Isotopic proxies for microbial and environmental change : insights hydrogen isotopes and the Ediacaran Khufai Formation

Microbes have profoundly influenced the Earth’s environments through time. Records of these interactions come primarily from the development and implementation of proxies that relate known modern processes to chemical signatures in the sedimentary record. This thesis is presented in two parts, focusing first on novel proxy development in the modern and second on interpretation of past environments using well-established methods. Part 1, presented in two chapters, builds on previous observations that different microbial metabolisms produce vastly different lipid hydrogen isotopic compositions. Chapter 1 evaluates the potential environmental expression of metabolism-based fractionation differences by exploiting the natural microbial community gradients in hydrothermal springs. We find a very large range in isotopic composition that can be demonstrably linked to the microbial source(s) of the fatty acids at each sample site. In Chapter 2, anaerobic culturing techniques are used to evaluate the hydrogen isotopic fractionations produced by anaerobic microbial metabolisms. Although the observed fractionation patterns are similar to those reported for aerobic cultures for some organisms, others show large differences. Part 2 changes focus from the modern to the ancient and uses classical stratigraphic methods combined with isotope stratigraphy to interpret microbial and environmental changes during the latest Precambrian Era. Chapter 3 presents a detailed characterization of the facies, parasequence development, and stratigraphic architecture of the Ediacaran Khufai Formation. Chapter 4 presents measurements of carbon, oxygen, and sulfur isotopic ratios in stratigraphic context. Large oscillations in the isotopic composition of sulfate constrain the size of the marine sulfate reservoir and suggest incorporation of an enriched isotopic source. Because this data was measured in stratigraphic context, we can assert with confidence that these isotopic shifts are not related to stratigraphic surfaces or facies type but instead reflect the evolution of the ocean through time. This data integrates into the chemostratigraphic global record and contributes to the emerging picture of changing marine chemistry during the latest Precambrian Era.

