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Giant Polyoxometalates : Dynamic Structure and Reactivity. In this thesis different methods were used to study several systems in which giant polyoxometalates are involved. The validity of the theoretical methods applied and the results obtained were always contrasted with the experimental evidence provided by the groups of Prof. Achim Müller (Bielefeld) and Prof. Marcella Bonchio (Padova). In certain cases the theoretical results provided an explanation for experimental observations and in other cases they had allowed prediction as main objective.Chapter IV presents the results regarding encapsulated water molecules inside the giant polyoxometalate cavities. Chapter V presents the results of the studies about ion pairing on polyoxometalates. Chapters VI and VII presents the results of two different polyoxometalates and their catalytic activity. Finally Chapter VIII presents a theoretical study on the effect of counterions on the growth of giant uranium polyperoxometalates. / Polioxometal·lats Gegants: Estructura Dinàmica i Reactivitat.En la present tesi diferents mètodes han estat utilitzats per estudiar diversos sistemes on els polyoxometalats gegants juguen un paper fonamental. La validesa dels mètodes computacionals utilitzats i dels resultats obtinguts han estat sempre contrastats amb les evidencies experimentals facilitades pels grups del Prof. Achim Müller (Bielefeld) i Prof. Marcella Bonchio (Padova). En alguns casos els resultats computacionals han permès explicar les observacions experimentals i en d'altres han permet fer prediccions com a principal objectiu.En el capítol IV es presenten els resultats referents a l'estructura de l'aigua encapsulada en les cavitats presents a polioxometal·lats gegants. El capítol V presenta els resultats dels estudis sobre ion pairing en polioxometal·lats. Els capítols VI i VII presenten els resultats de dos sistemes diferents i la seva activitat com a catalitzadors. Finalment, el capítol VIII presenta un estudi teòric sobre l'efecte dels contraions en el creixement de poliperoxometal·lats gegants d'urani.

We report for the first time a broad equilibrium model describing the complexation of ionic species in non-aqueous media that explicitly includes ion pairing for one of the components and that relies upon activities rather than molar concentrations. This model directly contradicts existing commonplace equilibrium treatments, which were shown to be incomplete, often invalid, and misleading. Experimental validation of our model was achieved through studies of pseudorotaxane formation between dibenzylammonium salts (DBAm-X) and dibenzo-24-crown-8 (DB24C8) in CDCl3:CD3CN (3:2). In that particular case, we showed that fluctuations in the apparent Ka,exp values as usually reported are attributable to ion pairing, with a dissociation constant Kipd, and that the constant Kassoc for pseudorotaxane complexation is independent of the counterion, a result of the complex existing in solution as a free cation. In accord with this model, we further described a straightforward and simple method to increase the extent of complexation by using either a ditopic cation and anion host, or adding to the charged host/guest solution a molecularly separate host capable of complexing the dissociated counterion. Also in accord with this model, we investigated the influence of the solvent¡¯s dielectric constant on Kipd and Kassoc. On the basis of competing condensation reactions between amines and ketones which were shown to occur within the timescale of host/guest recognition, we also challenged the commonly employed use of acetone in similar complexation studies involving 2o ammonium ions. Because a major goal of this work was to ultimately increase binding efficiency and selectivity, we explored new methods to drive complexation in related pseudorotaxane systems. We noted that addition of di- or tri-topic hydrogen bond accepting anions to solutions of bis(5-hydroxymethyl-1,3-phenylene)-32-crown-10 or bis(5-carboxy-1,3-phenylene)-32-crown-10 and paraquat di(hexafluorophosphate) served to significantly enhance host/guest interaction. The addition of Et4N+TFA- to an acetone solution of diacid crown and paraquat 2PF6 effectively boosted Ka,exp 40-fold, as estimated by 1H NMR studies. Similar increases in the apparent Ka,exp were observed upon the addition of n-Bu4N+OTs-. Evidenced by crystal structures, the increase in association resulted from chelation of the OH moieties of the crown by the di- or tri-topic anions, forming supramolecular bicyclic macrocycles (pseudocryptands) and stabilizing the complex in a cooperative manner. Significantly, Ka,exp of one of the pseudocryptands was shown to equal that determined in the corresponding cryptand complex. / Ph. D.

