by Yau Ming Hon. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (leaves 131-154). / Abstracts in English and Chinese. / Contents --- p.i / Acknowledgements --- p.ix / Abstract --- p.x / 槪論 --- p.xi / List of abbreviations --- p.xii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Reactive oxygen species (ROS) --- p.2 / Chapter 1.1.1 --- Hydrogen peroxide --- p.2 / Chapter 1.1.2 --- Superoxide anion --- p.3 / Chapter 1.1.3 --- Hydroxyl radical --- p.3 / Chapter 1.1.4 --- Carbon centered radical --- p.4 / Chapter 1.1.5 --- Nitric oxide --- p.4 / Chapter 1.2 --- Physiological roles of ROS --- p.5 / Chapter 1.2.1 --- Signal transduction --- p.5 / Chapter 1.2.2 --- Phagocytic activity --- p.6 / Chapter 1.3 --- Defense systems against ROS --- p.7 / Chapter 1.3.1 --- Endogenous antioxidant enzymes --- p.8 / Chapter 1.3.1.1 --- Catalase --- p.8 / Chapter 1.3.1.2 --- Superoxide dismutase --- p.8 / Chapter 1.3.1.3 --- Selenium-glutathione peroxidase --- p.9 / Chapter 1.3.1.4 --- Glutathione reductase --- p.10 / Chapter 1.3.1.5 --- Glutathione-S-transferases --- p.10 / Chapter 1.3.2 --- Non-enzymatic antioxidants --- p.12 / Chapter 1.3.2.1 --- Vitamin E (tocopherols and tocotrienols) --- p.12 / Chapter 1.3.2.2 --- Vitamin C (L-ascorbic acid) --- p.13 / Chapter 1.3.2.3 --- Glutathione --- p.14 / Chapter 1.3.2.4 --- Flavonoids and polyphenols --- p.15 / Chapter 1.3.2.5 --- Uric acid --- p.16 / Chapter 1.4 --- Roles of ROS in pathogenesis --- p.16 / Chapter 1.4.1 --- Liver diseases --- p.17 / Chapter 1.4.2 --- Genital malfunctioning --- p.19 / Chapter 1.5 --- "The traditional Chinese medicinal formula, Wu-zi-yan-zong-wan" --- p.19 / Chapter 1.5.1 --- Pharmacology of individual herbal components --- p.20 / Chapter 1.5.1.1 --- Semen Cuscuta --- p.20 / Chapter 1.5.1.2 --- Fructus Lycii --- p.21 / Chapter 1.5.1.3 --- Fructus Schisandrae --- p.21 / Chapter 1.5.1.4 --- Fructus Rubi --- p.22 / Chapter 1.5.1.5 --- Semen Plantaginis --- p.22 / Chapter 1.5.2 --- Effect of Wu-zi-yan-zong-wan on infertility --- p.23 / Chapter 1.5.3 --- Effect of Wu-zi-yan-zong-wan on liver disease --- p.23 / Chapter 1.6 --- Objectives of the present study --- p.24 / Chapter Chapter 2 --- Antioxidant Activity of Aqueous Extracts of the Herbal Components of Wu-zi-yan-zong-wan in in vitro Free Radical Generating Systems --- p.26 / Chapter 2.1 --- Introduction --- p.27 / Chapter 2.1.1 --- Application of in vitro ROS generating systems --- p.27 / Chapter 2.1.1.1 --- Superoxide generation --- p.27 / Chapter 2.1.1.2 --- Hydroxyl radical generation system --- p.28 / Chapter 2.1.1.3 --- "2,2'-Azobis(2-amidinopropane) dihydrochloride- induced hemolysis" --- p.28 / Chapter 2.1.1.4 --- Bleomycin-iron-dependent DNA damage --- p.28 / Chapter 2.1.2 --- Objective --- p.29 / Chapter 2.2 --- Materials and methods --- p.30 / Chapter 2.2.1 --- Materials --- p.30 / Chapter 2.2.2 --- Preparation of aqueous herbal extracts --- p.30 / Chapter 2.2.3 --- Superoxide-scavenging assay --- p.30 / Chapter 2.2.4 --- Microsome lipid peroxidation inhibition assay --- p.31 / Chapter 2.2.5 --- "2,2'-Azobis(2-amidinopropane) dihydrochloride-induced hemolysis inhibition assay" --- p.32 / Chapter 2.2.6 --- Bleomycin-iron-dependent DNA damage inhibition assay --- p.32 / Chapter 2.2.7 --- Statistical analysis --- p.33 / Chapter 2.3 --- Results --- p.34 / Chapter 2.3.1 --- Extraction yield --- p.34 / Chapter 2.3.2 --- Free radical scavenging activity of Wu-zi-yan-zong-wan extract --- p.34 / Chapter 2.3.3 --- Free radical scavenging activity of FR extract --- p.37 / Chapter 2.3.3.1 --- Superoxide-scavenging activity --- p.37 / Chapter 2.3.3.2 --- Effect on hydroxyl radical-induced lipid peroxidation --- p.37 / Chapter 2.3.3.3 --- Effect on AAPH-induced hemolysis --- p.40 / Chapter 2.3.3.4 --- Effect on bleomycin-iron-dependent DNA damage --- p.40 / Chapter 2.3.4 --- Pro-oxidant activity of FR extract --- p.40 / Chapter 2.3.5 --- Free radical scavenging activity of the remaining herbal extracts --- p.44 / Chapter 2.4 --- Discussion --- p.46 / Chapter Chapter 3 --- Effect of Aqueous Extract of the Herbal Components of Wu- zi-yan-zong-wan