This diploma thesis deals with acid-base and electrolytic behavior of hyaluronan solutions at different ionic strength. Acid-base behavior of hyaluronan was investigated by acid-base titrations which were carried out with two different methods, acid and alkaline acid-base titration. Dissociation constants at different ionic strength at zero degree of dissociation and at 50% degree of dissociation were evaluated from the results of acid-base titrations. Dissociation constants obtained from acid acid-base titrations have values between 3,0 and 3,6. Dissociation constants obtained from alkaline acid-base titrations are not very informative because their values are much higher than the expected values. The study of degradation of hyaluronan during acid-base titration was performed to complete study of acid-base behavior. Electrolytic behavior of hyaluronan solution was performed by conductometric titrations in three different environments.

Les biocapteurs sont des outils de détection et d'analyse puissants qui ont été largement utilisés dans les domaines de la santé, de la recherche biomédicale et de l’environnement. Cependant, différents biocapteurs utilisent différents transducteurs qui varient par la nature des substrats utilisés et par la chimie de surface. Tous ces paramètres peuvent avoir un effet sur les réactions biomoléculaires aux interfaces et conduire à des variations de la mesure de la constante de dissociation Kd. Dans ce contexte, ce travail de thèse visait à comparer trois techniques différentes : biopuce avec une détection par fluorescence, biocapteur à fluorescence par champ évanescent et biocapteur par résonance de plasmon de surface (SPR). Ces trois techniques ont été comparées pour la détermination de la constant de dissociation de l'hybridation de l'ADN. Pour la biopuce à fluorescence classique, le substrat est une lame de verre et la mesure est effectuée à la fin de l'expérience. Dans le cas du biocapteur à fluorescence à champ évanescent, le polystyrène est le substrat et une détection en temps réel est réalisée. La SPR est réalisée sur un film d'or mince. C'est une technique en temps réel et sans marquage. Les deux techniques basées sur la fluorescence nécessitent de marquer les cibles avec un fluorophore avant la mesure. Un facteur important déterminant la performance de l'analyse est la chimie de surface du capteur. Ici, nous avons optimisé la chimie de la surface de l'or pour le greffage d'ADN modifié thiol. Nous avons étudié deux méthodes de nettoyage: la solution de piranha et le plasma d'oxygène, dans le but d'obtenir une surface d'or propre sans oxydation de l'or. Ensuite, nous avons optimisé les paramètres lors de la mesure SPR comme par exemple la structure interfaciale du capteur, la force ionique .... Enfin, ces trois techniques ont été utilisées pour mesurer la constante de formation du duplex ADN/ADN. Les résultats ont montré que les Kd sont du même ordre de grandeur pour les trois techniques. De plus, pour les trois techniques, une augmentation de la densité de sonde de surface a entraîné une baisse d’affinité telle que mesurée. / Biosensors are powerful detection and analysis tools that have been widely applied in pharmaceuticals, healthcare, biomedical research, and environmental monitoring. However different biosensors use different transducers and therefore different substrates and surface chemistries. All of these parameters may have an effect on the biomolecular reactions at the interface and lead to a deviation in dissociation constant Kd measurements. In this context, this PhD work aimed at comparing three different techniques: fluorescent microarray, evanescent field fluorescence biosensor and surface plasmon resonance (SPR) biosensor, to determine DNA hybridization Kd. For the classical fluorescence microarray, the substrate is a glass slide and the detection is performed at the end of the experiment. In the case of evanescent field fluorescence biosensor, polystyrene is the substrate and it permits a real-time detection. SPR is performed on thin gold film. It is a real-time and a label-free technique. The two fluorescent based techniques require to label the targets with fluorescent dyes prior to the measurements. One important factor determining the performance of the analysis is the surface chemistry of the sensor chip. Herein, we have optimized gold surface chemistry for thiol modified DNA grafting. We studied two cleaning methods: piranha solution and oxygen plasma, aiming at obtaining a clean gold surface without oxidation of the gold. Then, we optimized SPR assay parameters such as interfacial structure of sensor chip, ionic strength... After, these three techniques were used to measure the DNA hybridization Kd. The results showed that the Kds measured are similar for the three techniques. In addition, increasing surface probe density resulted in an increase of Kd of DNA hybridization.

