Le terme folate (vitamine B9) désigne une famille de molécules ayant une structure de base composée de 3 parties : un noyau pterine, un acide para-aminobenzoïque (pABA) et une chaine de glutamates. Le rôle de ces cofacteurs est de transporter des groupements monocarbonés. Ils interviennent dans de nombreuses réactions comme la synthèse des bases nucléiques, la synthèse de méthionine et la synthèse et le turnover de la S-adenosylmethionine,. Le folate est synthétisé chez les plantes et un grand nombre de micro-organismes dont les parasites du phylum des apicomplexes, tels que Plasmodium falciparum, et Toxoplasma gondii. Les enzymes impliquées dans cette voie de biosynthèse étant absentes chez l'homme, elles représentent des cibles herbicides, antibiotiques et antiparasitaires potentielles. Les inhibiteurs de la voie de biosynthèse du folate (tels que les sulfamides, analogues du pABA et inhibiteurs de la dihydroptéroate synthase, ou les inhibiteurs de la dihydrofolate réductase), sont souvent utilisés comme antibiotiques et antiparasitaires. Un problème majeur dans le traitement de ces maladies infectieuses est la résistance développée contre ces molécules, ce qui nécessite la recherche permanente de nouveaux médicaments. Le pABA est synthétisé en plusieurs étapes qui sont autant de cibles intéressantes pour développer de nouveaux inhibiteurs. Tout d'abord l'aminodeoxychorismate (ADC) synthase transforme le chorismate en ADC, puis dans une seconde étape, l'ADC est transformé en pABA par une ADC lyase. Chez les plantes supérieures et les parasites apicomplexes l'ADC synthase est une enzyme bifonctionnelle composée de deux grands domaines, un domaine glutamine amidotranferase (GAT) qui permet de produire le NH3 nécessaire à l'amination du chorismate, et un domaine ADC synthase (ADCS). Nous avons pu déterminer les paramètres cinétiques de la GAT-ADCS d'Arabidopsis. Nous avons constaté que ces deux domaines fonctionnent indépendamment, c'est-à-dire soit en présence de glutamine seule pour le domaine GAT (pas de chorismate), soit en présence de chorismate et de NH3 pour le domaine ADCS (pas de glutamine). Toutefois, le fonctionnement en tandem des deux domaines (tous les substrats sont présents) améliore les propriétés cinétiques (kcat) de chacun d'eux. Nos résultats montrent aussi que le NH3 produit par le domaine GAT et nécessaire à la synthèse de l'ADC n'est pas relargué dans le milieu extérieur mais canalisé (channeling) vers le domaine ADCS. Finalement, nous avons observé que l'ADC, produit final de la réaction, retro-inhibe le domaine ADCS en absence d'ADC lyase. Pris dans son ensemble, nos résultats indiquent que l'amination du chorismate est l'étape la plus limitante de la synthèse du pABA,.. Des expériences de criblage à haut débit nous ont permis d'identifier une molécule, la rubreserine, qui inhibe in vitro le domaine GAT de l'ADC synthase d'Arabidopsis avec un Ki autour de 8 µM. Nous avons observé que cette molécule inhibe la croissance de plantules d'Arabidopsis thaliana et la prolifération des parasites Toxoplasma gondii et Plasmodium falciparum avec des IC50 respectif de 65 µM, 20 µM et 1.2 µM. Chez Arabidopsis, la concentration en folate des cellules traitées est abaissée d'environ 40% par rapport au contrôle, une diminution qui n'a plus lieu en présence de pABA. L'ajout de pABA et de 5-formyltetrahydrofolate dans les milieux de culture d'Arabidopsis ou de Toxoplasma supprime en grande partie l'inhibition de croissance liée à la rubreserine, ce qui montre bien la connexion entre rubreserine et voie de biosynthèse du folate. Avec Toxoplama gondii, la rubreserine apparait plus efficace que les sulfamides pour