This work sought to enforce aromatic interactions between compatible π-molecular orbital systems with ionic bonding. In this case the interacting partners are oppositely charged discotic triangulene derivatives. The observed properties of the heterodimeric ion-pairs likely arise due to a hypothetical synergy between electrostatics and π-interactions. The work presented here describes investigation of putative covalency arising from this hypothetical synergy in the electrostatics driven π-stacking. In order to probe this, various hypotheses were made and experiments were designed to test their validity. The results from the experiments show existence of contact ion-pairs and complex solvent-separated discotic ions in solution. The formation of complex ion-pairs arise due to the fact that the electrostatic interaction that brings the discotic ions together is strong, but does not neutralize when the contact is made. So, the dipole created by the monopoles in a dimeric contact ion-pair can attract ions at both termini forming oligomers. This process apparently continues towards highly aggregated states and then to nanometric species and at some point the material precipitates. The propensity to aggregate and form complex-ions limited our approach to the measurement of the energetics of the ion-pairing for two reasons: (1) the observables had a complex dependence on temperature, solvent, concentration and ionic strength; and (2) the mass in solution was undergoing kinetic evolution towards solid states. The turbidimetric effects arising due to aggregate formation further complicated the extraction of weak interactions between the ions and hence effects determination of ion-pairing constants.

Apesar da rápida expansão das aplicações da cromatografia líquida acoplada à espectrometria de massas em química clínica, a análise de metabólitos de baixo peso molecular e alta polaridade em matrizes biológicas ainda permanece como um grande desafio analítico. Dentre os compostos de grande importância no diagnóstico de doenças metabólicas que ainda carecem de melhores alternativas bioanalíticas destacam-se os aminoácidos. O presente estudo descreve o desenvolvimento e a validação de um novo método para a quantificação de 24 aminoácidos em plasma explorando a cromatografia líquida acoplada a espectrômetros de massas em tandem. Foi construído um método de detecção baseado em SRM (múltiplas reações selecionadas) com duas transições de massas para cada um dos 24 aminoácidos e os 19 padrões internos marcados com isótopos estáveis. Foram avaliadas três estratégias de separação cromatográfica e o melhor desempenho foi obtido com fase reversa com octadecilsilano (C18) com pareamento iônico com o ácido perfluoropentanoico. O método cromatográfico final permitiu a separação dos 24 aminoácidos, com resolução completa dos isômeros: leucina, isoleucina e allo-isoleucina, em 11 minutos incluindo o tempo de re-estabilização da coluna cromatográfica. Os limites de quantificação variaram em 113 fmol a 6 pmol injetados na coluna cromatográfica. A imprecisão obtida nos níveis testados para todos os aminoácidos foi inferior a 14%. O método apresentou linearidade para os intervalos testados chegando a 1,5 mmol.L-1 para vários compostos. Os ensaios de arraste mostraram que os limites máximos obtidos na linearidade não geram nenhuma interferência subsequente. A exatidão do método foi avaliada com amostras provenientes do programa de referência interlaboratorial European Research Network for evaluation and improvement of screening, Diagnosis and treatment of Inherited disorders of Metabolism (ERNDIM) e com o material de referência certificado do National Institute of Standards and Technology (NIST). Todos os analitos mostraram equivalência estatística com o método desenvolvido. / Despite the widespread use of liquid chromatography coupled to mass spectrometry applications in clinical chemistry, the analysis of low molecular weight and high polar metabolites in biological matrices remains as a major analytical challenge. Notwithstanding the key role played by amino acids in the diagnosis of metabolic diseases, there is still need for improvements in bioanalytical process of these analytes. The present study describes the development and validation of a new method for quantification of 24 amino acids in plasma based on liquid chromatography coupled to tandem mass spectrometry. Detection and quantification were achieved building a selected reaction monitoring method two mass transitions for each 24 amino acids and 19 stable isotope internal standards. Three chromatographic strategies for separation were evaluated, and best performance was achieved using reversed-phase octadecylsilane with perfluropentanoic acid as ion pairing agent. The separation method allowed separation of 24 amino acids with full resolution for isomers leucine, isoleucine and alloisoleucine in 11 minutes, including column equilibration time. The limits of quantification ranged from 113 fmol to 6 pmol (on column injection). Imprecisions for all evaluated levels and amino acids were less than 14%. The method is linear in all clinical intervals and extending up to 1.5 mmol.L-1. Carryover evaluation demonstrated absence of interference in the following injection throughout the analytical interval. Method accuracy was evaluated analyzing reference samples from European Research Network for evaluation and improvement of screening, Diagnosis and treatment of Inherited disorders of Metabolism (ERNDIM) and National Institute of Standards and Technology (NIST). Statistical equivalence was demonstrated for all analytes using the present method.

