Le nombre de cibles potentielles pour la conception de nouvelles molécules à activité thérapeutique ne cesse de croître. Pour chaque cible, il est nécessaire d’identifier des molécules actives et de les optimiser afin d’atteindre l’affinité et la sélectivité recherchées. Ces nouveaux défis accentuent la nécessité d’améliorer notre compréhension des facteurs qui mènent à la reconnaissance moléculaire entre une drogue potentielle et une macromolécule biologique, et particulièrement des facteurs énergétiques à la base de la stabilisation d’un complexe d’interaction. Dans le cadre de ce travail, nous nous sommes intéressés à l’effet que pouvaient avoir les équilibres de protonation/déprotonation des résidus ionisables d’une protéine sur les paramètres thermodynamiques caractérisant la complexation d’un ligand. Dasns ce but, nous avons étudié l’interaction entre l’α-chymotrypsine et un de ses inhibiteurs compétitifs, la proflavine. Cette protéine est représentative d’un nombre important d’enzymes présentant le même mécanisme catalytique. La compréhension des facteurs qui régissent les équilibres de protonation/déprotonation des résidus ionisables présents dans son site actif ainsi que de l’effet sur ceux-ci de l’interaction avec des ligands est d’une importance primordiale pour le développement d’inhibiteurs plus sélectifs de ces protéases.<p>Cette étude s’est essentiellement composée de trois volets. (i) La réalisation d’un modèle du complexe d’interaction afin de confronter des données structurales aux données expérimentales recueillies. (ii) L’étude de l’interaction entre l’α-chymotrypsine et la proflavine par spectroscopie de Résonance Magnétique Nucléaire (RMN) afin de mettre en évidence les résidus ionisables dont les équilibres de protonation/déprotonation sont influencés par la complexation du ligand. (iii) L’étude de la thermodynamique de l’interaction par Calorimétrie à Titrage Isotherme (ITC) et spectroscopie d’absorption en fonction de l’état d’ionisation des résidus identifiés par l’étude RMN.<p>Le modèle du complexe d’interaction entre l’α-chymotrypsine et la proflavine a été réalisé sur base de la structure cristallographique du complexe entre cet inhibiteur et une protéase apparentée à la chymotrypsine, la thrombine. Il ressort de l’analyse du modèle obtenu que la proflavine est profondément enfouie dans le subsite S1 de l’enzyme et présente une très grande complémentarité de surface avec cette poche hydrophobe. Nous avons également pu constater la présence de plusieurs molécules d’eau immobilisées au sein du complexe, et d’une molécule en particulier faisant office de relais de liens-H.<p>L’étude de l’interaction entre l’α-chymotrypsine et la proflavine par RMN du 1H a été précédée par une étude de l’effet du degré de maturité de l’enzyme sur les interactions liant les différents résidus composant la triade catalytique (Asp102, His57 et Ser195). Lors de l’activation du précurseur inactif de l’enzyme, le chymotrypsinogène, vers la forme mature, l’α-chymotrypsine, il semble en effet que le lien-H entre le NH&949;2 de l’His57 et le Oγ de la Ser195 soit affaibli, contrairement à celui qui relie le NHδ1 de cette même histidine au Oδ1 de l’Asp102. Nous rapportons pour la première fois l’observation de l’influence de la protonation de l’Asp102 sur les déplacements chimiques des protons NHδ1 et NH&949;2 de l’His57. L’étude de l’interaction entre l’α-chymotrypsine et la proflavine par RMN, nous a permis de mettre en évidence l’effet de la complexation du ligand sur l’état d’ionisation des résidus His57 et Asp102 de la triade catalytique, les pKa de ces résidus dans l’enzyme libre valant respectivement 7 et approximativement 4.<p>Les paramètres thermodynamiques de l’interaction α-chymotrypsine - proflavine et des différents équilibres de protonation/déprotonation qui y sont liés ont été obtenus par spectroscopie d’absorption et ITC. Cette dernière technique constitue un outil précieux pour l’étude d’interactions moléculaires car il s’agit de la seule technique expérimentale permettant la mesure directe de l’enthalpie d’interaction. Lorsque des équilibres de protonation/déprotonation sont thermodynamiquement liés à l’interaction, il s’agit également de la seule technique permettant la quantification de ces effets. En mesurant la constante d’affinité et l’enthalpie d’interaction observées à différents pH et dans différents tampons, nous avons pu, sur base du modèle obtenu par RMN, déterminer les paramètres thermodynamiques intrinsèques des différents équilibres.