bloquer l'invasion et la prolifération de ces parasites dans les fibroblastes humains. Ces résultats valident la GAT-ADCS comme cible anti-folate et montrent que la rubreserine a des propriétés anti-parasitaires intéressantes. / The term folate (vitamin B9) is a family of molecules with a basic structure composed of 3 parts: a core pterin, a para amino benzoic acid (PABA) moiety and a chain of glutamate. The role of these cofactors is to carry one-carbon groups. They are involved in many reactions such as the synthesis of nucleic acids, the synthesis of methionine and the synthesis and turnover of S-adenosylmethionine. Folate is synthesized in plants and many micro-organisms including parasites of the Apicomplexa phylum such as Plasmodium falciparum and Toxoplasma gondii. Several enzymes involved in the pathway are absent in humans, and so they are potential targets for herbicide, antibiotic and antiparasitic drugs. Inhibitors of folate biosynthesis (such as dihydropteroate synthase inhibitors, or inhibitors of dihydrofolate reductase), are often used as antibiotics and pesticides. A major problem in treating these infectious diseases is the resistance developed against these molecules, which requires a constant search for new drugs. pABA is synthesized in several steps which are all attractive targets for developing new inhibitors. First the aminodeoxychorismate (ADC) synthase converts chorismate into ADC, and then, in a second step, the ADC is converted to pABA by an ADC lyase. In higher plants and apicomplexan parasites the ADC synthase is a bifunctional enzyme composed of two main domains: a glutamine amidotranferase (GAT) domain that produces NH3, and an ADC synthase domain (ADCS) that catalyzes the amination of chorismate. We determined the kinetic parameters of the Arabidopsis GAT-ADCS. We found that these two domains function independently, that is to say either in the presence of glutamine alone for the GAT domain (no chorismate) or in the presence of chorismate and NH3 for the ADCS domain (no glutamine). However, the tandem operation of the two domains (all substrates are present) improves the kinetic properties (kcat) of each one. Our results also show that the NH3 produced by the GAT domain and required for the synthesis of ADC is not released into the surroundings but rather channeled to the active site of ADCS. Finally, we observed that ADC, the final product of the reaction, retro-inhibits the ADCS domain in the absence of ADC lyase. Taken together, our results indicate that the amination reaction of chorismate is the most limiting step of the synthesis of pABA. Using high-throughput screening approaches we have identified a molecule, rubreserine, which inhibits in vitro the GAT domain of Arabidopsis GAT-ADCS with a Ki value around 8 µM. We observed that this molecule inhibits the growth of Arabidopsis thaliana seedlings and the proliferation of Toxoplasma gondii and Plasmodium falciparum parasites with respective IC50 of 65 µM, 20 µM and 1 µM. In Arabidopsis, the concentration of folate in rubreserine-treated cells is lowered by about 40% compared to controls, a decrease that is suppressed in the presence of pABA. The addition of pABA and 5-Formyltetrahydrofolate in the culture media of Arabidopsis and Toxoplasma partly reverses the growth inhibition due to rubreserine, which shows the connection between the drug and folate biosynthesis. Rubreserine appears more effective than sulfa-drugs to block the invasion and proliferation of Toxoplasma gondii in human fibroblasts. These results validate the GAT-ADCS as an anti-folate target and show that rubreserine has interesting anti-parasitic properties.

