Studies on the reduction of the nitro group in 3-aryl-2-methylene-4-nitro-alkanoates afforded by the Baylis-Hillman adducts: Synthesis of 4-aryl-3-methylene-2-pyrrolidinones and 3-(1-alkoxycarbonyl-vinyl)-1H-indole-2-carboxylates

The formation of substituted 2-pyrrolidinones and indoles by the reduction of the secondary nitro group in appropriate 3-aryl-2-methylene-4-nitroalkanoates afforded by Baylis-Hillman chemistry via different reducing agents is described. The 3-aryl-2-methylene-4-nitroalkanoate obtained from SN2 nucleophilic reaction between the acetate of Baylis-Hillman adducts and ethyl nitroacetate upon reduction with indium-HCl furnishes a mixture of cis and trans substituted phenyl-3-methylene-2-pyrrolidinones. In contrast, similar reductions of analogous substrates derived from nitroethane stereoselectively furnished only the trans substituted phenyl-3-methylene-2-pyrrolidinones. On the other hand the SnCl2.2H2O-promoted reductions of substrates derived from nitro ethylacetate give oxime derivatives while the ones obtained from nitroethane yield a mixture of cis and trans 4-aryl-3-methylene-2-pyrrolidinones. Alternatively, the SnCl2.2H2O-promoted reduction of substituted 2-nitrophenyl-2-methylene-alkanoate furnished from ethyl nitroacetate yields 3-(1-alkoxycarbonyl-vinyl)-1H-indole-2-carboxylate while indium-promoted reaction of this substrate leads to a complex mixture. Analogous reactions with SnCl2.2H2O of substituted 2-nitrophenyl-2-methylene-alkanoate obtained from nitroethane yield 4-alkyl-3-methylene-2-quinolones in moderate yields

An alternate approach to quinoline architecture via Baylis-Hillman chemistry: SnCl2-mediated tandem reaction toward synthesis of 4-(substituted vinyl)-quinolines

An alternate approach to densely substituted quinolines from the products of SN2 nucleophilic substitution reaction between the acetyl derivatives of the Baylis-Hillman adducts obtained from 2-nitrobenzaldehydes and the carbonyl group containing carbon nucleophiles is described. Treatment of these compounds with SnCl2, trigger a tandem reaction wherein reduction of the nitro group is followed by a remarkably regioselective intramolecular cyclization and subsequent dehydrogenation to afford 4-(substituted vinyl)-quinolines.

Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis

Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered hydrolysis

Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. (1) In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered hydrolysis

Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. (1) In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

Sulfate assimilation in higher plants. Characterization of a stable intermediate in the adenosine 5′-phosphosulfate reductase reaction

The enzyme catalysing the reduction of adenosine 5′-phosphosulfate (AdoPS) to sulfite in higher plants, AdoPS reductase, is considered to be the key enzyme of assimilatory sulfate reduction. In order to address its reaction mechanism, the APR2 isoform of this enzyme from Arabidopsis thaliana was overexpressed in Escherichia coli and purified to homogeneity. Incubation of the enzyme with [35S]AdoPS at 4 °C resulted in radioactive labelling of the protein. Analysis of APR2 tryptic peptides revealed 35SO2–3 bound to Cys248, the only Cys conserved between AdoPS and prokaryotic phosphoadenosine 5′-phosphosulfate reductases. Consistent with this result, radioactivity could be released from the protein by incubation with thiols, inorganic sulfide and sulfite. The intermediate remained stable, however, after incubation with sulfate, oxidized glutathione or AdoPS. Because truncated APR2, missing the thioredoxin-like C-terminal part, could be labelled even at 37 °C, and because this intermediate was more stable than the complete protein, we conclude that the thioredoxin-like domain was required to release the bound SO2–3 from the intermediate. Taken together, these results demonstrate for the first time the binding of 35SO2–3 from [35S]AdoPS to AdoPS reductase and its subsequent release, and thus contribute to our understanding of the molecular mechanism of AdoPS reduction in plants.

