Orientador: Watson Loh / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-27T11:59:07Z (GMT). No. of bitstreams: 1 Ferreira_GuilhermeAugusto_M.pdf: 3614152 bytes, checksum: 568d89fdf3adc43ec1f13c46bc935cad (MD5) Previous issue date: 2015 / Resumo: Surfactantes são moléculas anfifílicas que, em solução, se organizam dando origem a uma série de estruturas de associação, dentre as quais destacam-se os cristais líquidos. Especialmente os brometos de dialquildimetilamônio se associam formando principalmente estruturas líquido-cristalinas lamelares. Nesse trabalho, foram estudadas as propriedades estruturais de fases lamelares formadas pela auto-organização, em solução aquosa, de dois surfactantes dessa classe: o DDAB (brometo de didodecildimetilamônio) e o DODAB (brometo de dioctadecildimetilamônio). Através das técnicas de caracterização utilizadas, foi verificado que, nas condições de concentração e temperatura estudadas, ambos os surfactantes, DDAB e DODAB, se associam em duas fases lamelares, La e Lß, fases essas que diferem pela organização das cadeias carbônicas nas bicamadas e intumescimento. Além de formarem diferentes fases lamelares, essas também apresentaram distintas propriedades estruturais, dependendo do surfactante utilizado. Estudos de calorimetria diferencial de varredura também permitiram acompanhar as transições entre as fases lamelares obtidas causadas por variação da temperatura. As bicamadas formadas pela auto-associação do surfactante DDAB apresentaram um intumescimento menor do que as formadas pelo análogo DODAB, porém, com esse último, houve a formação de bicamadas menos espessas. Misturas preparadas com ambos os surfactantes em diferentes proporções também indicaram a variação das propriedades investigadas, intumescimento e espessura das bicamadas, aumentando o teor de DODAB. A hipótese levantada é que as propriedades estruturais investigadas são fortemente influenciadas pelas forças eletrostáticas atuantes no sistema. A caracterização de amostras formuladas com os tensoativos acima da temperatura de transição para fase fluída e na presença de sal confirmou esta ideia. O maior intumescimento e a pequena espessura das bicamadas formadas pelo DODAB se devem, provavelmente, à interdigitação das cadeias carbônicas e ao efeito de correlação iônica, respectivamente, descritos em mais detalhes nessa dissertação / Abstract: Surfactants are amphiphilic molecules that self-assemble, in solution, giving rise to a number of association structures, among which the liquid crystals stand out. Particularly the dialkyldimethylammonium bromides associate to form mosty lamellar liquid crystalline structures. In this work, we studied the structural properties of lamellar phases formed by self-organization, in aqueous solution, of two surfactants from this class: DDAB (didodecyldimethylammonium bromide) and DODAB (dioctadecyldimethylammonium bromide). Through the used characterization techniques, we found that under the conditions of concentration and temperature studied, both surfactants, DDAB and DODAB are associated in two lamellar phases, La and Lß, phases that differ by the organization of the carbonic chains in bilayers and swelling degree. In addition to forming different lamellar phases, these also showed distinct structural properties, depending on the surfactant used. Studies with differential scanning calorimetry also allowed us to follow the transitions between the lamellar phases caused by temperature variation. The bilayers formed by self-association of DDAB showed a lower swelling degree than those formed by DODAB, however, with the later, there was the formation of thinner bilayers. Mixtures prepared with both surfactants in different proportions also indicated the variation of the investigated properties, swelling degree and bilayer thickness, upon increasing the DODAB content. We propose that the structural properties investigated are strongly influenced by electrostatic forces acting on the system. The characterization of samples formulated with surfactants above the transition temperature to the fluid phase and in the presence of salt confirmed this hypothesis / Mestrado / Físico-Química / Mestre em Química

<p>Zemlji&scaron;te predstavlja bogat izvor različitih mikroorganizama čiji<br />produkti metabolizma mogu biti od izuzetnog značaja za čoveka.<br />Dosada&scaron;nja ispitivanja mikrobnog diverziteta u zemlji&scaron;tu su<br />otkrila bogati biosintetski potencijal za proizvodnju novih<br />prirodnih proizvoda kod velikog broja mikroorganizama, naročito<br />kada je u pitanju klasa Actinobacteria. Među zemlji&scaron;nim izolatima,<br />rod Streptomyces prednjači po broju identifikovanih bioaktivnih<br />molekula u odnosu na sve ostale bakterije. Stoga je jedan od<br />ciljeva u okviru ove doktorske disertacije izolacija streptomiceta iz<br />rizosfera medicinski značajnih biljaka sakupljenih na teritoriji<br />Republike Srbije (Papaver rhoeas, Matricaria chamomilla, i Urtica<br />dioica) i ispitivanje njihovog antifungalnog potencijala na različite<br />vrste kandida. Morfolo&scaron;ki različiti izolati (ukupno 103) su izolovani<br />iz uzoraka rizosfera i okarakterisani kao streptomicete. Dve<br />različite podloge i dve procedure za ekstrakciju su kori&scaron;ćene da bi<br />se pospe&scaron;ila