<p>La corrélation entre les données thermodynamiques obtenues par ITC et spectroscopie d’absorption et les données structurales obtenues par RMN et sur base de l’analyse du modèle du complexe d’interaction, nous a permis de rationaliser les facteurs à la base de l’interaction préférentielle de l’inhibiteur avec une des formes de l’enzyme. L’interaction entre l’α-chymotrypsine et la proflavine est la plus favorable lorsqu’à la fois l’His57 et l’Asp102 sont déprotonnés. Cette interaction est caractérisée par un terme enthalpique favorable et un terme entropique légèrement défavorable. Ce dernier terme s’expliquerait en partie par l’immobilisation dans le site d’interaction de plusieurs molécules d’eau. L’affinité entre l’α-chymotrypsine et la proflavine diminue lorsque l’His57 se protonne. La répulsion électrostatique entre les charges positives de la proflavine et de l’His57 est vraisemblablement un des facteurs permettant d’expliquer cette diminution de la constante d’affinité. Nous n’avons pu mettre en évidence d’interaction entre ces deux molécules dès lors que l’Asp102 est protonné, malgré que ce résidu soit situé relativement loin de la proflavine dans le complexe. Il s’agit donc d’un effet indirect, probablement relayé par l’His57. Tant que l’Asp102 est déprotonné, sa charge négative compenserait la charge positive de l’His57 et réduirait la répulsion électrostatique avec la proflavine, ce qui n’est plus le cas lorsque l’aspartate se protonne. / Doctorat en sciences appliquées / info:eu-repo/semantics/nonPublished

The central topic of this dissertation is to seek the answer to the question: Is the single transition state model appropriate for (1) the proton transfer reactions of nitroalkanes and (2) the aromatic nucleophilic reactions of trinitroarenes? If not, what are the real mechanisms? This objective has been accomplished by careful kinetic and mechanistic studies which take advantage of modern digital acquisition of absorbance - time data, combined with extensive new data analysis of results from pseudo-first-order kinetic measurements. Several new analysis procedures for pseudo-first-order kinetics that are capable of distinguishing between single-step and multi-step mechanisms have been introduced and intensively confirmed during the application in the kinetic study of the target reactions. The procedures include (1) half-life dependence of apparent rate constant, (2) sequential linear pseudo-first-order correlation, (3) approximate instantaneous rate constant analysis, and (4) time-dependent apparent kinetic isotope effects. Various conventional and nonconventional pseudo-first-order kinetic analyses of the reactions of nitroalkanes in aqueous solutions revealed that the reactions are complex and involve kinetically significant intermediates. The spectral evidence for the formation of reactive intermediates was obtained by carrying out the kinetic experiments at the isosbestic points where changes in reactant and product absorbance cancel. The apparent deuterium kinetic isotope effects studies indicated that the deuterium kinetic isotope effects are not associated with the formation of the intermediates. The observations of anomalous Brønsted exponents previously found for this reaction series could be rationalized well with the complex mechanisms proposed in this work, which indicate that the nitroalkane anomaly does not exist, but arises from an interpretation based upon the incorrect assumption that the reactions follow a simple one-step mechanism. Simulations revealed that the generally accepted competitive mechanism was not appropriate to describe the Meisenheimer complex formation during the reaction of 2,4,6-trinitroanisole with methoxide ion in methanol. This conclusion is supported by the conventional pseudo-first-order kinetic analysis. A reversible consecutive mechanism that accounts for the kinetic behavior has been proposed, which involves an intermediate dianion complex that is formed reversibly from the initial 1,3-σ-complex, and then eliminates methoxide ion to form the 1,1-σ-complex product.