Advanced Reaction Systems for Hydrogen Production

[EN] This PhD work started in March 2010 with the support of the University of the Basque Country (UPV/EHU) under the program named “Formación de Personal Investigador” at the Chemical and Environmental Engineering Department in the Faculty of Engineering of Bilbao. The major part of the Thesis work was carried out in the mentioned department, as a member of the Sustainable Process Engineering (SuPrEn) research group. In addition, this PhD Thesis includes the research work developed during a period of 6 months at the Institut für Mikrotechnik Mainz GmbH, IMM, in Germany. During the four years of the Thesis, conventional and microreactor systems were tested for several feedstocks renewable and non-renewable, gases and liquids through several reforming processes in order to produce hydrogen. For this purpose, new catalytic formulations which showed high activity, selectivity and stability were design. As a consequence, the PhD work performed allowed the publication of seven scientific articles in peer-reviewed journals. This PhD Thesis is divided into the following six chapters described below. The opportunity of this work is established on the basis of the transition period needed for moving from a petroleum based energy system to a renewable based new one. Consequently, the present global energy scenario was detailed in Chapter 1, and the role of hydrogen as a real alternative in the future energy system was justified based on several outlooks. Therefore, renewable and non-renewable hydrogen production routes were presented, explaining the corresponding benefits and drawbacks. Then, the raw materials used in this Thesis work were described and the most important issues regarding the processes and the characteristics of the catalytic formulations were explained. The introduction chapter finishes by introducing the concepts of decentralized production and process intensification with the use of microreactors. In addition, a small description of these innovative reaction systems and the benefits that entailed their use were also mentioned. In Chapter 2 the main objectives of this Thesis work are summarized. The development of advanced reaction systems for hydrogen rich mixtures production is the main objective. In addition, the use and comparison between two different reaction systems, (fixed bed reactor (FBR) and microreactor), the processing of renewable raw materials, the development of new, active, selective and stable catalytic formulations, and the optimization of the operating conditions were also established as additional partial objectives. Methane and natural gas (NG) steam reforming experimental results obtained when operated with microreactor and FBR systems are presented in Chapter 3. For these experiments nickel-based (Ni/Al2O3 and Ni/MgO) and noble metal-based (Pd/Al2O3 and Pt/Al2O3) catalysts were prepared by wet impregnation and their catalytic activity was measured at several temperatures, from 973 to 1073 K, different S/C ratios, from 1.0 to 2.0, and atmospheric pressure. The Weight Hourly Space Velocity (WHSV) was maintained constant in order to compare the catalytic activity in both reaction systems. The results obtained showed a better performance of the catalysts operating in microreactors. The Ni/MgO catalyst reached the highest hydrogen production yield at 1073 K and steam-to-carbon ratio (S/C) of 1.5 under Steam methane Reforming (SMR) conditions. In addition, this catalyst also showed good activity and stability under NG reforming at S/C=1.0 and 2.0. The Ni/Al2O3 catalyst also showed high activity and good stability and it was the catalyst reaching the highest methane conversion (72.9 %) and H2out/CH4in ratio (2.4) under SMR conditions at 1073 K and S/C=1.0. However, this catalyst suffered from deactivation when it was tested under NG reforming conditions. Regarding the activity measurements carried out with the noble metal-based catalysts in the microreactor systems, they suffered a very quick deactivation, probably because of the effects attributed to carbon deposition, which was detected by Scanning Electron Microscope (SEM). When the FBR was used no catalytic activity was measured with the catalysts under investigation, probably because they were operated at the same WHSV than the microreactors and these WHSVs were too high for FBR system. In Chapter 4 biogas reforming processes were studied. This chapter starts with an introduction explaining the properties of the biogas and the main production routes. Then, the experimental procedure carried out is detailed giving concrete information about the experimental set-up, defining the parameters measured, specifying the characteristics of the reactors used and describing the characterization techniques utilized. Each following section describes the results obtained from activity testing with the different catalysts prepared, which is subsequently summarized: Section 4.3: Biogas reforming processes using γ-Al2O3 based catalysts The activity results obtained by several Ni-based catalysts and a bimetallic Rh-Ni catalyst supported on magnesia or alumina modified with oxides like CeO2 and ZrO2 are presented in this section. In addition, an alumina-based commercial catalyst was tested in order to compare the activity results measured. Four different biogas reforming processes were studied using a FBR: dry reforming (DR), biogas steam reforming (BSR), biogas oxidative reforming (BOR) and tri-reforming (TR). For the BSR process different steam to carbon ratios (S/C) from 1.0 to 3.0, were tested. In the case of BOR process the oxygen-to-methane (O2/CH4) ratio was varied from 0.125 to 0.50. Finally, for TR processes different S/C ratios from 1.0 to 3.0, and O2/CH4 ratios of 0.25 and 0.50 were studied. Then, the catalysts which achieved high activity and stability were impregnated in a microreactor to explore the viability of process intensification. The operation with microreactors was carried out under the best experimental conditions measured in the FBR. In addition, the physicochemical characterization of the fresh and spent catalysts was carried out by Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES), N2 physisorption, H2 chemisorption, Temperature Programmed Reduction (TPR), SEM, X-ray Photoelectron Spectroscopy (XPS) and X-ray powder Diffraction (XRD). Operating with the FBR, conversions close to the ones predicted by thermodynamic calculations were obtained by most of the catalysts