detekcija antifungalnih jedinjenja. Ispitan je uticaj<br />ukupno 412 ekstrakata na rast Candida albicans disk difuzionim<br />esejem pri čemu je utvrđeno da 42% (43/103) izolata imaju<br />sposobnost proizvodnje antifungalnih jedinjenja pri ispitivanim<br />uslovima. Pojedini ekstrakti su inhibirali rast važnih humanih<br />patogena poput Candida krusei, Candida parapsilosis, i Candida<br />glabrata. Na osnovu stepena i spektra antifungalne aktivnosti<br />devet izolata je odabrano za dalja istraživanja. Ispitana je<br />sposobnost njihovih ekstrakata da inhibiraju rast kandida u tečnoj<br />kulturi i u formi biofilma, a takođe je ispitan i njihov uticaj na već<br />formirane biofilmove kandide u koncentracijama od 8 do 250<br />pg/ml. Hromatografski profili ovih ekstrakata i uvid u njihovu<br />metaboličku raznolikost dobijeni su kori&scaron;ćenjem tečne<br />hromatografije visokih performansi. Tri ekstrakta sa specifičnom<br />antifungalnom aktivno&scaron;ću podvrgnuta su hemijskim analizama s<br />ciljem da se detektuju i strukturno okarakteri&scaron;u molekuli koji su<br />nosioci antifungalne aktivnosti. Na osnovu rezultata nuklearnomagnetno-<br />rezonantne spektroskopije otkriveno je da su aktivni<br />molekuli genistein, daidzein i staurosporin. Genistein i daidzein<br />koji su poznati fitoestrogeni poreklom iz sojinog bra&scaron;na za koje je<br />poznato da inhibiraju ključne enzime u biosintetskom putu<br />steroida. Njihovo prisustvo je u ovom istraživanju detektovano<br />usled kori&scaron;ćenja sojinog bra&scaron;na u hranljivoj podlozi. Kako<br />streptomicete u čijim ekstraktima su detektovani ovi molekuli<br />pokazuju sposobnost oslobađanja ovih važnih jedinjenja iz<br />kompleksne hranljive podloge, mogu se uzeti u razmatranje za<br />biotehnolo&scaron;ku proizvodnju fitoestrogena. Staurosporin je<br />detektovan kao nosilac antifungalne aktivnosti kod ekstrakta soja<br />Streptomyces sp. BV410. Staurosporin je inhibitor protein kinaza i<br />njegovi derivati i analozi se koriste u kao antitumorski agensi.<br />Biosinteza ovog molekula je optimizovana do prinosa od 36,94<br />mg/l nakon 14 dana gajenja u hranljivoj podlozi koja sadrži<br />glukozu, skrob, manitol i sojino bra&scaron;no (JS). Dalja optimizacija<br />hranljive podloge za biosintezu staurosporina ukazala je na<br />sledeći sastav hranljive podloge: 20 g/l glukoze, 0,36 g/l skroba,<br />21,46 g/l manitola, 17,32 g/l sojinog bra&scaron;na. Primenom<br />definisanih optimalnih vrednosti i kori&scaron;ćenjem odgovarajućih<br />matematičkih modela, predviđeno je da će se na ovaj način<br />postići prinosi od 46,88 mg/l staurosporina i 12,05 mg/ml<br />biomase. Validnost predviđenih rezultata potvrđena je<br />izvođenjem bioprocesa u optimizovanoj hranljivoj podlozi (JSSta).<br />Ispitana je kinetika biosinteze staurosporina i produkcije biomase,<br />kao i potro&scaron;nje izvora ugljenika i razvijeni su odgovarajući<br />procesni modeli. Dodatna optimizacija je podrazumevala dodatak<br />suplemenata koji prema literature stimuli&scaron;u sekundarni<br />metabolizam streptomiceta (joni cinka, gvožđa, fosfati, metil<br />oleat, ulje semenki grožđa). Ovi eksperimenti su izvođeni na tri pH<br />vrednosti (6,5, 7,5 i 8,5) a uspe&scaron;nost bioprocesa je procenjivana 7.,<br />10. i 14. dana gajenja. Dodatna optimizacija je dovela do podatka<br />da dodatak soli gvožđa značajno pospe&scaron;uje biosintezu<br />staurosporina sa povećanjem prinosa od 25%. Dobijeni rezultati<br />potvrđuju da su rizosfere medicinski značajnih biljaka značajan<br />izvor streptomiceta koje proizvode komponente sa<br />antifungalnom aktivno&scaron;ću. Izolacija novog proizvođača<br />staurosporina i optimizacija procesa njegove biosinteze<br />omogućiće dalja istraživanja ovog jedinjenja koje može biti<br />osnova za razvoj novih antifungalnih i jedinjenja koja inhibiraju<br />angiogenezu. Rezultati dobijeni u okviru ovih istraživanja<br />predstavljaju početni korak ka potencijalnoj industrijalizaciji<br />proizvodnje staurosporina.</p> / <p>Different soils are still a source of remarkable microbial diversity<br />which also reflects in the unexplored chemical diversity. Recent<br />advances in assessment of microbial diversity from soil have<br />revealed the extraordinarily rich biosynthetic potential for the<br />production of new natural products among different microbial<br />strains, especially within the group of Actinobacteria. Among<br />bacterial soil isolates, representatives of Streptomyces genus are<br />the most prolific producers of bioactive compounds. One of the<br />objectives of the present study was to isolate Streptomyces spp.