The goal of this study was to characterize the binding sites on the surface of wheat roots, Triticum turgidum, involved in the adsorption of protons and metals, and quantify the thermodynamic constants needed for a surface complexation model to predict metal binding. The adsorption of protons, Cd(II), Cu(II), and Ni(II) to the root surface as a function of pH and ionic strength in single metal exposure scenarios was quantitatively described using potentiometric titrations, batch metal adsorption experiments, and the least squares fitting program FITEQL. Model predictions from single metal exposures were compared to measured metal adsorption concentrations when roots were exposed to binary and ternary combinations of the metals. Proton dissociation was a function of three discrete monoprotic acid sites on the root surface with log proton dissociation constants of -4.50, -6.23, and -7.37 respectively, upon which varied ionic strength had no effect. The total proton binding capacities for the three sites were 2.58 x 10-4, 1.29 x 10-4, and 2.58 x 10-4 M, respectively. Metal complexation was best described by a two-site model having conditional stability constant log values of 3.04 and 3.30 for Cd(II), 3.21 and 3.25 for Cu(II), and 2.83 and 2.84 for Ni(II) at ionic strength 0.01M. At ionic strength 0.1 M the conditional stability constants log values were 2.37 and 3.36 for Cd(II), 3.11 and 2.56 for Cu(II), and 2.18 and 3.00 for Ni(II). When roots were exposed to binary or ternary mixtures of the metals, the two monoprotic acid single metal model did not provide ideal fits to the data indicating that adsorption in a metal mixture scenario cannot be considered additive and is dependent on the combination of metals present in the exposure environment. The experimentally determined proton dissociation constants and metal stability constants could be used in commercial geochemical speciation programs such as Visual MINTEQ to predict metal adsorption to plants. / Natural Sciences and Engineering Research Council of Canada, The Mining Association of Canada, Ontario Power Generation, Environment Canada.

Knowledge of the dissociation constants of the ionizable protons of weak acids in aqueous media is of fundamental importance in many areas of chemistry and biochemistry. The pKa value, or equilibrium dissociation constant, of a molecule determines the relative concentration of its protonated and deprotonated forms at a specified pH and is therefore an important descriptor of its chemical reactivity. Considerable efforts have been devoted to the determination of pKa values by deferent experimental techniques. Although in most cases the determination of pKa values from experimental is straightforward, there are situations where interpretation is difficult and the results ambiguous. It is, therefore, not surprising that the capability to provide accurate estimates of the pKa value has been a central goal in theoretical chemistry and there has been a large effort in developing methodologies for predicting pKa values for a variety of chemical systems by differing quantum chemical techniques. A prediction accuracy within 0.5 pKa units of experiment is the desirable level of accuracy. This is a non-trivial exercise, for an error of 1 kcal/mol in estimates of the free energy value would result in an error of 0.74 pKa units. In this thesis ab initio Car-Parrinello molecular dynamics (CPMD) has been used for investigating the Brϕnsted acid-base chemistry of weak acids in aqueous solution. A key issue in any dissociation event is how the solvating water molecules arrange themselves spatially and dynamically around the neutral and dissociated acid molecule. Ab initio methods have the advantage that all solvent water molecules can, in principle, be con- sidered explicitly. One of the factors that has inhibited the widespread use of ab initio MD methods to study the dissociation reaction is that dissociation of weak acids are rare events that require extremely long simulation times before one is observed. The metady- namics formalism provides a solution to this conundrum by preventing the system from revisiting regions of configuration space where it has been in the past. The formalism allows the system to escape the free-energy minima by biasing the dynamics with a history dependent potential (or force) that acts on select degrees of freedom, referred to as collective variables. The bias potentials, modeled by repulsive inverted Gaussians that are dropped during propagation, drive the system out of any free-energy minima and allow it to explore the configuration space by a relatively quick and efficient sampling. The the- sis deals with a detailed investigation of the Brϕnsted acid-base chemistry of weak acids in aqueous solutions by the CPMD-metadynamics procedure. In Chapter 1, current approaches for the theoretical estimation of pKa values are summarized while in Chapter 2 the simulation methodology and the metadynamics sampling techniques used in thisstudy are described. The potential of the CPMD-metadynamics procedure to provide estimates of the acid dissociation constant (pKa) is explored in Chapter 3, using acetic acid as a test sys- tem. Using the bond-distance dependent coordination number of protons bound to the dissociating carboxylic groups as the collective variable, the free-energy profile for the dissociation reaction of acetic acid in water was computed. Convergence of the free-energy profiles and barriers for the simulations parameters is demonstrated. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid and the deference in their values provides the estimate for pKa. The estimated value of pKa for acetic acid from the simulations, 4.80, is in good agreement with the experiment at value of 4.76. It is shown that the good agreement with experiment is a consequence of the cancellation of errors, as the pKa values are computed as the difference in the free energy values at the minima corresponding to the neutral and dissociated state. The chapter further explores the critical factors required for obtaining accurate estimates of the pKa values by the CPMD-metadynamics procedure. It is shown that having water molecules sufficient to complete three hydration shells as well as maintaining water density in the simulation cell as close to unity is important. In Chapter 4, the CPMD-metadynamics procedure described in Chapter-3 has been used to investigate the dissociation of a series of weak organic acids in aqueous solutions. The acids studied were chosen to highlight some of the major factors that influence the dissociation constant. These include the influence of the inductive effect, the stabilization of the dissociated anion by H-bonding as well as the presence of multiple ionizable groups. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cid and trans-butenedioic, the isomers of hydroxybenzoic acid and phthalic acids and its isomers. It was found that in each of these examples the CPMD-metadynamics procedure correctly estimates the pKa values, indicating that the formulism is capable of capturing these influences and equally importantly indicating that the cancellation of errors is indeed universal. Further, it is shown that the procedure can provide accurate estimates of the successive pKa values of polypro tic acids as well as the subtle deference in their values for deterrent isomers of the acid molecule. Changes in protonation-deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. It is shown that CPMD simulations in conjunction with metadynamics calculations of the free energy profile of the protonation- deprotonation reaction can provide estimates of the multiple pKa values of the 20 canonical α-amino acids in aqueous solutions in good agreement with experiment (Chapter 5). The distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic and the amine groups is used as the collective variable to explore the free energy profiles of the Brϕnsted acid-base chemistry of amino acids in aqueous solutions. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule were included explicitly in the computation procedure. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error with respect to experimental results, of 0.2 pKa units. The tripeptide Glutathione (GSH) is one of the most abundant peptides and the major repository for non-protein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thioldisulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influences the redox couple and hence the pKa value of the cysteine residue of GSH is critical to its functioning. In Chapter 6, it has been reported that ab initio Car-Parrinello Molecular Dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. It is shown that the free-energy landscape for the protonation - deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared to the isolated cysteine amino acid. The dissociation constants of weak acids are commonly determined from pH-titration curves. For simple acids the determination of the pKa from the titration curves using the Henderson-Hasselbalch equation is relatively straightforward. There are situations, however, especially in polypro tic acids with closely spaced dissociation constants, where titration curves do not exhibit clear inflexion and equivalence stages and consequently the estimation of multiple pKa values from a single titration curve is no longer straightfor- ward resulting in uncertainties in the determined pKa values. In Chapter 7, the multiple dissociation constant of the hexapeptide glutathione disulfide (GSSG) with six ionizable groups and six associated dissociation constants has been investigated. The six pKa values of GSSG were estimated using the CPMD-metadynamics procedure from the free-energy profiles for each dissociation reaction computed using the appropriate collective variable. The six pKa values of GSSG were estimated and the theoretical pH-titration curve was then compared with the experimentally measured pH-titration curve and found to be in excellent agreement. The object of the exercise was to establish whether interpretation of pH-titration curves of complex molecules with multiple ionizable groups could be facilitated using results of ab initio molecular dynamics simulations.

