Photocatalytic decomposition of organophosphonates fluorophenols in irradiated titanium dioxide suspensions

Dimethyl methyl phosphonate (DMMP), diethyl methyl phosphonate (DEMP), and fluorophenols undergo rapid decomposition upon TiO2 catalyzed photooxidation in air saturated aqueous solution. The degradation rates of DMMP were determined over a range of temperatures, under solar and artificial irradiation with and without simultaneous sonication. Solar illumination is effective for the degradation and the use of low energy of sonication increases the rate of mineralization. The surface area and the type of TiO2 dramatically affect the photoactivity of the catalyst. A number of intermediate products are formed and ultimately oxidized to phosphate and carbon dioxide. Possible reaction mechanisms and pathways for DMMP and DEMP are proposed. The Langmuir- Hinshelwood kinetic parameters for the photocatalysis of fluorophenols suggest modestly different reactivity for each isomer. The adsorption constant is largest for the ortho isomer consistent with the adsorption onto TiO2 through both hydroxyl and fluoride groups to form a chelated type structure.

Aplicação de tecnologias eletroquímicas (oxidação via radicais hidroxila, oxidação mediada via cloro ativo e eletrocoagulação) para o tratamento de efluentes reais ou sintéticos

In this work the degradation of real and synthetic wastewater was studied using electrochemical processes such as oxidation via hydroxyl radicals, mediated oxidation via active chlorine and electrocoagulation. The real effluent used was collected in the decanter tank of the Federal University of Rio Grande do Norte (ETE-UFRN) of Effluent Treatment Plant and the other a textile effluent dye Ácido Blue 113 (AB 113) was synthesized in the laboratory. In the electrochemical process, the effects of anode material, current density, the presence and concentration of chloride as well as the active chlorine species on site generated were evaluated. Electrodes of different compositions, Ti/Pt, Ti/Ru0,3Ti0,7O2, BDD, Pb/PbO2 and Ti/TiO2-nanotubes/PbO2 were used as anodes. These electrodes were subjected to electroanalytical analysis with the goal of checking how happen the anodic and cathodic processes across the concentrations of NaCl and supporting electrolyte used. The potential of oxygen evolution reaction were also checked. The effect of active chlorine species formed under the process efficiency was evaluated by removing the organic matter in the effluent-ETE UFRN. The wastewater treatment ETE-UFRN using Ti/Pt, DDB and Ti/Ru0,3Ti0,7O2 electrodes was evaluated, obtaining good performances. The electrochemical degradation of effluent-UFRN was able to promote the reduction of the concentration of TOC and COD in all tested anodes. However, Ti/Ru0,3Ti0,7O2 showed a considerable degradation due to active chlorine species generated on site. The results obtained from the electrochemical process in the presence of chloride were more satisfactory than those obtained in the absence. The addition of 0.021 M NaCl resulted in a faster removal of organic matter. Secondly, was prepared and characterized the electrode Ti/TiO2-nanotubes/PbO2 according to what the literature reports, however their preparation was to disk (10 cm diameter) with surface area and higher than that described by the same authors, aiming at application to textile effluent AB 113 dye. SEM images were taken to observe the growth of TiO2 nanotubes and confirm the electrodeposition of PbO2. Atomic Force Microscope was also used to confirm the formation of these nanotubes. Furthermore, was tested and found a high electrochemical stability of the electrode Ti/TiO2-nanotubes/PbO2 for applications such as long-term indicating a good electrocatalytic material. The electrochemical oxidation of AB 113 using Ti/Pt, Pb/PbO2 and Ti/TiO2-nanotubes/PbO2 and Al/Al (electrocoagulation) was also studied. However, the best color removal and COD decay were obtained when Ti/TiO2-nanotubes/PbO2 was used as the anode, removing up to 98% of color and 92,5% of COD decay. Analysis of GC/MS were performed in order to identify possible intermediates formed in the degradation of AB 113.