tested. The Rh-Ni/Ce-Al2O3 catalyst obtained the highest hydrogen production yield in DR. In BSR process, the Ni/Ce-Al2O3 catalyst achieved the best activity results operating at S/C=1.0. In the case of BOR process, the Ni/Ce-Zr-Al2O3 catalyst showed the highest reactants conversion values operating at O2/CH4=0.25. Finally, in the TR process the Rh-Ni/Ce-Al2O3 catalyst obtained the best results operating at S/C=1.0 and O2/CH4=0.25. Therefore, these three catalysts were selected to be coated onto microchannels in order to test its performance under BOR and TR processes conditions. Although the operation using microreactors was carried out under considerably higher WHSV, similar conversions and yields as the ones measured in FBR were measured. Furthermore, attending to other measurements like Turnover Frequency (TOF) and Hydrogen Productivity (PROD), the values calculated for the catalysts tested in microreactors were one order of magnitude higher. Thus, due to the low dispersion degree measured by H2-chemisorption, the Ni/Ce-Al2O3 catalyst reached the highest TOF and PROD values. Section 4.4: Biogas reforming processes using Zeolites L based catalysts In this section three type of L zeolites, with different morphology and size, were synthesized and used as catalyst support. Then, for each type of L zeolite three nickel monometallic and their homologous Rh-Ni bimetallic catalysts were prepared by the wetness impregnation method. These catalysts were tested using the FBR under DR process and different conditions of BSR (S/C ratio of 1.0 and 2.0), BOR (O2/CH4 ratio of 0.25 and 0.50) and TR processes (at S/C=1.0 and O2/CH4=0.25). The characterization of these catalysts was also carried out by using the same techniques mentioned in the previous section. Very high methane and carbon dioxide conversion values were measured for almost all the catalysts under investigation. The experimental results evidenced the better catalytic behavior of the bimetallic catalysts as compared to the monometallic ones. Comparing the catalysts behavior with regards to their morphology, for the BSR process the Disc catalysts were the most active ones at the lowest S/C ratio tested. On the contrary, the Cylindrical (30–60 nm) catalysts were more active under BOR conditions at O2/CH4=0.25 and TR processes. By the contrary, the Cylindrical (1–3 µm) catalysts showed the worst activity results for both processes. Section 4.5: Biogas reforming processes using Na+ and Cs+ doped Zeolites LTL based catalysts A method for the synthesis of Linde Type L (LTL) zeolite under microwave-assisted hydrothermal conditions and its behavior as a support for heterogeneously catalyzed hydrogen production is described in this section. Then, rhodium and nickel-based bimetallic catalysts were prepared in order to be tested by DR process and BOR process at O2/CH4=0.25. Moreover, the characterization of the catalysts under investigation was also carried out. Higher activities were achieved by the catalysts prepared from the non-doped zeolites, Rh-Ni/D and Rh-Ni/N, as compared to the ones supported on Na+ and Cs+ exchanged supports. However, the differences between them were not very significant. In addition, the Na+ and Cs+ incorporation affected mainly to the Disc catalysts. Comparing the results obtained by these catalysts with the ones studied in the section 4.4, in general worst results were achieved under DR conditions and almost the same results when operated under BOR conditions. In Chapter 5 the ethylene glycol (EG) as feed for syngas production by steam reforming (SR) and oxidative steam reforming (OSR) was studied by using microchannel reactors. The product composition was determined at a S/C of 4.0, reaction temperatures between 625°C and 725°C, atmospheric pressure and Volume Hourly Space Velocities (VHSV) between 100 and 300 NL/(gcath). This work was divided in two sections. The first one corresponds to the introduction of the main and most promising EG production routes. Then, the new experimental procedure is detailed and the information about the experimental set-up and the measured parameters is described. The characterization was carried out using the same techniques as for the previous chapter. Then, the next sections correspond to the catalytic activity and catalysts characterization results. Section 5.3: xRh-cm and xRh-np catalysts for ethylene glycol reforming Initially, catalysts with different rhodium loading, from 1.0 to 5.0 wt. %, and supported on α-Al2O3 were prepared by two different preparation methods (conventional impregnation and separate nanoparticle synthesis). Then, the catalysts were compared regarding their measured activity and selectivity, as well as the characterization results obtained before and after the activity tests carried out. The samples prepared by a conventional impregnation method showed generally higher activity compared to catalysts prepared from Rh nanoparticles. By-product formation of species such as acetaldehyde, ethane and ethylene was detected, regardless if oxygen was added to the feed or not. Among the catalysts tested, the 2.5Rh-cm catalyst was considered the best one. Section 5.4: 2.5Rh-cm catalyst support modification with CeO2 and La2O3 In this part of the Chapter 5, the catalyst showing the best performance in the previous section, the 2.5Rh-Al2O3 catalyst, was selected in order to be improved. Therefore, new Rh based catalysts were designed using α-Al2O3 and being modified this support with different contents of CeO2 or La2O3 oxides. All the catalysts containing additives showed complete conversion and selectivities close to the equilibrium in both SR and OSR processes. In addition, for these catalysts the concentrations measured for the C2H4, CH4, CH3CHO and C2H6 by-products were very low. Finally, the 2.5Rh-20Ce catalyst was selected according to its catalytic activity and characterization results in order to run a stability test, which lasted more than 115 hours under stable operation. The last chapter, Chapter 6, summarizes the main conclusions achieved throughout this Thesis work. Although very high reactant conversions and rich hydrogen mixtures were obtained using a fixed bed reaction system, the use of microreactors improves the key issues, heat and mass transfer limitations, through which the reforming reactions are intensified. Therefore, they seem to be a very interesting and promising alternative for process intensification and decentralized production for remote application.

