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Hydrogen bonds are of great interest in the solid state due to their importance in structural, functional and dynamical properties of chemical systems. Moderate hydrogen bonds have been linked with proton transfer, whereas the short, strong hydrogen bonds enable proton migration. Previous work in our group on relatively simple hydrogen bonded adducts relied on the combination of ab initio computational modelling (molecular dynamics) with variable temperature diffraction results (X-ray and neutron). These demonstrated that the interplay of these techniques was successful in studying the phenomena of proton transfer and migration. The present work follows on from that, and focuses on the effects of temperature and pressure on proton transfer and migration using both experimental and computational methods. The systems studied continue to encapsulate adducts with N…O and O…O hydrogen bonds. The study of the adduct formed between squaric acid and 4,4’-bipyridine was found to exhibit proton transfer associated with a single-crystal to single-crystal phase transition at 450 K that is coupled to a colour change (yellow to red). X-ray and neutron diffraction initially revealed the heavy atom structure and secondly the location of the hydrogen atoms along the moderate N…O hydrogen bond (ca. 2.6 Å). Computational modelling supported this and deduced the reason for the striking colour change. Pressure studies also determined that the adduct underwent two phase-transitions with a similar colour change, indicating that proton transfer is also a factor here, but with powder patterns different from the high temperature form, indicating that further polymorphs for this interesting system must exist. In an attempt to lower the temperature at which proton transfer would occur the base was changed to one of a more basic nature, i.e. co-crystallisation of squaric acid and 2,2’-dimethyl–4,4’-bipyridine was pursued. This lead to the formation of two red crystals that were found to posses the base doubly protonated at all temperatures studied (from 300 K to 100 K). The adduct of N,N-dimethylurea with phosphoric acid was obtained from a systematic study designed to follow the success of a previously reported system that showed proton migration (the adduct of urea and phosphoric acid). The new material was found to crystallise as the 2:1 adduct and maintained the short, strong hydrogen bonds characteristic of the parent structure. As part of the systematic approach undertaken throughout the research presented here, co-crystallisation of a combination of acids and bases were attempted in order to synthesise new materials containing short, strong hydrogen bonds. These yielded the adducts between oxalic acid and 2,2’-dimethyl-4,4’-bipyridine, and oxamic acid and 4,4’-bipyridine. In addition to these adducts some compounds ended up reacting to create new ones, e.g. the fusing of dimethyl urea and squaric acid to give N-(2-hydroxycyclobutene-3,4-dione)-N’,N’-dimethylurea and N-(2- hydroxycyclobutene-3,4-dione)-N,N'-dimethylurea, while a new polymorphs of one of the precursors on its own was also obtained (N,N’-dimethylurea). The resulting co-crystallisations did not all follow the design quite as intended. They did, however, yield interesting new structures, some of which have the potential to be proton migration and transfer systems.

Proton exchange membrane (PEM) fuel cells are at the forefront among different types of fuel cells and are likely to be important power sources in the near future. PEM is a key component of the PEM fuel cells. The objective of this research is to investigate the fundamental aspects of PEM in terms of thermodynamics and proton transport in the membrane, so that the new proton conducting materials may be developed based on the detailed understanding. Since the proton conductivity increases dramatically with the amount of water in PEM, it is important to maintain a high humidification during the fuel cell operation. Therefore, the water uptake characteristics of the membrane are very important in developing fuel cell systems. Thermodynamic models are developed to describe sorption in proton-exchange membranes (PEMs), which can predict the complete isotherm as well as provide a plausible explanation for the long unresolved phenomenon termed Schroeder¡¯s paradox, namely the difference between the amounts sorbed from a liquid solvent versus from its saturated vapor. The sorption isotherm is a result of equilibrium established in the polymer-solvent system when the swelling pressure due to the uptake of solvent is balanced by the surface and elastic deformation pressures that restrain further stretching of the polymer network. The transport of protons in PEMs is intriguing. It requires knowledge of the PEM structure, water sorption thermodynamics in PEM, proton distribution in PEM, interactions between the protons and PEM, and proton transport in aqueous solution. Even proton conduction in water is anomalous that has received considerable attention for over a century because of its paramount importance in chemical, biological, and electrochemical systems. A pore transport model is proposed to describe proton diffusion at various hydration levels within Nafion¢ÃƒÂ§ by incorporating structural effect upon water uptake and various proton transport mechanisms, namely proton hopping on pore surface, Grotthuss diffusion in pore bulk, and ordinary mass diffusion of hydronium ions. A comprehensive random walk basis that relates the molecular details of proton transfer to the continuum diffusion coefficients has been applied to provide the transport details in the molecular scale within the pores of PEM. The proton conductivity in contact with water vapor is accurately predicted as a function of relative humidity without any fitted parameters. This theoretical model is quite insightful and provides design variables for developing high proton conducting PEMs. The proton transport model has been extended to the nanocomposite membranes being designed for higher temperature operation which are prepared via modification of polymer (host membrane) by the incorporation of inorganics such as SiO2 and ZrO2. The operation of fuel cells at high temperature provides many advantages, especially for CO poisoning. A proton transport model is proposed to describe proton diffusion in nanocomposite Nafion¢ÃƒÂ§/(ZrO2/SO42-) membranes. This model adequately accounts for the acidity, surface acid density, particle size, and the amount of loading of the inorganics. The higher proton conductivity of the composite membrane compared with that of Nafion is observed experimentally and also predicted by the model. Finally, some applications of PEM fuel cells are considered including direct methanol fuel cells, palladium barrier anode, and water electrolysis in regenerative fuel cells.