Tecnologia eletroquímica como tratamento alternativo de efluentes derivados da indústria têxtil e petroquímica

In this work, the treatment of wastewater from the textile industry, containing dyes as Yellow Novacron (YN), Red Remazol BR (RRB) and Blue Novacron CD (NB), and also, the treatment of wastewater from petrochemical industry (produced water) were investigated by anodic oxidation (OA) with platinum anodes supported on titanium (Ti/Pt) and boron-doped diamond (DDB). Definitely, one of the main parameters of this kind of treatment is the type of electrocatalytic material used, since the mechanisms and products of some anodic reactions depend on it. The OA of synthetic effluents containing with RRB, NB and YN were investigated in order to find the best conditions for the removal of color and organic content of the dye. According to the experimental results, the process of OA is suitable for decolorization of wastewaters containing these textile dyes due to electrocatalytic properties of DDB and Pt anodes. Removal of the organic load was more efficient at DDB, in all cases; where the dyes were degraded to aliphatic carboxylic acids at the end of the electrolysis. Energy requirements for the removal of color during OA of solutions of RRB, NB and YN depends mainly on the operating conditions, for example, RRB passes of 3.30 kWh m-3 at 20 mA cm-2 for 4.28 kWh m-3 at 60 mA cm-2 (pH = 1); 15.23 kWh m-3 at 20 mA cm-2 to 24.75 kWh m-3 at 60 mA cm-2 (pH 4.5); 10.80 kWh m-3 at 20 mA cm-2 to 31.5 kWh m-3 at 60 mA cm-2 (pH = 8) (estimated data for volume of treated effluent). On the other hand, in the study of OA of produced water effluent generated by petrochemical industry, galvanostatic electrolysis using DDB led to the complete removal of COD (98%), due to large amounts of hydroxyl radicals and peroxodisulphates generated from the oxidation of water and sulfates in solution, respectively. Thus, the rate of COD removal increases with increasing applied current density (15-60 mAcm-2 ). Moreover, at Pt electrode, approximately 50% removal of the organic load was achieved by applying from 15 to 30 mAcm-2 while 80% of COD removal was achieved for 60 mAcm-2 . Thus, the results obtained in the application of this technology were satisfactory depending on the electrocatalytic materials and operating conditions used for removal of organic load (petrochemical and textile effluents) as well as for the removal of color (in the case of textile effluents). Therefore, the applicability of electrochemical treatment can be considered as a new alternative like pretreatment or treatment of effluents derived from textiles and petrochemical industries.

Caracterização estrutural e atividades farmacológicas do alginato obtido da alga Dictyopteris delicatula (J.V. Lamouroux., 1809) e seu derivado sulfatado

Marine algae are rich sources of various structural compounds which recently has been increasingly studied as a new source of bioactive substances. The alginate, as come as fucans, are considered the main acidic polysaccharides found in brown seaweed. This molecule consists a linear natural polysaccharide, non-sulfated, and presents monosaccharides: acid β-D-mannuronic (M) and α-L-guluronic acid (G); in a vast amount compositions and threads. Alginate has been widely applied in food and pharmaceutical industries because of its ability to retain water, forming films and gels as well as thickening, stabilizing and form emulsions. In this work we aimed to extract, structurally characterize, compare and analyze the possible pharmacological activities of native alginate molecule obtained from brown seaweed Dyctiopteris delicatula (DYN), and its chemically sulfated derivative (DYS). The alginate structure and composition molecule can be proven through chemical dosing, that showed low protein contamination and high sugar level, existence and separation of M and G blocks in the descending paper chromatography, infrared spectroscopy and nuclear magnetic resonance. Molecule sulfation was proven with sulphate dosage, resulting in 28.56% sulphate in molecule; electrophoresis, verify metachromasia with toluidine blue; and infrared spectroscopy, that showed a characteristic band at 1221cm-1 corresponding a sulfate group vibration. For the pharmacological activities the tests was: antioxidant activity, changes in cell function (MTT test) and anticoagulant test. In the antioxidant activity we observed that DYN showed better results in the kidnapping of hydroxyl radicals and ferric chelation compared to DYS, this had the best result in the total antioxidant capacity. Both showed similar activity in reducing power and the kidnapping radicals DPPH. In MTT test DYN and DYS had not proliferative and cytotoxic activity in fibroblast cells (3T3) and showed antiproliferative and cytotoxic activity in cancer cell lines HeLa and B16 melanoma. In anticoagulant assay DYN showed good activity in the intrinsic pathway of blood coagulation, and a small activity in the extrinsic pathway, in the other hand DYS showed only a very small activity in the extrinsic pathway, but cannot come to be regarded as an anticoagulant agent. From these results it can be concluded that the alginate was extracted and sulfated, revealing a potential compound to be used in the pharmaceutical industry as an anticoagulant agent, antioxidant and antitumor and the sulfation has not been conclusively important to performance in the tested pharmacological activities

