Modeling Ultrafast Spectroscopy of the NADH Dimer: From UV-VIS to X-rays

Ultrafast pump-probe spectroscopy is a conceptually simple and versatile tool for resolving photoinduced dynamics in molecular systems. Due to the fast development of new experimental setups, such as synchrotron light sources and X-ray free electron lasers (XFEL), new spectral windows are becoming accessible. On the one hand, these sources have enabled scientist to access faster and faster time scales and to reach unprecedent insights into dynamical properties of matter. On the other hand, the complementarity of well-developed and novel techniques allows to study the same physical process from different points of views, integrating the advantages and overcoming the limitations of each approach. In this context, it is highly desirable to reach a clear understanding of which type of spectroscopy is more suited to capture a certain facade of a given photo-induced process, that is, to establish a correlation between the process to be unraveled and the technique to be used. In this thesis, I will show how computational spectroscopy can be a tool to establish such a correlation. I will study a specific process, which is the ultrafast energy transfer in the nicotinamide adenine dinucleotide dimer (NADH). This process will be observed in different spectral windows (from UV-VIS to X-rays), accessing the ability of different spectroscopic techniques to unravel the system evolution by means of state-of-the-art theoretical models and methodologies. The comparison of different spectroscopic simulations will demonstrate their complementarity, eventually allowing to identify the type of spectroscopy that is best suited to resolve the ultrafast energy transfer.

Distribuição de metais e caracterização das constantes de troca entre espécies metálicas e frações húmicas aquáticas de diferentes tamanhos moleculares

In this work the metal distribution and exchange constants between metal species and aquatic humic fractions with different molecular sizes were studied. The aquatic humic substances (AHS) were extracted by XAD-8 resin from water sample collected from Itapitanguí river, São Paulo State, Brazil. The AHS were fractionated in six fractions with different molecular sizes (>100 - <5 kDa) and characterized by several techniques. Molar ratios H/C suggested higher aromaticity for fractions F1 and F6 whereas molar ratios C/N didn´t show any differences regarding the humification degree between the fractions. The UV-Vis absorbance a254/a436 ratio showed higher results for F4 and F5, probably by less condensed features. FTIR studies showed high similarity in the functional groups in the fractions. The highest percentage of traces of Co, Al, Fe, Mn, Cu, Zn and Ni (determined by ICP-AES) was preferably complexed by fractions F3 and F4 with a greater amount of dissolved organic carbon (DOC). In addition, the exchange constants, determined by ultrafiltration method, showed complexes AHS-Fe and AHS-Al with higher stability than complexes AHS-Co in all fractions.

Marquage fluorescent des protéines pour étudier les enzymes protéolytiques solubles et immobilisées par la cartographie peptidique électrophorétique