The dependencies of electrophoretic mobility on pH were measured for a set of 14 markers used for isoelectric focusing that were developed by the group of Šlais and that are based on substitutions on the nitrophenol core, and for a kit consisting of 5 pI markers developed by Shimura, which have an oligopeptide structure. The dissociation constants and limiting electrophoretic mobilities of these compounds were obtained from the dependencies with the use of the program AnglerFish. The isoelectric point values of the compounds were consequently calculated using the obtained data. A comparison of the obtained pI values with the values that have been declared in literature, albeit gained by different analytical methods, has been made. Key Words capillary zone electrophoresis, isoelectric focusing, pI markers, isoelectric point, thermodynamic dissociation constant, limiting ionic mobility

Proline-rich antimicrobial peptides (PrAMPs) are promising candidates to treat bacterial infections. The designer peptide ARV-1502 exhibits strong antimicrobial effects against Enterobacteriaceae both in vitro and in vivo. Since the inhibitory effects of ARV-1502 reported for the 70 kDa heat-shock protein DnaK do not fully explain the antimicrobial activity of its 176 substituted analogs, we further studied their effect on the bacterial 70S ribosome of Escherichia coli, a known target of PrAMPs. ARV-1502 analogues, substituted in positions 3, 4, and 8 to 12 (underlined) of the binding motif D3KPRPYLPRP12 with aspartic acid, lysine, serine, phenylalanine or leucine, were tested in a competitive fluorescence polarization (FP) binding screening assay using 5(6)-carboxyfluoresceinlabeled (Cf-) ARV-1502 and the 70S ribosome isolated from E. coli BW25113. While their effect on ribosomal protein expression was studied for green fluorescent protein (GFP) in a cell-free expression system (in vitro translation), the importance of known PrAMP transporters SbmA and MdtM was investigated using E. coli BW25113 and the corresponding knockout mutants. The dissociation constant (Kd) of 201 16 nmol/L obtained for Cf-ARV-1502 suggests strong binding to the E. coli 70S ribosome. An inhibitory binding assay indicated that the binding site overlaps with those of other PrAMPs including Onc112 and pyrrhocoricin as well as the non-peptidic antibiotics erythromycin and chloramphenicol. All these drugs and drug candidates bind to the exit-tunnel of the 70S ribosome. Substitutions of the C-terminal fragment of the binding motif YLPRP reduced binding. At the same time, inhibition of GFP expression increased with net peptide charge. Interestingly, the MIC values of wild-type and DsbmA and DmdtM knockout mutants indicated that substitutions in the ribosomal binding motif altered also the bacterial uptake, which was generally improved by incorporation of hydrophobic residues. In conclusion, most substituted ARV-1502 analogs bound weaker to the 70S ribosome than ARV-1502 underlining the importance of the YLPRP binding motif. The weaker ribosomal binding correlated well with decreased antimicrobial activity in vitro. Substituted ARV-1502 analogs with a higher level of hydrophobicity or positive net charge improved the ribosome binding, inhibition of translation, and bacterial uptake.

