Influence of abiotic stress factors on VOCs emission from Portuguese rice paddy fields: relation with increased climate change

Dissertação para obtenção do Grau de Mestre em Engenharia do Ambiente Perfil de Gestão de Sistemas Ambientais

Functional characterization and directed engineering of redox proteins for a rational improvement of Bioelectrochemical systems

In recent years, new methods of clean and environmentally friendly energy production have been the focus of intense research efforts. Microbial fuel cells (MFCs) are devices that utilize naturally occurring microorganisms that feed on organic matter, like waste water, while producing electrical energy. The natural habitats of bacteria thriving in microbial fuel cells are usually marine and freshwater sediments. These microorganisms are called dissimilatory metal reducing bacteria (DMRB), but in addition to metals like iron and manganese, they can use organic compounds like DMSO or TMAO, radionuclides and electrodes as terminal electron acceptors in their metabolic pathways.(...)

Insights into the biochemical strategies of adaptation to heat stress in the hyperthermophilic archaeon Pyrococcus furiosus

Organisms that thrive optimally at temperatures above 80°C are called hyperthermophiles. These prokaryotes have been isolated from a variety of hot environments, such as marine geothermal areas, hence they are usually slightly halophilic. Like other halophiles, marine hyperthermophiles have to cope with fluctuations in the salinity of the external medium and generally use low-molecular mass organic compounds to adjust cell turgor pressure. These compounds can accumulate to high levels without interfering with cell metabolism, thereby deserving the designation of compatible solutes. Curiously, the accumulation of compatible solutes also occurs in response to supraoptimal temperatures.(...)

Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis.

Rubisco is responsible for the fixation of CO2 into organic compounds through photosynthesis and thus has a great agronomic importance. It is well established that this enzyme suffers from a slow catalysis, and its low specificity results into photorespiration, which is considered as an energy waste for the plant. However, natural variations exist, and some Rubisco lineages, such as in C4 plants, exhibit higher catalytic efficiencies coupled to lower specificities. These C4 kinetics could have evolved as an adaptation to the higher CO2 concentration present in C4 photosynthetic cells. In this study, using phylogenetic analyses on a large data set of C3 and C4 monocots, we showed that the rbcL gene, which encodes the large subunit of Rubisco, evolved under positive selection in independent C4 lineages. This confirms that selective pressures on Rubisco have been switched in C4 plants by the high CO2 environment prevailing in their photosynthetic cells. Eight rbcL codons evolving under positive selection in C4 clades were involved in parallel changes among the 23 independent monocot C4 lineages included in this study. These amino acids are potentially responsible for the C4 kinetics, and their identification opens new roads for human-directed Rubisco engineering. The introgression of C4-like high-efficiency Rubisco would strongly enhance C3 crop yields in the future CO2-enriched atmosphere.

Producción primaria en el ambiente marino en el Pacífico sudeste, Perú, 1960-2000

Los resultados de investigación sobre producción primaria dentro del alcance interdisciplinario del ambiente marino frente a la costa peruana incluyen estudios nacionales, extranjeros y de investigación conjunta a través de proyectos internacionales (1960-2000). La circulación en la costa peruana es dominada por una corriente hacia el ecuador en una capa de 20 a 50 m. La estructura de plumas del afloramiento se presenta en cada área y podría ser la clave para el desarrollo de cadenas cortas y productivas: fitoplancton peces clupeidos. La distribución de nutrientes sigue la pluma de temperatura, con altos valores en la costa y bajos lejos de la costa; la clorofila muestra mínimos valores cerca de la costa (10 mn) que se incrementa al alejarse. El crecimiento del fitoplancton en aguas peruanas, varía de 0,5 a 0,8 d/d. En aguas recién afloradas el crecimiento es limitado por falta de “condicionamiento biológico” y de compuestos orgánicos (15°S). Estos tipos de agua pueden estar relacionados con las “aguas azules” de altos nutrientes y pobre fitoplancton con células de pequeño tamaño (clorofila <2 μg/L) y con “aguas marrones” con denso fitoplancton, (clorofila >5 μg/L), mayor diversidad y con células de diámetro >5μ. La media de producción primaria fue 3 gC/m2/d (1960-1985), comparable a la mayoría de estudios en los cuales varía entre 3 y 4 gC/m2/d en la franja costera, el último valor es altamente variable en espacio, siendo más frecuente dentro de 10 km. Valores mayores de 12 gC/m2/d se encontraron en el afloramiento de Chimbote. El Niño, La Niña y fases del ENSO, afectan la producción primaria. Las temperaturas bajas originan cambios en la composición química del fitoplancton y reducen el índice de productividad mgC/mgclor-a/d que también es atribuido a limitaciones de luz.

