Protein dynamics play a key role in enzyme-catalyzed reactions. Vibrational spectroscopy provides a method to follow these structural changes and thereby describe the reaction coordinate as a function of space and time. A vibrational spectroscopic technique, reaction-induced FTIR spectroscopy, has been applied to the study of the oxygen-evolving complex (OEC) of photosystem II (PSII). In plant photosynthesis, PSII evolves oxygen from the substrate, water, by the accumulation of photo-oxidizing equivalents at the OEC. Molecular oxygen and protons are the products of this reaction, which is responsible for the maintenance of an aerobic atmosphere on earth. The OEC is a Mn4CaO5 cluster with nearby bound chloride ions. Sequentially oxidized states of the OEC are termed the S states. The dark-stable state is S1, and oxygen is released on the transition from S3 to S0. Using short laser flashes, individual S states are generated, allowing vibrational spectroscopy to be used to study these different oxidation states of the OEC. In current X-ray crystal structures, hydrogen bonds to water molecules are predicted to form an extensive network around the Mn4CaO5 cluster. In the OEC, four peptide carbonyl groups are linked to the water network, which extends to two Mn-bound and two Ca-bound water molecules. This dissertation discusses a vibrational spectroscopic method that uses these peptide carbonyl frequencies as reporters of solvatochromic changes in the OEC. This technique provides a new, high-resolution method with which to study water and protein dynamics in PSII and other enzymes.

Vibrational spectroscopy, mainly infrared spectroscopy, has been applied to bacteria, yeast and archaea cells for many years, for example, for the purpose of developing a rapid method of identification. More recently microcolonies have been used for consistency with the preparation and culture protocols of traditional microbiological methods. Heterogeneity of microcolonies has not been well studied. Investigation of heterogeneity may provide detailed biochemical information leading to an understanding of how colonies grow and the link to the growth cycle. Investigation of regions within bacterial colonies using FT-IR microspectroscopy was applied to two prokaryotes, the Gram-negative archaeon Halobacterium salinarium and the Gram-positive bacterium Bacillus stearothermophilus. Two-dimensional maps of the entire colony and point maps, spectra taken from key regions such as the periphery and centre of the colony, were acquired. The approximate size of the colonies ranged from 250-950 μm. The infrared data for the Gram-negative archaeon, H. salinarium supports that for the Gram-positive bacterium, B. stearothermophilus, despite the microorganisms being of different domains and Gram types. It was concluded that the periphery of the microcolony approximately equates to the exponential growth phase (and possibly the lag phase) where the younger cells reside, while the centre approximates to the death and stationary phases. However the spatial resolution proved to be a limiting factor, so Raman microspectroscopy was employed to address this. Raman spectra across the diameter of microcolonies ranging from 100-300 μm of the pigmented bacterial species Halobacterium salinarium revealed variations in the carotenoid bands. It was suggested that these variations correspond to growth rings, which relate to the growth cycle and the consolidation and migration phase of the cells. The carotenoid variation was rather clear mainly due to the enhanced spectral intensity due to resonance with the laser excitation source. Hence, pigmented bacterial colonies are ideal to study by Raman spectroscopy. The results of this particular aspect of the research are to be published in the Journal of Raman Spectroscopy [1]. In addition, a connection between the consolidation and migration phases and the phases of the growth cycle has been postulated as a novel hypothesis to link the periodic dynamics of the colony and the growth mechanisms at the cellular level. The Raman microspectroscopic study was extended to non-pigmented bacterial colonies directly on the growth medium. This was a more difficult endeavour as the spectra taken do not have the resonance enhanced advantage of a pigmented bacterium. In addition the sampling volume can consist of variable amounts of growth medium thus decreasing the signal-to-noise ratio and reducing the accuracy of subsequent spectral calculations. However, this was overcome to a large extent by the use of confocal microscopy. The non-pigmented bacterial colonies investigated were Bacillus stearothermophilus and Bacillus subtilis. Analysis, by band area ratios and by chemometric approaches, of radial line map spectra of both Bacillus species revealed variation of nucleic acid concentration. The higher nucleic acid concentration is likely to be a result of cells in the exponential growth phase as rapid growth of new cells is occurring.