Enhanced hydrogen desorption from Si sites during low-temperature Si1-xGex growth by disilane and solid-Ge molecular beam epitaxy

A phenomenological model is proposed to explain quantitatively the interesting compositional dependence on the Ge incorporation rate during low-temperature growth of Si1-xGex by disilane and solid-Ge molecular beam epitaxy, based on enhanced hydrogen desorption from Si sites due to the presence of Ge atoms. The hydrogen desorption rate constant for disilane on Si sites is fitted to an exponential function of Ge incorporation rate and a possible physical explanation is discussed. Simulated results are in excellent agreement with experimental data. (C) 1999 American Institute of Physics. [S0021-8979(99)02109-X].

Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T(3)) or antagonist (NH(3)). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, C-terminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T(3), but not NH(3), increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T(3) but not NH(3.) We present data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011)

Superoxide Dismutase 1-mediated Production of Ethanol- and DNA-derived Radicals in Yeasts Challenged with Hydrogen Peroxide MOLECULAR INSIGHTS INTO THE GENOME INSTABILITY OF PEROXIREDOXIN-NULL STRAINS

Peroxiredoxins are receiving increasing attention as defenders against oxidative damage and sensors of hydrogen peroxide-mediated signaling events. In the yeast Saccharomyces cerevisiae, deletion of one or more isoforms of the peroxiredoxins is not lethal but compromises genome stability by mechanisms that remain under scrutiny. Here, we show that cytosolic peroxiredoxin-null cells (tsa1 Delta tsa2 Delta) are more resistant to hydrogen peroxide than wildtype (WT) cells and consume it faster under fermentative conditions. Also, tsa1 Delta tsa2 Delta cells produced higher yields of the 1-hydroxyethyl radical from oxidation of the glucose metabolite ethanol, as proved by spin-trapping experiments. A major role for Fenton chemistry in radical formation was excluded by comparing WT and tsa1 Delta tsa2 Delta cells with respect to their levels of total and chelatable metal ions and of radical produced in the presence of chelators. The main route for 1-hydroxyethyl radical formation was ascribed to the peroxidase activity of Cu, Zn-superoxide dismutase (Sod1), whose expression and activity increased similar to 5- and 2-fold, respectively, in tsa1 Delta tsa2 Delta compared with WT cells. Accordingly, overexpression of human Sod1 in WT yeasts led to increased 1-hydroxyethyl radical production. Relevantly, tsa1 Delta tsa2 Delta cells challenged with hydrogen peroxide contained higher levels of DNA-derived radicals and adducts as monitored by immuno-spin trapping and incorporation of (14)C from glucose into DNA, respectively. The results indicate that part of hydrogen peroxide consumption by tsa1 Delta tsa2 Delta cells is mediated by induced Sod1, which oxidizes ethanol to the 1-hydroxyethyl radical, which, in turn, leads to increased DNA damage. Overall, our studies provide a pathway to account for the hypermutability of peroxiredoxin-null strains.

