Diss. (sammanfattning) Uppsala : Uppsala universitet, 2009. / Härtill 8 uppsatser.

Ph.D. afhandling, Roskilde universitetscenter 2005.

Perchlorate and chlorate are naturally occurring in the atmosphere, from here it sediments into groundwater and soil. The pollution is increased by discharges of perchlorate and chlorate from agriculture and paper mills. Bacteria capable of reducing perchlorate and chlorate to chloride and oxygen can be used to get rid of these contaminants. However an anaerobic environment needs to be sustained in order for this reaction to be used. For this reduction to work in an aerobic environment as well, a greater knowledge of the reducing enzymes, regulating factors and their corresponding genes is needed. One of these enzymes is called chlorite dismutase. The upstream region of this gene in Ideonella dechloratans bacteria is likely to contain a promoter sequence. The purpose of this work was to shorten this DNA sequence to get closer to the potential regulatory sequences and binding-site for RNA polymerase. Subsequently control if the sequence was active as an promoter. The potential promoter region was shortened and amplified by PCR. It was then ligated into the plasmid pRU1103which is carrying a reporter gene. Cloning of the construction into Escherichia coli resulted in a production of the reporter gene product. This indicates that the sequence contained a working promoter.

Oxochlorates are anions with a partially naturally occurrence in nature but are also spread by human activities, including the paper industry. These compounds are harmful to both nature and humans, which makes it necessary to find a good way for their degradation. There are two different kinds of bacteria that can use oxochlorates as electron acceptors in their metabolism, bacteria that break down perchlorate and bacteria that break down both perchlorate and chlorate. A bacterium that can break down chlorate under anaerobic conditions is Ideonella dechloratans which holds the genes for chlorite dismutase and chlorate reductase which are enzymes for the degradation of chlorate. Gene expression and enzyme activity of chlorite dismutase are induced under anaerobic conditions, which makes it interesting to find out how this regulation functions in order to better exploit these bacteria in biological wastewater treatment. To study the expression of the gene for chlorite dismutase a potential promoter and regulatory sequence has previously been cloned in a reporter vector and transformed into Escherichia coli (E.coli) bacterium XL-1 blue. This work was to develop a β-galactosidase assay for the quantification of gene expression in this system and apply it to aerobic and anaerobic bacterial cultures. The method was optimized for cultivation in LB-medium and measurements of gene expression showed higher promoter activity during anaerobic compared with aerobic culture conditions for all of the studied clones. This means that all the clones contain a sequence which can function as promoter in E. coli, and that its activity increases during anaerobic conditions.

Nanosized structures are of intermediate size between individual molecules and bulkmaterials which gives them several unique properties. At the same time their relative limitedsizes make them suitable for studies by the methods of computational chemistry. In this thesiswater clusters, ice clathrates and functionalized metal-oxide nanoparticles have been studiedby quantum-chemical calculations and statistical thermodynamics. The stabilities of water clusters composed of up to 100 molecules have been investigated. Themultitude of possible H-bonded topologies and their importance for determining theproperties of the clusters have been highlighted. Several structural characteristics of thehydrogen bonded network have been examined and the structural factors that determine thestability of an H-bonded network have been identified. The stability of two kinds of oxygenframeworks for water clusters have been analyzed, taking into account thermal energy andentropy corrections. Clusters with many 4-coordinated molecules have been found to be lowerin energy at low temperatures whereas the clusters with less-coordinated molecules dominateat higher temperatures. The equilibrium size distribution of water clusters as a function oftemperature and pressure has been computed using statistical thermodynamics. Themicroscopic local structure of liquid water has been probed by utilizing information from thestudied water clusters. The average number of H-bonds in liquid water has been predicted byfitting calculated average IR spectra for different coordination types in water clusters toexperimental IR spectra. Water can form an ice-like structure that encloses various molecules such as methane. Thesemethane hydrates are found naturally at the ocean floor and in permafrost regions and canconstitute a large unemployed energy resource as well as a source of an effective green-housegas. The pressure dependencies of the crystal structures, lattice energies and phase transitionsfor the three methane hydrates with the clathrate structures I, II and H have been mapped out. Zinc oxide is a semiconducting material with interesting luminescence properties that can beutilized in optical devices, such as photodetectors, light emitting devices and biomarkers. Theeffect of water molecules adsorbed on the ZnO surface when adsorbing organic acids havebeen investigated. Changes in optical properties by the adsorption of carboxylic acids havebeen studied and compared with experimental results. Aromatic alcohols at TiO2 metal-oxidenanoparticles have been studied as model systems for dye-sensitizied solar cells. Adsorptiongeometries are predicted and the influence from the adsorbed molecules on the electronicproperties has been studied.