Six new multi-component crystals between 4-phenylpyridine and substituted benzoic acids (3-nitrobenzoic acid, 3,5-dinitrobenzoic acid, gallic acid, 4-aminobenozic acid, salicylic acid and 2-aminobenzoic acid) were created and characterized crystallographically to investigate the influence of chemical and structural factors on the hydrogen location between the two components. While the expected intermolecular interactions are formed between the acid and pyridine group in most cases, the gallic acid structure is anomalous forming an unexpected salt with pyridine to hydroxyl interactions. Calculations of the hydrogen bonding motifs indicate that the level of proton transfer (e.g. salt versus co-crystal formation) is not solely a function of the dimer geometry but influenced by the local crystallographic environment. Analysis of the crystal structures indicates the strength of the hydrogen bonding into this motif alters the expected protonation state from chemical considerations.

Stroke is one of the leading causes of death and adult disability worldwide. The major therapeutic intervention for acute ischemic stroke is the administration of recombinant tissue plasminogen activator (rtPA) to help to restore blood flow to the brain. This has been shown to increase the survival rate and to reduce the disability of ischemic stroke patients. However, rtPA is associated with intracranial haemorrhage and thus its administration is currently limited to only about 5% of ischemic stroke patients. More advanced imaging techniques can be used to better stratify patients for rtPA treatment. One new imaging technique, chemical exchange saturation transfer (CEST) magnetic resonance imaging, can potentially image intracellular pH and since tissue acidification happens prior to cerebral infarction, CEST has the potential to predict ischemic injury and hence to improve patient selection. Despite this potential, most studies have generated pH-weighted rather than quantitative pH maps; the most widely used metric to quantify the CEST effect is only able to generate qualitative contrast measurements and suffers from many confounds. The greatest clinical benefit of CEST imaging lies in its ability to non-invasively measure quantitative pH values which may be useful to identify salvageable tissue. The quantitative techniques and work presented in this thesis thus provide the necessary analysis to determine whether a threshold for the quantified CEST effect or for pH exists to help to define tissue outcome following stroke; to investigate the potential of CEST for clinical stroke imaging; and subsequently to facilitate clinical translation of CEST for acute stroke management.

Disertacijoje nagrinėjamas galimas aplinkos poveikis organinių molekulių elektroninių būsenų savybėms. Tam tikslui yra naudojami kompiuterizuotieji kvantinės mechanikos metodai, kuriais remiantis nagrinėjamos įvairių molekulių savybės. Ištirtos 2-(N-metil-α-iminoethyl)-fenol ir N-triphenylmethylsalicylidene imine molekelulių, esančių poliniame tirpiklyje, struktūros pagrindinėje ir sužadintose elektroninėse būsenose. Pirmą kartą parodyta, kad, norint gauti teisingą kokybinį ir artimą kiekybiniam vidujmolekulinės protono pernašos potencinės energijos paviršių, būtina atsižvelgti į polinių tirpiklio molekulių kuriamą vandenilinių ryšių tinklą bei į nulinių svyravimų energijas. Pastarieji ir nulemia protono pernašos vyksmo kryptį bei efektyvumą. Parodyta, kad anilų klasės molekulių konformerų susiformavimas priklauso nuo tirpiklio poliškumo, o jų susidarymas savo ruožtu konkuruoja su klasterių iš tirpiklio molekulių susiformavimo galimybėmis. Pirmą kartą parodyta, kad dipolinio momento vertė bakteriorodopsine yra nulemta membranos paviršiuose esančių radikalų. Pademonstruota, kad stilbazolio molekulė deformuojasi ir sudaro naujus konformerus (pademonstruota dviejų formų atsiradimo galimybė) tik esant molekulėms tirpalo apsuptyje. Šis rezultatas paaiškino eksperimente stebimus skirtuminių spektrinių pokyčių evoliucijos prigimtį. Apskaičiuotos ir išanalizuotos karotinoidų - luteino, violaksantino ir zeaksantino molekulių - žemiausios sužadintos elektroninės būsenos. Parodyta... [toliau žr. visą tekstą] / To explore changes