Analysis of agonist and antagonist effects on thyroid hormone receptor conformation by hydrogen/deuterium exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T 3) or antagonist (NH3). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/ deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, Cterminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T 3, but not NH3, increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T 3 but not NH3.Wepresent data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011). Copyright © 2011 by The Endocrine Society.

Thermodynamic and economic analysis of hydrogen production integration in the Brazilian sugar and alcohol industry

One of the biggest challenges today is to develop clean fuels, which do not emit pollutant and with viable implementation. One of the options currently under study is the hydrogen production process. In this context, this work aims to study the technical and economical aspects of the incorporation process of hydrogen producing by ethanol steam reforming in the sugar cane industry and MCFC (molten carbonate fuel cell) application on it to generate electric power. Therefore, it has been proposed a modification in the traditional process of sugar cane industry, in order to incorporate hydrogen production, besides the traditional products (sugar, ethylic, hydrated and anhydric alcohol). For this purpose, a detailed theoretical study of the ethanol production process, describing the considerations to incorporate the hydrogen production will be performed. After that, there will be a thermodynamic study for analysing the innovation of this production chain, as well as a study of economic engineering to allocate the costs of products of the new process, optimising it and considering the thermoeconomics as being as an analysis tool. This proposal aims to improve Brazil's position in the ranking of international biofuels, corroborating the nation to be a power in the hydrogen era. (C) 2013 Elsevier Ltd. All rights reserved.

Effect of incorporation of remineralizing agents into bleaching gels on the microhardness of bovine enamel in situ

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hydrogen peroxide monitoring in Fenton reaction by using a ruthenium oxide hexacyanoferrate/multiwalled carbon nanotubes modified electrode

A novel amperometric sensor based on the incorporation of ruthenium oxide hexacyanoferrate (RuOHCF) into multiwalled carbon nanotubes (MWCNTs) immobilized on a glassy carbon electrode is described. Cyclic voltammetry experiments indicated that the cathodic reduction of hydrogen peroxide at the RuOHCF/MWCNTs100/GC modified electrode is facilitated, occurring at 0.0 V vs. Ag/AgCl/KCl(sat). Following the optimization of the experimental conditions, the proposed sensor presented excellent analytical properties for hydrogen peroxide determination, with a low limit of detection (4.7 mu mol L-1), a large dynamic concentration range (0.1-10 mmol L-1) and a sensitivity of 1280 mu A mmol(-1) L cm(-2). The usefulness of the RuOHCF/MWCNTs100/GC electrochemical sensor was confirmed by monitoring the consumption of hydrogen peroxide during the degradation of phenol by the Fenton reaction. (C) 2012 Elsevier B.V. All rights reserved.

Incorporation of RANKL promotes osteoclast formation and osteoclast activity on β-TCP ceramics.

