Structural and optical properties of InAs/GaAs quantum structures

The goal of the thesis was to study fundamental structural and optical properties of InAs islands and In(Ga)As quantum rings. The research was carried out at the Department of Micro and Nanosciences of Helsinki University of Technology. A good surface quality can be essential for the potential applications in optoelectronic devices. For such device applications it is usually necessary to control size, density and arrangement of the islands. In order to study the dependence of the structural properties of the islands and the quantum rings on growth conditions, atomic force microscope was used. Obtained results reveal that the size and the density of the In(Ga)As quantum rings strongly depend on the growth temperature, the annealing time and the thickness of the partial capping layer. From obtained results it is possible to conclude that to get round shape islands and high density one has to use growth temperature of 500 ̊C. In the case of formation of In(Ga)As quantum rings the effect of mobility anisotropy is observed that so the shape of the rings is not symmetric. To exclude this effect it is preferable to use a higher annealing temperature of 570 ̊C. Optical properties were characterized by PL spectroscopy. PL emission was observed from buried InAs quantum dots and In(Ga)As quantum rings grown with different annealing time and temperature and covered with a various thickness of the partial capping layer.

Application of cerium oxide thin films grown by atomic layer deposition for soot removal

The objective of the thesis is to study cerium oxide thin films grown by the atomic layer deposition (ALD) for soot removal. Cerium oxide is one of the most important heterogeneous catalysts and can be used in particulate filters and sensors in a diesel exhaust pipe. Its redox/oxidation properties are a key factor in soot oxidation. Thus, the cerium oxide coating can help to keep particulate filters and sensors clean permanently. The literature part of the thesis focuses on the soot removal, introducing the origin and structure of soot, reviewing emissions standards for diesel particulate matter, and presenting methods and catalysts for soot removal. In the experimental part the optimal ALD conditions for cerium oxide were found, the structural properties of cerium oxide thin films were analyzed, and the catalytic activity of the cerium oxide for soot oxidation was investigated. Studying ALD growth conditions of cerium oxide films and determining their critical thickness range are important to maximize the catalytic performance operating at comparatively low temperature. It was found that the cerium oxide film deposited at 300 °C with 2000 ALD cycles had the highest catalytic activity. Although the activity was still moderate and did not decrease the soot oxidation temperature enough for a real-life application. The cerium oxide thin film deposited at 300 °C has a different crystal structure, surface morphology and elemental composition with a higher Ce3+ concentration compared to the films deposited at lower temperatures. The different properties of the cerium oxide thin film deposited at 300 °C increase the catalytic activity most likely due to higher surface area and addition of the oxygen vacancies.

DPS-Like Peroxide Resistance Protein: Structural and Functional Studies on a Versatile Nanocontainer

Oxidative stress is a constant threat to almost all organisms. It damages a number of biomolecules and leads to the disruption of many crucial cellular functions. It is caused by reactive oxygen species (ROS), such as hydrogen peroxide (H2O₂), superoxide (•O₂ -), and hydroxyl radical (•OH). The most harmful of these compounds is •OH, which is only formed in cells in the presence of redox-cycling transition metals, such as iron and copper. Bacteria have developed a number of mechanisms to cope with ROS. One of the most widespread means employed by bacteria is the DNA-binding proteins from starved cells (Dps). Dps proteins protect the cells by binding and oxidizing Fe2+, thus greatly reducing the production of •OH. The oxidized iron is stored inside the protein as an iron core. In addition, Dps proteins bind directly to DNA forming a protective coating that shields DNA from harmful agents. Moreover, Dps proteins have been found to elicit other protective functions in cells and to participate in bacterial virulence. Dps proteins are of special importance to Streptococci owing to the lack of catalase in this genus of bacteria.This study was focused on structural and functional characterization of streptococcal Dpslike peroxide resistance (Dpr) proteins. Initially, crystal structures of Streptococcus pyogenes Dpr were determined. The data confirmed the presence of a di-metal ferroxidase center (FOC) in Dpr proteins and revealed the presence of a novel N-terminal helix as well as a surface metal-binding site. The crystal structures of Streptococcus suis Dpr complexed with transition metals demonstrated the metal specificity of the FOC. Solution binding studies also indicated the presence of a di-metal FOC. These results suggested a possible role for Dpr in the detoxification of various metals. Iron was found to mineralize inside the protein as ferrihydrite based on X-ray absorption spectroscopy data. The iron core was found to exhibit clear superparamagnetic behaviour using magnetic and Mössbauer measurements. The results from this study are expected to further increase our understanding on the binding, oxidation, and mineralization of iron and other metals in Dpr proteins. In particular, the structural and magnetic properties of the iron core can form a basis for potential new applications in nanotechnology. From the streptococcal viewpoint, the results would help in understanding better the complicated picture of bacterial pathogenesis. Dpr proteins may also provide a novel target for drug design due to their tight involvement in bacterial virulence.