caused by the environment on the internal characteristics of an organic molecule is the objective of the thesis. For this purpose we investigate a variety of organic molecules. Using various methods of quantum mechanics calculations possible influence of a polar solvent on the ground and excited states of 2-(N-metil-α-iminoethyl)-fenol and N-triphenylmethylsalicylidene imine is considered. It is shown for the first time that in order to obtain the correct qualitative and quantitative interpretation of possible pathways of the intermolecular proton transfer the hydrogen network of the polar solvent molecules together with the zero point energy have to be taken into consideration. It is also shown that conformational variability of anil-type molecules in polar solvents is competing with clusters formation of solvent molecules. It is shown for the first time that the dipole moment of bacteriorhodopsin is mainly defined by cytoplasmic and extracellular coils on the surfaces of the membrane. It is also demonstrated that the stilbazole molecule experiences the deformation resulting in formation of new conformers (at least two forms are present) in the solvent surrounding. The experimental data of the transient spectroscopy were explained in the basis of these model calculations. The lowest excited states of carotinoids, such as lutein, zeaxanthin and violoxantin are calculated and analyzed. Sensitivity of the excited electronic state on the polar environment is... [to full text]

In dieser Arbeit wird Femtosekunden-Spektroskopie im mittleren Infrarot angewandt auf einige der am gründlichsten studierten fotoinduzierten Reaktionen: der Wasserstoff-Protonentransfer im elektronischen angeregten Zustand, für einen intramolekularen und einen intermolekularen Fall, sowie die Isomerisation fotochromer Verbindungen. Elektronische Spektroskopie ist die am häufigsten verwendete Methode zur Untersuchung ultraschneller Reaktionsdynamik in der kondensierten Phase, wobei Übergänge zwischen elektronischen Zuständen der reagierenden molekularen Systeme beobachtet werden. Häufig werden elektronische Übergänge abgetastet, deren Wellenfunktionen delokalisiert sind, so dass kaum ortspezifische Information erhalten wird. Außerdem ist aufgrund der breiten Absorptionslinien, die aus den schnellen Dephasierungszeiten elektronischer Übergänge resultieren, eine verlässliche Interpretation der experimentellen Daten schwierig; dies umso mehr, je komplexer der Reaktion ist, z.B. durch die Anwesenheit verschiedener Isomere oder durch das Zusammenwirken vieler elektronischer Zustände. Femtosekunden-Infrarotspektroskopie wird in dieser Arbeit als leistungsfähige Alternative eingesetzt, um ultraschnelle Reaktionsdynamik zu beobachten, und so den hohen Grad an Korrelation zwischen Infrarotspektren und molekularer Struktur sowie die Vorteile schmaler Bandbreiten IR-aktiver Schwingungsmoden auszunutzen. / In this thesis femtosecond mid-infrared spectroscopy has been applied to the investigation of some of the most thoroughly studied photoinduced reactions: the excited state hydrogen/proton transfer, both in an intramolecular and in an intermolecular case, and the isomerization of photochromic compounds. Electronic spectroscopy is the most commonly used method for ultrafast studies of molecular reaction dynamics in the condensed phase, whereby the electronic states of the reacting molecular systems are monitored. These techniques typically probe electronic transitions occurring between delocalized orbitals and - thus - do not provide site-specific information. Besides, the broad absorption lines resulting from the fast dephasing times of electronic transitions in solutions may hinder a reliable interpretation of the experimental results, especially when the complexity of the reaction increases, due e.g. to the presence of different isomers or to the involvement of numerous electronic states. Femtosecond infrared spectroscopy has been used in this work as a powerful and complementary alternative to probe ultrafast reaction dynamics, exploiting the high degree of correlation between the infrared spectra and the molecular structure and the advantages stemming from the narrow bandwidths of IR-active vibrational modes.