<br />from the rhizosphere soils of three ethno-medicinal plants<br />collected in Serbia (Papaver rhoeas, Matricaria chamomilla, and<br />Urtica dioica) and to screen their antifungal activity against<br />Candida spp. Morphologically different sporulating isolates (103<br />in total) were collected from rhizosphere soil samples and<br />determined as Streptomyces spp. Two different media and two<br />extraction procedures were used to induce the production and<br />facilitate identification of antifungals. Overall, 412 crude cell<br />extracts were tested against Candida albicans using disk<br />diffusion assays, with 42% (43/103) of the strains showing the<br />ability to produce antifungal agents. Also, extracts inhibited<br />growth of other important human pathogens: Candida krusei,<br />Candida parapsilosis, and Candida glabrata. Based on the<br />established degree and range of antifungal activity, nine isolates<br />were selected for further testing. Their ability to inhibit Candida<br />growth in liquid culture, to inhibit biofilm formation, and to<br />disperse pre-formed biofilms was assessed with active<br />concentrations from 8 to 250 pg/ml. High-performance liquid<br />chromatographic profiles of extracts derived from selected<br />strains were recorded, revealing moderate metabolic diversity.<br />The most potent extracts were subjected to comprehensive<br />identification and structural characterization of antifungal<br />compounds. Applying a bioactivity-guided isolation approach,<br />active compounds of three extracts were separated, and based<br />on NMR structure elucidation it was shown that active<br />compounds were genistein, daidzein and staurosporine.<br />Genistein and daidzein, soy phytoestrogens, are known to inhibit<br />key enzymes in the steroid metabolism pathway and were<br />coming from the fermentation medium containing soy flower.<br />Since isolated Streptomyces spp. showed good ability to extract<br />these molecules from complex medium, they can be further<br />considered for biotechnological production of these<br />phytoestrogens. One of the isolates, Streptomyces sp. BV410,<br />was characterized as an efficient staurosporine producer.<br />Staurosporine is a potent inhibitor of protein kinases and is<br />considered in anticancer therapy. The biotechnological<br />production of staurosporine by strain BV410 was optimized to<br />yield 36.94 mg/l after 14 days of incubation in soy flowerglucose-<br />starch-mannitol based fermentation medium (JS).<br />Further optimization of medium for biosynthesis of<br />staurosporine indicated the following optimal values of the<br />examined factors: the content of glucose of 20 g/l, starch 0.36<br />g/l, mannitol 21.46 g/l, soy flower 17.32 g/l. By applying the<br />defined optimal values and using the appropriate mathematical<br />models, the following responses were predicted: concentration<br />of staurosporine 46.88 mg/l and biomass yield 12.05 mg/ml. The<br />validity of the results was confirmed by performing the<br />biosynthesis of the staurosporine in the medium with optimal<br />composition (JSSta). Kinetics of staurosporine and biomass<br />production and carbon source consumption were examined and<br />process models were developed. Additionally, optimization of<br />staurosporine production was performed with different<br />supplements which, according to literature data, had stimulative<br />effect on secondary metabolism (Zn, Fe and P salts, methyl<br />oleate, grape seed oil). In order to improve the production of<br />staurosporine, effects of pH (6.5, 7.5 and 8.5) and incubation time<br />(7, 10 and 14 days) were also examined. It was found that<br />addition of FeS04 significantly improved the staurosporine yield<br />in comparison to the starting conditions (increase of 25%). Our<br />results proved that rhizosphere soils of ethno-medicinal plants<br />are a prolific source of streptomycetes, producers of compounds<br />with good antifungal activity. Isolation of the new staurosporine<br />producing strain, allowed for its detailed bioactivity assessment.<br />Staurosporine scaffold might serve as a lead structure for the<br />development of new antifungal and antiangiogenic agents. Also,<br />results obtained within this research represent the basis for the<br />further scale-up and potential industrialization of the proposed<br />production process.</p>

This thesis summarizes our latest findings on liquid-solid equilibria for fluids in confined spaces. In the first part of the thesis we introduce a microscopic lattice model which we have developed for the exploration of the freezing and melting phenomena in mesoporous solids with arbitrary geometries of the pore spaces. By applying this model to materials with well-ordered pore structures we (i) establish the mechanisms of the freezing and melting transitions and identify the equilibrium and metastable transition branches for different boundary conditions, (ii) illuminate the role of thermodynamic fluctuations, and (iii) find rigorous equations governing the transition temperatures for the lattice model considered. In the second part of the thesis the results obtained with the ordered pore systems are used for an in-depth analysis of the transitions occurring in geometrically disordered porous solids. First, by considering the ink-bottle pore geometry the efficacies of the different phase transition mechanisms established in the first part are elucidated. As a particularly important result, it is shown that thermodynamic fluctuations may alter the transition mechanisms. In the light of these findings the freezing and melting behaviors in statistically disordered porous materials are discussed. In the third part of the thesis several experimentally-relevant topics are considered and the potentials of the microscopic model for evaluation of the experimental data are demonstrated.