Electrochemical and spectroelectrochemical characterization of alkylated and thiolated polyanilines

Vi omges i vardagen av alla sorters plaster, som kemiskt kallas för polymerer. Vi anknyter dem oftast till vardagliga föremål såsom muggar, leksaker eller platskassar. Det finns dock en särklass av polymerer som fås elektriskt ledande genom en så kallad dopningsprocess. Dopning innebär i detta fall oxidation eller reduktion av konjugerade dubbelbindningar i polymerstrukturen. Detta har lett till utveckling av elektriska apparater där dyra, och i vissa fall även sällsynta, metall och halvledarmaterial ersätts genom av elektriskt ledande polymerer (plaster). Utöver elektronisk ledningsförmåga uppvisar dessa polymerer också jonisk ledningsförmåga. Denna kombination av unika egenskaper möjliggör skapandet av t.ex. nya sensormaterial som kan överföra kemisk information till en mätbar elektronisk signal. Detta öppnar i sin tur möjligheter att göra snabba, billiga och känsliga sensorer för bl.a. mediciniska analyser. I denna avhandling karakteriserades elektrokemiskt och spektroelektrokemiskt N- och ring-substituerade polyanilinfilmer. Polyanilin (PANI) hör till de mest studerade elektriskt ledande polymererna. Den är stabil och lätt att framställa. Substituerade polyaniliner har ändå studerats måttligt, mest p.g.a. att substituerade PANIs ledningsförmåga är lägre än PANIs och deras framställning kan vara svår. De nya grupperna i PANI-kedjan ger dock en möjlighet att binda ytterligare molekyler av intresse till PANI-kedjan, som t.ex. jonselektiva grupper. Kovalent bundna selektiva molekyler ger upphov till stabila, känsliga och selektiva sensormaterial. Karakteriseringen av de studerade polymerer är viktig för den fundamentala förståelsen av deras unika egenskaper och för utvecklingen av framtidens sensormaterial. -------------------------------------- Käytämme joka päivä monenlaisia muoveja, joita kutsutaan kemiassa myös polymeereiksi. Olemme tottuneet yhdistämään muovit arkisiin esineisiin kuten mukeihin, leluihin tai muovikasseihin. On kuitenkin olemassa erityisiä polymeerejä, jotka voidaan saada sähköä johtaviksi hapetus- ja pelkistysreaktioiden avulla. Tästä johtuen on kehitteillä sähköisiä laitteita, joissa kalliit ja jossain tapauksissa myös harvinaisia metalleja sisältävät osat ja puolijohteet voidaan korvata johdepolymeereillä (eli muoveilla). Sähkönjohtavuuden lisäksi johdepolymeereillä on myös ionijohtavuutta. Näiden erityislaatuisten ominaisuuksien yhdistelmä on mahdollistanut mm. sensorimateriaalin kehittämisen, sillä kemiallinen tieto voidaan kääntää mitattavaksi sähköiseksi signaaliksi. Tämä taas omalta osaltaan mahdollistaisi nopeiden, halpojen ja herkkien sensorien valmistuksen, mm. diagnostiikkaan. Tässä väitöksessä on tutkittu sähkökemiallisesti valmistettuja N- ja rengassubstituoituja polyaniliinikalvoja. Polyaniliini (PANI) on yksi eniten tutkituista johdepolymeereistä. Se on stabiili ja helppo valmistaa. Substituoidut polyaniliinit ovat herättäneet vain kohtalaista tieteellistä kiinnostusta, lähinnä, koska niiden sähköinen johdekyky on alhaisempi kuin PANIn. Myös niiden valmistus voi olla vaikeaa. Substituoidut molekyylit PANI-ketjussa mahdollistavat kuitenkin, että niihin voi liittää uusia molekyylejä, esim. ioniherkkiä ryhmiä. Kovalentisti sitoutuneilla selektiivisillä molekyyleillä saadaan tehtyä stabiileja, herkkiä ja selektiivisiä sensorimateriaaleja. Väitöksessä käytettyjen polymeerien karakterisointi on tärkeää, jotta niiden erityisominaisuuksia pystyttäisiin ymmärtämään paremmin ja myös kehittämään sopivia tulevaisuuden sensorimateriaaleja.