β-Tricalcium phosphate (β-TCP) ceramics are approved for the repair of osseous defects. In large defects, however, the substitution of the material by authentic bone is inadequate to provide sufficient long-term mechanical stability. We aimed to develop composites of β-TCP ceramics and receptor activator of nuclear factor κ-B ligand (RANKL) to enhance the formation of osteoclasts and promote cell mediated calcium phosphate resorption. RANKL was adsorbed superficially onto β-TCP ceramics or incorporated into a crystalline layer of calcium phosphate by the use of a co-precipitation technique. Murine osteoclast precursors were seeded onto the ceramics. After 15 days, the formation of osteoclasts was quantified cytologically and colorimetrically with tartrate-resistant acidic phosphatase (TRAP) staining and TRAP activity measurements, respectively. Additionally, the expression of transcripts encoding the osteoclast gene products cathepsin K, calcitonin receptor, and of the sodium/hydrogen exchanger NHA2 were quantified by real-time PCR. The activity of newly formed osteoclasts was evaluated by means of a calcium phosphate resorption assay. Superficially adsorbed RANKL did not induce the formation of osteoclasts on β-TCP ceramics. When co-precipitated onto β-TCP ceramics RANKL supported the formation of mature osteoclasts. The development of osteoclast lineage cells was further confirmed by the increased expression of cathepsin K, calcitonin receptor, and NHA2. Incorporated RANKL stimulated the cells to resorb crystalline calcium phosphate. Our in vitro study shows that RANKL incorporated into β-TCP ceramics induces the formation of active, resorbing osteoclasts on the material surface. Once formed, osteoclasts mediate the release of RANKL thereby perpetuating their differentiation and activation. In vivo, the stimulation of osteoclast-mediated resorption may contribute to a coordinated sequence of material resorption and bone formation. Further in vivo studies are needed to confirm the current in vitro findings.

Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns.

The ability of DNA polymerases (pols) to catalyze the template-directed synthesis of duplex oligonucleotides containing a nonstandard Watson-Crick base pair between a nucleotide bearing a 5-(2,4-diaminopyrimidine) heterocycle (d kappa) and a nucleotide bearing either deoxyxanthosine (dX) or N1-methyloxoformycin B (pi) has been investigated. The kappa-X and kappa-pi base pairs are jointed by a hydrogen bonding pattern different from and exclusive of those joining the AT and GC base pairs. Reverse transcriptase from human immunodeficiency virus type 1 (HIV-1) incorporates dXTP into an oligonucleotide opposite d kappa in a template with good fidelity. With lower efficiency and fidelity, HIV-1 reverse transcriptase also incorporates d kappa TP opposite dX in the template. With d pi in the template, no incorporation of d kappa TP was observed with HIV reverse transcriptase. The Klenow fragment of DNA pol I from Escherichia coli does not incorporate d kappa TP opposite dX in a template but does incorporate dXTP opposite d kappa. Bovine DNA pols alpha, beta, and epsilon accept neither dXTP opposite d kappa nor d kappa TP opposite d pi. DNA pols alpha and epsilon (but not beta) incorporate d kappa TP opposite dX in a template but discontinue elongation after incorporating a single additional base. These results are discussed in light of the crystal structure for pol beta and general considerations of how polymerases must interact with an incoming base pair to faithfully copy genetic information.

Incorporation of glutamine repeats makes protein oligomerize: implications for neurodegenerative diseases.

Many transcription factors and some other proteins contain glutamine repeats; their abnormal expansion has been linked to several dominantly inherited neuro-degenerative diseases. Having found that poly(L-glutamine) alone forms beta-strands held together by hydrogen bonds between their amide groups, we surmised that glutamine repeats may form polar zippers, an unusual motif for protein-protein interactions. To test this hypothesis, we have engineered a Gly-Gln10-Gly peptide into the inhibitory loop of truncated chymotrypsin inhibitor 2 (CI2), a small protein from barley seeds, by both insertion and replacement. Gel filtration resolved both mutant inhibitors into at least three fractions, which analytical ultracentrifugation identified as monomers, dimers, and trimers of the recombinant protein; the truncated wild-type CI2 formed only monomers. CD difference spectra of the dimers and trimers versus wild type indicated that their glutamine repeats formed beta-pleated sheets, while those of the monomers versus wild type were more suggestive of type I beta-turns. The CD spectra of all three fractions remained unchanged even after incubation at 70 degrees C; neither the dimers nor the trimers dissociated at this temperature. We argue that the stability of all three fractions is due to the multiplicity of hydrogen bonds between extended strands of glutamine repeats in the oligomers or within a beta-hairpin formed by the single glutamine repeat of each monomer. Pathological effects may arise when expanded glutamine repeats cause proteins to acquire excessively high affinities for each other or for other proteins with glutamine repeats.