on tert-Butyl Hydroperoxide-Induced Oxidative Damage in Primary Rat Hepatocyte --- p.51 / Chapter 3.1 --- Introduction --- p.52 / Chapter 3.1.1 --- Primary rat hepatocyte as pharmacological model --- p.52 / Chapter 3.1.2 --- tert-Butyl hydroperoxide as an oxidative stress inducer --- p.53 / Chapter 3.1.3 --- Detection of ROS --- p.54 / Chapter 3.1.4 --- Objective --- p.55 / Chapter 3.2 --- Materials and methods --- p.56 / Chapter 3.2.1 --- Materials --- p.56 / Chapter 3.2.2 --- Primary rat hepatocyte isolation --- p.56 / Chapter 3.2.2.1 --- Liver perfusion --- p.56 / Chapter 3.2.2.2 --- Collagen pre-coated plates preparation --- p.57 / Chapter 3.2.2.3 --- Hepatocyte culture --- p.58 / Chapter 3.2.3 --- Drug treatment and oxidative stress induction --- p.58 / Chapter 3.2.4 --- Cytotoxicity assessment --- p.58 / Chapter 3.2.4.1 --- Lactate dehydrogenase leakage measurement --- p.59 / Chapter 3.2.4.2 --- MTT assay --- p.59 / Chapter 3.2.5 --- Cellular GSH content determination --- p.59 / Chapter 3.2.6 --- Protein determination by Lowry's method --- p.60 / Chapter 3.2.7 --- MDA measurement --- p.60 / Chapter 3.2.8 --- GSSG measurement --- p.61 / Chapter 3.2.9 --- ROS measurement with fluorescent dye --- p.61 / Chapter 3.2.10 --- "Vitamin C, vitamin E and butylated hydroxytoluene treatment" --- p.62 / Chapter 3.2.11 --- Antioxidant enzyme activity measurement --- p.62 / Chapter 3.2.11.1 --- Catalase activity measurement --- p.62 / Chapter 3.2.11.2 --- Superoxide dismutase activity measurement --- p.63 / Chapter 3.2.11.3 --- Glutathione peroxidase activity measurement --- p.63 / Chapter 3.2.11.4 --- Glutathione-S-transferases activity measurement --- p.63 / Chapter 3.2.11.5 --- Glutathione reductase activity measurement --- p.64 / Chapter 3.2.12 --- Statistical analysis --- p.64 / Chapter 3.3 --- Results --- p.65 / Chapter 3.3.1 --- Cytotoxicity of FR extract on rat hepatocyte --- p.65 / Chapter 3.3.2 --- Effect of tBHP and FR extract on hepatocyte viability --- p.65 / Chapter 3.3.3 --- Time-dependent effect of FR extract on tBHP-induced cytotoxicity --- p.69 / Chapter 3.3.4 --- Effect of tBHP and FR extract on hepatocyte GSH content --- p.69 / Chapter 3.3.5 --- Effect of tBHP and FR extract on GSSG formation in hepatocyte --- p.72 / Chapter 3.3.6 --- Effect of tBHP and FR extract on MDA formation in hepatocyte --- p.72 / Chapter 3.3.7 --- ROS-scavenging activity of FR extract in hepatocyte --- p.77 / Chapter 3.3.8 --- Effect of FR extract on antioxidant enzymes activities --- p.77 / Chapter 3.3.9 --- Comparison between typical antioxidants --- p.77 / Chapter 3.3.10 --- Effect of WZ and remaining herbal extracts on tBHP-induced oxidative damage in hepatocyte --- p.81 / Chapter 3.4 --- Discussion --- p.84 / Chapter Chapter 4 --- Effect of Aqueous Extract of Wu-zi-yan-zong-wan and Fructus Rubi on tert-Buty Hydroperoxide Induced Oxidative Damage in Mouse Model --- p.91 / Chapter 4.1 --- Introduction --- p.92 / Chapter 4.2 --- Materials and methods --- p.93 / Chapter 4.2.1 --- Materials --- p.93 / Chapter 4.2.2 --- Animal treatments --- p.93 / Chapter 4.2.3 --- Serum preparation --- p.94 / Chapter 4.2.4 --- Marker enzyme measurement --- p.94 / Chapter 4.2.5 --- Liver MDA and GSH determination --- p.95 / Chapter 4.2.6 --- Statistical analysis --- p.95 / Chapter 4.3 --- Results --- p.97 / Chapter 4.3.1 --- Effect of tBHP and FR extract on mouse serum ALT and AST activities --- p.97 / Chapter 4.3.2 --- Effect of tBHP and FR extract on mouse liver MDA and GSH content --- p.97 / Chapter 4.3.3 --- Effect of WZ extract on tBHP-induced increase in serum ALT and AST activities --- p.97 / Chapter 4.4 --- Discussion --- p.102 / Chapter Chapter 5 --- Characterization of the Active Antioxidant Principlein Aqueous Extract of FR --- p.105 / Chapter 5.1 --- Introduction --- p.106 / Chapter 5.2 --- Materials and methods --- p.107 / Chapter 5.2.1 --- Materials --- p.107 / Chapter 5.2.2 --- Chemical/physical treatments on FR extract --- p.107 / Chapter 5.2.3 --- Digestion with enzymes --- p.108 / Chapter 5.2.4 --- Antioxidant activity determination --- p.109 / Chapter 5.2.5 --- Chemical composition determination --- p.109 / Chapter 5.2.5.1 --- Uronic acid determination --- p.109 / Chapter 5.2.5.2 --- Hexose determination --- p.109 / Chapter 5.2.5.3 --- Tannin determination --- p.110 / Chapter 5.2.5.4 --- Protein determination --- p.110 / Chapter 5.2.6 --- Column chromatography --- p.110 / Chapter 5.2.6.1 --- Polyamide CC6 resin column chromatography --- p.111 / Chapter 5.2.6.2 --- Sephadex LH-20 gel column chromatography --- p.111 / Chapter 5.2.7 --- Antioxidant activity of commercially available tannin --- p.111 / Chapter 5.2.8 --- Bovine serum albumin precipitation --- p.112 / Chapter 5.2.9 --- Statistical analysis --- p.112 / Chapter 5.3 --- Results --- p.113 / Chapter 5.3.1 --- Effect of chemical/physical treatments on antioxidant activity of FR extract --- p.113 / Chapter 5.3.2 --- Effect of enzyme digestions on antioxidant activity of FR extract --- p.113 / Chapter 5.3.3 --- Chemical composition of FR extract --- p.118 / Chapter 5.3.4 --- Polyamide CC6 resin column chromatography --- p.118 / Chapter 5.3.5 --- Sephadex LH-20 gel column chromatography --- p.118 / Chapter 5.3.6 --- Antioxidant activity of commercially available tannin --- p.123 / Chapter 5.3.7 --- Effect of BSA precipitation on superoxide-scavenging activity --- p.123 / Chapter 5.4 --- Discussion --- p.127 / Conclusion --- p.131 / References --- p.132

Methyl tert-butyl ether (MTBE) has been used as a gasoline additive to improve the combustion efficiency and to replace lead since 1978. It is the most commonly used oxygenate now due to its low cost, convenience of transfer, and ease of blending and production. MTBE has become a prevalent groundwater contaminant because it is widely used and it has been disposed inappropriately. MTBE has been demonstrated an animal carcinogen. The US Environmental Protection Agency (US EPA) has temporarily classified MTBE as a possible human carcinogen and has set its advisory level for drinking water at 20-40 µg/L based on taste and odor concerns. The Taiwan Environmental Protection Administration (TEPA) also classifies it as the Class IV toxic chemical substances. Currently, natural attenuation (NA) as well as natural bioremediation or enhanced bioremediation are attractive remediation options for contaminated sites due to their economic benefit and environmental friendly. In general, in situ microorganisms at the contaminated site play a very important role in site restoration. Although early studies suggested that the biodegradability of MTBE was not significant, recent laboratory and field reports reveal that MTBE can be biodegraded under aerobic and anaerobic conditions. In addition, evidences and some successful cases of MTBE attenuation have been reported that make natural attenuation a considerable remedial strategy. However, the biodegrading rate might decrease if the nutritional and physiological requirements are not met. Thus, it is important to assess the biodegradability of natural microorganisms under various site conditions to obtain optimal remedial conditions. Contributions of intrinsic biodegradation and other abiotic mechanisms to the removal and control of contaminants should also be evaluated to provide sufficient information for remedial option determination. Moreover, isolation and identification of the dominant native microorganisms will be helpful to following remediation tasks. In the first part of this study, microcosm study and microbial identification technologies (denaturing gradient gel electrophoresis, DGGE) were applied to assess the biodegradability of MTBE by indigenous microbial consortia and to identify the dominant microorganisms at a MTBE-contaminated site (Site A). In the second part of this study, thorough field investigations were performed to evaluate the occurrence of natural attenuation of MTBE at two MTBE-contaminated sites (Site A and Site B). In addition, a natural attenuation model, BIOSCREEN, was performed to assess the effectiveness of natural attenuation on MTBE containment. The main objectives of this study contained the following: (1)Evaluate MTBE biodegradability