Public health assessment : Railroad Avenue groundwater contamination, West Des Moines, Polk County, Iowa EPA facility ID: IA0001610963 (2004)

The Railroad Avenue groundwater contamination site (the site) is in West Des Moines, Polk County, Iowa. Located on approximately 120 acres. The site comprises mixed residential, industrial and commercial properties. Underneath the site, chlorinated volatile organic compounds (VOCs) have contaminatcd the shallow (i.e., 30-50 feet deep) groundwater. These compounds have compromised several shallow wells within the West Des Moines water works system. A contamination source, however, has not yet been identified. In 1993, routine water analysis by the City of West Des Moines identified 1, 2 cis-dichlorocthylcne (1, 2 cis-DCE) at a concentration of 1.2 μg/L (micrograms) per liter of water) in the water supply. Subsequently. several shallow municipal wells were found to be contaminated by VOCs, including 1. 2 cis-DCE, trichloroethylene (TCE), tetrachloroethylene (PCE) and benzene. Five of these wells have been taken out of service. Because of the impact on the West Des Moines water supply, the U.S. Environmental Protection Agency (USEPA) has assigned the site to the National Priorities List. Surface water und sediment at the site have not been impacted by the VOCs. Testing for VOCs in surface soils has not revealed any significant VOC contamination. Subsurface soils -- generally 8 feet or greater in depth -- are contaminated with VOCs, but at levels which should not present a health hazard. The past, present, and future health hazard category chosen for this site is no apparent public health hazard. This category is used when exposure to toxins might be occurring or might have occurrcd in the past, but at levels below any known health hazard. Analysis of available environmental data has not revealed that residental or commercial water customers are or have been exposed to VOCs at concentrations that might cause any adverse health effects.

Biotransformations of water insoluble substrates in aqueous, two-phase and encapsulated systems /

The biotransformation of water insoluble substrates by mammalian and bacterial cells has been problematic, since these whole cell reactions are primarily performed in an aqueous environment The implementation of a twophase or encapsulated system has the advantages of providing a low water system along with the physiological environment the cells require to sustain themselves. Encapsulation of mammalian cells by formation of polyamide capsules via interfacial polymerization illustrated that the cells could not survive this type of encapsulation process. Biotransformation of the steroid spironolactone [3] by human kidney carcinoma cells was performed in a substrate-encapsulated system, yielding canrenone [4] in 70% yield. Encapsulation of nitrile-metabolizing Rhodococcus rhodochrous cells using a polyamide membrane yielded leaky capsules, but biotransformation of 2-(4- chlorophenyl)-3-methylbutyronitrile (CPIN) [6] in a free cell system yielded CPIN amide [7] in 40% yield and 94% ee. A two-phase biotransformation of CPIN consisting of a 5:1 ratio of tris buffer, pH 7.2 to octane respectively, gave CPIN acid [8] in 30% yield and 97% ee. It was concluded that Rhodococcus rhodochrous ATCC 17895 contained a nonselective nitrile hydratase and a highly selective amidase enzyme.