A molécula de ácido orto-aminobenzóico tem sido intensamente empregada como sonda fluorescente no estudo de peptídeos e membranas e o entendimento dos efeitos de solvente sobre suas propriedades espectroscópicas apresenta grande interesse científico. Neste trabalho realizamos um estudo experimental e cálculos DFT sobre alterações nos espectros de absorção e emissão da sonda em solução aquosa, em função do pH do meio. Examinamos também o seu derivado 2-amino-N-metil benzamida (o-Abz-NHCH3) e as mudanças espectrais na interação com micelas de SDS. Resultados de experimentos de titulação mostraram-se coerentes com a existência de três estados de protonação para o-Abz à medida em que o pH torna-se ácido, resultantes da protonação dos grupos amino e carboxila, de modo semelhante ao que ocorre com aminoácidos. Para cada estado de protonação, realizamos cálculos de otimização de geometria e verificação de mínima energia com a teoria DFT utilizando diferentes funcionais e conjuntos de bases para orbitais atômicos. Partindo das geometrias de menor energia, com a teoria TD-DFT (B3LYP/311++G(d,p)) fizemos cálculos das transições eletrônicas. A melhor concordância com os resultados experimentais foi obtida com a molécula na forma aniônica. Na comparação dos resultados da posição espectral da transição de mais baixa energia, no processo de absorção ótica, observamos uma diferença relativa de 0,6%. Para a fluorescência otimizamos e verificamos a geometria do estado excitado e obtivemos as energias de transição vertical com o método TD-DFT (B3LYP/Def2-TZVP) com o qual tivemos um resultado de lambda = 407nm considerado satisfatório quando comparado com o valor experimental lambda= 394nm. Nas formas neutra e catiônica, as diferenças relativas entre os cálculos e os experimentos foram maiores, chegando a 11% na posição da banda de fluorescência da molécula neutra. Usando simulações de Dinâmica Molecular conseguimos estimar quantas moléculas de água se distribuem em torno do o-Abz. Os resultados mostram que, embora exista um número parecido de moléculas de água solvatando a molécula nas formas aniônica e catiônica, há uma redução na quantidade de ligações de hidrogênio realizadas pela protonação catiônica em relação à aniônica. O modelo utilizado para simular o o-Abz-NH(CH3) em micelas de SDS apresentou resultados satisfatórios com erro relativo entre 0,7\\% e 0,9%, no entanto são necessárias outras abordagens computacionais e experimentais para indicar em qual região a molécula se encontra na micela, dando assim mais confiabilidade e uma melhor interpretação aos resultados. / The ortho-aminobenzoic acid is a molecule largely employed as a fluorescent probe in peptide and membrane studies. The solvent dependence of its spectroscopic properties deserves great interest and we describe here results of experimental measurements and computational calculations by \\textit and Molecular Dynamics methods about spectroscopic and solvation properties of the molecule in aqueous medium at different pH values. We also examined the derivative 2-amino-N-methyl-benzamide (o-Abz-NHCH3), investigating the spectral modifications in its interaction with SDS micelles. The results of titration experiments could be interpreted as originated from three protonation states for o-Abz: in neutral pH and above, both carboxy and amine groups are deprotonated, and the molecule is in the anionic form. Decreasing the pH, protonation of amino group or carboxy renders the molecule neutral (pK = 5.0) and at low pH both groups are protonated and the molecule is in the cationic form (pK = 2.3). Geometry optimization and determination of energy minima were performed with the molecule in each protonation state using Density Functional Theory (DFT) with different functionals and basis set for atomic orbitals. Eletronic transitions were calculated from lowest energy geometry using TD-DFT (B3LYP/311++G(d,p)). The best agreement with experimental results were obtained for the anionic molecule: we observed a relative difference of 0.6\\% for the lowest energy optical transition. From the optimized geometry of the excited state the vertical transition was calculated with TD-DFT (B3LYP/Def2-TZVP), and the emission was predicted to occur at 407nm, a reasonable result compared with the experimental value or 394nm. For the molecule in neutral or cationic state, the relative differences between experimental and calculation results were greater, amounting to 11\\% for the fluorescence band in the neutral species. From Molecular Dynamics simulation we estimated the number of water molecules distributed aroud the o-Abz molecule. The results show that, although there is similar number of water molecules solvating the o-Abz in anionic and cationic state, there is a decrease in the amount of hydrogen bond in the cationic molecule. The simulation of the derivative o-Abz-NHCH3 in SDS micelles by implicit solvent methods gave results comparable to the experimental ones, with relative deviations lower than 1\\%. It should be noted that further study should be carried out in order to have a better knowledge about the location of the probe in the micelle, and to afford a beter interpretation of the results.