La cartographie peptidique est une méthode qui permet entre autre d’identifier les modifications post-traductionnelles des protéines. Elle comprend trois étapes : 1) la protéolyse enzymatique, 2) la séparation par électrophorèse capillaire (CE) ou chromatographie en phase liquide à haute performance (HPLC) des fragments peptidiques et 3) l’identification de ces derniers. Cette dernière étape peut se faire par des méthodes photométriques ou par spectrométrie de masse (MS). Au cours de la dernière décennie, les enzymes protéolytiques immobilisées ont acquis une grande popularité parce qu’elles peuvent être réutilisées et permettent une digestion rapide des protéines due à un rapport élevé d’enzyme/substrat. Pour étudier les nouvelles techniques d’immobilisation qui ont été développées dans le laboratoire du Professeur Waldron, la cartographie peptidique par CE est souvent utilisée pour déterminer le nombre total de peptides détectés et leurs abondances. La CE nous permet d’avoir des séparations très efficaces et lorsque couplée à la fluorescence induite par laser (LIF), elle donne des limites de détection qui sont 1000 fois plus basses que celles obtenues avec l’absorbance UV-Vis. Dans la méthode typique, les peptides venant de l’étape 1) sont marqués avec un fluorophore avant l’analyse par CE-LIF. Bien que la sensibilité de détection LIF puisse approcher 10-12 M pour un fluorophore, la réaction de marquage nécessite un analyte dont la concentration est d’au moins 10-7 M, ce qui représente son principal désavantage. Donc, il n’est pas facile d’étudier les enzymes des peptides dérivés après la protéolyse en utilisant la technique CE-LIF si la concentration du substrat protéique initial est inférieure à 10-7 M. Ceci est attribué à la dilution supplémentaire lors de la protéolyse. Alors, afin d’utiliser le CE-LIF pour évaluer l’efficacité de la digestion par enzyme immobilisée à faible concentration de substrat,nous proposons d’utiliser des substrats protéiques marqués de fluorophores pouvant être purifiés et dilués. Trois méthodes de marquage fluorescent de protéine sont décrites dans ce mémoire pour étudier les enzymes solubles et immobilisées. Les fluorophores étudiés pour le marquage de protéine standard incluent le naphtalène-2,3-dicarboxaldéhyde (NDA), la fluorescéine-5-isothiocyanate (FITC) et l’ester de 6-carboxyfluorescéine N-succinimidyl (FAMSE). Le FAMSE est un excellent réactif puisqu’il se conjugue rapidement avec les amines primaires des peptides. Aussi, le substrat marqué est stable dans le temps. Les protéines étudiées étaient l’-lactalbumine (LACT), l’anhydrase carbonique (CA) et l’insuline chaîne B (INB). Les protéines sont digérées à l’aide de la trypsine (T), la chymotrypsine (CT) ou la pepsine (PEP) dans leurs formes solubles ou insolubles. La forme soluble est plus active que celle immobilisée. Cela nous a permis de vérifier que les protéines marquées sont encore reconnues par chaque enzyme. Nous avons comparé les digestions des protéines par différentes enzymes telles la chymotrypsine libre (i.e., soluble), la chymotrypsine immobilisée (i.e., insoluble) par réticulation avec le glutaraldéhyde (GACT) et la chymotrypsine immobilisée sur billes d’agarose en gel (GELCT). Cette dernière était disponible sur le marché. Selon la chymotrypsine utilisée, nos études ont démontré que les cartes peptidiques avaient des différences significatives selon le nombre de pics et leurs intensités correspondantes. De plus, ces études nous ont permis de constater que les digestions effectuées avec l’enzyme immobilisée avaient une bonne reproductibilité. Plusieurs paramètres quantitatifs ont été étudiés afin d’évaluer l’efficacité des méthodes développées. La limite de détection par CE-LIF obtenue était de 3,010-10 M (S/N = 2,7) pour la CA-FAM digérée par GACT et de 2,010-10 M (S/N = 4,3) pour la CA-FAM digérée par la chymotrypsine libre. Nos études ont aussi démontrées que la courbe d’étalonnage était linéaire dans la région de travail (1,0×10-9-1,0×10-6 M) avec un coefficient de corrélation (R2) de 0,9991.

Langmuir and Langmuir-Blodgett (LB) films of tetrapyridyl metalloporphyrins

We report on the formation of Langmuir films of 5,10,15,20-tetra(4-pyridyl) 21H,23H-porphine,hereafter named tetrapyridyl porphyrins with distinct central ions (2H(+), Zn(2+), Cu(2+), Ni(2+)). The films were characterized with surface pressure and surface potential isotherms and in situ UV-vis absorbance. The measurements indicated strong aggregation of porphyrin monomers at the air-water interface, with a red shift of the Soret band in comparison with the spectrum obtained from CHCl(3) solutions. The shift was larger for the non-substituted H(2)TPyP, and depended on the metal ion. Significantly, aggregation occurred right after spreading of the Langmuir film, with on further shifts in the UV-vis spectra upon compression of the film, or even after transferring them onto solid substrates in the form of Langmuir-Blodgett (LB) films. The buildup of LB films from H(2)TPyP and ZnTPyP was monitored with UV-vis spectroscopy, indicating an equal amount of material deposited in each deposition step. Using FTIR in the transmission and reflection modes, we inferred that the H(2)TPyP molecules exhibit no preferential orientation in the LB films, while for ZnTPyP there is preferential orientation, with the porphyrin molecules anchored to the substrate by the lateral pyridyl groups. (C) 2008 Elsevier B.V. All rights reserved.