Made available in DSpace on 2014-06-11T19:27:13Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-08-29Bitstream added on 2014-06-13T18:55:41Z : No. of bitstreams: 1 volpati_d_me_bauru.pdf: 5747357 bytes, checksum: 51588cae60e48257109b7cd67deb6faa (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Filmes finos do bis benzimidazo perileno (AzoPTCD) foram fabricados usando as técnicas de Langmuir, Langmuir-Blodgett (LB) e evaporação a vácuo (PVD). A estabilidade térmica durante a fabricação dos filmes PVD ('DA ORDEM DE' '400 GRAUS' a '10 POT. -6' Torr) e a integridade da estrutura molecular pela dissolução do AzoPTCD em ácidos fortes para a fabricação dos filmes de Langmuir e LB foram monitoradas pelo espalhamento Raman. Complementarmente a análise termogravimétrica revelou que a degradação térmica do AzoPTCD ocorre a '675 GRAUS'. Os filmes de Langmuir revelaram um alto empacotamento molecular do AzoPTCD sobre a subfase aquosa, onde as moléculas estão apoiadas sobre seu eixo maior ou menor. A adição de íons metálicos na subface aquosa revelou uma sensibilidade do AzoPTCD a presença destes íons, deslocando as isotermas para maiores valores de área molecular média. O crescimento dos filmes LB e PVD sobre substratos sólidos foi monitorado através da espectroscopia de absorção UV-Vis, e a morfologia dos filmes PVD foi estudada via microscopia de força atômica (AFM) em função da espessura em massa. A organização molecular dos filmes PVD foi determinada usando as regras de seleção de superfície aplicadas na espectroscopia de absorção no infravermelho (modos de transmissão e reflexão). Apesar da organização molecular, a difração de raios-x revelou que os filmes PVD são amorfos. Cálculos teóricos (Density functional theory -B3LYP) foram usados para atribuição dos modos vibracionais nos espectros de absorção no infravermelho e espalhamento Raman ressoante Nanoestruturas metálicas, capazes de ativar os fenômenos de amplificação em superfície foram usadas para estudos de espalhamento Raman ressonante amplificado em superfície (SERRS) e fluorescência amplificada em superfície (SEF) nos filmes LB e PVD. Através... / Thin solid films of bis benzimidazo perylene (AzoPTCD) were fabricated using Langmuir, Langmuir-Blodgett (LB) and physical vapor deposition (PVD) techniques. Thermal stability during the fabrication of PVD films ('DA ORDEM DE' '400 GRAUS' a '10 POT. -6' Torr) and chemical structure integrity by dissolution of the AzoPTCD in a strong acid were monitored by Raman scattering. Complementary thermogravimetric results showed that thermal degradation of AzoPTCD occurs at '675 GRAUS'. Langmuir films showed a high molecular packing with the molecules tilted onto the aqueous subphase. Besides, the AzoPTCD л-A isotherms were shifted to larger areas due to the addition of metallic ions in the subphase. The growth of the LB and PVD films were established through UV-Vis absorption spectroscopy, and the surface morphology in PVD films was probed by atomic force microscopy (AFM) as function of the mass thickness. The AzoPTCD molecular organization in the PVD films was determined using the selection rules of infrared absorption spectroscopy (transmission and reflection-absorption modes). Despite the molecular organization, X-ray diffraction revealed that the PVD films are amorphous. Theoretical calculations (Density Functional Theory, B3LYP) were used to assign the vibrational modes in the infrared and Raman spectra. Metallic nanostructures, able to sustain localized surface plasmons (LSP) were used to achieve surface-enhanced resonance Raman scattering (SERRS) and surface-enhanced fluirescence (SEF) in the LB and PVD films. The conductivity and rectifier character of the PVD films of AzoPTCD were determined by current as function of tension curves (I(V)) in dc measurements. The impedance spectroscopy in ac measurements was used to study the performance of PVD films of the AzoPTCD as transductor elements in sensing units applied to discriminate... (Complete abstract click electronic access below)