Nanoarchitectures Based on Layered Titanosilicates Supported on Glass Fibers: Application to Hydrogen Storage

This work reports on the synthesis of nanosheets of layered titanosilicate JDF-L1 supported on commercial E-type glass fibers with the aim of developing novel nanoarchitectures useful as robust and easy to handle hydrogen adsorbents. The preparation of those materials is carried out by hydrothermal reaction from the corresponding gel precursor in the presence of the glass support. Because of the basic character of the synthesis media, silica from the silicate-based glass fibers can be involved in the reaction, cementing its associated titanosilicate and giving rise to strong linkages on the support with the result of very stable heterostructures. The nanoarchitectures built up by this approach promote the growth and disposition of the titanosilicate nanosheets as a house-of-cards radially distributed around the fiber axis. Such an open arrangement represents suitable geometry for potential uses in adsorption and catalytic applications where the active surface has to be available. The content of the titanosilicate crystalline phase in the system represents about 12 wt %, and this percentage of the adsorbent fraction can achieve, at 298 K and 20 MPa, 0.14 wt % hydrogen adsorption with respect to the total mass of the system. Following postsynthesis treatments, small amounts of Pd (<0.1 wt %) have been incorporated into the resulting nanoarchitectures in order to improve their hydrogen adsorption capacity. In this way, Pd-layered titanosilicate supported on glass fibers has been tested as a hydrogen adsorbent at diverse pressures and temperatures, giving rise to values around 0.46 wt % at 298 K and 20 MPa. A mechanism of hydrogen spillover involving the titanosilicate framework and the Pd nanoparticules has been proposed to explain the high increase in the hydrogen uptake capacity after the incorporation of Pd into the nanoarchitecture.

Van der Waals-corrected density functional theory: benchmarking for hydrogen-nanotube and nanotube-nanotube interactions

Density functional theory (DFT) is a powerful approach to electronic structure calculations in extended systems, but suffers currently from inadequate incorporation of long-range dispersion, or Van der Waals (VdW) interactions. VdW-corrected DFT is tested for interactions involving molecular hydrogen, graphite, single-walled carbon nanotubes (SWCNTs), and SWCNT bundles. The energy correction, based on an empirical London dispersion term with a damping function at short range, allows a reasonable physisorption energy and equilibrium distance to be obtained for H-2 on a model graphite surface. The VdW-corrected DFT calculation for an (8, 8) nanotube bundle reproduces accurately the experimental lattice constant. For H-2 inside or outside an (8, 8) SWCNT, we find the binding energies are respectively higher and lower than that on a graphite surface, correctly predicting the well known curvature effect. We conclude that the VdW correction is a very effective method for implementing DFT calculations, allowing a reliable description of both short-range chemical bonding and long-range dispersive interactions. The method will find powerful applications in areas of SWCNT research where empirical potential functions either have not been developed, or do not capture the necessary range of both dispersion and bonding interactions.

Chapter 1 : nucleobases with designed patterns of hydrogen bonding

The chemistry used in key bond-forming steps to prepare nucleobases with designed patterns of hydrogen bonding is surveyed. Incorporation of the nucleobases into DNA and RNA oligomers is achieved either chemically using building blocks such as nucleoside phosphoramidites or enzymatically using nucleotide triphosphates. By varying the hydrogen bonding pattern within nucleobases, and by incorporating additional substituents, new structures have been designed that "reach over" so that contacts with both strands in targeted duplex DNA can be made in antigene strategies to control gene expression. Various new base-pairing systems have been evaluated that expand the genetic alphabet beyond Watson-Crick base pairs A.T and G.C. For example, benzo-homologated analogs of the natural DNA bases represent a new genetic set of orthogonal, size-expanded derivatives that have been shown to encode amino acids of a protein in a living organism.