In a previous ICFCA paper we have shown that, in the Description Logics EL and ELgfp, the set of general concept inclusions holding in a finite model always has a finite basis. In this paper, we address the problem of how to compute this basis efficiently, by adapting methods from formal concept analysis.

<p> Non-homologous end joining (NHEJ) is the predominant mode of DNA double strand break (DSB) repair pathway in mammalian cells. At the heart of this repair pathway is Xrcc4-DNA ligase IV complex, which mediates ligation of the broken DNA strands. The C-terminal tandem BRCT repeats of human DNA ligase IV spanning residues 654-911 in complex with the functional fragment of Xrcc4 comprised of residues 1-203 were crystallized by the hanging drop vapour diffusion method at 20°C. Generation of single, well-packed, diffraction quality crystals suitable for structure determination involved usage of an Xrcc4 point mutant (A60E). Arriving at the crystallization condition included optimization of pH, variation of the precipitant concentration, investigation of the effects of small molecules, and alteration of the amount of crystal seed used as initial nuclei. A Crystal of selenomethionine-derived protein complex was grown using the above optimization steps and diffracted to 2.4 A resolution. Data processing revealed that the crystal belonged to space group P1 with unit cell dimensions a= 67.33 b = 86.00 c = 111.52; a= 67.37 ~ = 83.00 y = 74.56. The crystal structure of Xrcc4-DNA ligase IV complex was solved by single-wavelength anomalous diffraction using data collected at a wavelength of 0.9785A corresponding to peak energy. </p> <p> The structure maintains a 2:1 stoichiometry of Xrcc4 to the C-terminal domain of DNA ligase IV. The structure of the complex not only confirms the overall novel mode of interaction first observed in the 3.9 A structure of the yeast ortholog liflp-lig4p complex, but it also discloses additional key features such as the DNA binding surface of the complex and the striking conformational changes occurring within Xrcc4 upon interaction with DNA ligase IV. Together, the structural information procured forms an important basis for a better understanding of the mechanism involved in the NHEJ repair pathway. </p> / Thesis / Master of Science (MSc)

Previous studies of supramolecular association through chalcogen-centred secondary bonding interactions (SBIs) demonstrated the versatility of 1,2,5-telluradiazoles and their annulated congeners, the benzo-2,1,3-telluradiazoles, as supramolecular building blocks. Key to the properties of those compounds is their propensity to undergo auto-association through the [Te-N]2 supramolecular synthon leading to dimers or supramolecular ribbon polymers. Moderate steric repulsion induces structural distortions of [Te-N]2 without dissociation and, in doing so, enables properties of practical interest such as chromotropism and second-order non-linear optical responses. However, moisture sensitivity discourages wide-spread application of these compounds. While being more tolerant of the atmosphere, the analogous selenadiazoles form weaker intermolecular interactions. Using a combined experimental and computational approach, this thesis investigates methods by which the selenium-centred supramolecular interactions can be enhanced and applied in the construction of supramolecular architectures. The quantum mechanical description of the SBIs formed by 1,2,5-chalcogenadiazoles was updated with the application of modern dispersion corrections to relativistic density functional theory calculations (PBE-D3, ZORA). While in all cases the dispersion effect on optimized SBI distances is small (< 0.03 Å), the dispersion corrections to the calculated interaction energy range from 6 to 10 kJ mol-1 and increase with the weight of the chalcogen. The total interaction energy increases faster, however, therefore the relative weight of dispersion for the telluradiazole (10%) is significantly less than for the sulfur analogue (40%). The same dispersion-corrected functional was applied to the identification of the secondary ions observed in the Laser Desorption Ionization mass spectrum of benzotelluradiazoles. The most stable structure of the [2M+H]+ ion was shown to feature the [Te-N]2 supramolecular synthon and would be preferred over alternatives held by hydrogen bonding alone, one TeN SBI, a combination of the two or -stacking. The [2M]+ would also feature the [Te-N]2 supramolecular synthon. Shortening of the TeN distances in these ions