under different redox conditions by the indigenous microorganisms. (2)Determine the dominant native microorganisms in MTBE biodegradation for further application. (3)Assess the feasibility of using natural attenuation to control the MTBE plume. (4)Evaluate the contributions of intrinsic biodegradation patterns on natural attenuation processes by BIOSCREEN. Results from the microcosm study reveal that MTBE could be biodegraded by aquifer sediments without the addition of extra carbon sources under aerobic conditions. The production of tert-butyl alcohol (TBA), a degradation byproduct of MTBE, was detected. Complete removal of TBA was also observed by the end of the experiment. Results from aerobic microcosms study indicate that oxygen might be the major limiting factor of MTBE biodegradation at Site A. Thus, MTBE at this site could be removed via natural biodegradation processes with the supplement of sufficient oxygen. Microcosm study with extracted supernatant of aquifer sediments as the inocula show that the indigenous microorganisms were capable of using MTBE as the sole carbon and energy source. The calculated MTBE degradation rate was 0.597 mg/g cells/h or 0.194 nmole/mg cells/h. No MTBE removal was observed under various anaerobic conditions. Results suggest that aerobic biodegradation was the dominant degradation process and aerobic bioremediation might be a more appropriate option for the site remediation. According to the results of DGGE analysis, aerobic MTBE-biodegrading bacteria, Pseudomonas sp. and Xanthomonas sp., might exist at this site. Although results of microcosm study show that MTBE could not be degraded under anaerobic conditions, the microbial identification indicates that some novel anaerobic microbes, which could degraded MTBE, might be present at this site. In addition, anaerobic microbes caused the consumption of electron acceptors (e.g., nitrate, ferric iron) and removal of benzene, toluene, ethylbenzene, xylenes (BTEX), 1,2,4-trimethyl benzene (1,2,4-TMB), and 1,3,5-trimethyl benzene (1,3,5-TMB) (TMBs) in the anaerobic microcosms. These results also indicate that the potential of anaerobes activities was high at Site A. Based on the results from the field investigation, natural attenuation of MTBE was occurring at both sites. MTBE plume at Site B could be effectively controlled via natural attenuation processes. Nevertheless, MTBE plume at Site A has migrated to a farther downgradient area and passed the boundary of the site. Field investigation results indicate that the natural attenuation mechanisms of MTBE at both sites were occurring with the first-order attenuation rates of 0.0021 and 0.0048 1/day at Sites A and B, respectively. According to BIOSCREEN simulation, biodegradation was responsible for 78% and 59% of MTBE mass reduction at Sites A and B, respectively. The intrinsic biodegradation had significant contributions on the control of MTBE plumes. Moreover, the dilution and dispersion processes might be the major mechanisms for the attenuation of MTBE in the downgradient areas. However, results also reveal that intrinsic biological processes might still fail to contain the plume if the selected point of compliance is not appropriate. Results of this study suggest that natural attenuation might be feasible to be used as a remedial option for the remediation of MTBE-contaminated site on the premise that (1) detailed site characterization has been conducted, and (2) the occurrence and effectiveness of natural attenuation processes have been confirmed. Based on the results from the field investigation and laboratory microcosm studies, MTBE could be biodegraded by natural microbial populations at the studied sites under both aerobic and anaerobic conditions and natural attenuation would be applied as a remedial option at MTBE-contaminated sites. Results from this study would be useful in determining the favorable bioremediation conditions and designing an efficient and cost-effective bioremediation system such as monitored natural attenuation (MNA) or in situ or on-site MTBE bioremediation system for field application.