Modelagem da degradação de fenol em efluentes aquosos através do processo de foto-fenton

Advanced Oxidation Processes (AOP) are techniques involving the formation of hydroxyl radical (HO•) with high organic matter oxidation rate. These processes application in industry have been increasing due to their capacity of degrading recalcitrant substances that cannot be completely removed by traditional processes of effluent treatment. In the present work, phenol degrading by photo-Fenton process based on addition of H2O2, Fe2+ and luminous radiation was studied. An experimental design was developed to analyze the effect of phenol, H2O2 and Fe2+ concentration on the fraction of total organic carbon (TOC) degraded. The experiments were performed in a batch photochemical parabolic reactor with 1.5 L of capacity. Samples of the reactional medium were collected at different reaction times and analyzed in a TOC measurement instrument from Shimadzu (TOC-VWP). The results showed a negative effect of phenol concentration and a positive effect of the two other variables in the TOC degraded fraction. A statistical analysis of the experimental design showed that the hydrogen peroxide concentration was the most influent variable in the TOC degraded fraction at 45 minutes and generated a model with R² = 0.82, which predicted the experimental data with low precision. The Visual Basic for Application (VBA) tool was used to generate a neural networks model and a photochemical database. The aforementioned model presented R² = 0.96 and precisely predicted the response data used for testing. The results found indicate the possible application of the developed tool for industry, mainly for its simplicity, low cost and easy access to the program.

Modelagem da degradação de fenol em efluentes aquosos através do processo de foto-fenton

Advanced Oxidation Processes (AOP) are techniques involving the formation of hydroxyl radical (HO•) with high organic matter oxidation rate. These processes application in industry have been increasing due to their capacity of degrading recalcitrant substances that cannot be completely removed by traditional processes of effluent treatment. In the present work, phenol degrading by photo-Fenton process based on addition of H2O2, Fe2+ and luminous radiation was studied. An experimental design was developed to analyze the effect of phenol, H2O2 and Fe2+ concentration on the fraction of total organic carbon (TOC) degraded. The experiments were performed in a batch photochemical parabolic reactor with 1.5 L of capacity. Samples of the reactional medium were collected at different reaction times and analyzed in a TOC measurement instrument from Shimadzu (TOC-VWP). The results showed a negative effect of phenol concentration and a positive effect of the two other variables in the TOC degraded fraction. A statistical analysis of the experimental design showed that the hydrogen peroxide concentration was the most influent variable in the TOC degraded fraction at 45 minutes and generated a model with R² = 0.82, which predicted the experimental data with low precision. The Visual Basic for Application (VBA) tool was used to generate a neural networks model and a photochemical database. The aforementioned model presented R² = 0.96 and precisely predicted the response data used for testing. The results found indicate the possible application of the developed tool for industry, mainly for its simplicity, low cost and easy access to the program.

(Table 1) Ratio of hydroxy-GDGT vs. the total core GDGT was calculated based on the detection of hydroxy-GDGT