Langmuir and Langmuir-Blodgett (LB) films of tetrapyridyl metalloporphyrins

We report on the formation of Langmuir films of 5,10,15,20-tetra(4-pyridyl) 21H,23H-porphine,hereafter named tetrapyridyl porphyrins with distinct central ions (2H(+), Zn(2+), Cu(2+), Ni(2+)). The films were characterized with surface pressure and surface potential isotherms and in situ UV-vis absorbance. The measurements indicated strong aggregation of porphyrin monomers at the air-water interface, with a red shift of the Soret band in comparison with the spectrum obtained from CHCl(3) solutions. The shift was larger for the non-substituted H(2)TPyP, and depended on the metal ion. Significantly, aggregation occurred right after spreading of the Langmuir film, with on further shifts in the UV-vis spectra upon compression of the film, or even after transferring them onto solid substrates in the form of Langmuir-Blodgett (LB) films. The buildup of LB films from H(2)TPyP and ZnTPyP was monitored with UV-vis spectroscopy, indicating an equal amount of material deposited in each deposition step. Using FTIR in the transmission and reflection modes, we inferred that the H(2)TPyP molecules exhibit no preferential orientation in the LB films, while for ZnTPyP there is preferential orientation, with the porphyrin molecules anchored to the substrate by the lateral pyridyl groups. (C) 2008 Elsevier B.V. All rights reserved.

Oxidation of melatonin and its catabolites, N-1-acetyl-N (2)-formyl-5-methoxykynuramine and N-1-acetyl-5-methoxykynuramine, by activated leukocytes

N-1-acetyl-N-2-formyl-5-methoxykynuramine (AFMK) and N-1-acetyl-5-methoxykynuramine (AMK), two melatonin catabolites, have been described as potent antioxidants. We aimed to follow the kinetics of AFMK and AMK formation when melatonin is oxidized by phorbol myristate acetate (PMA) and lipopolysaccharide (LPS)-activated leukocytes. An HPLC-based method was used for AFMK and AMK determination in neutrophil and peripheral blood mononuclear cell cultures supernatants. Samples were separated isocratically on a C18 reverse-phase column using acetonitrile/H2O (25:75) as the mobile phase. AFMK was detected by fluorescence (excitation 340 nm and emission 460 nm) and AMK by UV-VIS absorbance (254 nm). Activation of neutrophils and mononuclear cells with PMA produces larger amounts of AFMK than activation with LPS, probably due to the lower levels of reactive oxygen species formation and myeloperoxidase (MPO) degranulation that occurs when cells are stimulated with LPS. The concentration of AMK found in the supernatant was about 5-10% (from 18-hr cultures) compared with AFMK. This result may reflect its reactivity. Indeed AMK, but not AFMK, is easily oxidized by activated neutrophils in a MPO and hydrogen peroxide-dependent reaction. In conclusion, we defined a simple procedure for the determination of AFMK and AMK in biological samples and demonstrated the capacity of leukocytes to oxidize melatonin and AMK.

Distribuição de metais e caracterização das constantes de troca entre espécies metálicas e frações húmicas aquáticas de diferentes tamanhos moleculares

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Multi-method Study on Aquatic Humic Substances from the Rio Negro - Amazonas State/Brazil: Emphasis on Molecular-Size Classification of their Metal Contents

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Synthesis of PTSH-modified CeO2 nanoparticles: Effect of the modifier on structure, optical properties, and dispersibility

CeO2 nanoparticles were synthesized by the precipitation method and modified with para-toluene sulfonic acid (PTSH), either in situ or post-synthesis. The presence of PTSH in the samples was confirmed by FTIR. PXRD and FTIR analyses showed that the post-synthesis PTSH modification altered the CeO2 structure, whereas the in situ modification maintained intact the crystalline structure and UV-vis absorbance properties. For both in situ and post-synthesis modifications, TEM images revealed the presence of nanoparticles that were 5nm in size. The dispersibility of the in situ PTSH-modified material in a hydrophilic ureasil-poly(ethylene oxide) matrix was investigated using SAXS measurements, which indicated that CeO2 nanoparticles modified with PTSH in situ were less aggregated within the matrix, compared to unmodified CeO2 nanoparticles. © 2013 Elsevier B.V.