implies that electron withdrawing groups strengthen the SBIs. The updated computational method was also applied to characterize the bonding in the adducts of a N-heterocyclic carbene with benzo-2,1,3-telluradiazole and 3,4-dicyano-2,1,5-telluradiazole recently prepared by the Zibarev group. The long TeC distances (2.53 and 2.34 Å) correspond to fractional bond orders (<0.6) but display a significant covalent character. Attachment of the carbene nearly erases the remaining σ-hole on tellurium, raises the LUMO energy and consequently prevents the dimerization of these adducts, in contrast to what has been observed with the pyridine and DMSO adducts of other telluradiazoles. Benzo-2,1,3-selenenadiazole reacted with boranes (BR3, R = Ph, F, Cl, Br) yielding 1:1 (R = Ph, F, Cl, Br) and 1:2 (R = Cl) adducts. The crystal structure the BPh3 adduct features molecules organized in pairs connected by long SeC SBIs but no SeN SBIs. The BF3 and BCl3 1:1 adducts dimerize forming the [Se-N]2 supramolecular synthon. In contrast, the BBr3 adduct does not dimerize although SeBr, BrBr SBIs are formed through the lattice. The 1:2 adduct displays SeCl SBIs accompanied by distortion of the N-B-Cl bond angle due to the enhanced electrophilicity of the chalcogen. DFT calculations were performed to evaluate the energies of dimerization of the 1:1 adducts, the calculated SBI energies are greater than those for the dimer of the parent heterocycle (benzo-2,1,3-selenadiazole, 3b). The products of the combination of benzo-2,1,3-selenenadiazole with chloride salts of divalent Mn, Fe, Co, Ni, and Cd crystallized from DMSO in two distinct structural types. While the smaller ions (FeII, CoII and NiII) form infinite chains of metal atoms N,N’-bridged by the heterocycle΄ the larger ions (MnII and CdII) stabilize infinite chains of metal atoms bridged by 2 halide ions. In the latter case, two heterocycle molecules cap each metal ion and are able to establish a link to the next chain in the lattice through the [Se‑N]2 supramolecular synthon. Despite the large (>9.2 Å) distance between [M(-Cl)2]∞ chains, the manganese derivative is only paramagnetic, not ferromagnetic. Symmetry-broken DFT calculations for small models were unable to quantitatively reproduce the measured couplings (J) but do indicate that the heterocycle acquires significant spin density in the MnII compound enabling paramagnetic coupling through the [Se‑N]2 supramolecular synthon. General methods for the synthesis of N-alkylated selenadiazolium cations were investigated. Methyl, iso-propyl and tert-butyl benzo-2,1,3-selenadiazolium cations were prepared by direct alkylation or cyclo-condensation of the alkyl-phenylenediamine with selenous acid. While the former reaction only proceeds with the primary and tertiary alkyl iodides, the latter is very efficient. Difficulties reported in earlier literature are attributable to the formation of adducts of benzoselenadiazole with its alkylated cations and side reactions initiated by aerobic oxidation of iodide. However, the cations themselves are resilient to oxidation and stable in acidic to neutral aqueous media. X-ray crystallography was used in the identification and characterization of the following compounds: [C6H4N2(R)Se]+X-, (R = CH(CH3)2, C(CH3)3; X = I-, I3-), [C6H4N2(CH3)Se]+I-, and [C6H4N2Se][C6H4N2(CH3)Se]2I2. Formation of SeN SBIs was only observed in the last structure because anion binding to selenium is stronger. The relative strengths of those forces and the structural preferences they enforce were assessed with DFT-D3 calculations supplemented by AIM analyses of the electron density. The methods developed for the preparation of N-alkyl benzoselenadiazolium cations were extended to the syntheses of dications intended for use as building blocks of supramolecular polymers. The structure of several salts was established by single-crystal X-ray diffraction. [H4C6NSeN-CH2-CH2-NSeNC6H4]Cl2 crystallized forming a macrocyclic structure in which two dications are bridged by SeCl SBIs; a third halide anion sits at the centre of the macrocycle. [1,2-(H4C6NSeN)2-C6H10]Cl2 features two selenadiazolium cations bridged by a 1‑(R),2‑(R)‑substituted cyclohexane and short SeCl SBIs. [1,4-(H4C6NSeN-CH2)2-C6H4](BF4)2, featuring a p-xylene bridge, crystallizes in two pseudopolymorphs; with dications in anti or syn conformations making SeF contacts. [H4C6NSeN-CH2-CH2-NSeNC6H4](CF3SO3)2 does dimerize though the [Se-N]2 supramolecular synthon, although SeO interactions with the anions cap the second