Tendo em conta os constantes problemas que apresentasse com os processos de corrosão, o presente trabalho de pesquisa tem como foco principal a alteração nas propriedades de superfície das ligas de alumínio empregadas nas aeronaves, AA2024 e AA7075, utilizando mono e bicamadas baseadas de octadecil-trimetóxi-silano (ODTMS) + poli(anilina-co-3-aminobenzoico/PAni3ABA) a fim de encontrar melhores condições para a redução da corrosão puntiformes. Posteriormente, avalia-se as características protetoras dos filmes através de testes de corrosão, como potencial de circuito aberto, curvas de polarização anódica e espectroscopia de impedância eletroquímica visando a caracterização do comportamento eletroquímico das amostras. Também foram realizadas análises de microscopia óptica para verificar a eficiência de proteção contra a corrosão dos revestimentos propostos antes e após os ensaios de corrosão. Os resultados obtidos demonstram que as camadas utilizadas melhoram a resistência contra a corrosão na seguinte ordem: PAni3ABA > ODTMS + PAni3ABA > ODTMS, sendo a primeira a que apresentou os melhores resultados como maiores deslocamentos do Ecorr para valores mais positivos, diminuição da icorr e menor número de pontos de corrosão após a realização das curvas de polarização. Além de testes de aderência para os filmes também foram efetuadas caracterizações das ligas por MEV. / Taking into account the constant problems that presents with corrosion processes, this research work has focused primarily on the change in surface properties of aluminum alloys used in aircraft, AA2024 and AA7075, with mono and bilayers using as a base octadecyl trimethoxy silane (ODTMS) + poly (aniline-co-3-aminobenzoic / PAni3ABA) to find optimum conditions for reducing corrosion punctiform. Later, it evaluates the protective features of the films through corrosion tests such as open circuit potential, anodic polarization curves and electrochemical impedance spectroscopy in order to characterize the electrochemical behavior of the samples. They were also carried out optical microscopy analysis to verify the efficiency of protection against corrosion of the coatings proposed before and after corrosion testing. The results obtained show that the layers used improve corrosion resistance in the following order: PAni3ABA> ODTMS + PAni3ABA> ODTMS, the first being the one that presented the best results as larger shifts towards more positive values, reduced and fewer corrosion points after performing the polarization curves. In addition to compliance tests for the films were also made characterizations of alloys by SEM.

A molécula de ácido orto-aminobenzóico tem sido intensamente empregada como sonda fluorescente no estudo de peptídeos e membranas e o entendimento dos efeitos de solvente sobre suas propriedades espectroscópicas apresenta grande interesse científico. Neste trabalho realizamos um estudo experimental e cálculos DFT sobre alterações nos espectros de absorção e emissão da sonda em solução aquosa, em função do pH do meio. Examinamos também o seu derivado 2-amino-N-metil benzamida (o-Abz-NHCH3) e as mudanças espectrais na interação com micelas de SDS. Resultados de experimentos de titulação mostraram-se coerentes com a existência de três estados de protonação para o-Abz à medida em que o pH torna-se ácido, resultantes da protonação dos grupos amino e carboxila, de modo semelhante ao que ocorre com aminoácidos. Para cada estado de protonação, realizamos cálculos de otimização de geometria e verificação de mínima energia com a teoria DFT utilizando diferentes funcionais e conjuntos de bases para orbitais atômicos. Partindo das geometrias de menor energia, com a teoria TD-DFT (B3LYP/311++G(d,p)) fizemos cálculos das transições eletrônicas. A melhor concordância com os resultados experimentais foi obtida com a molécula na forma aniônica. Na comparação dos resultados da posição espectral da