Towards the enantioselective synthesis of lycoricidine alkaloids /

Two efficient, regio- and stereo controlled synthetic approaches to the synthesis of racemic analogs of pancratistatin have been accomplished and they serve as the model systems for the total synthesis of optically active 7-deoxy-pancratistatin. In the Diels-Alder approach, an efficient [4+2] cycloaddition of 3,4-methylenedioxyco- nitrostyrene with Danishefsky's diene to selectively form an exo-nitro adduct has been developed as the key step in the construction of the C-ring of the target molecule. In the Michael addition approach, the key step was a conjugate addition of an organic zinc-cuprate to the 3,4-methylenedioxy-(B-nitrostyrene, followed by a diastereocontroUed closure to form the cyclohexane C-ring of the target molecule via an intramolecular nitro-aldol cyclization on a neutral alumina surface. A chair-like transition state for such a cyclization has been established and such a chelation controlled transition state can be useful in the prediction of diastereoselectivity in other related 6-exo-trig nitroaldol reactions. Cyclization of the above products fi^om both approaches by using a Bischler-Napieralski type reaction afforded two lycoricidine derivatives 38 and 50 in good yields. The initial results from the above modeling studies as well as the analysis of the synthetic strategy were directed to a chiral pool approach to the total synthesis of optically active 7-deoxy-pancratistatin. Selective monsilylation and iodination of Ltartaric acid provided a chiral precursor for the proposed key Michael transformation. The outlook for the total synthesis of 7-deoxy-pancratistatin by this approach is very promising.A concise synthesis of novel designed, optically pure, Cz-symmetrical disulfonylamide chiral ligands starting from L-tartaric acid has also been achieved. This sequence employs the metallation of indole followed by Sfj2 replacement of a dimesylate as the key step. The activity for this Cz-symmetric chiral disulfonamide ligand in the catalytic enantioselective reaction has been confirmed by nucleophilic addition to benzaldehyde in the disulfonamide-Ti (0-i-Pr)4-diethylzinc system with a 48% yield and a 33% e.e. value. Such a ligand tethered with a suitable metal complex should be also applicable towards the total synthesis of 7-deoxy-pancratistatin.

Molecular mechanics calculations of tin-bis (triphenylphosphine oxide) complexes

The capability of molecular mechanics for modeling the wide distribution of bond angles and bond lengths characteristic of coordination complexes was investigatecl. This was the preliminary step for future modeling of solvent extraction. Several tin-phosphine oxide COrnI)le:){es were selected as the test groUl) for t.he d,esired range of geometry they eX!libi ted as \-vell as the ligands they cOD.tained r Wllich were c\f interest in connection with solvation. A variety of adjustments were made to Allinger's M:M2 force·-field ill order to inl.prove its performance in the treatment of these systems. A set of u,nique force constants was introduced for' those terms representing the metal ligand bond lengths, bond angles, and, torsion angles. These were significantly smaller than trad.itionallY used. with organic compounds. The ~1orse poteIlt.ial energ'Y function was incorporated for the M-X l')ond lE~ngths and the cosine harmonic potential erlerg-y function was invoked for the MOP bond angle. These functions were found to accomodate the wide distribution of observed values better than the traditional harmonic approximations~ Crystal packing influences on the MOP angle were explored thr"ollgh ttle inclusion of the isolated molecule withil1 a shell cc)ntaini11g tl1e nearest neigl1'bors duri.rlg energy rninimization experiments~ This was found to further improve the fit of the MOP angle.