Study of Basic Wood Decay Mechanisms and Their Biotechnological Applications

The overall objective of this thesis was to gain further understanding of the non-enzymatic mechanisms involved in brown-rot wood decay, especially the role of pH, oxalic acid, and low molecular catecholate compounds on the dissolution and reduction of iron, and the formation of reactive oxygen species. Another focus of this study will be the potential application of a biomimetic free radical generating system inspired from fungi wood decay process, especially the non-enzymatic mechanism. The possible pathways of iron uptake and iron redox cycling in non-enzymatic brown-rot decay were investigated in this study. UV-Vis spectroscopy and HPLC were employed to study the kinetics and pathways of the interaction between iron and model catecholate compounds under different pH and chelator/iron molar ratio conditions. Iron chelation and reduction during early non-enzymatic wood decay processes have been studied in this thesis. The results indicate that the effects of the chelator/iron ratio, the pH, and other reaction parameters on the hydroxyl radical generation in a Fenton type system can be determined using ESR spin-trapping techniques. Data also support the hypothesis that superoxide radicals are involved in chelator-mediated Fenton processes. The mechanisms involved in free radical activation of Thermal Mechanical Pulp fibers were investigated. The activation of TMP fibers was evaluated by ESR measurement of free phenoxy radical generation on solid fibers. The results indicate that low molecular weight chelators can improve Fenton reactions, thus in turn stimulating the free radical activation of TMP fibers. A mediated Fenton system was evaluated for decolorization of several types of dyes. The result shows that the Fenton system mediated by a catecholate-type chelator effectively reduced the color of a diluted solution of synthetic dyes after 90 minutes of treatment at room temperature. The results show that compared to a neat Fenton process, the mediated Fenton decolorization process increased the production, and therefore the effective longevity, of hydroxyl radical species to increase the decolorization efficiency.

Kinetics and Mechanism of Oxygen Delignification

Considerable research has been conducted into the kinetics and selectivity of the oxygen delignification process to overcome limitation in its use. However most studies were performed in a batch reactor whereby the hydroxide and dissolved oxygen concentrations are changing during the reaction time in an effort to simulate tower performance in pulp mills. This makes it difficult to determine the reaction order of the different reactants in the rate expressions. Also the lignin content and cellulose degradation of the pulp are only established at the end of the experiment when the sample is removed from the batch reactor. To overcome these deficiencies, we have adopted a differential reactor system used frequently for fluid-solid rate studies (so-called Berty reactor) for measurement of oxygen delignification kinetics. In this reactor, the dissolved oxygen concentration and the alkali concentration in the feed are kept constant, and the rate of lignin removal is determined from the dissolved lignin content in the outflow stream measured by UV absorption. The mass of lignin removed is verified by analyzing the pulp at several time intervals. Experiments were performed at different temperatures, oxygen pressures and caustic concentrations. The delignification rate was found to be first order in HexA-free residual lignin content. The delignification rate reaction order in caustic concentration and oxygen pressure were determined to be 0.42 and 0.44 respectively. The activation energy was found to be 53kJ/mol. The carbohydrate degradation during oxygen delignification can be described by two contributions: one due to radicals produced by phenolic delignification, and a much smaller contribution due to alkaline hydrolysis. From the first order of the reaction and the pKa of the active lignin site, a new oxygen delignification mechanism is proposed. The number 3 carbon atom in the aromatic ring with the attached methoxyl group forms the lignin active site for oxygen adsorption and subsequent electrophic reaction to form a hydroperoxide with a pKa value similar to that of the present delignification kinetics. The uniform presence of the aromatic methoxyl groups in residual lignin further support the first order in lignin kinetics.