transição de mais baixa energia, no processo de absorção ótica, observamos uma diferença relativa de 0,6%. Para a fluorescência otimizamos e verificamos a geometria do estado excitado e obtivemos as energias de transição vertical com o método TD-DFT (B3LYP/Def2-TZVP) com o qual tivemos um resultado de lambda = 407nm considerado satisfatório quando comparado com o valor experimental lambda= 394nm. Nas formas neutra e catiônica, as diferenças relativas entre os cálculos e os experimentos foram maiores, chegando a 11% na posição da banda de fluorescência da molécula neutra. Usando simulações de Dinâmica Molecular conseguimos estimar quantas moléculas de água se distribuem em torno do o-Abz. Os resultados mostram que, embora exista um número parecido de moléculas de água solvatando a molécula nas formas aniônica e catiônica, há uma redução na quantidade de ligações de hidrogênio realizadas pela protonação catiônica em relação à aniônica. O modelo utilizado para simular o o-Abz-NH(CH3) em micelas de SDS apresentou resultados satisfatórios com erro relativo entre 0,7\\% e 0,9%, no entanto são necessárias outras abordagens computacionais e experimentais para indicar em qual região a molécula se encontra na micela, dando assim mais confiabilidade e uma melhor interpretação aos resultados. / The ortho-aminobenzoic acid is a molecule largely employed as a fluorescent probe in peptide and membrane studies. The solvent dependence of its spectroscopic properties deserves great interest and we describe here results of experimental measurements and computational calculations by \\textit and Molecular Dynamics methods about spectroscopic and solvation properties of the molecule in aqueous medium at different pH values. We also examined the derivative 2-amino-N-methyl-benzamide (o-Abz-NHCH3), investigating the spectral modifications in its interaction with SDS micelles. The results of titration experiments could be interpreted as originated from three protonation states for o-Abz: in neutral pH and above, both carboxy and amine groups are deprotonated, and the molecule is in the anionic form. Decreasing the pH, protonation of amino group or carboxy renders the molecule neutral (pK = 5.0) and at low pH both groups are protonated and the molecule is in the cationic form (pK = 2.3). Geometry optimization and determination of energy minima were performed with the molecule in each protonation state using Density Functional Theory (DFT) with different functionals and basis set for atomic orbitals. Eletronic transitions were calculated from lowest energy geometry using TD-DFT (B3LYP/311++G(d,p)). The best agreement with experimental results were obtained for the anionic molecule: we observed a relative difference of 0.6\\% for the lowest energy optical transition. From the optimized geometry of the excited state the vertical transition was calculated with TD-DFT (B3LYP/Def2-TZVP), and the emission was predicted to occur at 407nm, a reasonable result compared with the experimental value or 394nm. For the molecule in neutral or cationic state, the relative differences between experimental and calculation results were greater, amounting to 11\\% for the fluorescence band in the neutral species. From Molecular Dynamics simulation we estimated the number of water molecules distributed aroud the o-Abz molecule. The results show that, although there is similar number of water molecules solvating the o-Abz in anionic and cationic state, there is a decrease in the amount of hydrogen bond in the cationic molecule. The simulation of the derivative o-Abz-NHCH3 in SDS micelles by implicit solvent methods gave results comparable to the experimental ones, with relative deviations lower than 1\\%. It should be noted that further study should be carried out in order to have a better knowledge about the location of the probe in the micelle, and to afford a beter interpretation of the results.