Dual-host combinations of cation and anion sensors have unique potential for selective detection of ion pairs, such as NH4NO3, via solvent extraction. Selective sensors for NH4+ and NO3- were synthesized and used together for ion-pair sensing of ammonium nitrate both in organic solvents (using Bu4N+NO3 - and NH4+PF6-) and in extraction of NH4NO3 from water into dichloromethane. A fluorescent sensor for NH4+ based on 1,3,5-triethylbenzene shows remarkable binding and sensing selectivity for NH4+ vs. K+. Fluorescence and 1H-NMR titrations reveal surprising differences in sensing properties and binding constants for the tris-(3,5-dimethyl)pyrazole vs. the tris(3,5-diphenyl)pyrazole. The role of ion pairing and solvation is revealed by X-ray and theoretical DFT studies. We have also demonstrated a unique dual-host extraction-based ion-pair sensing paradigm using Förster Resonance Energy Transfer (FRET), showing selectivity for NH4NO3. The fluorescence emission of the NH4+ sensor tris-(3,5-dimethyl)pyrazole (305-340 nm), is compatible with the excitation wavelength of the dansyl fluorophore of the nitrate sensor 1,3,5-Tris-(5-dimethylamino-1-naphthalenesulfonamido)methyl]-2,4,6-triethylbenzene, thus resulting in FRET emission upon combined use of these two sensors for the NH4NO3 ion pair. Contact of dichloromethane solutions containing the two hosts with aqueous solutions of NH4NO3 (1 x 10-5 M to 1 x 10-4 M ), resulted in FRET fluorescence enhancements at 510 nm, with increasing concentrations of NH4NO3, while NaNO3, KNO3, NaCl and KCl showed only minimal fluorescence responses, under identical conditions. The ability of the tris-pyrazole to bind cations, such as NH4+, was also exploited in a detailed fluorescence and 1H-NMR Ln(III), binding study using tris-pyrazoles with varying substitution patterns. The dependence of fluorescence responses on pyrazole substitution that had been observed for NH4+ was also observed for different Ln(III), indicating the significant role of ion pairing for Ln(III) binding and fluorescence sensing. Likewise, the tris-dansyl nitrate receptor, in its deprotonated form, was also found to be an efficient Hg(II) fluorescent sensor. An X-ray crystal structure showed the ability of the trianionic version of this receptor to bind three Hg(II) atoms, also containing three CH3COO- counteranions. The X-ray crystal structure of the same receptor with HgCl2 gave a 2:1 complexation pattern, with one Hg atom complexed by two bis-deprotonated receptor molecules

Glycosaminoglycans (GAGs) are sulfated polysaccharides that mediate a variety of extracellular interactions. Heparan sulfate (HS) is one of the most prominent GAGs on human cell surfaces. Both endogenous proteins, such as growth factors, and exogenous proteins, such as pathogen surface proteins, recognize and bind GAGs to gain access to human cells. Oligosaccharides and other structural analogs of HS and GAGs have been evaluated for a variety of therapeutic targets including angiogenesis and infectious diseases. Development of compounds to block HS-protein interactions has primarily focused on optimizing the degree and orientation of anionic substituents on a scaffold, to mimic HS structure, but their utility is diminished by their large size and non-specific interactions with many proteins. To overcome these limitations, it has been demonstrated that replacing N-sulfo groups on heparin with non-anionic N-arylacyl groups increased affinity and selectivity for binding different heparin-binding proteins. However, the heparin-derived compounds in that work were heterogeneous polysaccharides. Strategies to obtain small, structurally-defined and lower charge ligands are needed to ultimately obtain specific bind-and-block antagonists of HS-binding proteins. This study addresses these challenges by synthesizing N-arylacyl O-sulfonated aminoglycosides as small molecule, structurally-defined ligands to identify novel structures that selectively bind to HS-binding proteins. This study details development of new HPLC and LC-MS methods to separate, characterize, and purify amphiphilic oligosaccharides. The development of these methods enabled the synthesis of a panel of N-arylacyl O-sulfonated aminoglycosides. The compounds in this panel were screened for affinity and selectivity in binding with HS-binding proteins. This work demonstrates for the first time the selective binding of small amphiphilic oligosaccharides with HS-binding proteins. Significantly, individual compounds demonstrate heparin-like affinity for binding with select HS-binding proteins. Structural differences between the N-arylacyl O-sulfonated aminoglycosides, including changing the aminoglycoside core or the structure of the N-arylacyl moiety, are shown to impart specificity for these compounds to selectively bind different HS-binding proteins.