The complementary value of vibrational spectroscopy and mass spectrometry in obtaining structural information on a range of tricyclic indoles with various ring patterns has been investigated, focusing particularly on whether these heterocycles with a functional group containing oxygen in the third ring should be described as ketoindoles or hydroxindolenines. Parallels between certain fragmentations of ionised indoles and electrophilic substitution in solution have been identified. A mechanistically interesting and analytically useful interesting dimerisation, leading to the formation of [2M-H]+ ions, has been discovered in the positive ion electrospray mass spectra of 3-alkylindoles. This dimerisation, which occurs in the nebuliser of the instrument, offers a potential new route to bisindoles under milder conditions than those employed in classical solution chemistry. Facile formation of C=N bonds by condensation of C=O and H2N has been shown to provide a means of preparing protonated imines and protonated quinoxalines from mixtures of the requisite (di)carbonyl compounds and (di)amines, thus further illustrating how organic synthesis is possible in the droplets in the nebuliser of the instrument. Possible metal catalysed coupling reaction routes to bisindoles have been explored. Acyl transfer reactions from nitrogen to carbon have been investigated in 1-acyl-2-methylindoles and orthogonally protected sulphonamides. These processes have been shown to be intermolecular and intramolecular, respectively. The latter rearrangement, which may be prevented when necessary by choosing the nitrophenylsulphonamide protecting group, offers a route to acyl, carboalkoxy and carboaryloxy aromatic compounds, some of which are difficult to prepare.

The spectral analysis techniques afforded us from the field of physics has enabled us to explore the spectral signatures of trace contaminants and degradation products in used or in service engine oil through atomic and molecular spectroscopy. Here we have examined the need to address proper preparation of calibrating samples for infrared spectroscopy analysis by inducing emulsification and have evaluated multiple procedures for proper emulsification of samples with the intent to help establish the protocols that are not explicitly set forth in the ASTM International standard. We have also explored the use of Fourier-transform infrared spectroscopy techniques to examine the suppression of the O–H stretching mode of water due to the influence of ethylene glycol, which may help in the quantification of water when both are present in oil. This was done in conjunction with exploring alternative methods for direct and indirect measurement of the glycol contamination by use of UV/Vis spectroscopy, Raman, and laser-induced breakdown spectroscopy. An exploration of FT-IR and UV/Vis data on the oxidation of oil by means of ANOVA calculations has led to the reporting of highly significant differences in the data of differing oxidation times and in regions of the spectrum not known to have been previously reported.

L’un des enjeux actuels dans le domaine de la chimie des nanomatériaux est de développer des stratégies visant à contrôler la synthèse, l’organisation et la réactivité de nanoparticules (NPs) métalliques, y compris sous forme cœur (métal)@coquille (oxyde(s)). Dans ce contexte, en revisitant la synthèse par voie micellaire, a été établi une stratégie basée sur la modification des interactions ligand-ligand contrôlées par le solvant, suivant la modélisation de la solubilité de Hansen, afin de contrôler de la taille des NPs de cobalt entre 3,8 nm et 9,1 nm (mesure MET). De l’acide dodécanoïque passive les NPs et protège de l’oxydation et de la coalescence. Des monocouches en réseau hexagonal et des supercristaux cfc ont été obtenus. En utilisant deux méthodes d’oxydation combinées à des recuits, par voie sèche et en solution, des NPs coeur/coquille [Co(ferro)@CoO(antiferromagnétique)] ont été préparées avec un cœur métallique polycristallin cfc ou monocristallin hcp. L’étude préliminaire des propriétés magnétiques (mesures SQUID) montre que l’interface Co/CoO favorise une interaction d’échange ferromagnétique/antiferromagnétique faible. La spectroscopie Raman, méthode non-invasive, sous différentes excitations laser permet d’analyser simultanément la particule métallique (contrôle de la phase et mesure des diamètres à partir des modes de Lambs), l’agent