Die Reaktionspfade und Reaktionsdynamik photoinduzierter bimolekularer Ladungstransferreaktionen werden mit Hilfe der ultraschnellen polarisationsabhängigen UV-Pump/IR-Probe-Spektroskopie charakterisiert. Allgemein akzeptierte Modelle zur Beschreibung von bimolekularen Elektrontranserreaktionen nehmen an, dass Ladungstrennung in polaren Lösungsmitteln zu zwei Arten von Ionenpaaren führt, den lockeren (LIPs) und den engen Ionenpaaren (TIPs). TIPs und LIPs können durch die Beobachtung von Schwingungsmoden spektroskopisch unterschieden werden. Allerdings deuten die multiplen Zeitskalen sowohl für die Bildung von TIPs als auch LIPs darauf hin, dass eine Unterscheidung in zwei Arten von Ionenpaaren mit definierter Geometrie eine erhebliche Vereinfachung ist. TIPs und LIPs sind vielmehr als Grenzfälle zu betrachten, zwischen derer eine kontinuierliche Verteilung verschiedener Ionenpaare existiert. Die Natur der Ionenpaare wird durch die Verteilung der neutralen Reaktionspaare vor Initiation der Reaktion bestimmt. Außerdem wird gezeigt, dass TIPs höchst anisotrop sind. Die Wichtigkeit der beidseitigen Orientierung der Reaktanten wird dabei offengelegt. Weiterhin wird erstmalig ein femtosekundenspektroskopischer Beweis für die Existenz von Kohlensäure in wäßriger Lösung präsentiert. Eine Photosäure wurde verwendet, um die ultraschnelle Protonierung von Bikarbonat optisch auszulösen. Kohlensäure wurde bisher als Feststoff in Eismatrizen und in der Gasphase detektiert. Da Kohlensäure als Intermediat zwischen Kohlenstoffdioxid und Bikarbonat postuliert wird, ist ihre Charakterisierung von immenser Bedeutung für das Verständnis grundlegender Säure-Base Chemie von Karbonaten in wäßriger Lösung. Die Analyse der zeitabhängigen Signale unter Verwendung eines theoretischen Modells erlaubt die Bestimmung der bimolekularen Reaktionsdynamik. Dies ermöglicht einen Einblick in die Säure-Base Chemie von Kohlensäure. / The reaction pathways and dynamics of photoinduced bimolecular charge transfer reactions are characterised with ultrafast polarisation-sensitive UV-pump/IR-probe-spectroscopy. Generally accepted models for bimolecular electron transfer reactions suppose that charge separation in polar solvents leads to two geminate ion pairs, namely loose (LIPs) and tight ion pairs (TIPs). By monitoring vibrational marker modes TIPs and LIPs can be distinguished spectroscopically. However, multiple time scales for the formation of TIPs and LIPs indicate that a distinction between two kinds of ion pairs with well-defined geometries is a considerable simplification. TIPs and LIPs should rather be regarded as limiting cases, as there is a continuous distribution of different ion pairs between these two limits. The crucial parameter governing the nature of the ion pairs is the distribution of neutral reaction pairs subsequent to initiation of the reaction. Furthermore, TIPs are found to be highly anisotropic, revealing the importance of mutual orientation of the reactants. This thesis also presents for the first time femtosecond infrared spectroscopic results proving the existence of carbonic acid in aqueous solution. A photoacid is used to optically trigger the ultrafast protonation of bicarbonate. Carbonic acid has only been detected as solid existing in ice matrices and in the gas phase, so far. Because carbonic acid is often postulated as intermediate between carbon dioxide and bicarbonate its characterisation is of substantial support in understanding fundamental acid-base chemistry of carbonates in aqueous solution as well as in biophysical situations. Analysing the time-dependent signals using a theoretical model to describe bimolecular reaction dynamics an on-contact proton transfer reaction rate is derived. This gives an insight into the acid-base chemistry of carbonic acid.