Depuis le milieu du 20ème siècle, les techniques de récupération assistée du pétrole (RAP) ont été beaucoup utilisées afin d’améliorer le rendement d’extraction du pétrole brut. Des polyacrylamides modifiés hydrophobiquement ont montré des propriétés intéressantes en tant que modificateurs de rhéologie en vue d’une application en RAP. Cependant, la synthèse de polymères hydrosolubles comportant des segments hydrophobes le long de la chaîne est un défi puisque les monomères hydrophiles et hydrophobes sont rarement miscibles dans le même solvant. Le but de cette thèse a été de développer des copolymères à base d’acrylamide pouvant ensuite être utilisés en RAP. Au cours de l’extraction du pétrole, des polymères possédant des longues chaînes sont mélangés à l’eau puis injecté dans le puits afin de pousser le pétrole brut en dehors de celui-ci. Le polymère a alors pour rôle d’accroître la viscosité de l’eau de sorte qu’elle puisse déplacer plus efficacement le pétrole hors du réservoir. Au cours de cette thèse, la technique RAFT/MADIX a été combinée à la polymérisation micellaire dans le but de synthétiser de nouveaux copolymères associatifs d’architectures contrôlées et possédant de nombreux blocs hydrophobes distribués le long de la chaîne. En phase aqueuse, les segments hydrophobes s’associent et forment un réseau viscoélastique résultant en une augmentation de la viscosité. La combinaison de RAFT/MADIX avec la polymérisation micellaire nous permet également de limiter la dérive en composition observée en polymérisation micellaire conventionnelle. Dans un premier temps, l’étude de l’effet des monomères et de sels sur le comportement des micelles de tensio-actif a montré que la présence de NaAMPS gouverne le procédé de micellisation du SDS par rapport à l’acrylamide. Cette étude a également prouvé qu’il est possible de prévoir l’évolution du NH en fonction de la composition du milieu réactionnel au cours de la synthèse. La compréhension des interactions tensio-actif-monomères permet ainsi de prévoir la microstructure du polymère. Dans un second temps, il a été démontré que les polymères associatifs synthétisés ici se comportent comme des chaînes vivantes et peuvent être étendus avec de l’acrylamide pour former des polymères à bloc de haute masse molaire. L’addition d’un sel monovalent tel que le chlorure de sodium (NaCl) s’est révélée un outil efficace pour contrôler la microstructure du polymère, rendant possible le passage d’une composition de type gradient vers une composition plus homogène (rmonomères hydrophiles/tBS proche de 1). Enfin, l’analyse des relations structure-propriété a montré que tous les polymères synthétisés possèdent un comportement associatif et accroissent la viscosité de l’eau comparé à l’homopolyacrylamide. La présence de NaAMPS dans la chaîne diminue fortement la viscosité du polymère alors qu’elle n’est pas affectée par celle du chlorure de sodium. Le polymère présentant les meilleures propriétés en vue d’une application en RAP est P(Am90-co-AMPS10-co-(Am/NaCl)10-co-tBS1). L’utilisation de NaCl assure de bonnes propriétés rhéologiques tandis que le NaAMPS favorise la solubilité du copolymère en solution aqueuse. / Since the middle of the 20th century, enhanced oil recovery (EOR) techniques have been used to improve the extraction of crude oil. Hydrophobically modified polyacrylamides have shown great properties as rheology modifiers for EOR purposes. However, the synthesis of water-soluble polymers containing hydrophobic segments along the backbone is challenging as hydrophilic and hydrophobic monomers are rarely soluble in the same solvent. The aim of this project was to develop acrylamide-based copolymers for enhanced oil recovery (EOR). In this process, long chain polymer molecules are mixed with water and injected into the oil field in order to drive the oil out of the well. The polymer serves to increase the viscosity of the water, making it more effective at displacing the oil. In this thesis, RAFT/MADIX technique has been combined with micellar polymerization in order to synthesize new associative copolymers with controlled architectures and numerous hydrophobic blocks distributed along the backbone. The associations generate a viscoelastic network in aqueous media resulting in a viscosity increase. The combination of RAFT/MADIX with micellar polymerization allows us to limit the compositional drift observed in conventional micellar polymerization. First, the study of the effect of monomers and salts on the behavior of surfactant micelles has shown that the influence of NaAMPS dominates that of acrylamide in its effect on the micellization behavior of SDS. This study has proven that it is possible to predict how NH would vary depending on the composition of the reactive medium during the synthesis. Understanding the surfactant-monomer interactions thus enables prediction of the microstructure of the polymer. In a second step, it has been demonstrated that the associative polymeric chains were living chains and could be further extended to high molar masses with acrylamide. Increasing the content of NaAMPS in the hydrophilic backbone led to a significant increase in the reactivity ratio. The addition of monovalent salt (especially NaCl) is a useful tool to control the polymer microstructure, enabling switching between a gradient-type composition and a more homogeneous one (rhydrophilic monomers/tBS close to 1). Finally, the examination of structure-property relationships of the associative polymers has highlighted that all polymers displayed associating properties as well as enhanced viscosity compared to homopolyacrylamide. The polymer viscosity strongly decreased upon incorporation of NaAMPS within the backbone while it was unaffected by the presence of NaCl during the synthesis. The polymer displaying the best properties for use in EOR is P(Am90-co-AMPS10-co-(Am/NaCl)10-co-tBS1). The use of NaCl ensures good rheological properties while AMPS enhances the solubility of the copolymer.