Silicon carbide (SiC) is a promising material for high power and high frequency devices due to its wide bandgap, high break down field and high thermal conductivity. The most established technique for growth ofepitaxial layers of SiC is chemical vapor deposition (CVD) at around 1550 °C using silane, SiH4, and lighthydrocarbons e g propane, C3H8, or ethylene, C2H4, as precursors heavily diluted in hydrogen. For high-voltagedevices made of SiC thick (> 100 μm), low doped epilayers are needed. Normal growth rate in SiC epitaxy is~ 5 μm/h, rendering long growth times for such SiC device structures. The main problem when trying to achievehigher growth rate by increasing the precursor flows is the formation of aggregates in the gas phase; for SiCCVD these aggregates are mainly silicon droplets and their formation results in saturation of the growth ratesince if the gas flow does not manage to transport these droplets out of the growth zone, they will eventuallycome in contact with the crystal surface and thereby creating very large defects on the epilayer making theepilayer unusable. To overcome this problem, high temperature- as well as low pressure processes have beendeveloped where the droplets are either dissolved by the high temperature or transported out of the susceptor bythe higher gas flow. A different approach is to use chloride-based epitaxy that uses the idea that the silicondroplets can be dissolved by presence of species that bind stronger to silicon than silicon itself. An appropriatecandidate to use is chlorine since it forms strong bonds to silicon and chlorinated compounds of high purity canbe purchased. In this thesis the chloride-based CVD process is studied by using first a single molecule precursor,methyltrichlorosilane (MTS) that contributes with silicon, carbon and chlorine to the process. Growth of SiCepilayers from MTS is explored in Paper 1 where growth rates up to 104 μm/h are reported together withmorphology studies, doping dependence of growth rate and the influence of the C/Si- and Cl/Si-ratios on thegrowth rate and doping. In Paper 2 MTS is used for the growth of 200 μm thick epilayers at a growth rate of 100μm/h, the epilayers are shown to be of very high crystalline quality and the growth process stable. The growthcharacteristics of the chloride-based CVD process, is further studied in Paper 3, where the approach to add HClgas to the standard precursors silane and ethylene is used as well as the MTS approach. A comparison betweenliterature data of growth rates for different approaches is done and it is found that a precursor molecule withdirect Si-Cl bonds should be more efficient for the growth process. Also the process stability and growth ratedependence on C/Si- and Cl/Si are further studied. In Paper 4 the standard growth process for growth on 4° offaxis substrates is improved in order to get better morphology of the epilayers. It is also shown that the optimizedprocess conditions can be transferred to a chloride-based process and a high growth rate of 28 μm/h wasachieved, using the HCl-approach, while keeping the good morphology. In Paper 5 chloride-based CVD growthon on-axis substrates is explored using both the HCl- and MTS-approaches. The incorporation of dopants in SiCepilayers grown by the chloride-based CVD process is studied in Papers 6 and 7 using the HCl-approach. InPaper 6 the incorporation of the donor atoms nitrogen and phosphorus is studied and in Paper 7 theincorporation of the acceptor atoms boron and aluminum. The incorporation of dopants is found to follow thetrends seen in the standard growth process but it is also found that the Cl/Si-ratio can affect the amount ofincorporated dopants. / Kiselkarbid (SiC) är ett fascinerande material som samtidigt är mycket enkelt och mycketkomplicerat. Det är enkelt eftersom det byggs upp av bara två sorters atomer, kisel och kol.Atomerna bygger upp kristallens struktur genom att bilda Si-C bindningar och man kan beskrivakristallstrukturen som uppbyggd av tetraedrar med en kiselatom (eller kolatom) i mitten och enkolatom (eller kiselatom) i varje hörn på tetraedern. Samtidigt är SiC komplicerat eftersomberoende på hur man staplar dessa tetraedrar kan man få olika varianter på kristallstrukturen, såkallade polytyper. Det finns drygt 200 kända polytyper av kiselkarbid, men det är dock bara enhandfull av dessa polytyper som är tekniskt intressanta. Kiselkarbid är intressant eftersom det ärett hårt material som inte heller påverkas nämnvärt av kemiskt aggressiva miljöer ellertemperaturer upp till 2000 °C; dessutom är SiC en halvledare och tack vare dess tålighet är det ettmycket bra material för elektriska komponenter för högspänningselektronik eller för användningi