selenium atom. In contrast, [H4C6NSeN-CH2-CH2-CH2-NSeNC6H4](CF3SO3)2 only displays SeO contacts. An oligonucleotide analogue containing N-substituted selenadiazolium cations was designed to create foldamers with structures controlled by main-group secondary bonding. The target structures take advantage of the methods developed in this thesis for the functionalization of selenadiazoles and is meant to be compatible with automated methods for oligonucleotide synthesis. The proposed synthesis begins with the preparation of 1-(α,β)-O-methyl-2-deoxy-D-ribose, which was chlorinated and treated with phenylenediamine. High-resolution mass spectrometry confirmed the attachment of the diamine to the ribose, however, the yield was too low to continue this synthetic project. A ground-breaking development in the application of secondary bonding in supramolecular chemistry is the discovery of the reversible auto-association of iso-tellurazole N-oxides through TeO SBIs into annular structures. These rings are persistent in solution and behave as actual macrocycles able to complex transition metal ions, form adducts with fullerenes, and host small molecules. Single-crystal X-ray diffraction was critical to the characterization of these structures and required careful disorder modelling for tetrahydrofuran molecules included in a macrocyclic hexamer and the occupational disorder of CH2Cl2 and BF4- anions due to metal depletion in the crystal of a PdII complex. / Thesis / Doctor of Philosophy (PhD) / Supramolecular chemistry is a prominent area of research that pursues the construction of large structures by the spontaneous assembly and organization of molecular building blocks. Its fundamental premise is that the judicious use of intermolecular forces allows the design of a structure and control of its properties. Most of the work in supramolecular chemistry has relied on hydrogen atoms bridging molecules and the bonding of metal ions to atoms rich in electrons. This thesis pursued the use of a different type of intermolecular force, termed “secondary bonding”, which is characteristic of the heaviest elements at the right of the periodic table (the “main-group” of elements). Previous work at McMaster demonstrated that cyclic molecules containing carbon, nitrogen and tellurium were particularly efficient as supramolecular building blocks. However, they are easily degraded by atmospheric water, this fact severely limits practical applications of these compounds. In this thesis, the tellurium atoms are replaced by selenium, a lighter element in the same family. The resulting molecules are more tolerant of atmospheric conditions but form weaker intermolecular links. Through a combination of quantum mechanical, synthetic, spectroscopic and structural studies, it is shown that certain modifications to the molecular structure increase the affinity of the selenium atoms for electrons. In this way, it is possible to strengthen the intermolecular interactions and promote the spontaneous assembly of supramolecular structures. These investigations eminently fall in the category of fundamental research but have broad-reaching implications for practical applications in optical and electronic technologies.

An infinitesimal fraction of the practically infinite sequence space has achieved enormous functional diversity of proteins during evolution. Intrinsically disordered proteins (IDPs) which lack a fully defined three-dimensional structure are the most likely precursors to today's proteins because of their flexible conformation and functional diversity. But how have these proteins evolved into often rigid and highly specialized protein structures? This evolutionary trajectory has the greatest support in the theory of induced fold whereby the development of the structure was mediated by the interaction and coevolution of primordial unstructured proteins with different cofactors or RNA molecules. Although some random sequences from the sequence space which is not used by nature are also able to form folded proteins the more suitable candidates for evolution of structure and function appear to be random sequences with a high content of disordered which have low aggregation propensity. The selected random protein sequences with high disorder content have been structurally characterized in this work for their further use in evolutionary studies. Three artificial proteins were selected from a random-sequence library based on previous study in our laboratory. In the present work they were purified and...