Structural and functional Studies of angucycline tailoring enzymes

Polyketides are a diverse group of natural products produced in many bacteria, fungi and plants. These metabolites have diverse biological activities and several members of this group are in clinical use as antibiotics, anticancer agents, antifungals and immunosuppressants. The different polyketides are produced by polyketide synthases, which catalyze the condensation of extender units into various polyketide scaffolds. After the biosynthesis of the polyketide backbone, more versatility is created to the molecule by tailoring enzymes catalyzing for instance hydroxylations, methylations and glycosylations. Flavoprotein monooxygenases (FPMO) and short-chain alcohol dehydrogenases/reductases (SDR) are two enzyme families that catalyze unusual tailoring reactions in the biosynthesis of natural products. In the experimental section, functions of homologous FPMO and SDR tailoring enzymes from five different angucycline pathways were studied in vitro. The results revealed how different angucyclinones are produced from a common intermediate and that FPMO JadH and SDR LanV are responsible for the divergence of jadomycins and landomycins, respectively, from other angucyclines. Structural studies of these tailoring enzymes revealed differences between homologous enzymes and enabled the use of structure-based protein engineering. Mutagenesis experiments gave important information about the enzymes behind the evolution of distinct angucycline metabolites. These experiments revealed a correlation between the substrate inhibition and bi-functionality in JadH homologue PgaE. In the case of LanV, analysis of mutagenesis results revealed that the difference between the stereospecificities of LanV and its homologues CabV and UrdMred is unexpectedly related to the conformation of the substrate rather than to the structure of the enzyme. Altogether, the results presented here have improved our knowledge about different steps of angucycline biosynthesis and the reaction mechanisms used by the tailoring enzymes behind these steps. This information can hopefully be used to modify these enzymes to produce novel metabolites, which have new biological targets or possess novel modes-of-action. The understanding of these unusual enzyme mechanisms is also interesting to enzymologists outside the field of natural product research.

Structural and Mechanistic Studies of Phosphoserine Aminotransferase

Phosphoserine aminotrasferase (PSAT: EC 2.6.1.52) is a vitamin B6-dependent enzyme and a member of the subgroup IV in the aminotransferase superfamily. Here, X-ray crystallography was used to determine the structure of PSAT from Bacillus alcalophilus with pyridoxamine 5′-phosphate (PMP) at high resolution (1.57 Å). In addition, analysis of active residues and their conformational changes was performed. The structure is of good quality as indicated, for example, by the last recorded Rwork and Rfree numbers (0.1331 and 0.1495, respectively). The enzyme was initially crystallized in the presence of substrate L-glutamate with the idea to produce the enzyme-substrate complex. However, the structure determination revealed no glutamate bound at the active site. Instead, the Schiff base between Lys196 and PLP appeared broken, resulting in the formation of PMP owing to the excess of the donor substrate used during co-crystallization. Structural comparison with the free PSAT enzyme and the PSAR-PSER complex showed that the aromatic ring of the co-factor remains in almost the same place in all structures. A flexible nearby loop in the active site was found in the same position as in the free PSAT structure while in the PSAT-PSER structure it moves inwards to interact with PSER. B-factors comparison in all three structures (PSAT-PMP complex, free PSAT, and PSAT-PSER complex) showed elevated loop flexibility in the absence of the substrate, indicating that loop flexibility plays an important role during substrate binding. The reported structure provides mechanistic details into the reaction mechanism of PSAT and may help in understanding better the role of various parts in the structure towards the design of novel compounds as potential disruptors of PSAT function. This may lead to the development of new drugs which could target the human and bacterial PSAT active site.