Hydroxylated glycerol dialkyl glycerol tetraethers (hydroxy-GDGTs) were detected in marine sediments of diverse depositional regimes and ages. Mass spectrometric evidence, complemented by information gleaned from two-dimensional (2D) 1H-13C nuclear magnetic resonance (NMR) spectroscopy on minute quantities of target analyte isolated from marine sediment, allowed us to identify one major compound as a monohydroxy-GDGT with acyclic biphytanyl moieties (OH-GDGT-0). NMR spectroscopic and mass spectrometric data indicate the presence of a tertiary hydroxyl group suggesting the compounds are the tetraether analogues of the widespread hydroxylated archaeol derivatives that have received great attention in geochemical studies of the last two decades. Three other related compounds were assigned as acyclic dihydroxy-GDGT (2OH-GDGT-0) and monohydroxy-GDGT with one (OH-GDGT-1) and two cyclopentane rings (OH-GDGT-2). Based on the identification of hydroxy-GDGT core lipids, a group of previously reported unknown intact polar lipids (IPLs), including the ubiquitously distributed H341-GDGT (Lipp J. S. and Hinrichs K. -U. (2009) Structural diversity and fate of intact polar lipids in marine sediments. Geochim. Cosmochim. Acta 73, 6816-6833), and its analogues were tentatively identified as glycosidic hydroxy-GDGTs. In addition to marine sediments, we also detected hydroxy-GDGTs in a culture of Methanothermococcus thermolithotrophicus. Given the previous finding of the putative polar precursor H341-GDGT in the planktonic marine crenarchaeon Nitrosopumilus maritimus, these compounds are synthesized by representatives of both cren- and euryarchaeota. The ubiquitous distribution and apparent substantial abundance of hydroxy-GDGT core lipids in marine sediments (up to 8% of total isoprenoid core GDGTs) point to their potential as proxies.

Degradação de paracetamol empregando tecnologia oxidativa avançada baseada em fotocatálise heterogênea usando irradiação artificial e solar

In this work, the oxidation and mineralization of paracetamol, based in an advanced oxidative process promoted by heterogeneous photocatalysis, was evaluated. The action of two photocatalysts (titanium dioxide, and a composite based on the association between titanium dioxide and zinc phthalocyanine dye) was studied. First of all, experiments in laboratory scale were performed using as radiation font a 400 W high pressure mercury lamp. The mineralization of paracetamol, promoted by both photocatalysts, was evaluated working with 4L of solution containing 10 mg L-1 of paracetamol and 100 mg L-1 of photocatalyst. To find the best experimental conditions, the influence of hydrogen peroxide concentration and pH was evaluated for the reactions. The best results for the reactions in laboratory scale was obtained using 33,00 mg L-1 of hydrogen peroxide in natural pH (6,80). Under these conditions, 100% oxidation was reached in just 40 minutes of reaction using TiO2 P25, while the mineralization was 78%. Using the composite, the mineralization was 63% in 2 hours of reaction and a oxidation of almost 100% was reached after 60 minutes. A CPC reactor (compound parabolic concentrator) was employed in the expanded work scale, using the sun as irradiation source. In this case the experiments were performed using 50 L of aqueous solution containing 10 mg L-1 of paracetamol and 100 mg L-1 of photocatalyst. The assays were done at pH 3,00 and natural pH (6,80). The used concentration of hydrogen peroxide was 33,00 mg L-1, adopted after laboratory scale studies. The reaction at pH 3,00 shows to be more advantageous, since under natural pH (6,80), the use of deionized water was necessary to prepare the solutions, probably because the deleterious action of carbonate ions, known hydroxyl radical scavengers. Using solar irradiation, the reaction mediated by the composite was more efficient when compared with the assays under laboratory scale since the composite presents the advantage of promoting a better use of visible radiation. Under these conditions, the mineralization increased from 40% to 56% under pH 3,00. At natural pH the oxidation occurred more slowly and the mineralization decreased from 56% to 50%. Thus, the use of pH 3,00 will be more interesting in real scale applications, even if it is necessary the pH correction before the discard of the treated effluent to the environment.

Structural and Biochemical Dissection of the Trehalose Biosynthetic Complex in Pathogenic Fungi

Trehalose is a non-reducing disaccharide essential for pathogenic fungal survival and virulence. The biosynthesis of trehalose requires the trehalose-6-phosphate synthase, Tps1, and trehalose-6-phosphate phosphatase, Tps2. More importantly, the trehalose biosynthetic pathway is absent in mammals, conferring this pathway as an ideal target for antifungal drug design. However, lack of germane biochemical and structural information hinders antifungal drug design against these targets.