Planktonic foraminifera in the latest Maastrichtian of Walvis Ridge, South Atlantic

An abrupt global warming of 3-4°C occurred near the end of the Maastrichtian at 65.45-65.10 Ma. The environmental effects of this warm event are here documented based on stable isotopes and quantitative analysis of planktonic foraminifera at the South Atlantic DSDP Site 525A. Stable isotopes of individual species mark a rapid increase in temperature and a reduction in the vertical water mass stratification that is accompanied by a decrease in niche habitats, reduced species diversity and/or abundance, smaller species morphologies or dwarfing, and reduced photosymbiotic activity. During the warm event, the relative abundance of a large number of species decreased, including tropical-subtropical affiliated species, whereas typical mid-latitude species retained high abundances. This indicates that climate warming did not create favorable conditions for all tropical-subtropical species at mid-latitudes and did not cause a massive retreat in the local mid-latitude population. A noticeable exception is the ecological generalist Heterohelix dentata Stenestad that dominated during the cool intervals, but significantly decreased during the warm event. However, dwarfing is the most striking response to the abrupt warming and occurred in various species of different morphologies and lineages (e.g. biserial, trochospiral, keeled globotruncanids). Dwarfing is a typical reaction to environmental stress conditions and was likely the result of increased reproduction rates. Similarly, photosymbiotic activity appears to have been reduced significantly during the maximum warming, as indicated by decreased delta13C values. The foraminiferal response to climate change is thus multifaceted resulting in decreased species diversity, decreased species populations, increased competition due to reduced niche habitats, dwarfing and reduced photosymbiotic activity.

Chemistry of sediment profile GeoB4906

Mineralization of organic matter and the subsequent dissolution of calcite were simulated for surface sediments of the upper continental slope off Gabon by using microsensors to measure O2, pH, pCO2 and Ca2+ (in situ), pore-water concentration profiles of NO3-, NH4+, Fe2+, and Mn2+ and SO42- (ex situ), as well as sulfate reduction rates derived from incubation experiments. The transport and reaction model CoTReM was used to simulate the degradation of organic matter by O2, [NO3]-, Fe(OH)3 and [SO4]2-, reoxidation reactions involving Fe2+ and Mn2+, and precipitation of FeS. Model application revealed an overall rate of organic matter mineralization amounting to 50 µmol C cm**-2 yr**-1, of which 77% were due to O2, 17% to [NO3]- and 3% to Fe(OH)3 and 3% to [SO4]2-. The best fit for the pH profile was achieved by adapting three different dissolution rate constants of calcite ranging between 0.01 and 0.5% d-1 and accounting for different calcite phases in the sediment. A reaction order of 4.5 was assumed in the kinetic rate law. A CaCO3 flux to the sediment was estimated to occur at a rate of 42 g m**-2 yr**-1 in the area of equatorial upwelling. The model predicts a redissolution flux of calcite amounting to 36 g m**-2 yr**-1, thus indicating that ~90% of the calcite flux to the sediment is redissolved.

Element contents, sulfur and oxygen isotopes, and molecular biomarkers of phosphatic crust samples from the Chimbote Platform of the shelf off Peru

Authigenic phosphatic laminites enclosed in phosphorite crusts from the shelf off Peru (10°01' S and 10°24' S) consist of carbonate fluorapatite layers, which contain abundant sulfide minerals including pyrite (FeS2) and sphalerite (ZnS). Low d34Spyrite values (average -28.8 per mill) agree with bacterial sulfate reduction and subsequent pyrite formation. Stable sulfur isotopic compositions of sulfate bound in carbonate fluorapatite are lower than that of sulfate from ambient sea water, suggesting bacterial reoxidation of sulfide by sulfide-oxidizing bacteria. The release of phosphorus and subsequent formation of the autochthonous phosphatic laminites are apparently caused by the activity of sulfate-reducing bacteria and associated sulfide-oxidizing bacteria. Following an extraction-phosphorite dissolution-extraction procedure, molecular fossils of sulfate-reducing bacteria (mono-O-alkyl glycerol ethers, di-O-alkyl glycerol ethers, as well as the short-chain branched fatty acids i/ai-C15:0, i/ai-C17:0 and 10MeC16:0) are found to be among the most abundant compounds. The fact that these molecular fossils of sulfate-reducing bacteria are distinctly more abundant after dissolution of the phosphatic laminite reveals that the lipids are tightly bound to the mineral lattice of carbonate fluorapatite. Moreover, compared with the autochthonous laminite, molecular fossils of sulfate-reducing bacteria are: (1) significantly less abundant and (2) not as tightly bound to the mineral lattice in the other, allochthonous facies of the Peruvian crusts consisting of phosphatic coated grains. These observations confirm the importance of sulfate-reducing bacteria in the formation of the phosphatic laminite. Model calculations highlight that organic matter degradation by sulfate-reducing bacteria has the potential to liberate sufficient phosphorus for phosphogenesis.