passivant et les éventuelles coquilles d’oxyde (CoO/CoOH, Co3O4) ainsi que la dynamique des chaines dodécanoates. L’analyse infrarouge indique une hydroxylation des NPs non oxydées. Les techniques vibrationnelles apparaissent bien adaptées au contrôle multi-échelle des assemblées et supracristaux de NPs. / One of the present challenges in the field of nanomaterial chemistry is to develop strategies aimed at controlling not only the growth of metal nanoparticles (NPs), but also their long-distance organization. Another important goal is controlling the oxidation of NPs and especially the formation of complex oxides having a core (metal) @ shell (metal oxide) architecture. In this context, by revisiting micellar synthesis, a strategy based on the modification of solvent-controlled ligand-ligand interactions was established, following the modeling of the Hansen solubility, of controlling the size of cobalt NPs (3.8 nm to 9.1 nm). Dodecanoic acid NPs passives and protects from oxidation and coalescence (TEM & SAXS control). Hexagonal lattice monolayers and face-centered 3D fcc superlattices were obtained. Using two oxidation strategies combined with annealing, dry and in solution, core / shell NPs: Co (ferro) @CoO (antiferromagnetic)/ were prepared with a polycrystalline metal core cfc or monocrystalline hcp. The preliminary study of the magnetic properties (SQUID) shows that the Co / CoO interface favors a moderate ferromagnetic / antiferromagnetic exchange interaction. Raman spectroscopy, a non-invasive method, under different laser excitations allows the simultaneous analysis of the metal particle (phase control and measurement of diameters from Lamb's modes), coating agent and its interaction with the NP and the possible oxide shells (CoO/CoOH, CO3O4) as well as the dynamics of the dodecanaote chains. Infrared analysis indicates hydroxylation of the unoxidized NPs. The vibrational techniques appear well adapted to the multi-scale control of NPs assemblies and supracrystals.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / Compostos ferroelÃsticos sÃo caracterizados pela possibilidade de apresentarem dois ou mais estados de deformaÃÃo ou strain espontÃneos devendo haver a possibilidade de permutaÃÃo entre estes estados atravÃs da aplicaÃÃo de um stress mecÃnico. O Pb8O5(VO4)2 pode ser classificado como pertencente a este grupo. Sua estrutura cristalina ainda nÃo à bem definida na literatura por conta de certas adversidades encontradas durante as anÃlises das mesmas, no entanto, fazendo uso de difraÃÃo de raios-X em diversos cristais deste composto discutiremos seus provÃveis grupos pontuais. Sabe-se tambÃm que hà uma relaÃÃo direta entre os estados de strain e as estruturas de domÃnios sob condiÃÃes ambientes de temperatura e pressÃo. Diversas tÃcnicas espectroscÃpicas foram empregadas afim de analisar como a estrutura cristalina destes compostos pode variar de acordo com as dimensÃes de cada cristal. Dessa forma, verificamos a existÃncia de trÃs fases sob condiÃÃes ambiente, bem como a possibilidade de uma transiÃÃo de fase espontÃnea para cristais da ordem de unidades de micrometros quadrados. O comportamento estrutural do Pb8O5(VO4)2 com o aumento de temperatura foi estudado detalhadamente por diversos autores. Eles reportaram a existÃncia de duas transiÃÃes de fase durante o aquecimento, uma transiÃÃo de segunda ordem por volta de 440 K e outra de primeira ordem por volta de 520 K. A transiÃÃo de primeira ordem leva os cristais de Pb8O5(VO4)2 da fase ferroelÃstica para a fase paraelastica. Contudo, uma vez que cristais ferroelÃsticos apresentam mudanÃas de estados de strain espontÃneos atravÃs da aplicaÃÃo de stress mecÃnico, fizemos uso de medidas de espalhamento Raman com aumento de pressÃo hidrostÃtica em amostras de Pb8O5(VO4)2 para acompanhar o comportamento espectral dos mesmos durante estas variaÃÃes de pressÃo. Assim, observamos um fenÃmeno de amorfizaÃÃo da amostra por volta de 11 GPa e obtivemos fortes indÃcios de trÃs transiÃÃes de fase em aproximadamente 1, 3.5 e 6 GPa. / Ferroelastic compounds are characterized by the possibility to present two or more states of spontaneous strain which could be permuted by application of mechanical stress. Pb8O5(VO4)2 can be classified