In this dissertation, macromolecular X-ray crystallography and biochemical assays were employed to understand the structures and functions of proteins involved in the trehalose biosynthetic pathway. I report here the first eukaryotic Tps1 structures from Candida albicans (C. albicans) and Aspergillus fumigatus (A. fumigatus) with substrates or substrate analogs. These structures reveal the key residues involved in substrate binding and catalysis. Subsequent enzymatic assays and cellular assays highlight the significance of these key Tps1 residues in enzyme function and fungal stress response. The Tps1 structure captured in its transition-state with a non-hydrolysable inhibitor demonstrates that Tps1 adopts an “internal return like” mechanism for catalysis. Furthermore, disruption of the trehalose biosynthetic complex formation through abolishing Tps1 dimerization reveals that complex formation has regulatory function in addition to trehalose production, providing additional targets for antifungal drug intervention.

I also present here the structure of the Tps2 N-terminal domain (Tps2NTD) from C. albicans, which may be involved in the proper formation of the trehalose biosynthetic complex. Deletion of the Tps2NTD results in a temperature sensitive phenotype. Further, I describe in this dissertation the structures of the Tps2 phosphatase domain (Tps2PD) from C. albicans, A. fumigatus and Cryptococcus neoformans (C. neoformans) in multiple conformational states. The structures of the C. albicans Tps2PD -BeF3-trehalose complex and C. neoformans Tps2PD(D24N)-T6P complex reveal extensive interactions between both glucose moieties of the trehalose involving all eight hydroxyl groups and multiple residues of both the cap and core domains of Tps2PD. These structures also reveal that steric hindrance is a key underlying factor for the exquisite substrate specificity of Tps2PD. In addition, the structures of Tps2PD in the open conformation provide direct visualization of the conformational changes of this domain that are effected by substrate binding and product release.

Last, I present the structure of the C. albicans trehalose synthase regulatory protein (Tps3) pseudo-phosphatase domain (Tps3PPD) structure. Tps3PPD adopts a haloacid dehydrogenase superfamily (HADSF) phosphatase fold with a core Rossmann-fold domain and a α/β fold cap domain. Despite lack of phosphatase activity, the cleft between the Tps3PPD core domain and cap domain presents a binding pocket for a yet uncharacterized ligand. Identification of this ligand could reveal the cellular function of Tps3 and any interconnection of the trehalose biosynthetic pathway with other cellular metabolic pathways.

Combined, these structures together with significant biochemical analyses advance our understanding of the proteins responsible for trehalose biosynthesis. These structures are ready to be exploited to rationally design or optimize inhibitors of the trehalose biosynthetic pathway enzymes. Hence, the work described in this thesis has laid the groundwork for the design of Tps1 and Tps2 specific inhibitors, which ultimately could lead to novel therapeutics to treat fungal infections.

Development and Application of Covalent-Labeling Strategies for the Large-Scale Thermodynamic Analysis of Protein Folding and Ligand Binding

Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional calorimetric or spectroscopic approaches for measuring protein stability typically require large amounts of purified protein. This requirement has precluded their use in proteomic applications. Stability of Proteins from Rates of Oxidation (SPROX) is a recently developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new SPROX-like protocol was developed that measured protein folding free energies using the denaturant dependence of the rate at which globally protected tryptophan and methionine residues are modified with dimethyl (2-hydroxyl-5-nitrobenzyl) sulfonium bromide and hydrogen peroxide, respectively. This so-called Hybrid protocol was applied to proteins in yeast and MCF-7 cell lysates and achieved a ~50% increase in proteomic coverage compared to probing only methionine-containing peptides. Subsequently, the Hybrid protocol was successfully utilized to identify and quantify both known and novel protein-ligand interactions in cell lysates. The ligands under study included the well-known Hsp90 inhibitor geldanamycin and the less well-understood omeprazole sulfide that inhibits liver-stage malaria. In addition to protein-small molecule interactions, protein-protein interactions involving Puf6 were investigated using the SPROX technique in comparative thermodynamic analyses performed on wild-type and Puf6-deletion yeast strains. A total of 39 proteins were detected as Puf6 targets and 36 of these targets were previously unknown to interact with Puf6. Finally, to facilitate the SPROX/Hybrid data analysis process and minimize human errors, a Bayesian algorithm was developed for transition midpoint assignment. In summary, the work in this dissertation expanded the scope of SPROX and evaluated the use of SPROX/Hybrid protocols for characterizing protein-ligand interactions in complex biological mixtures.