Synthesis and spectral studies of methyl heterocylic systems

2-Carboxy-2?-methyldiphenyl sulfide was prepared by the Ullmann reaction and cyclodehydrated by sulfuric acid to afford 4-methylthioxanthone. 1-Methylthioxanthone was separated from the reaction mixture obtained upon cyclodehydration of 2-carboxy-3f-methyldiphenyl sulfide. In addition, 1-, 2-, 3- and 4-methylthioxanthone 10,10-dioxides were synthesized by oxidation of the corresponding thioxanthones. o-, m- and p-N-Tolylanthranilic acids were prepared by the Ullmann reaction and used as precursors for the preparation of 1-, 2- and 4- methyl-9-chloroacridine and finally 1-, 2-, 3- and 4-methylacridone. High resolution, 60 MHz PMR spectra were obtained on the four monomethyl isomers of xanthone, thioxanthone, thioxanthone 10,10-dioxide and acridone, and on 1-, 2- and 4-methyl-9-chloroacridine. For some compounds, coupling of all three different aromatic protons to the methyl was observed, two of the couplings typically being smaller than the third. With the large (ortho) coupling being on the order of 0.5 to 1.0 Hz, it was necessary to decouple the aromatic part of the spectrum. The magnitude of the ortho benzylic constant may be related to an incomplete Tr-bond delocalization in the molecules.

Modifications to the Suzuki reaction and mechanistic insights on the NBS mediated cleavage of benzylidene acetals /

One of the most challenging tasks for a synthetic organic chemist today, is the development of chemo, regio, and stereoselective methodologies toward the total synthesis of macromolecules. r . The objective of my thesis was to develop methodologies towards this end. The first part of my project was to develop highly functionalized chirons from D-glucose, a cheap, chiral starting material, to be utilized in this capacity. The second part of the project dealt with modifying the carbon-carbon bond forming Suzuki reaction, which is utilized quite often as a means of combining molecular sub units in total synthesis applications. As previously stated the first area of the project was to develop high value chirons from D-glucose, but the mechanism of their formation was also investigated. The free radical initiated oxidative fragmentation of benzylidene acetals was investigated through the use of several test-case substrates in order to unravel the possible mechanistic pathways. This was performed by reacting the different acetals with N-bromosuccinimide and benzoyl peroxide in chlorobenzene at 70^C in all cases. Of the three mechanistic pathways discussed in the literature, it was determined, from the various reaction products obtained, that the fragmentation of the initial benzylic radical does not occur spontaneously but rather, oxidation proceeds to give the benzyl bromide, which then fragments via a polar pathway. It was also discovered that the regioselectivity of the fragmentation step could be altered through incorporation of an allylic system into the benzylidene acetal. This allows for the acquisition of a new set of densely functionalized. chiral, valuable synthetic intermediates in only a few steps and in high yields from a-Dglucose. The second part of the project was the utilization of the phosphonium salt room temperature ionic liquid tetradecyltrihexylphosphonium chloride (THPC) as an efficient reusable medium for the palladium catalyzed Suzuki cross-coupling reaction of aryl halides, including aryl chlorides, under mild conditions. The cross-coupling reactions were found to proceed in THPC containing small amounts of water and toluene using potassium phosphate and 1% Pd2(dba)3. Variously substituted iodobenzenes, including electron rich derivatives, reacted efficiently in THPC with a variety of arylboronic acids and afforded complete conversion within 1 hour at 50 ^C. The corresponding aryl bromides also reacted under these conditions with the addition of a catalytic amount of triphenylphosphine that allowed for complete conversion and high isolated yields. The reactions involving aryl chlorides were considerably slower, although the addition of triphenylphosphine and heating at 70 ^C allowed high conversion of electron deficient derivatives. Addition of water and hexane to the reaction products results in a triphasic system in which the top hexane phase contained the biaryl products, the palladium catalyst remained fully dissolved in the central THPC layer, while the inorganic salts were extracted into the lower aqueous phase. The catalyst was then recycled by removing the top and bottom layers and adding the reagents to the ionic liquid which was heated again at 50 ^C; resulting in complete turnover of iodobenzene. Repetition of this procedure gave the biphenyl product in 82-97% yield (repeated five times) for both the initial and recycled reaction sequences.