This work consists of an introduction, 3 chapters, a conclusion and a list of references. The work is devoted to the development of a method for determining the pKa of compounds from a number of nitrotriazolo[5,1-c][1,2,4]triazines and nitrotriazolo[1,5-a]pyrimidines in aprotic and mixed media by potentiometric titration and spectrophotometry. The relevance of the definition of pKa in mixed and aprotic media is substantiated. Two different ways of defining it in these environments are considered. The paper examines the possibility of determining pKa by potentiometric titration and spectrophotometric analysis in aprotic and mixed media of compounds from a number of nitrotriazolo[5,1-c][1,2,4]triazines and nitrotriazolo[1,5-a]pyrimidines. The algorithms of the developed methods for determining pKa are given. / Настоящая работа состоит из введения, 3 глав, заключения и списка литературы. Работа посвящена разработка способа определения рКа соединений из ряда нитротриазоло[5,1-c][1,2,4]триазинов и нитротриазоло[1,5-а]пиримидинов в апротонных и смешанных средах методами потенциометрического титрования и спектрофотометрии. Обоснована актуальность определения рКа в смешанных и апротонных средах. Рассмотрены два различных способа по её определению в данных средах. В работе изучена возможность определения рКа методами потенциометрического титрования и спектрофотометрического анализа в апротонных и смешанных средах соединений из ряда нитротриазоло[5,1-c][1,2,4]триазинов и нитротриазоло[1,5-а]пиримидинов. Приведены алгоритмы разработанных способов определения рКа.

<p>Specific and non-specific interactions of solutes with immobilized biomembranes were studied using chromatographic methods. Liposomes, proteoliposomes and red blood cell (RBC) membrane vesicles were immobilized by a freeze-thawing procedure, whereas whole RBCs were adsorbed in the gel beds using electrostatic interaction, binding to wheat germ agglutinin (WGA) or the streptavidin-biotin interaction. </p><p>Superporous agarose gel with coupled WGA was the most promising matrix for RBC adsorption and allowed frontal chromatographic analyses of the cells for about one week. Dissociation constants for the binding of cytochalasin B and glucose to the glucose transporter GLUT1 were determined under equilibrium conditions. The number of cytochalasin B-binding sites per GLUT1 monomer was calculated and compared to corresponding results measured on free and immobilized membrane vesicles and GLUT1 proteoliposomes. This allowed conclusions about the protein´s binding state <i>in vitro</i> and <i>in vivo</i>. </p><p>Partitioning of drugs into biomembranes was quantified and the system was suggested as a screening method to test for possible intestinal absorption of drug candidates. We also studied how membrane partitioning of drugs is affected by the presence of integral membrane proteins or of charged phospholipids.</p><p>An attempt to combine the theory for specific binding and membrane partitioning of solutes in a single equation is briefly presented. </p>

<p>The human glucose transporter GLUT1 is abundant in red blood cells, the blood-brain barrier and epithelial cells, where it mediates the transport of the energy metabolite, glucose. In the present work some properties of GLUT1, including affinity binding of both substrates and inhibitors, transport rates as well as permeabilities of aromatic amino acids and drug-membrane interactions were analyzed by chromatographic methods.</p><p>Reconstitution by size-exclusion chromatography on Superdex 75 from a detergent with a low CMC that provides monomeric GLUT1 was examined regarding D-glucose- and CB binding as well as D-glucose transport. Upon steric immobilization in Superdex 200 gel beads, residual detergent could be washed away and dissociation constants in the same range as reported for binding to GLUT1 reconstituted from other detergents were obtained. The transport rate into the GLUT1 proteoliposomes was low, probably due to residual detergent. Binding to GLUT1 at different pH was analyzed and the affinity of glucose and GLUT1 inhibitors was found to decrease with increasing pH (5–8.7). The average number of cytochalasin B-binding sites per GLUT1 monomers was, in most cases, approximately 0.4. GLUT1 may work as a functional monomer, dimer or oligomer. To determine whether GLUT1 was responsible for the transport of the aromatic amino acids tyrosine and tryptophan, uptake values and permeabilities of these amino acids into liposomes and GLUT1 proteoliposomes were compared to the permeabilities of D- and L- glucose in the same systems. Dihydrocytochalasin B was identified to be a new inhibitor of tyrosine and tryptophan transport into red blood cells. Ethanol turned out to inhibit the specific binding between CB and GLUT1 and also to decrease the partitioning of CB and drugs into lipid bilayers. A capacity factor for drug partitioning into membranes that allows comparison between columns with different amount of immobilized lipids was validated, and turned out to be independent of flow rate, amount of lipids and drug concentration in the ranges tested.</p>