Effect of reaction mechanism on precursor exposure time in atomic layer deposition of silicon oxide and silicon nitride

Atomic layer deposition (ALD) of highly conformal, silicon-based dielectric thin films has become necessary because of the continuing decrease in feature size in microelectronic devices. The ALD of oxides and nitrides is usually thought to be mechanistically similar, but plasma-enhanced ALD of silicon nitride is found to be problematic, while that of silicon oxide is straightforward. To find why, the ALD of silicon nitride and silicon oxide dielectric films was studied by applying ab initio methods to theoretical models for proposed surface reaction mechanisms. The thermodynamic energies for the elimination of functional groups from different silicon precursors reacting with simple model molecules were calculated using density functional theory (DFT), explaining the lower reactivity of precursors toward the deposition of silicon nitride relative to silicon oxide seen in experiments, but not explaining the trends between precursors. Using more realistic cluster models of amine and hydroxyl covered surfaces, the structures and energies were calculated of reaction pathways for chemisorption of different silicon precursors via functional group elimination, with more success. DFT calculations identified the initial physisorption step as crucial toward deposition and this step was thus used to predict the ALD reactivity of a range of amino-silane precursors, yielding good agreement with experiment. The retention of hydrogen within silicon nitride films but not in silicon oxide observed in FTIR spectra was accounted for by the theoretical calculations and helped verify the application of the model.

Enzymatic Polymerization of High Molecular Weight DNA

The use of DNA as a polymeric building material transcends its function in biology and is exciting in bionanotechnology for applications ranging from biosensing, to diagnostics, and to targeted drug delivery. These applications are enabled by DNA’s unique structural and chemical properties, embodied as a directional polyanion that exhibits molecular recognition capabilities. Hence, the efficient and precise synthesis of high molecular weight DNA materials has become key to advance DNA bionanotechnology. Current synthesis methods largely rely on either solid phase chemical synthesis or template-dependent polymerase amplification. The inherent step-by-step fashion of solid phase synthesis limits the length of the resulting DNA to typically less than 150 nucleotides. In contrast, polymerase based enzymatic synthesis methods (e.g., polymerase chain reaction) are not limited by product length, but require a DNA template to guide the synthesis. Furthermore, advanced DNA bionanotechnology requires tailorable structural and self-assembly properties. Current synthesis methods, however, often involve multiple conjugating reactions and extensive purification steps.

The research described in this dissertation aims to develop a facile method to synthesize high molecular weight, single stranded DNA (or polynucleotide) with versatile functionalities. We exploit the ability of a template-independent DNA polymerase−terminal deoxynucleotidyl transferase (TdT) to catalyze the polymerization of 2’-deoxyribonucleoside 5’-triphosphates (dNTP, monomer) from the 3’-hydroxyl group of an oligodeoxyribonucleotide (initiator). We termed this enzymatic synthesis method: TdT catalyzed enzymatic polymerization, or TcEP.

Specifically, this dissertation is structured to address three specific research aims. With the objective to generate high molecular weight polynucleotides, Specific Aim 1 studies the reaction kinetics of TcEP by investigating the polymerization of 2’-deoxythymidine 5’-triphosphates (monomer) from the 3’-hydroxyl group of oligodeoxyribothymidine (initiator) using in situ 1H NMR and fluorescent gel electrophoresis. We found that TcEP kinetics follows the “living” chain-growth polycondensation mechanism, and like in “living” polymerizations, the molecular weight of the final product is determined by the starting molar ratio of monomer to initiator. The distribution of the molecular weight is crucially influenced by the molar ratio of initiator to TdT. We developed a reaction kinetics model that allows us to quantitatively describe the reaction and predict the molecular weight of the reaction products.