Binding of antioxidant flavone isovitexin to human serum albumin investigated by experimental and computational assays

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Application of chromatographic and spectroscopic techniques in the evaluation of the lipid fraction of animal products

Lipolysis and oxidation of lipids in foods are the major biochemical and chemical processes that cause food quality deterioration, leading to the characteristic, unpalatable odour and flavour called rancidity. In addition to unpalatability, rancidity may give rise to toxic levels of certain compounds like aldehydes, hydroperoxides, epoxides and cholesterol oxidation products. In this PhD study chromatographic and spectroscopic techniques were employed to determine the degree of rancidity in different animal products and its relationship with technological parameters like feeding fat sources, packaging, processing and storage conditions. To achieve this goal capillary gas chromatography (CGC) was employed not only to determine the fatty acids profile but also, after solid phase extraction, the amount of free fatty acids (FFA), diglycerides (DG), sterols (cholesterol and phytosterols) and cholesterol oxidation products (COPs). To determine hydroperoxides, primary products of oxidation and quantify secondary products UV/VIS absorbance spectroscopy was applied. Most of the foods analysed in this study were meat products. In actual fact, lipid oxidation is a major deterioration reaction in meat and meat products and results in adverse changes in the colour, flavour and texture of meat. The development of rancidity has long recognized as a serious problem during meat handling, storage and processing. On a dairy product, a vegetal cream, a study of lipid fraction and development of rancidity during storage was carried out to evaluate its shelf-life and some nutritional features life saturated/unsaturated fatty acids ratio and phytosterols content. Then, according to the interest that has been growing around functional food in the last years, a new electrophoretic method was optimized and compared with HPLC to check the quality of a beehive product like royal jelly. This manuscript reports the main results obtained in the five activities briefly summarized as follows: 1) comparison between HPLC and a new electrophoretic method in the evaluation of authenticity of royal jelly; 2) study of the lipid fraction of a vegetal cream under different storage conditions; 3) study of lipid oxidation in minced beef during storage under a modified atmosphere packaging, before and after cooking; 4) evaluation of the influence of dietary fat and processing on the lipid fraction of chicken patties; 5) study of the lipid fraction of typical Italian and Spanish pork dry sausages and cured hams.

Food lipids: their effects on quality and oxidative stability of animal tissues and emulsions

Lipolysis and oxidation of lipids in foods are the major biochemical and chemical processes that cause food quality deterioration, leading to the characteristic, unpalatable odour and flavour called rancidity. In addition to unpalatability, rancidity may give rise to toxic levels of certain compounds like aldehydes, hydroperoxides, epoxides and cholesterol oxidation products. In this PhD study chromatographic and spectroscopic techniques were employed to determine the degree of lipid oxidation in different animal products and its relationship with technological parameters like feeding fat sources, packaging, processing and storage conditions. To achieve this goal capillary gas chromatography (CGC) was employed not only to determine the fatty acids profile but also, after solid phase extraction, the amount of sterols (cholesterol and phytosterols) and cholesterol oxidation products (COPs). To determine hydroperoxides, primary products of oxidation and quantify secondary products UV/VIS absorbance spectroscopy was applied. Beef and pork meat in this study were analysed. In actual fact, lipid oxidation is a major deterioration reaction in meat, meat products and results in adverse changes in the colour, flavour, texture of meat and develops different compounds which should be a risk to human health as oxysterols. On beef and pork meat, a study of lipid fraction during storage was carried out to evaluate its shelf-life and some nutritional features life saturated/unsaturated fatty acids ratio and sterols content, in according to the interest that has been growing around functional food in the last years. The last part of this research was focused on the study of lipid oxidation in emulsions. In oil-in-water emulsions antioxidant activity of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) was evaluated. The rates of lipid oxidation of 1.0% stripped soybean oil-in-water emulsions with DOPC were followed by monitoring lipid hydroperoxide and hexanal as indicators of primary and secondary oxidation products and the droplet surface charge or zeta potential (ζ) of the emulsions with varying concentrations of DOPC were tested. This manuscript reports the main results obtained in the three activities briefly summarized as follows: 1. study on effects of feeding composition on the photoxidative stability of lipids from beef meat, evaluated during storage under commercial retail conditions; 2. evaluation of effects of diets and storage conditions on the oxidative stability of pork meat lipids; 3. study on oxidative behavior of DOPC in stripped soybean oil-in-water emulsions stabilized by nonionic surfactant.