aggressiva miljöer. För att kunna tillverka dessa komponenter måste man kunna odla kristaller av kiselkarbid. Detfinns i princip två typer av kristallodling; i) odling av bulkkristaller, där stora kristaller odlas föratt sedan kan skivas och poleras till kristallskivor (dessa skivor benämns oftast substrat), och ii)odling av epitaxiella skikt, där man odlar ett tunt lager kristall med mycket hög renhet ovanpå ettsubstrat (ordet epitaxi kommer från grekiskans epi = ovanpå och taxis = i ordning, epitaxiellaskikt odlas alltså ovanpå ett substrat och kopierar den kristallina ordningen hos substratet). I detepitaxiella skiktet, eller epilagret som det även kallas, kan man styra den elektriskaledningsförmågan med mycket hög precision genom att blanda in små mängder orenheter iepilagret, man pratar här om att dopa halvledarkristallen. För att odla epilager av SiC använderman CVD, CVD betyder Chemical Vapor Deposition, någon riktigt bra svensk översättningfinns inte men det är en teknik för att framställa ett tunt lager av ett material genom kemiskareaktioner med gaser som startmaterial. I standard CVD-processen för odling av SiC epilager använder man silan (SiH4) som kiselkälla och lätta kolväten som eten (C2H4) eller propan (C3H8) som kolkälla. Dessa gaser späds kraftigtut i vätgas och man odlar epilagret vid ungefär 1500-1600 °C. Med denna process kan man odlaca 5 mikrometer (mikrometer = miljondelsmeter) epilager på en timme. Men för vissakomponenter behöver man ett epilager som är över 100 mikrometer tjockt, vilket görtillverkningen av sådana komponenter både tidsödande och kostsam. Ett problem som manmåste lösa för att få högre tillväxthastighet i processen är att när man ökar mängden silan,kommer kiseldroppar att bildas i gasfasen och om de kommer i kontakt med substratet blirepilagret förstört. I denna avhandling undersöks ett sätt att lösa problemet med kiseldropparnaoch därmed kunna tillåta höga tillväxthastigheter för SiC epilager. Idén är att man kan lösa uppkiseldropparna genom att tillsätta något i gasblandningen som binder starkare till kisel än kisel.En mycket bra atom att använda för detta ändamål är klor eftersom klor binder mycket starkt tillkisel. Man kallar denna process för klorid-baserad CVD. Till att börja med använde vi molekylen metyltriklorsilan (MTS), som innehåller både kol, kiseloch klor, för klorid-baserad tillväxt av SiC epilager. Genom att använda MTS lyckades vi fåtillväxthastigheter mellan 2 och 104 mikrometer i timmen. Vi har även visat att det är möjligtanvända MTS för att odla 200 mikrometer tjocka epilager med en tillväxthastighet på 100mikrometer i timmen utan att den kristallina kvalitén på epilagren försämras. Ett alternativ till attanvända MTS är att addera saltsyra (HCl) i gasform till standard processen. För att förstå denklorid-baserade processen bättre, jämfördes de olika alternativen med litteraturdata från enprocess där man istället för vanlig silan hade använt triklorsilan (TCS) för att få en klorid-baserad process. Det visade sig att MTS- och TCS-processerna krävde mindre kiselhalt i gasfasen för attfå en hög tillväxthastighet, med andra ord var de mer effektiva. Vi förklarade detta med atteftersom dessa startmolekyler har tre kisel-kol bindningar är det enkelt att bilda SiCl2 molekylen,som har visat sig vara ett viktigt mellansteg i den klorid-baserade processen, eftersom man dåbara behöver bryta kemiska bindningar. Om man istället börjar från silan och saltsyra måstekemiska reaktioner ske för att skapa kisel-kol bindningar och därmed SiCl2. När man odlar kristaller underlättar man tillväxten genom att preparera ytan på substratet medatomära steg. Om man tittar på ytan med atomär förstoring kan säga att ytan liknar en trappa,detta är bra eftersom atomerna som bygger upp epilagret gärna fastnar vid atomära steg eftersomde kan binda in till kristallen både neråt och åt sidan. Vi har optimerat standard processen för attfå bättre morfologi, alltså en finare yta, när man odlar på substrat som har mindre andel atomärasteg på ytan och visat att denna optimering går att överföra till en klorid-baserad process medhög tillväxthastighet . Vi har även visat att man kan använda den klorid-baserade processen föratt odla epilager med hög tillväxthastighet på substrat helt utan atomära steg. Slutligen har vi studerat doping av kiselkarbid vid höga tillväxthastigheter med den kloridbaseradeprocessen, både n-typ doping (där man dopar med ämnen som har fler valenselektronerän kol och kisel så att man får ett överskott av elektroner i materialet) med kväve och fosfor, ochp-typ doping (där man dopar med ämnen som har färre valenselektroner än kol och kisel så attman får ett underskott av elektroner i materialet) med bor och aluminium.