Specific Aim 2 further explores TcEP’s ability to transcend homo-polynucleotide synthesis by varying the choices of initiators and monomers. We investigated the effects of initiator length and sequence on TcEP, and found that the minimum length of an effective initiator should be 10 nucleotides and that the formation of secondary structures close to the 3’-hydroxyl group can impede the polymerization reaction. We also demonstrated TcEP’s capacity to incorporate a wide range of unnatural dNTPs into the growing chain, such as, hydrophobic fluorescent dNTP and fluoro modified dNTP. By harnessing the encoded nucleotide sequence of an initiator and the chemical diversity of monomers, TcEP enables us to introduce molecular recognition capabilities and chemical functionalities on the 5’-terminus and 3’-terminus, respectively.

Building on TcEP’s synthesis capacities, in Specific Aim 3 we invented a two-step strategy to synthesize diblock amphiphilic polynucleotides, in which the first, hydrophilic block serves as a macro-initiator for the growth of the second block, comprised of natural and/or unnatural nucleotides. By tuning the hydrophilic length, we synthesized the amphiphilic diblock polynucleotides that can self-assemble into micellar structures ranging from star-like to crew-cut morphologies. The observed self-assembly behaviors agree with predictions from dissipative particle dynamics simulations as well as scaling law for polyelectrolyte block copolymers.

In summary, we developed an enzymatic synthesis method (i.e., TcEP) that enables the facile synthesis of high molecular weight polynucleotides with low polydispersity. Although we can control the nucleotide sequence only to a limited extent, TcEP offers a method to integrate an oligodeoxyribonucleotide with specific sequence at the 5’-terminus and to incorporate functional groups along the growing chains simultaneously. Additionally, we used TcEP to synthesize amphiphilic polynucleotides that display self-assemble ability. We anticipate that our facile synthesis method will not only advance molecular biology, but also invigorate materials science and bionanotechnology.

Design and Synthesis of 4-N-Alkanoyl and 4-N-Alkyl Gemcitabine Analogues Suitable for Positron Emission Tomography

Gemcitabine is a highly potent chemotherapeutic nucleoside agent used in the treatment of several cancers and solid tumors. However, it is therapeutically limitated because of toxicity to normal cells and its rapid intracellular deamination by cytidine deaminase into the inactive uracil derivative. Modification at the 4-(N) position of gemcitabine's exocyclic amine to an -amide functionality is a well reported prodrug strategy which has been that confers a resistance to intracellular deamination while also altering pharmacokinetics of the parent drug. Coupling of gemcitabine to carboxylic acids with varying terminal moieties afforded the 4-N-alkanoylgemcitabines whereas reaction of 4-N-tosylgemcitabine with the corresponding alkyl amines gave the 4-N-alkylgemcitabines. The 4-N-alkanoyl and 4-N-alkyl gemcitabine analogues with a terminal hydroxyl group on the 4-N-alkanoyl or 4-N-alkyl chain were efficiently fluorinated either with diethylaminosulfur trifluoride or under conditions that are compatible with the synthetic protocols for 18F labeling, such as displacement of the corresponding mesylate with KF/Kryptofix 2.2.2. The 4-N-alkanoylgemcitabine analogues displayed potent cytostatic activities against murine and human tumor cell lines with 50% inhibitory concentration (IC50) values in the range of low nM, whereas cytotoxicity of the 4-N-alkylgemcitabine derivatives were in the low to modest µM range. The cytostatic activity of the 4-N-alkanoylgemcitabines was reduced by several orders of magnitude in the 2'-deoxycytidine kinase (dCK)-deficient CEM/dCK- cell line while the 4-N-alkylgemcitabines were only lowered by 2-5 times. None of the 4-N-modified gemcitabines were found to be substrates for cytosolic dCK, however all were found to inhibit DNA synthesis. As such, the 4-N-alkanoyl gemcitabine derivatives likely need to be converted to gemcitabine prior to achieving their significant cytostatic potential, whereas the 4-N-alkylgemcitabines reach their modest activity without "measurable" conversion to gemcitabine. Thus, the 4-N-alkylgemcitabines provide valuable insight on the metabolism of 4-N-modified gemcitabine prodrugs.