<div> <div> <div> <p>The Effective Fragment Potential (EFP) is a quantum-mechanical based model potential for accurate calculations of non-covalent interactions between molecules. It can be coupled with ab initio methods in so-called QM/EFP models to explore the electronic properties of extended molecular systems by providing rigorous description of surrounding environments. The current EFP formulation is, however, not well suited for large-scale simulations due to its inherent limitation of representing effective fragments as rigid structures. The process of utilizing EFP method for the molecular systems with flexible degrees of freedom entails multiple sets of parameter calculations requiring intensive computational resources. This work presents development of the EFP method for describing flexible molecular systems, so-called Flexible EFP. To validate the applicability of the Flexible EFP method, extensive benchmark studies on the amino acid interactions, binding energies, and electronic properties of flavin chromophore of the cryptochrome protein have been demonstrated. In addition to methodological developments, excitonic properties of the Fenna-Matthews-Olson (FMO) photosynthetic pigment-protein complex are explored. In biological systems where intermolecular interactions span a broad range from non-polar to polar and ionic forces, EFP is superior to the classical force fields. In the present study, we demonstrate excellent performance of the QM/EFP model for predicting excitonic interactions and spectral characteristics of the FMO wildtype complex. We characterize the key factors for accurate modeling of electronic properties of bacteriochlrophyll a (BChl a) photosynthetic pigments and suggest a robust computational protocol that can be applied for modeling other photosynthetic systems. Developed computational procedures were also successfully utilized to elucidate photostability and triplet dynamics in the FMO complex and spectroscopic effects of single-point mutagenesis in FMO. A combination of polarizable EFP molecular dynamics and QM/EFP vibrational frequency calculations were also applied to understanding and interpreting structures and Raman spectroscopy of tert-butyl alcohol solutions. </p> </div> </div> </div>

Esta tesis describe el estudio de la aplicación en síntesis de N-terc-butanosulfinil derivados de alquil, alquenil, homoalil y homopropargil aminas como intermedios para acceder a moléculas orgánicas de mayor complejidad. Por un lado, se ha estudiado la adición de compuestos organomagnesianos y organolíticos a N-terc-butanosulfinil iminas, y los distintos derivados de aminas que se obtienen como resultado se han usado como precursores de alcaloides pirrolodínicos y piperidínicos, así como para acceder a anillos tipo azepano. Por otro lado, también se presentan aplicaciones en síntesis de N-terc-butanosulfinil homoalil y homopropargil aminas, que pueden participar en reacciones de oxidación allílica y cicloadiciones [2+2+2], respectivamente, para dar lugar a compuestos polifuncionalizados, en el caso de los derivados de homoalil aminas, y derivados de 9-amino-9, 10-dihidrofenantrenos y 1,2,3,4-tetrahidroisoquinolinas, en el cado de los derivados de homopropargil aminas.

Palladium complexes of bis(di-tert-butylphosphinomethyl)benzene (DTBPMB) show remarkably high activity as alkene methoxycarbonylation catalysts, in addition to numerous other catalytic conversions, and are currently being commercialised by Lucite in ethene methoxycarbonylation to methyl propanoate. Any large-scale exploitation of this catalyst system for heavier products, however, is likely to be hindered by catalyst-product separation problems common to homogeneous catalysts; hence modification of this catalyst system to allow facile product separation was investigated. Tethering of DTBPMB residues onto polystyrene via Suzuki-type coupling of suitable precursors onto bromopolystyrene and boronic acid functionalised polystyrene resins was investigated and the phosphine was successfully immobilised. Phosphination of the resins was not complete however and as such there is concern that other phosphine residues may be present which do not exhibit a bidentate binding motif. The synthesis of a potassium sulfonate derivative of DTBPMB (KBPMBS) was successful and immobilisation of this onto ion exchange resins was also investigated. Some preliminary results from studies into 1-octene methoxycarbonylation using palladium complexes of these resins were obtained. Supporting of this diphosphine onto silica via a sol-gel co-condensation methodology was also investigated; the synthesis of a suitably functionalised precursor containing a sulfonamide linkage was successful via protection of the diphosphine using borane. Although formation of the silica support was successful, attempts to deprotect the phosphine-borane resulted in cleavage of the ligand from the support. An alternative route to this supported ligand was attempted and others discussed. Synthesis of a suitable sol-gel precursor via alkene hydrosilation was also attempted and is discussed. Supporting of the sulfonated phosphine, KBPMBS onto silica functionalised with imidazolium tethered residues was also investigated, although complete leaching of the phosphine from the support by methanol washing was observed. Immobilisation of the synthesised KBPMBS ligand in an ionic liquid (IL) phase was investigated. Complex formation and catalytic activity were demonstrated and a positive effect on conversion was observed upon addition of carbon dioxide to the system; possibly due to the increased CO solubility within the IL phase. Efficient product separation from the IL-immobilised catalyst system was demonstrated, both by organic extraction and using supercritical carbon dioxide flow. However, poor catalyst stability under these conditions appears to present a barrier to recycling this system, with loss of conversion observed on catalyst recycling. Other attempts to immobilise the DTBPMB ligand are discussed and reduction of the sulfide derivative of DTBPMB was demonstrated using hexachlorodisilane, which could be used as a general synthetic strategy for protecting highly electron rich phosphines. It is possible that increasing the bulk of the DTBPMB ligand may increase catalyst stability and result in catalyst systems with higher turnover numbers. Therefore syntheses of bulky ligands based on the DTBPMB backbone were investigated. 1,2,4,5-tetrakis(di(tert-butyl)phosphinomethyl)benzene was successfully synthesised although palladium complexes of this showed no activity in catalytic methoxycarbonylation. Attempts to synthesise a related biphenyl-based tetraphosphine is also discussed, although isolation of this in a pure form was not achieved. Routes toward tetraphenyl and dimethyl-diphenyl functionalised derivatives of DTBPMB have also been explored, although only a monophosphine was isolated due to difficulties in obtaining an intermediate di(chloromethyl) precursor in both synthetic pathways, although this now appears to have been overcome.