Ce travail constitue une approche innovante mettant en complémentarité diverses techniques de caractérisation physicochimique, électrique et structurale. Menées sur un polymère époxyde, ces études ont pour principal objectif la compréhension des phénomènes et propriétés diélectriques associés aux charges d’espace, ainsi que le suivi de leur évolution dans le temps ou suite à l’application de contraintes extérieures. Les mesures de spectroscopie d’impédance et de courant de dépolarisation thermo-stimulé (CDTS), ont mis en évidence des processus de relaxations dipolaires et interfaciales. L’origine de ces phénomènes a pu être expliquée à partir des analyses physico-chimiques et structurales. Tout d’abord à l’aide des mesures de fluorescence X qui ont révélé la présence de deux types d’impuretés, pouvant créer des états énergétiques plus ou moins profonds dans la bande interdite. Ensuite, par des mesures en réflectométrie X qui ont mis en évidence plusieurs structures ordonnées au sein d’une matrice amorphe. Cette hétérogénéité structurale explique les mécanismes de piégeage et d’accumulation des charges d’espaces aux interfaces. De même, l’ordre local favorisant la mobilité des charges, ces résultats donnent une première réponse quant à la valeur relativement élevée de la conductivité électrique du polymère, telle qu’elle a pu être déterminée à partir des mesures des caractéristiques courant-tension. Des études de vieillissement accéléré ont également été menées. Les différents recuits appliqués ont contribué à la création de charges qui sont piégées dans des niveaux énergétiques de plus en plus profonds. Cela s’est traduit par une diminution de la quantité de charges qui relaxent par activation thermique ainsi que par une diminution de la conductivité électrique des échantillons. Ces changements de propriétés électriques ont été corrélés aux changements structuraux qui se sont produits au sein du polymère, et dont la principale manifestation est la disparition progressive des structures ordonnées. Cette disparition de l’ordre local a aussi été observée en l’absence de contraintes thermiques (vieillissement naturel), où il a été montré que le comportement superficiel et en volume des échantillons n’était pas identique. / This work constitutes an innovative approach in epoxy based polymer characterization, where complementary physico-chemical, electric and structural techniques are used. The main objective of these studies is to understand both dielectric phenomena and properties associated to the space charges, as well as to follow-up their evolution in time or after the application of external constraints.Impedance spectroscopy and thermo-stimulated depolarization current (TSDC), measurements have highlighted dipolar and interfacial relaxations processes. Origin of these phenomena has been explained from physico-chemical and structural analyses. First, X-ray fluorescence measurements revealed the presence of two types of impurities, which are able to create deep energetic levels in the forbidden energy band. Then, X ray reflectometry measurements highlighted several periodic structures within an amorphous matrix. This structural heterogeneity explains the mechanisms of trapping and accumulation of space charges at the interfaces and gives a first reply as for the relatively high value of the polymer electric conductivity, calculated from current-voltage measurements.Accelerated ageing studies have been also carried out. They have shown that annealing creates charges which are trapped in increasingly deep energetic levels. Consequently, both the quantity of released charges and annealed samples conductivities have decreased.These electric properties changes have been correlated with the structural changes occurring within the polymer, and whose principal manifestation is the progressive disappearance of the ordered structures. This disappearance of the local periodicity has also been observed in the absence of thermal constraints (natural ageing), where it was shown that samples surface’s behavior is different from the bulk.

As proteínas pertencentes à família das septinas foram originalmente descobertas em 1971 em decorrencia de estudos genéticos em células mutantes. Essas proteínas encontradas em fungos e animais, mas não em plantas apresentam como principais características a presença de um domínio conservado de ligação aos nucleotídeos de guanina (GTP) e a formação de filamentos homo- e hetero-oligoméricos, que são estruturas altamente organizadas. Estudos filogenéticos e moleculares em humanos identificaram 14 septinas que são divididas em 4 grupos (I, II, III e IV). Estas moléculas associam-se com membranas celulares, actina, microtúbulos do citoesqueleto e estão envolvidas em inúmeros processos que ocorrem no córtex celular e requerem organização espacial, tais como: citocinese, ciclo celular, formação de barreiras de difusão, alinhamento de fuso. Alterações na expressão das septinas estão associadas a vários tipos de tumores e a doenças de Parkinson e Alzheimer. Neste trabalho, com o objetivo de obter informações estruturais e bioquímicas das septinas 7 e 9 humanas. Este projeto é parte de um esforço conjunto coordenado pelo Prof. Dr. Richard C. Garratt e conhecido informalmente como Septimoma. As construções recombinantes SEPT 7, SEPT 7G, e SEPT 9G foram expressas em Escherichia coli e as proteínas recombinantes obtidas. As análises em eletroforese SDS-Page e em gel nativo indicam que essas proteínas foram purificadas com sucesso. A atividade GTPase e o estado oligomérico na forma dimérica foram verificados. Estudos de dicroísmo circular e fluorescência determinaram que esses recombinantes são formados por uma mistura de estruturas secundárias &alfa; e &beta;, e também que o C e o N terminais aumentam a estabilidade das proteínas. Foram obtidos cristais da SEPT 7G e, por meio da técnica de raios-X, foi determinado um modelo tridimensional da proteína com resolução de 3,4o. / Proteins belonging to the septin family were originally discovered in 1971 through genetic studies of mutant cells. These proteins found in fungi and animals, but not in plants present, as their main characteristics, a conserved guanine nucleotide-binding domain (GTP) and they also form homo and hetero-oligomeric filaments that are highly organized structures. Phylogenetic and molecular studies in humans have identified 14 septins which are divided into 4 subfamilies (groups I, II, III and IV). These molecules associate with cell membranes, actin, cytoskeleton microtubules and they are related to a number of processes that take place in the cell cortex and that require spatial organization, such as cytokinesis, cell cycle, diffusion barrier formation and spindle alignment. Alterations in the expression of septins are associated with several types of tumors and with Parkinsons and Alzheimers diseases. In this work, with the goal of obtaining structural and biochemical information of human septins 7 and 9, the recombinants SEPT 7, SEPT 7G and SEPT 9G were expressed in E. coli. Analyses both in SDS-Page electroforesis and in native gel suggest that these proteins were purified successfully for they are soluble and homogeneous. GTpase activity has been verified in all of these recombinants, which shows that these proteins are present in native form and that additional molecules are not needed for this activity. It was possible to determine through different techniques such as molecular exclusion chromatography and SAXS that all the molecules in solution are grouped as dimeric form. Circular dichroism and fluorescence spectroscopic studies have determined both that such recombinants are formed by means of a mixture of &alfa; and &beta; secondary structures and that the C and N-terminals increase the stability of proteins. Protein stability studies under different pH and temperature conditions show that the raise of the latter produces a greater molecular aggregation. Measurements of fluorescence emissions have indicated that the SEPT 7, SEPT 7G and SEPT 9G form structures of amyloid-like filaments found in many septins. Crystal structures of SEPT 7G have been obtained and, by means of the X-ray technique, a 3-D model of the protein has been determined with a resolution of 3.4o. It has been possible to predict, with molecular modeling studies, regions formed by loops that showed low electronic density in the GTPase crystallographic model. Therefore, it has been possible to add more structural information to this domain and to form the complete polypeptide without cuts.