Neste trabalho de Mestrado, foram feitos estudos do comportamento fotofísico da fisetina em diversos solventes através de medidas de absorção de luz UV-Visível, fluorescência estática e resolvida no tempo e da interação entre fisetina (3,3\',4\',7-tetrahidroxiflavona) e 7-hidroxiflavona com ciclodextrinas ( beta e gama) (CDs) através de experimentos de absorção de luz UV-Visível, sinal induzido de dicroísmo circular, fluorescência estática e resolvida no tempo, anisotropia de estado estacionário e RMN de 1H, focando a dependência destas medidas em função da temperatura e do pH. Os resultados experimentais foram comparados com estudos mecânico-quânticos baseados no modelo semi-empírico SAM1 (AMPAC), e nos funcionais B3LYP e MPW1PW91, da Teoria do Funcional de Densidade, empregando os conjuntos de funções de base 6-311G* e 3-21G**. Os estudos da fisetina em diferentes solventes próticos e apróticos mostraram que a fluorescência da sonda é fortemente dependente do solvente. Resultados experimentais indicam a formação de complexos de inclusão entre as CDs e os flavonóides acima. A fisetina com ?-CD forma complexo de estequiometria 1:1 nos meios neutro/ácido e básico, cujos valores de constante de complexação são 900 +- 100 +_ 240 +_ 90 (L/mol), respectivamente. Os dados teóricos evidenciaram que a inclusão da fisetina na beta-CD ocorre preferencialmente pelo anel fenila. O complexo com a gama-CD apresenta estequiometria de 1:1 em meio ácido/neutro e de 1:2 em meio básico, com constantes de complexação de 94 +- 30 e 130 +- 10 (L/mol), respectivamente. Os estudos com a 7-hidroxiflavona revelaram que somente ocorre a formação de complexos com a beta-CD de estequiometria 1:1 e não há dependência do pH. As constantes de complexação obtidas nos meios ácido/neutro e básico são similares, 1430 +-- 510 e 1220 +- 165 L/mol, respectivamente. / In this work, the photophysics of fisetin (3,3\',4\',7-tetrahydroxyflavone) in several solvents was studied through UV-vis absorption spectra, steady-state and time-resolved fluorescence measurements. The interaction between fisetin and 7-hydroxyflavone and cyclodextrins (b- e g-) (CDs) was also investigated by UV-vis absorption spectra, induced signal of circular dichroism, steady-state and time-resolved fluorescence, steady-state anisotropy, and 1H NMR, with dependence on pH and temperature. Some experimental data were compared with quantum-mechanics studies based on the SAM1 (AMPAC) semi-empirical model, as well as with the B3LYP and MPW1PW91 functional models from the Density Functional Theory using the 6-311G* and 3-21G* basis sets. The study of the photophysics of fisetin in protic and aprotic solvents showed a complex behavior and a strong dependence on the solvent. The occurrence of many equilibria between the possible structures of fisetin, e.g. the normal, a few deprotonated ones, and the tautomer due to the excited state intramolecular proton transfer can be responsible for the complex analyses of these experimental data. The spectroscopic measurements show that, at pH 4.0 and 6.5, the complex fisetin - b-CD is formed in a Fis:b-CD 1:1 stoichiometry and an equilibrium constant (K) of 900 ± 100 L/mol. In basic medium (pH 11.5), K decreases to 240 ± 90 L/mol. Molecular modeling points out that the inclusion complex is formed preferentially via entry of the fisetin phenyl group into b-CD. On the other hand, the fisetin - g-CD has a stoichiometry of 1:1 in acid/neutral solutions and of 1:2 in basic conditions. The K values are 94 ± 30 e 130 ± 10 (L/mol), respectively. The 7-hydroxyflavone can only form inclusion complexes with b-CD. The stoichiometry is 1:1 and there is no dependence on pH. Both equilibrium constants determined either in acid or basic medium is very similar to each other, 1430 ± 510, and 1220 ± 165 L/mol, respectively. For this reason, we suppose that the inclusion of this compound into b-CD is also through the phenyl ring of the flavonoid.