Molecular simulations have become an important tool within the last few decades to understand physical processes in the microscale and customize processes in the macroscale according to the understanding developed at the molecular level. We present results from molecular simulations we performed to study the adsorption of hazardous organics in nanoporous materials. Adsorption of water in silicalite, a hydrophobic material, and the effect of defects were investigated by Monte Carlo simulations. Silanol nests were found to have a big impact on the hydrophobicity of silicalite. Even the presence of one silanol nest per unit cell caused a significant amount of water adsorption. We also investigated the effect of four different cations, H+, Li+, Na+, and Cs+. Their presence in silicalite increased the amount of water adsorbed. Monte Carlo and molecular dynamics simulations of MTBE adsorption in silicalite, mordenite, and zeolite beta with different Na+ cation loadings were carried out. The results revealed the importance of the pore structure on the adsorption of MTBE. Although these three zeolites have similar pore volumes, zeolite beta, with its pore structure which is mostly accessible to MTBE molecules, is predicted to adsorb significantly more MTBE than silicalite and mordenite. The Na+ cation loading, up to four cations does not have a significant effect on the adsorption capacity of the zeolites studied here, however, for silicalite and zeolite beta increasing the Na+ content increases the amount adsorbed at very low pressures. A new force field was developed by Monte Carlo simulations for 1,4-Dioxane, an important industrial solvent which has emerged as a potentially significant threat to human health. The objective was to develop reliable atom-atom interaction parameters to use in the simulations of the adsorption of 1,4-Dioxane in different adsorbent materials. Predictions of critical point data, liquid and vapour densities, heats of vaporization with our new force field were in good agreement with experimental data and outperformed predictions from simulations with other force field parameters available in literature. To obtain the isotherms of MTBE and 1,4-Dioxane adsorption from water in silicalite Monte Carlo simulations were performed. First we optimized the interaction parameters between the atoms of silicalite and the atoms of MTBE and 1,4-Dioxane. Using these optimized parameters we simulated the adsorption of MTBE and 1,4-Dioxane from water in silicalite. Despite the agreement of simulated and experimental isotherms of pure components, simulated isotherms of MTBE and 1,4-Dioxane adsorption from water in silicalite did not yield satisfactory results. Monte Carlo simulations were performed to investigate the affinity between two hazardous materials, PFOA and 1,1-DCE; and four different zeolites. Binding energies and Henry's constants were computed. For both PFOA and 1,1-DCE zeolite-beta had the highest affinity. The affinity between activated carbon with polar surface groups and water, and 1,4-Dioxane were investigated to shed light on why activated carbon is ineffective to remove 1,4-Dioxane from water. Results showed that presence of polar surface groups increased the affinity between water and activated carbon, while the affinity between 1,4-Dioxane and activated carbon was not effected by the presence of polar surface groups.