as belonging to this group. Its crystal structure is not well defined in the literature due to certain adversities found during the data analysis. However, making use of X-ray diffraction in several crystals of this compound we will discuss their probable point groups. It is also known that there is a direct relation between the states of strain and the domains pattern at ambient conditions of temperature and pressure. Several spectroscopic techniques were employed in order to analyze how the crystal structure of these compounds varies according to the dimensions of each crystal. Therefore, we observed the existence of three phases under ambient conditions as well as the possibility of a spontaneous phase transition in crystals of order to units of square micrometers. The structural behavior of Pb8O5(VO4)2 with increasing temperature has been studied in detail by different authors. They reported the existence of two phase transitions on heating, one second-order transition at about 440 K and another first-order around 520 K. The first-order phase transition leads the Pb8O5(VO4)2 crystals of ferroelastic phase to paraelastic phase. However, since ferroelastics crystals show changes of state of spontaneous strain through the application of mechanical stress, we made use of Raman scattering measures with increasing of hydrostatic pressure on samples of Pb8O5(VO4)2 to accompany the spectral behavior of the same during these pressure variations. This way we observed a phenomenon of amorphization of the sample around 11 GPa and obtained strong evidences from three phase transitions at approximately 1, 3.5 and 6 GPa.

A presente tese descreve e discute as síntese de alguns mercaptais e mercaptóis e apresenta atribuições a várias frequências do espectro vibracional. Um apanhado bibliográfico sôbre a absorção no lnfra-Vermelho e Raman de tióis, sulfetos, dissulfetos e alguns mercaptais indica que acham-se descritas as frequências para os seguintes modos de vibração: estiramento de C-H deformação de CH3, CH2 e CH estiramento de S-H, C-S e S-S deformação de C-S-S, C-S-C, C-C-S e C-S-H. Para fins de comparação incluem-se também os dados da literatura referentes às frequências vibracionais de CH3, CH2 e CH nos hidrocarbonetos e compostos oxigenados. São descritas as sínteses de 20 dialquil e diarilmer-captais de aldeídos e cetonas alifáticas e aromáticas pelo emprêgo de dois métodos: (1) Reação entre tiol e composto carbonílico na presença de gás clorídrico sêco. (2) Reação entre ortotioformiato de alquila ou arila e composto carbonílico na presença de ácido sulfúrico concentrado. É fornecida uma prova da formação do intermediário catiônico pela catálise ácida do ortotioformiato de etila como primeiro passo de (2) por meio da reação tipo Friedel Crafts entre anisol e ortotioformiato, em presença de ácido sulfúrico concentrado, que conduziu ao dietilmercaptal do anisaldeído. É sugerido também um provável mecanismo para a reação do intermediário catiônico com o composto carbonílico. A reação do ortotioformiato com anisol, ainda não descrita na literatura, poderá se constituir f\'uturamente num novo método de obtenção de mercaptaisde aldeídos aromáticos. Observa-se que: Os espectros no Infra-Vermelho de compostos que contém os grupos C6H5-CH2S, C6H5-CHS2 e (C6H5)2CS2, nos quais o anel aromático não está ligado diretamente ao enxôfre, mostram, como a maioria dos compostos aromáticos monosubstituídos, um grupo de quatro bandas na região de 1610-1450cm-1. Entretanto, o grupo C6H5S, presente em difenilmercaptais, difenilsulfeto e difenildissulfeto, é caracterizado por três bandas na região de 1590-1435cm-1. As bandas correspondentes às vibrações de deformação no plano de C-H do anel aromático, na região de 1100-1000cm-1 do Infra-Vermelho são geralmente de fraca intensidade e de limitado uso analítico. Entretanto, nos espectros dos compostos contendo os grupos C6H5-CHS2, (C6H5)2CS2 e C6H5CH2S nota-se a presença de duas bandas de média ou forte intensidade. No caso de compostos que contém os grupos C6H5S, o número de bandas de média ou forte intensidade é aumentado para três. Os grupos SC2H5 e SCH2C6H5 nos mercaptais semelhantemente aos sulfetos e dissulfetos diferem entre si pelo wagging de CH2, em 1265 