Ziel der vorliegenden Arbeit war die Herstellung, der Einsatz und die Bewertung von Durchfluss-Photoreaktoren für online Prüfungen zur photochemischen Stabilität im HPLC-System (hn- HPLC). Neben der Anfertigung eines für dieses Anforderungsprofil geeigneten Reaktors war es von Interesse, Strahlungsintensitäten zu bestimmen, die Photostabilität von UV-Filtern zu bewerten, sowie analytische Verfahren zu optimieren. Als wichtigste Ergebnisse dieser Arbeit sind: (1) erstmalig aktinometrische Messungen im Durchfluss durchgeführt worden, (2) die eingestrahlten Intensität im Durchfluss-Reaktor mit dem Standard-Sonnenspektrum (COLIPA) verglichen worden, (3) die Bestimmung von 4-Aminobenzoesäure (PABA) und 4-Acetamidobenzoesäure (PAABA) mittels HPLC-hn optimiert und (4) photochemische Umsätze an folgenden UV-Filtern festgestellt worden: 4-Methoxy-zimtsäure-2-ethyl-hexylester, 3-(4'-Methyl)benzyliden-bornan-2-on,1-(4-tert.-Butylphenyl)-3-(4-methoxyphenyl)propan-1.3-dion und 4-Aminobenzoesäure. / The aim of the present thesis was the construction and evaluation of an on-line photochemical reactor for photochemical stability tests in an HPLC-system (hn- HPLC). The work was focused on the production of a functional and effective photochemical reactor, the determination of radiation intensities and the optimisation of analytical methods. Furthermore the stability of UV-filters under exposure to UV-radiation was investigated. The main results of these thesis are presented in the following: (1) the determination of radiation intensities in online photochemical reactors, (2) the comparison of spectra with standard-sun spectra (COLIPA), (3) the optimisation of the determination of 4-aminobenzoic acid (PABA) and 4-acetamidobenzoic acid (PAABA) with an HPLC-hn method (4) the characterisation of photochemical changes of UV-filters: p-methoxy-cinnamic acid-2-ethyl-hexyl ester, 3-(4'-methyl)benzylidene-bornan-2-on,1-(4-tert.-butylphenyl)-3-(4-methoxyphenyl)propan-1,3-dion and p-aminobenzoic acid.

The Ph.D. project compiled in this thesis has focused on the role of the solvent in solid-liquid phase equilibria and in nucleation kinetics. Six organic substances have been selected as model compounds, viz. ortho-, meta- and para-hydroxybenzoic acid, salicylamide, meta- and para-aminobenzoic acid. The different types of crystal phases of these compounds have been explored, and their respective solid-state properties have been determined experimentally. The solubility of these crystal phases has been determined in various solvents between 10 and 50 oC. The kinetics of nucleation has been investigated for salicylamide by measuring the metastable zone width, in five different solvents under different experimental conditions. A total of 15 different crystal phases were identified among the six model compounds. Only one crystal form was found for the ortho-substituted compounds, whereas the meta-isomeric compounds crystallized as two unsolvated polymorphs. The para-substituted isomers crystallized as two unsolvated polymorphs and as several solvates in different solvents. It was discovered that the molar solubility of the different crystal phases was linked to the temperature dependence of solubility. In general, a greater molar solubility corresponds to a smaller temperature dependence of solubility. The generality of this relation for organic compounds was investigated using a test set of 41 organic solutes comprising a total of 115 solubility curves. A semi-empirical solubility model was developed based on how thermodynamic properties relate to concentration and temperature. The model was fitted to the 115 solubility curves and used to predict the temperature dependence of solubility. The model allows for entire solubility curves to be constructed in new solvents based on the melting properties of the solute and the solubility in that solvent at a single temperature. Based on the test set comprising the 115 solubility curves it was also found that the melting temperature of the solute can readily be predicted from solubility data in organic solvents. The activity of the solid phase (or ideal solubility) of four of the investigated crystal phases was determined within a rigorous thermodynamic framework, by combining experimental data at the melting temperature and solubility in different solvents and temperatures. The results show that the assumptions normally used in the literature to determine the activity of the solid phase may give rise to errors up to a factor of 12. An extensive variation in the metastable zone width of salicylamide was obtained during repeated experiments performed under identical experimental conditions. Only small or negligible effects on the onset of nucleation were observed by changing the saturation temperature or increasing the solution volume. The onset of nucleation was instead considerably influenced by different cooling rates and different solvents. A correlation was found between the supersaturation ratio at the average onset of nucleation and the viscosity of the solvent divided by the solubility of the solute. The trends suggest that an increased molecular mobility and a higher concentration of the solute reduce the metastable zone width of salicylamide. / QC 20100831