Isotopic composition of oxygen, carbon, and sulfur in interstitial water and cores at DSDP Leg 59 Holes

Comprehensive isotopic studies based on data from the Deep Sea Drilling Project have elucidated numerous details of the low- and high-temperature mechanisms of interaction between water and rocks of ocean crustal seismic Layers 1 and 2. These isotopic studies have also identified climatic changes during the Meso-Cenozoic history of oceans. Data on the abundance and isotopic composition of sulfur in the sedimentary layer as well as in rocks of the volcanic basement are more fragmentary than are oxygen and carbon data. In this chapter we specifically concentrate upon isotopic data related to specific features of the mechanisms of low-temperature interaction of water with sedimentary and volcanogenic rocks. The Leg 59 data provide a good opportunity for such lithologic and isotopic studies, because almost 600 meters of basalt flows and sills interbedded with tuffs and volcaniclastic breccias were cored during the drilling of Hole 448A. Moreover, rocks supposedly exposed to hydrothermal alteration play an important role at the deepest horizons of that mass. Sulfur isotopic studies of the character of possible biogenic processes of sulfate reduction in sediments are another focus, as well as the nature and origin of sulfide mineralization in Layer-2 rocks of remnant island arcs. Finally, oxygen and carbon istopic analyses of biogenic carbonates in the cores also enabled us to investigate the effects of changing climatic conditions during the Cenozoic. These results are compared with previous data from adjacent regions of the Pacific Ocean. Thus this chapter describes results of isotopic analyses of: oxygen and sulfur of interstitial water; oxygen and carbon of sedimentary carbonates and of calcite intercalations and inclusions in tuffs and volcaniclastic breccias interbedded with basalt flows; and sulfur of sulfides in these rocks.

Pliocene-Pleistocene oxygen isotope record DSDP Site 586, Ontong Java Plateau, Pacific Ocean i

Oceanographic changes in the western equatorial Pacific during the past 6 Ma are inferred from oxygen isotopic analyses of planktic and benthic foraminifera from Ontong Java Plateau (DSDP Site 586). The taxa are Globigerinoides sacculifer, Pulleniatina, Cibicidoides wuellerstorfi, and Oridorsalis umbonatus. Cooling and ice buildup are indicated by an 18O enrichment of 0.3 per mil in the planktic species near 3.4 Ma. This shift apparently is compensated in the benthic data by a warming of the deep waters by between 1° and 2° C. We suggest that the dominant source of upper deep water supply to the Pacific changed from Antarctic to North Atlantic at that time, the North Atlantic-derived water being warmer. Near 2.8 Ma (approximately) the planktic foraminifera again record an enrichment in 18O (Delta delta18O=0.25 per mil). We suggest ice buildup in the northern hemisphere as the cause, because of subsequent sharp increase in fluctuations of the delta18O signal, that is, instability. The enrichment is magnified in the benthic foraminifera (Delta delta18O = 0.5 per mil) by a cooling of the deep water by 1.5° at the time, presumably signalling a glacial-type reduction of North Atlantic Deep Water (NADW) production. Episodic divergence between the signals of G. sacculifer and Pulleniatina in the Pleistocene apparently reflects periods of increased upwelling in the western equatorial Pacific. The amplitude of ice volume fluctuations cannot be reconstructed from delta18O data alone, unless there are constraints on temperature variations. The increase in amplitude of fluctuation of the benthic and planktic signals during the Pleistocene may be attributed either to an increase in maximum ice volume, or to an increase in the fractionation of continental ice, or a combination of both causes.