This thesis describes ruthenium(II) polypyridyl-type complexes tailored for artificial photosynthesis. Inspired by Nature, the primary events in photosystem II are mimicked by donor-photosensitizer-acceptor (D-P-A) assemblies. The photosensitizer plays a key role in such processes, and the combination of structural and photophysical properties is essential to control the electron transfer steps. In the first part, the general requirements for photosensitizers are discussed. The second part deals with [Ru(bpy)3]2+-benzoquinone (Q) dyads (bpy is 2,2´-bipyridine) based on an asymmetric 5,5´-bisamide substituted bpy. Rapid electron-transfer from the excited state is observed to generate the RuIII-Q- charge separated states but preliminary results show no effect of the directionality of the amide link. In the main part, a strategy to overcome the photophysical limitations of RuII bistridentate complexes (e.g. [Ru(tpy)2]2+, tpy is 2,2´:6´,2´´-terpyridine) is explored. The prototypical [Ru(dqp)2]2+ complex (dqp is 2,6-di(quinolin-8-yl)pyridine) is synthesized which displays a 3000 ns excited state lifetime at room temperature, reversible redox chemistry and high photostability. The synthesis of 4-substituted dqp is achieved via SUZUKI coupling using 8-quinoline boronic acid or ring-formation of the central pyridine. A markedly rich Ru coordination chemistry was observed, e.g. facial and meridional isomers of [Ru(dqp)2]2+. Using a chloride-free [Ru(dqp-R)(MeCN)3]2+ intermediate allows the synthesis of heteroleptic meridional [Ru(dqp-R)(dqp-R’)]2+ (R,R’ = -H, -CO2Et, -NH2, -OMe, -Br, -PhBr, …) in high yields. The meridional complexes show long-lived luminescence (450 - 5500 ns) and reversible redox chemistry. The photochemical reactivity has been investigated in typical electron-transfer reactions, e.g. in a supramolecular P-A dyad and in a multimolecular approach using biomimetic components (Mn and Fe complexes). The dqp ligand is further used to synthesize FeII, RhIII, cyclometallating RuII complexes and an aza-analogue of [Ru(dqp)2]2+ and is discussed in the final part. These complexes were prepared with the aim to further tune the redox properties while maintaining good photophysical properties.