Artificial photosynthesis is used to harvest solar energy and store it in the form of chemical bonds. The system of interest in this study does this by splitting water into hydrogen and oxygen gas through a plasmon assisted process, collective oscillations from free electron gas. This is a renewable way to store energy that could be used as an alternative to fossil based fuel. In this study, a small part of this photo catalytic system is studied, namely the interaction between plasmonically active silver nanoparticles (Ag NPs) transferring photo-excited electrons via a linker molecule, 4-aminobenzoic acid (pABA). The pABA linker molecule transfers charge from the Ag surface to a semiconductor and a catalyst performing the water splitting. The pABA can bind in different ways onto the Ag-surface and the aim of this study is to examine which bond is strongest and which best enables charge transfer. To this purpose three systems where simulated quantum mechanically using a supercomputer. The total free energy of the systems was computed and compared. Out of the three studied binding sites, the hollow-site bond (pABA binding to three silver atoms) was found to have the lowest energy, meaningit's the strongest of the possible bonds. Additionally it was found that the band gap (the energy needed to transfer charge) for the pABA decreased when bound to the Ag-surface. The hollow-site bound pABA also had the smallest band gap, meaning it requires the least energy to transfer a charge and should therefore be the best bond fitted for the photo catalytic system. / Artificiell fotosyntes används för att absorbera solenergi och förvara den i formen av kemiska bindningar. Systemet som används i denna studie gör detta genom att splittra vatten till vätgas och syrgas genom en plasmon assisterad process. Detta är ett förnyelsebart sätt att förvara energi och kan användas som ett alternativ till fossila bränslen. I denna studie studeras en liten del utav detta fotokatalytiska system nämligen interaktionen där plasmonaktiva silvernanopartiklar (Ag NPs) överför foto-exciterade elektroner genom molekyllänken 4-aminobensoesyra (pABA). Molekyllänken pABA överför laddning från silverytan till en halvledare och en katalys som utför splittringen av vattnet. pABA kan binda på olika sätt tillen silveryta och denna studie syftar till att undersöka vilken utav bindningarna som är starkast och vilken som effektivast överför laddning. För att göra detta simulerades tre system kvantmekaniskt med hjälp av en superdator, ett system för varje sorts bindning. Den totala fria energin av systemen beräknades och jämfördes. Av de tre undersökta bindningarna hadehollow-site bindningen (pABA som binder till tre silveratomer) längst energi, vilket betyder att det är den starkaste av bindningarna. Utöver detta så visade det sig att bandgapet (energin som krävs för att överföra laddning) minskade för pABA när den var bunden till Ag-ytan. Hollow-site bundet pABA hade även minst bandgap, vilket betyder att den kräver minst energi för att överföra laddning och är därmed den mest effektiva bindningen för det fotokatalytiska systemet.

Work presented in this thesis is in two parts. Part one: The X-ray crystal structures of potential antimicrobial drug targets. The protein IspF (2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase, EC: 4.6.1.12) from two pathogens (Burkholderia cenocepacia and Plasmodium falciparum) has been investigated. IspF is an enzyme of isoprenoid-precursor biosynthesis and is considered to be a potential drug target. The results of structural and fragment-screening efforts presented here inform early stage drug discovery efforts. The structure of the PabC protein (4-amino-4-deoxychorismate lyase, EC: 4.1.3.38) from the Gram-negative pathogen Pseudomonas aeruginosa was also determined. PabC is involved in the production of para-aminobenzoic acid on the path to folate. Comparisons with previously solved PabC structures identified a spatially conserved tyrosine residue in the active site and suggest that a re-evaluation of a published mechanism is warranted. Part two: Immunity proteins in the Gram-negative Type VI secretion system. The X-ray crystal structures of the proteins Rap1a and Rap2a from Serratia marcescens, inhibitors of the peptidoglycan amidase toxins secreted by some Gram-negative bacteria employing the Type VI secretion pathway, were determined by molecular replacement and analysed.