Even though electrophoretic NMR (eNMR) experiments may provide unique chemical information and have been performed for three decades, the technique is still rarely applied, mainly because several experimental sources of artifacts have to be controlled to achieve accurate results. In this thesis, new experimental setups and protocols for accurate and precise eNMR experiments are presented. These include a novel eNMR sample cell, a radiofrequency filter and methods to suppress bulk flow effects. These developments improved the signal-to-noise ratio by roughly an order of magnitude compared to the U-tube setup previously used for eNMR. Convection-compensated pulse sequences in combination with a phase correction method were found to efficiently suppress bulk flow effects in the experiments and greatly increase experimental accuracy. These experimental setups and protocols were applied to probe association of ions and molecules in solution. It is particularly illustrated that the combination of diffusion and eNMR has great potential to provide quantitative results on ionic and molecular association in a variety of systems. The extent to which ionic surfactants associate with uncharged cyclodextrin probed by eNMR yielded very similar results to those obtained by diffusion NMR experiments. Complexation of a large set of small mono- and polyvalent metal cations to poly(ethylene oxide) was quantified by estimating the effective charge of the polymer through combined diffusion and eNMR information. Significant association was found for cations that have a surface charge density below a critical value. Ion pairing between tetramethylammonium cations and a series of anions in several solvents was also probed by diffusion NMR and eNMR experiments. For the monovalent anions in ethanol and ethanol-water mixture a dependence on ionic size was demonstrated. In water, dimethylsulfoxide, and methanol no such trend and very little pairing was observed. In acetonitrile, a different pattern was seen that did not correlate well with any single ionic parameter. An experimental cell and procedures for electrokinetic studies of solvated proton-conducting polymer materials is also presented. Electro-osmotic flow and diffusion were studied for each molecular component in water-methanol mixtures that swell Nafion membranes. / Elektroforetisk NMR (eNMR) är en experimentell metod som funnits i tre decennier och som kan ge unik kemisk information. Ändå används den sällan då flera experimentella artefakter måste korrigeras för, om man ska få korrekta resultat. I denna avhandling presenteras nya experimentella uppställningar och protokoll ämnade att uppnå korrekta och noggranna resultat. Dessa inkluderar en ny mätcell, ett radiofrekvensfilter och metoder för att minimera effekten av samtidiga bulkflöden i provlösningen. Sammantaget uppnås ungefär en storleksordning högre signal-brus-förhållande jämfört med den U-rörsuppställning som tidigare använts. Konvektions-kompenserande pulssekvenser i kombination med en faskorrektionsteknik minskade också bulkflödeseffekter effektivt, vilket ökade resultatens noggrannhet högst avsevärt. De experimentella uppställningarna och protokollen användes här för att mäta association av joner och molekyler i lösning. Mätningarna visar att kombinationen diffusions- och eNMR har en stor potential att kvantitativt kunna bestämma associationgraden i många olika typer av kemiska system. Associationsgraden mellan joniska tensider och cyklodextriner undersöktes både med eNMR och diffusions-NMR, och resultaten var mycket lika. Komplex-bildningen mellan en serie enkel- och flerladdade metalljoner och poly-(etylenoxid) kvantifierades genom att uppskatta polymerens effektiva laddning från kombinerad diffusions- och eNMR. Betydande komplexbildning hittades för katjoner med ytladdningstäthet under ett kritiskt värde. Jonparbildning mellan tetrametylammoniumjoner och en serie av anjoner i flera olika lösningsmedel undersöktes också med diffusions- och eNMR. För de monovalenta anjonerna i etanol och etanol-vatten-blandning påvisades ett samband med jonstorleken. I vatten, dimetylsulfoxid och metanol var däremot jonparbildningen låg och inget liknande samband hittades. I acetonitril observerades ett annat mönster, som inte korrelerade bra med någon av anjonernas normala joniska karakteristika. Slutligen presenteras en mätcell och procedurer för elektrokinetiska studier i de solvatiserade protonledande polymermaterial som bland annat används i bränsleceller. Elektroosmotiskt flöde och diffusion uppmättes för varje molekylär komponent i Nafion-membran solvatiserade av vatten-metanol-blandningar. / QC20100709