Role of Platinum Deposited on TiO2 in Photocatalytic Methanol Oxidation and Dehydrogenation Reactions

Titania modified nanoparticles have been prepared by the photodeposition method employing platinum particles on the commercially available titanium dioxide (Hombikat UV 100). The properties of the prepared photocatalysts were investigated by means of the Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), atomic force microscopy (AFM), and UV-visible diffuse spectrophotometry (UV-Vis). XRD was employed to determine the crystallographic phase and particle size of both bare and platinised titanium dioxide. The results indicated that the particle size was decreased with the increasing of platinum loading. AFM analysis showed that one particle consists of about 9 to 11 crystals. UV-vis absorbance analysis showed that the absorption edge shifted to longer wavelength for 0.5% Pt loading compared with bare titanium dioxide. The photocatalytic activity of pure and Pt-loaded TiO2 was investigated employing the photocatalytic oxidation and dehydrogenation of methanol. The results of the photocatalytic activity indicate that the platinized titanium dioxide samples are always more active than the corresponding bare TiO2 for both methanol oxidation and dehydrogenation processes. The loading with various platinum amounts resulted in a significant improvement of the photocatalytic activity of TiO2. This beneficial effect was attributed to an increased separation of the photogenerated electron-hole charge carriers.

Transport in the blood of an anti-tumor water-soluble rutheniun cyclopentadienyl complex: a fluorescence study on albumin binding

Dissertação de mestrado, Qualidade em Análises, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014

Nanocomposites based on poly(caprolactone)-chitosan electrospun nanofibers and metallic oxide nanoparticles. Their potential use to adsorption and photocatalytic degradation of organic contaminants

Pollution of water bodies is one of the most common environmental problems today. Organic pollutants are one of the main drawbacks in this natural resource, among which the following stand out long-lived dyes, pharmaceuticals, and pesticides. This research aims at obtaining nanocomposites based on polycaprolactone-chitosan (PCL-CS) electrospun nanofibers (NFs) containing TiO2 nanoparticles (NPs) for the adsorption and photocatalytic degradation of organic pollutants, using Rhodamine B as a model. The fabricated hybrid materials were characterized by FT-IR, TGA, DSC, SEM, TEM, tensile properties, and the contact angle of water drops. The photoactivity of the NFs was investigated using a batch-type system by following UV-Vis absorbance and fluorescence of rhodamine B (RhB). For this purpose, TiO2NPs were successfully ex-situ incorporated into the polymer matrix promoting good mechanical properties and higher hydrophilicity of the material. The results showed that CS in the NFs increased the absorption and degradation of RhB by the TiO2NPs. CS attracted the pollutant molecules to the active sites vicinity of TiO2NPs, favoring initial adsorption and degradation. In other words, a bait-hook-and-destroy effect was evidenced. It also was demonstrated that the sensitization of TiO2 by organic dyes (e.g., perylene derivative) considerably improves the photocatalytic activity under visible radiation, allowing the use of low amounts of TiO2. (≈0.05 g/1 g of fiber). Hence, the current study is expected to contribute with an environmentally friendly green alternative solution.