This work concerns the interrelationship between thermodynamic, kinetic and structural aspects of crystal polymorphism. It is both experimental and theoretical, and limited with respect to compounds to substituted monocyclic aromatics. Two polymorphs of the compound m-aminobenzoic acid have been experimentally isolated and characterized by ATR-FTIR spectroscopy, X-ray powder diffraction and optical microscopy. In addition, two polymorphs of the compound m-hydroxybenzoic acid have been isolated and characterized by ATR-FTIR spectroscopy, high-temperature XRPD, confocal Raman, hot-stage and scanning electron microscopy. For all polymorphs, melting properties and specific heat capacity have been determined calorimetrically, and the solubility in several pure solvents measured at different temperatures with a gravimetric method. The solid-state activity (ideal solubility), and the free energy, enthalpy and entropy of fusion have been determined as functions of temperature for all solid phases through a thermodynamic analysis of multiple experimental data. It is shown that m-aminobenzoic acid is an enantiotropic system, with a stability transition point determined to be located at approximately 156°C, and that the difference in free energy at room temperature between the polymorphs is considerable. It is further shown that m-hydroxybenzoic acid is a monotropic system, with minor differences in free energy, enthalpy and entropy. 1393 primary nucleation experiments have been carried out for both compounds in different series of repeatability experiments, differing with respect to solvent, cooling rate, saturation temperature and solution preparation and pre-treatment. It is found that in the vast majority of experiments, either the stable or the metastable polymorph is obtained in the pure form, and only for a few evaluated experimental conditions does one polymorph crystallize in all experiments. The fact that the polymorphic outcome of a crystallization is the result of the interplay between relative thermodynamic stability and nucleation kinetics, and that it is vital to perform multiple experiments under identical conditions when studying nucleation of polymorphic compounds, is strongly emphasized by the results of this work. The main experimental variable which in this work has been found to affect which polymorph will preferentially crystallize is the solvent. For m-aminobenzoic acid, it is shown how a significantly metastable polymorph can be obtained by choosing a solvent in which nucleation of the stable form is sufficiently obstructed. For m-hydroxybenzoic acid, nucleation of the stable polymorph is promoted in solvents where the solubility is high. It is shown how this partly can be rationalized by analysing solubility data with respect to temperature dependence. By crystallizing solutions differing only with respect to pre-treatment and which polymorph was dissolved, it is found that the immediate thermal and structural history of a solution can have a significant effect on nucleation, affecting the predisposition for overall nucleation as well as which polymorph will preferentially crystallize. A set of polymorphic crystal structures has been compiled from the Cambridge Structural Database. It is found that statistically, about 50% crystallize in the crystallographic space group P21/c. Furthermore, it is found that crystal structures of polymorphs tend to differ significantly with respect to either hydrogen bond network or molecular conformation. Molecular mechanics based Monte Carlo simulated annealing has been used to sample different potential crystal structures corresponding to minima in potential energy with respect to structural degrees of freedom, restricted to one space group, for each of the polymorphic compounds. It is found that all simulations result in very large numbers of predicted structures. About 15% of the predicted structures have excess relative lattice energies of <=10% compared to the most stable predicted structure; a limit verified to reflect maximum lattice energy differences between experimentally observed polymorphs of similar compounds. The number of predicted structures is found to correlate to molecular weight and to the number of rotatable covalent bonds. A close study of two compounds has shown that predicted structures tend to belong to different groups defined by unique hydrogen bond networks, located in well-defined regions in energy/packing space according to the close-packing principle. It is hypothesized that kinetic effects in combination with this structural segregation might affect the number of potential structures that can be realized experimentally. The experimentally determined crystal structures of several compounds have been geometry-optimized (relaxed) to the nearest potential energy minimum using ten different combinations of common potential energy functions (force fields) and techniques for assigning nucleus-centred point charges used in the electrostatic description of the energy. Changes in structural coordinates upon relaxation have been quantified, crystal lattice energies calculated and compared with experimentally determined enthalpies of sublimation, and the energy difference before and after relaxation computed and analysed. It is found that certain combinations of force fields and charge assignment techniques work reasonably well for modelling crystal structures of small aromatics, provided that proper attention is paid to electrostatic description and to how the force field was parameterized. A comparison of energy differences for randomly packed as well as experimentally determined crystal structures before and after relaxation suggests that the potential energy function for the solid state of a small organic molecule is highly undulating with many deep, narrow and steep minima. / QC 20110527