Phospha-adamantane ligands and phosphorous ionic liquids for palladium-catalyzed cross-coupling reactions /

New and robust methodologies have been designed for palladiumcatalyzed cross-coupling reactions involving a library of novel tertiary phosphine ligands incorporating a phospha-adamantane framework. The secondary phosphine, l,3,5,7-tetramethyl-2,4,8-trioxa-6-phospha-adamantane was converted into a small library of tertiary phosphine derivatives and the ability of these tertiary phosphaadamantanes to act as effective ligands in the palladium-catalyzed amination reaction and p-alkyl-Suzuki cross-coupling was examined. l,3,5,7-Tetramethyl-6- phenyl-2,4,8-trioxa-6-phosphaadamantane (PA-Ph) used in combination with Pd2(dba)3 CHCI3 facilitated the reaction of an array of aryl iodides, bromides and chlorides with a variety secondary and primary amines to give tertiary and secondary amines respectively in good to excellent yields. 8-(2,4-Dimethoxyphenyl)- l,3,5,7-tetramethyl-2,4,6-trioxa-8-phospha-tricyclo[3.3.1.1*3,7*]decane used in combination with Pd(0Ac)2 permitted the reaction of an array of alkyl iodides, and bromides with a variety aryl boronic acids and alkyl 9-BBN compounds in good to excellent yields. Subsequent to this work, the use of phosphorous based ionic liquids, specifically tetradecyltrihexylphosphonium chloride (THPC), in the Heck reaction provided good to excellent yields in the coupling of aryl iodides and bromides with a variety of olefins.

Asymmetric cyclopropanation via catalysts incorporating the 1,4-diol ligands and the newly designed dioxaborolane /

The development of new methodology for the asymmetric synthesis of chiral organic compounds is a major focus in modem organic chemistry. The use of chiral catalysts is replacing chiral auxiliaries as a new tool for synthetic chemists. An efficient chiral catalyst allows for large quantities of optically active product to be obtained on use of relatively small amount of enantiopure material, without the need for the removal and recovery of a chiral auxiliary. Furthermore, the most practical catalytic methods utilize an inexpensive and readily available chiral ligand that can provide high and predictable enantioselectivity across a wide range of substrates. In our project, two type of versatile, upgraded chiral ligands have been designed and synthesized. Their application in Simmons-Smith type cyclopropanation is investigated, and the pleasing results suggest that they are the potential catalytic enantioselective candidates to build C-C bonds.

Enantiodivergent chemoenzymatic synthesis of Balanol and approaches to the synthesis of (+)-Codine

The present thesis reviews the development of a formal enantiodivergent synthesis of the (+)- and (-)-isomers of balanol. This approach commences from a cis-dihydrodiol derived from the enzymatic dihydroxylation of bromobenzene. The stereochemistry of the diol is used to direct the synthesis of two different aziridines, each used in the formal synthesis of one enantiomer of balanol. Also described are several enantioselective approaches to (+ )-codeine. Each strategy begins with the enzymatic dihydroxylation of p-bromoethylbenzene and involves a Mitsunobu inversion and intramolecular Heck reaction as key steps.

Two enantiodivergent syntheses of balanol and the chemoenzymatic synthesis of oseltamivir

The present thesis outlines our latest findings on the reactivity of the Burgess reagent with oxiranes. Structural, mechanistic, and computational studies are presented. Included is the development of a (-)-menthyl version of the Burgess reagent and its application to the synthesis of enantiomerically pure ~-amino alcohols. This methodology has been exploited in the formal enantiodivergent synthesis of the (+)- and (-)-isomers of balanol. Also described is a second generation approach to both balanol enantiomers; each commencmg with the chemoenzymatic dihydroxylation of bromobenzene. This study also describes the steric and functional limitations of the toluene dioxygenase-mediated oxidation of benzoate esters. The metabolite derived from ethyl benzoate was employed in a formal synthesis of oseltamivir. Finally, several synthetic approaches to oseltamivir and its analogs are presented, each proceeding through a different vinyl aziridine derived from bromobenzene and ethyl benzoate.