O petróleo é a principal fonte de energia no mundo, mas alguns de seus derivados podem ser prejudiciais à natureza e à saúde. O BTEX, um derivado do petróleo, é usado em combustíveis, sendo estes a maior causa de contaminação ambiental, pois no transporte ou armazenamento destes ocorrem vazamentos que poluem solo e fontes de água. Como alternativas para diminuir a concentração do BTEX no combustível surgiram os aditivos oxigenados, os quais melhoram a qualidade do combustível e reduzem as emissões de monóxido de carbono. Os aditivos mais comuns são o MTBE e o etanol. No entanto, o MTBE é oncogênico e por isso, alguns países o substituem pelo etanol. Porém, o etanol aumenta a solubilidade do BTEX na água, a migração deste no solo, e diminui sua degradação natural. A degradação destes compostos é possível pela ação de microrganismos nativos. Em vista disto, no presente trabalho, bactérias foram isoladas de uma planta de tratamento de águas residuais da indústria petroquímica, com o objetivo de encontrar bactérias tolerantes com capacidade de degradação do BTEX. Os 30 isolados obtidos foram identificados como pertencentes aos gêneros Bacillus, Enterococcus, Staphylococcus, Streptococcus, Pseudomona, Lysinobacterium, Neisseria, Corynobacterium e Leucobacter. Quinze isolados foram tolerantes ao B, T, E, X, e destes, os isolados 16 e 25 pertencentes ao gênero Bacillus, foram testados para a degradação de BTEX, BTEX/MTBE, BTEX/Etanol. A maior porcentagem de degradação foi detectada no tratamento com BTEX seguido por BTEX/MTBE e BTEX/Etanol. O isolado 25 mostrou maior capacidade de degradação dos compostos. / Oil is the main source of energy in the world; nevertheless, some of its derivatives could be harmful to the environment and health. BTEX is a petroleum derivative. It is used in fuels; this one is the main cause of environmental pollution, because during the transport or storage of them there are leaks that pollute the soil and water sources. In order to reduce BTEX concentration in fuel, oxygenated additives emerged; these improve the quality of the fuel and reduce carbon monoxide emissions. The most common additives are MTBE and ethanol. Due to fact that MTBE is oncogenic, some countries replace it with ethanol. Ethanol increases the solubility of BTEX in water, its migration in the ground and decreases its natural degradation. The degradation of harmful compounds by action of native microorganisms has proven to be effective. With this purpose, in the current research, bacteria were isolated from a wastewater treatment plant of petrochemical industry, in order to find tolerant bacteria and with ability to degrade BTEX. The 30 isolates obtained were identified as belonging to the genus Bacillus, Enterococcus, Staphylococcus, Streptococcus, Pseudomonas, Lysinobacterium, Neisseria, Corynobacterium, and Leucobacter. Fifteen isolates were tolerant to B, T, E, X, and out them, isolates 16 and 25 belong to genus Bacillus were tested for degradation of BTEX BTEX / MTBE, BTEX / Ethanol. The highest percentage of degradation was found in the assay with BTEX followed by BTEX / MTBE and BTEX / Ethanol. Isolate 25 showed the highest capacity of degradation.

The synthetic progress towards yaku'amide A is described. The study leads to development of new synthetic methodologies. Base-free regioselective aminohydroxylation is convenient to deliver β-tert-hydroxyamino acids. A sequence consisting of alkylative esterification, Martin sulfurane mediated anti dehydration, a tandem azide reduction-O→N acyl transfer allows the rapid access of E- and Z-dehydroisoleucine-containing peptides from β-tert-hydroxyisoleucine derivatives. Those methods are effective in constructing complicated peptides and advanced subunits of yaku'amide A.

Anthraquinone (AQ) has been used in electron transfer studies in DNA. The focus of this dissertation is the synthesis of conjugates between AQ derivatives and 2’-deoxyadenosine (dA), which can be used to induce adenine oxidation in DNA. Different AQ derivatives were attached to dA via ethynyl or ethanyl linkers. If incorporated into DNA, these short linkers should enable regiocontrol for electron transfer from adenine within the DNA duplex structure. The challenge in working with anthraquinone-2’-deoxynucleosides conjugates is that they and their intermediates are insoluble in water and only sparingly soluble in most organic solvents. A strategy used to overcome this problem was the use of either tert-butyldiphenylsilyl (TBDPS) or 4’,4-dimethoxytrityl (DMTr) 5’-protected deoxynucleosides as starting materials. A water-soluble, ethynyl-linked AQ-dA conjugate with a 3’-benzyl hydrogen phosphate was synthesized using DMTr protection. The DMTr group was not stable to the hydrogenation required to make the ethanyl-linked AQ-dA conjugate with 3’-benzyl hydrogen phosphate. Hence the latter was synthesized starting with the TBDPS protecting group. Both of these syntheses were based on the Pd coupling between ethynylanthraquinone and 8-bromodeoxyadenosine derivatives. New conjugates between AQ and A, in which the AQ moieties have been modified with formyl, trifluoroacetyl and methyl ester groups as electron withdrawing substituents were also synthesized. The synthesis of these AQ-dA conjugates was based on Pd coupling between bromoanthraquinone and 8-ethynyldeoxyadenosine derivatives. This route avoided the use of ethynylanthraquinone derivatives that had extremely low solubility and photoinstability. Other anthraquinones with electron withdrawing groups (which should provide enhanced driving force to enable respective AQ derivative to oxidize adenine) were synthesized as models. Cyclic voltammetry showed that the conjugate with the two ester groups and ethynyl linker was the most easily reduced of the derivatives synthesized. Conjugates between AQ and dU were also synthesized. Those conjugates can potentially be used to oxidize guanine or adenine or they can be used as a deep trap for an electron in reduced DNA.