Apesar da rápida expansão das aplicações da cromatografia líquida acoplada à espectrometria de massas em química clínica, a análise de metabólitos de baixo peso molecular e alta polaridade em matrizes biológicas ainda permanece como um grande desafio analítico. Dentre os compostos de grande importância no diagnóstico de doenças metabólicas que ainda carecem de melhores alternativas bioanalíticas destacam-se os aminoácidos. O presente estudo descreve o desenvolvimento e a validação de um novo método para a quantificação de 24 aminoácidos em plasma explorando a cromatografia líquida acoplada a espectrômetros de massas em tandem. Foi construído um método de detecção baseado em SRM (múltiplas reações selecionadas) com duas transições de massas para cada um dos 24 aminoácidos e os 19 padrões internos marcados com isótopos estáveis. Foram avaliadas três estratégias de separação cromatográfica e o melhor desempenho foi obtido com fase reversa com octadecilsilano (C18) com pareamento iônico com o ácido perfluoropentanoico. O método cromatográfico final permitiu a separação dos 24 aminoácidos, com resolução completa dos isômeros: leucina, isoleucina e allo-isoleucina, em 11 minutos incluindo o tempo de re-estabilização da coluna cromatográfica. Os limites de quantificação variaram em 113 fmol a 6 pmol injetados na coluna cromatográfica. A imprecisão obtida nos níveis testados para todos os aminoácidos foi inferior a 14%. O método apresentou linearidade para os intervalos testados chegando a 1,5 mmol.L-1 para vários compostos. Os ensaios de arraste mostraram que os limites máximos obtidos na linearidade não geram nenhuma interferência subsequente. A exatidão do método foi avaliada com amostras provenientes do programa de referência interlaboratorial European Research Network for evaluation and improvement of screening, Diagnosis and treatment of Inherited disorders of Metabolism (ERNDIM) e com o material de referência certificado do National Institute of Standards and Technology (NIST). Todos os analitos mostraram equivalência estatística com o método desenvolvido. / Despite the widespread use of liquid chromatography coupled to mass spectrometry applications in clinical chemistry, the analysis of low molecular weight and high polar metabolites in biological matrices remains as a major analytical challenge. Notwithstanding the key role played by amino acids in the diagnosis of metabolic diseases, there is still need for improvements in bioanalytical process of these analytes. The present study describes the development and validation of a new method for quantification of 24 amino acids in plasma based on liquid chromatography coupled to tandem mass spectrometry. Detection and quantification were achieved building a selected reaction monitoring method two mass transitions for each 24 amino acids and 19 stable isotope internal standards. Three chromatographic strategies for separation were evaluated, and best performance was achieved using reversed-phase octadecylsilane with perfluropentanoic acid as ion pairing agent. The separation method allowed separation of 24 amino acids with full resolution for isomers leucine, isoleucine and alloisoleucine in 11 minutes, including column equilibration time. The limits of quantification ranged from 113 fmol to 6 pmol (on column injection). Imprecisions for all evaluated levels and amino acids were less than 14%. The method is linear in all clinical intervals and extending up to 1.5 mmol.L-1. Carryover evaluation demonstrated absence of interference in the following injection throughout the analytical interval. Method accuracy was evaluated analyzing reference samples from European Research Network for evaluation and improvement of screening, Diagnosis and treatment of Inherited disorders of Metabolism (ERNDIM) and National Institute of Standards and Technology (NIST). Statistical equivalence was demonstrated for all analytes using the present method.

Title: Solvent effects on ion pairing and photoionization in water Author: Mgr. et Ing. Eva Pluhařová Department: Physical and Macromoleculer Chemistry Advisor: Prof. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: Various methods of theoretical chemistry, namely classical molecular dynamics simulations with empirical force fields, ab initio molecular dynamics, enhanced sampling methods, and ab initio calculations were used to provide new insight into ion pairing and photoionization in aqueous solutions. Systems mod- eling aqueous solutions of decreasing size were investigated by computational methods of increasing level of sophistication. In a classical molecular dynamics study of concentrated lithium salt solutions, the electronic continuum correction to account for polarization provided qualita- tive improvement over the conventional non-polarizable force fields and enabled molecular interpretation of neutron scattering measurements. The same model- ing approach was also successful in predicting the affinity of halide ions to the solution/oil interface. By combining ab initio molecular dynamics and potential of mean force cal- culations, we designed a reliable computational protocol for calculating the free energy profile for an ion pair...