High-resolution in situ oxygen microprofiles, porewater and solid phase geochemistry from the Crimean shelf (Black Sea) from Maria S. Merian cruise MSM15/1

The outer western Crimean shelf of the Black Sea is a natural laboratory to investigate effects of stable oxic versus varying hypoxic conditions on seafloor biogeochemical processes and benthic community structure. Bottom-water oxygen concentrations ranged from normoxic (175 µmol O2/L) and hypoxic (< 63 µmol O2/L) or even anoxic/sulfidic conditions within a few kilometers' distance. Variations in oxygen concentrations between 160 and 10 µmol/L even occurred within hours close to the chemocline at 134 m water depth. Total oxygen uptake, including diffusive as well as fauna-mediated oxygen consumption, decreased from 15 mmol/m**2/d on average in the oxic zone, to 7 mmol/m**2/d on average in the hypoxic zone, correlating with changes in macrobenthos composition. Benthic diffusive oxygen uptake rates, comprising respiration of microorganisms and small meiofauna, were similar in oxic and hypoxic zones (on average 4.5 mmol/m**2/d), but declined to 1.3 mmol/m**2/d in bottom waters with oxygen concentrations below 20 µmol/L. Measurements and modeling of porewater profiles indicated that reoxidation of reduced compounds played only a minor role in diffusive oxygen uptake under the different oxygen conditions, leaving the major fraction to aerobic degradation of organic carbon. Remineralization efficiency decreased from nearly 100 % in the oxic zone, to 50 % in the oxic-hypoxic zone, to 10 % in the hypoxic-anoxic zone. Overall, the faunal remineralization rate was more important, but also more influenced by fluctuating oxygen concentrations, than microbial and geochemical oxidation processes.

Planktonic foraminifera oxygen isotope and trace metal data ODP Hole 172-1056A, 46-54 ka BP

Salinity increase in the subtropical gyre system may have pre-conditioned the North Atlantic Ocean for a rapid return to stronger overturning circulation and high-latitude warming following meltwater events during the Last Glacial period. Here we investigate the Gulf Stream - subtropical gyre system properties over Dansgaard-Oeschger (DO) cycles 14 to 12, including Heinrich ice-rafting event 5. During the Holocene and Last Glacial Maximum a positive gradient in surface dwelling planktonic foraminifera d18O (Globigerinoides ruber) can be observed between the Gulf Stream and subtropical gyre, due to decreasing temperature, increasing salinity, and a change from summer to year-round occurrence of G. ruber. We assess whether this gradient was a common feature during stadial-interstadial climate oscillations of Marine Isotope Stage 3, by comparing existing G. ruber d18O from ODP Site 1060 (subtropical gyre location) and new data from ODP Site 1056 (Gulf Stream location) between 54 and 46 ka. Our results suggest that this gradient was largely absent during the period studied. During the major warm DO interstadials 14 and 12 we infer a more zonal and wider Gulf Stream, influencing both ODP Sites 1056 and 1060. A Gulf Stream presence during these major interstadials is also suggested by the large vertical d18O gradient between shallow dwelling planktonic foraminifera species, especially G. ruber, and the deep dwelling species Globorotalia inflata at site 1056, which we associate with strong summer stratification and Gulf Stream presence. A major reduction in this vertical d18O gradient from 51 ka until the end of Heinrich event 5 at 48.5 ka suggests site 1056 was situated within the subtropical gyre in this mainly cold period, from which we infer a migration of the Gulf Stream to a position nearer to the continental shelf, indicative of a narrower Gulf Stream with possibly reduced transport.