No description available.

Phosphorus (P) is an essential nutrient. A significant amount of soil P may be in the form of organophosphates. Due to the size of these compounds, hydrolysis is often required before P can be assimilated by organisms. Hydrolysis may be mediated by mineral surfaces, or catalyzed by extra cellular enzymes. Since both organophosphates and enzymes have a strong affinity for environmental particles, a study of the hydrolysis of organophosphates must focus on reactions at the water/particle interface. This thesis is a summary of four papers, discussing the adsorption, desorption, and abiotic and enzymatic hydrolysis of glucose-1-phosphate (G1P) and glucose-6-phosphate (G6P) in aqueous goethite suspensions. A new technique for simultaneous infrared and potentiometric titrations (SIPT) allowed in-situ measurements of the interfacial reactions. It was found that glucose phosphates form pH-dependent inner sphere complexes on goethite, which coordinate in a monodentate fashion, and are stabilized by hydrogen bonding. Desorption involves a change in speciation of the surface complexes, illustrating the difficulty in determining desorption rates for individual complexes. The surface mediated hydrolysis is primarily base catalyzed for G1P, and acid catalyzed for G6P. The difference is partly due to electronic factors, and partly to differences in glucose group/goethite interactions. Considerably more extensive is the hydrolysis catalyzed by an acid phosphatase (AcPase). The rate of the enzymatic hydrolysis are strongly dependent on the glucose phosphate surface coverage, showing that surface properties affect the adsorption mode of enzymes, and thus their catalytic activity. In solution, AcPase showed a greater specificity towards G6P, but this specificity was partly lost after adsorption onto goethite.

Iron, an essential nutrient, is primarily present in soils in the form of iron-bearing minerals characterized with low solubilities. Under iron deficient conditions, some plants and microorganisms exude a mixture of iron-complexing agents, including carboxylates and siderophores, that can cause minerals to dissolve and increase iron solubility. Siderophores are chelating agents with functional groups such as hydroxamate, catecholate, or α-hydroxycarboxylate, that have high selectivity and specificity for Fe(III). This thesis is focused on adsorption/dissolution processes at the surface of a common soil mineral, goethite(α-FeOOH), in the presence of oxalate and a trihydroxamate siderophore, desferrioxamine-B (DFOB) at pH 4 and/or 6 in the absence of visible light. In order to characterize these processes at a molecular level and to understand the reaction mechanisms, a combination of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, extended X-ray absorption fine structure (EXAFS) spectroscopy and quantitative solution phase measurements were applied. In the oxalate-goethite system, four surface species were detected: 1) an electrostatically attracted outer-sphere complex, 2) a hydrogen bonded outer-sphere complex, 3) an inner-sphere oxalate coordinated to surface iron and 4) a ternary type A complex formed during a dissolution-readsorption process. Addition of Al(C 2O 4 ) 3 3-or Ga(C 2 O 4 ) 3 3- to a goethite suspension resulted in the formation of an additional surface complex - oxalate coordinated to Al or Ga in a ternary type A complex. In the DFOB-goethite system, DFOB is subjected to surface-mediated hydrolysis followed by the reduction of Fe(III) as evidenced by the release of acetate and a nitroso-DFOB fragment into the aqueous phase. It is postulated that Fe(II) is not detected in the solution phase due to its adsorption at the surface. At low surface coverage, a small fraction of dissolved FeHDFOB + complex is also likely to form ternary surface complexes and hydrolyze. These observations suggest that DFOB-promoted dissolution of goethite may proceed not only via purely ligand-exchange reactions, but also through reductive pathways. In the oxalate-DFOB-goethite system, the dissolution rates are greater than the sum of the dissolution rates in the single-ligand systems. Results presented demonstrate that this synergistic effect is due to the formation of the above mentioned ternary oxalate surface complex via dissolution and readsorption. Iron in this ternary complex is more labile than iron in the crystal lattice and thus more readily accessible for other complexing agents, e.g. siderophores. The results presented in this thesis provide a molecular-level view of ligand-promoted mineral dissolution in the presence of small carboxylates and/or siderophores, which improves our fundamental understanding of the role of surface complexation in mineral dissolution and iron bioavailability.