<p>Denitrification is an anaerobic process performed by several soil bacteria as an alternative to aerobic respiration. A key-step in denitrification (the N-N-bond is made) is catalyzed by nitric oxide reductase (NOR); 2NO + 2e^- + 2H⁺ → N₂O + H₂O. NOR from <i>Paracoccus denitrificans</i> is a member of the heme copper oxidase superfamily (HCuOs), where the mitochondrial cytochrome c oxidase is the classical example. NOR is situated in the cytoplasmic membrane and can, as a side reaction, catalyze the reduction of oxygen to water.</p><p>NORs have properties that make them divergent members of the HCuOs; the reactions they catalyze are not electrogenic and they do not pump protons. They also have five strictly conserved glutamates in their catalytic subunit (NorB) that are not conserved in the ‘classical’ HCuOs. It has been asked whether the protons used in the reaction really come from the periplasm and if so how do the protons proceed through the protein into the catalytic site?</p><p>In order to find out whether the protons are taken from the periplasm or the cytoplasm and in order to pinpoint the proton-route in NorB, we studied electron- and proton transfer during a single- as well as multiple turnovers, using time resolved optical spectroscopy. Wild type NOR and several variants of the five conserved glutamates were investigated in their solubilised form or/and reconstituted into vesicles.</p><p>The results demonstrate that protons needed for the reaction indeed are taken from the periplasm and that all but one of the conserved glutamates are crucial for the oxidative phase of the reaction that is limited by proton uptake to the active site.</p><p>In this thesis it is proposed, using a model of NorB, that two of the glutamates are located at the entrance of the proton pathway which also contains two of the other glutamates close to the active site.</p>

<p>Amino acid radicals are key redox intermediates in several natural enzymes including Cytochrome c peroxidase, DNA photolyase, ribonucletide reductase, cytochrome c oxidase and photosystem II. Electron transfer from amino acids is often coupled to deprotonation and this thesis concerns the coupling of electron transfer from tyrosine and tryptophan to trisbipyridineruthenium(III) with deprotonation in model complexes. Specifically the mechanisms for these proton coupled electron transfer reactions have been studied and the controlling parameters have been identified, the possible mechanisms being stepwise electron transfer followed by deprotonation and deprotonation followed by electron transfer or concerted electron transfer/deprotonation.</p><p>Proton coupled electron transfer reactions have been studied using nano-second flash photolysis in water solution and the effect of pH, temperature, reaction driving force, deuteration and nature of the amino acid has been determined. I have shown that the rate constant for the concerted reaction depends intrinsically on the mixing entropy of the released proton and that the pH-dependence can be used as an experimental tool for mechanistic discrimination. Moreover I have shown that the concerted reaction inherently has a high reorganisation energy due to the coupling of the electron motion with deprotonation. Hydrogen bonding to the transferring proton however significantly reduces this reorganisation energy. The concerted reaction also has a relatively high driving force counteracting the high reorganisation energy in the competition between the concerted reaction and the stepwise electron transfer first reaction. The relative importance of the high reorganisation energy and the high driving force for the concerted reaction determines the mechanistic outcome of the reaction, the stepwise reaction being favoured by high over-all driving forces and the concerted reaction by high pH.</p><p>By comparing my results from model complexes with tyrosineZ oxidation in photosystem II, I give strong evidence for a concerted electron transfer/deprotonation mechanism.</p>

Amino acid radicals are key redox intermediates in several natural enzymes including Cytochrome c peroxidase, DNA photolyase, ribonucletide reductase, cytochrome c oxidase and photosystem II. Electron transfer from amino acids is often coupled to deprotonation and this thesis concerns the coupling of electron transfer from tyrosine and tryptophan to trisbipyridineruthenium(III) with deprotonation in model complexes. Specifically the mechanisms for these proton coupled electron transfer reactions have been studied and the controlling parameters have been identified, the possible mechanisms being stepwise electron transfer followed by deprotonation and deprotonation followed by electron transfer or concerted electron transfer/deprotonation. Proton coupled electron transfer reactions have been studied using nano-second flash photolysis in water solution and the effect of pH, temperature, reaction driving force, deuteration and nature of the amino acid has been determined. I have shown that the rate constant for the concerted reaction depends intrinsically on the mixing entropy of the released proton and that the pH-dependence can be used as an experimental tool for mechanistic discrimination. Moreover I have shown that the concerted reaction inherently has a high reorganisation energy due to the coupling of the electron motion with deprotonation. Hydrogen bonding to the transferring proton however significantly reduces this reorganisation energy. The concerted reaction also has a relatively high driving force counteracting the high reorganisation energy in the competition between the concerted reaction and the stepwise electron transfer first reaction. The relative importance of the high reorganisation energy and the high driving force for the concerted reaction determines the mechanistic outcome of the reaction, the stepwise reaction being favoured by high over-all driving forces and the concerted reaction by high pH. By comparing my results from model complexes with tyrosineZ oxidation in photosystem II, I give strong evidence for a concerted electron transfer/deprotonation mechanism.