A utilização de novas rotas de síntese de materiais nanoestruturados tem levado à obtenção de materiais apresentando novas propriedades e aplicações. O presente trabalho teve como principal objetivo realizar a síntese e a caracterização de nanopartículas de óxido de vanádio obtidas pelo método da decomposição de peróxido utilizando o tratamento hidrotermal. Por meio do controle do tempo e da temperatura de síntese, foi possível obter nanoestruturas de pentóxido de vanádio com diferentes fases cristalinas e morfologias. Os resultados de espectroscopia Raman e difração de raios X (DRX) mostraram que o tratamento hidrotermal da solução em temperaturas de até 180oC, durante 2 horas, leva à formação da fase V2O5nH2O monoclínica, apresentando uma orientação preferencial na direção 00l. A partir desta temperatura, o material obtido passou a ter a fase ortorrômbica perdendo sua orientação preferencial. Através das medidas de termogravimetria (TG) foi observado que, dependendo da condição de síntese, as amostras apresentam diferentes quantidades de moléculas de água (H2O) intercaladas em sua estrutura. Imagens de microscopia eletrônica mostraram que as nanoestruturas obtidas podem possuir a forma de fitas, fios ou bastões. Utilizando a técnica de espectroscopia de absorção de raios X (XAS), foi possível verificar a presença de íons de V4+ nas amostras de fase monoclínica, o que não foi observado naquelas que possuem estrutura ortorrômbica. Pela técnica de XAS também foi possível constatar que as amostras de estrutura ortorrômbica possuem menor grau de desordem ao redor do átomo de vanádio. O estudo do mecanismo de crescimento da nanoestrutura de V2O5nH2O mostrou que ocorre um crescimento lateral, o qual pode ser descrito pelo mecanismo denominado Coalescência Orientada ou Oriented attachment (OA). Finalmente, através da decomposição do peróxido de vanádio, foi possível obter compostos vanadatos contendo cátions de Na+ em sua estrutura. / The use of new routes for nanostructured materials synthesis has lead to materials with new properties and applications. This PhD project aimed to realize the synthesis and the characterization of vanadium pentoxide nanoparticles obtained by peroxide decomposition using the hydrothermal treatment. By controlling synthesis time and temperature it was possible to achieve vanadium pentoxide nanoparticles with different crystalline phases and orphologies. The results of Raman spectroscopy and X-ray diffraction (XRD) showed that the hydrothermal treatment of the solution at temperatures up to 180oC for two hours leads to formation of the V2O5nH2O monoclinic phase with a preferential orientation on 00l direction. From this temperature on the material obtained began to present the orthorhombic phase misleading its preferential orientation. Through thermogravimetry (TG) measurements it was seen that depending on the synthesis condition the samples contains different amounts of water molecules (H2O) interleaved in their structure. Images of transmission electron microscopy (TEM) showed that the V2O5nH2O compound could have different morphologies such as ribbons, wires and rods. From X-Ray Absorption spectroscopy (XAS) measurements, it was observed the presence of V4+ ions in the monoclinic phase samples, which was not observed on orthorhombic structure samples. Through the XAS technique was also observed that the orthorhombic structure samples have a lower degree of disorder around the vanadium atom. Regarding the growth mechanism of these nanostructures, it was possible to verify that has been a wide growth which can be explained by the mechanism denominated Oriented Attachment (OA). Finally, through vanadium peroxide decomposition vanadates compounds containing Na+ cation in its structure were carried out.