Mineralogy, isotopic composition of oxygen, hydrogen and carbon, and oxygen isotopic temperature of deep-sea silica and coexisting carbonates (Table 1)

Water extracted from opal-CT ("porcellanite", "cristobalite"), granular microcrystalline quartz (chert), and pure fibrous quartz (chalcedony) in cherts from the JOIDES Deep Sea Drilling Project is 56? to 87? depleted in deuterium relative to the water in which the silica formed. This large fractionation is similar in magnitude and sign to that observed for hydroxyl in clay minerals and suggests that water extracted from these forms of silica has been derived from hydroxyl groups within the silica. Delta18O-values for opal-CT at sites 61, 64, 70B and 149 vary from 34.3? to 37.2? and show no direct correlation with depth of burial. Granular microcrystaUine quartz in these cores is 0.5 ? depleted in 18O relative to coexisting opal-CT at sediment depths of 100 m and the depletion increases to 2? for sediments buried below 384 m. These relationships suggest that opal-CT forms before significant burial while granular microcrystalline quartz forms during deeper burial at warmer temperatures. The temperature at which opal-CT forms is thus probably approximately equal to the temperature of the overlying bottom water. Isotopic temperatures deduced for opal-CT formation are preliminary and very approximate, but yield Eocene deep-water temperatures of 5-13°C, and 6°C for the upper Cretaceous sample. Pure euhedral quartz crystals lining a cavity in opal-CT at 388 m in core 8-70B-4-CC have a ~delta18O value of +29.8? and probably formed near maximum burial. The isotopic temperature is approximately 32 ° C.

BLOCK COPOLYMERS CONTAINING A LOW-SURFACE-ENERGY BLOCK AND THEIR APPLICATIONS

This thesis reports the synthesis and/or applications of three types of block copolymers that each bear a low-surface-energy block. First, poly(dimethylsiloxane)-block-poly(2-cinnamoyloxyethyl acrylate) (PDMS-b-PCEA) was synthesized and characterized. Cotton coating using a micellar solution of this block copolymer yielded superhydrophobic cotton fabrics. X-ray photoelectron spectroscopy (XPS) and surface property analyses indicated that the PDMS block topped the polymer coating. Photocuring the cotton swatches crosslinked the underlying PCEA layer and yielded permanent coatings. More interestingly, hydrophilically patterned superhydrophobic cotton fabrics were produced using photolithography that allowed the crosslinking of the coating around irradiated fibers but the removal, by solvent extraction, of the coating on fibers that were not irradiated. Since water-based ink only permeated the uncoated regions, such patterned fabric was further used to print ink patterns onto substrates such as fabrics, cardboard, paper, wood, and aluminum foil. Then, another PDMS-based diblock copolymer poly(dimethylsiloxane)-block-poly(glycidyl methacrylate) (PDMS-b-PGMA) was prepared. Different from PCEA that photocrosslinked around cotton fibers, PGMA reacted with hydroxyl groups on cotton fiber surfaces to get covalently attached. Further, different PGMA chains crosslinked with each other. PDMS-b-PGMA-coated cotton fabrics have been used for oil-water separations. In addition, polymeric nanoparticles were grafted onto cotton fiber surface before PDMS-b-PGMA was used to cover the surfaces of the grafted spheres and the residual surfaces of the cotton fibers. These two types of fabrics, coated by the block copolymer alone or by the polymer nanospheres and then the copolymer, were characterized by scanning electron microscope (SEM), Fourier transform infrared spectroscopy (FT-IR), and water repellency analyses. A comprehensive comparative study was made of their performances in oil-water separation. Finally, a fluorinated ABC triblock copolymer poly(acrylic acid)-block-poly(2-cinnamoyloxyethyl methacrylate)-block-poly(2-perfluorooctylethyl methacrylate) (PAA-b-PCEMA-b-PFOEMA) was used to iii encapsulate air nanobubbles. The produced air nanobubbles were thermodynamically stable in water and were some 100 times more stable than commercially available perfluorocarbon-filled microbubbles under ultrasound. These nanobubbles, due to their small sizes and thus ability to permeate the capillary networks of organs and to reach tumors, may expand the applications of microbubbles in diagnostic ultrasonography and find new applications in ultrasound-regulated drug delivery.