e 1240cm-1 respectivamente. A banda em 1050cm-1 de fraca intensidade atribuída na literatura ao rocking de CH3 em C2H5S, é também característica do grupo CH3 CHS2, sendo porém neste último caso, de forte intensidade. A banda de forte intensidade em 1110cm-1 nos espectros de Infra-Vermelho dos mercaptóis da acetona, que é fraca ou às vêzes omitida nos sulfetos e disulfetos contendo o grupo (CH3)2CHS, é característica do grupo (CH3)2C ligado a dois átomos de enxôfre. Os mercaptais de aldeídos alifáticos diferem dos correspondentes mercaptóis, no Infra-Vermelho pela presença de duas bandas em 1260 e 1180cm-1 de fraca e média intensidade respectivamente, correspondentes aos modos de deformação de C-H. As bandas em 1225 e 1155cm-1, presentes no dietilmercaptal do benzaldeído, mas ausentes no composto deuterado correspondente, são devidas aos modos de deformação de C-H nos mercaptais de aldeídos aromáticos. As bandas em 1260 e 1230cm-1, presentes em mercaptais de aldeídos alifáticos e aromáticos respectivamente, que se mostraram polarizados no espectro Raman, correspondem à deformaçao simétrica do grupo-C-H. As bandas em 1180 e 1155cm-1, não polarizadas no espectro Raman, são correspondentes à deformação assimétrica do mesmo grupo. Faz-se um estudo comparativo de: frequências de deformação de C-H vizinho aos átomos de enxôfre com as de C-H vizinho aos átomos de carbono, oxigênio e cloro. frequências de deformação no plano de C-H do anel aromático em compostos de enxôfre com as frequências correspondentes em compostos clorados. / Abstract not available

Des techniques de séquençage existent pour les biopolymères comme les protéines et l'ADN et ont permis de révolutionner la biologie moderne. Toutefois, des techniques similaires dédiées au séquençage des carbohydrates n'ont pas encore été développées à cause de la complexité de cette classe de biomolécules. Dans ce contexte, nous avons construit un instrument couplant spectroscopie vibrationnelle et spectrométrie de masse (MS/IR) afin de caractériser la structure des carbohydrates grâce à leur signature infrarouge.Dans cette thèse, nous avons démontré que cette métrique permet de différencier les différentes isoméries présentes dans la classe des carbohydrates : la nature des monosaccharides, la position des modifications fonctionnelles ainsi que la régio- et la stéréochimie de la liaison glycosidique. Ensuite la conservation de la structure moléculaire des ions après fragmentation a été démontrée sur des fragments de disaccharides permettant ainsi d'établir les règles du séquençage de carbohydrates par MS/IR. Cette méthode a ensuite été appliquée sur différents oligosaccharides.Enfin dans la dernière partie de ce manuscrit, le potentiel de la spectroscopie IRMPD dans l'infrarouge lointain est exploré pour la résolution des anomères, des isomères et des conformations. Finalement deux approches permettant une séparation en masse et en isomère en amont de l'analyse spectroscopique sont proposées : spectroscopie IRMPD 2 couleurs ou couplage avec la chromatographie liquide / Sequencing techniques have been established for proteins and DNA and have revolutionised modern biology but similar technique do not exist for carbohydrates due to their unique complexity. In this context, we have built an instrument coupling vibrational spectroscopy and mass spectrometry (MS/IR) dedicated to the structural characterization of carbohydrates.In this thesis, we have shown that the IR signature is a powerful metric which is able to resolve simultaneously all carbohydrate isomerisms: the monosaccharide content, the position of functional modifications, the regiochemistry and the stereochemistry of the glycosidic linkage. Then the conservation of the molecular structure of MS fragments has been revealed on disaccharide fragments. Following this demonstration we have established the carbohydrate sequencing rules using MS/IR and applied them for the determination of the sequence of different oligosaccharides.Finally the potential of the IRMPD spectroscopy in the Far-IR range is explored for anomers, isomers and conformations resolution as well as the utilisation of a two colors infrared spectroscopy or the coupling with an HPLC instrument

No description available.