Proton-transfer reactions are one of the most fundamental chemical reactions. However, the chemical dynamics of these processes remain elusive due to the difficulty of modeling these reactions. Establishing an experimental model system and using infrared absorption and two-dimensional infrared (2D IR) spectroscopies as means for detection, the chemical dynamics of the protonation states that are involved in a ground-electronic-state proton-transfer reaction in solution can be determined. In this study, experimental models are established with formic acid and nitrogenous bases in a low dielectric solvent. A hydrogen bond forms between the acid and the base, which will allow for the proton to transfer between the two molecules to form the neutral and the ion-pair protonation states. The carbon-deuterium (C-D) stretch and the carbonyl (C=O) stretch of the formic acid molecule are used as the reporter groups for the 2D IR measurements. The results of the C-D stretch demonstrate that there is a high sensitivity to the deprotonation, vibrational coupling, and vibrational dynamics trends that are linked to the solute-solvent interactions. The results of the C=O stretch demonstrate a sensitivity to the deprotonation and conformational disorder in which the position of the C=O changes the dynamics of the protonation state. Although, a proton-transfer is not detected, the experimental model system provides an understanding of the features that govern the chemical dynamics of proton-transfer reactions.

Le projet de cette thèse était l'évaluation du processus de réactivation et l'étude du site actif de l'AChE inhibée par un agent neurotoxique par des méthode computationnelles. L'objectif était de guider le design rationnel de nouveau réactivateurs. Une étude initiale avec un modèle QM tronqué a indiqué la nécessité de modéliser l'environnement enzymatique pour compenser la charge du Glu334. Elle a aussi confirmé le rôle du trou oxyanionique dans la stabilisation des états de transition de la réactivation. Des simulations QM/MM de la réactivation par le réactivateur classique 2-PAM, ainsi que par deux réactivateurs au coeur aromatique non chargé ont été effectuées. Il a été démontré que le Glu202, un résidu à proximité de la triade catalytique de l'AChE, doit être protoné pour que la réactivation ait lieu. Ces simulations ont aussi montré que le réactivateur peut être déprotoné dans le site actif de l'AChE par His447. Les réactivateurs au coeur aromatique non chargé sont plus nucléophiles que la 2-PAM et l'un d'entre eux est plus aisément déprotoné dans le site actif. Nos résultats indiquent que la capacité d'un réactivateur à être facilement déprotoné est plus importante que sa nucléophilie. Enfin, un mécanisme de migration de protons a été identifié par des calculs QM/MM et EVB. Il implique deux glutamates derrière le site actif, Glu450 et Glu452. La possibilité que ces deux protons soient temporairement protonés et donc impliqués dans une migration de protons a été confirmé par des calculs CpHMD. La migration de proton passe par la N-protonation d'une liaison amide, ce qui constitue un nouveau mécanisme. / The project of this PhD was to investigate the reactivation process and the active site of nerve agent inhibited AChE by computational methodologies to gain insight about the rational design of new reactivators. An initial truncated QM model study provided some insight in the necessary compensation of Glu334 by the enzyme. It also confirmed the role of the oxyanionic hole in the stabilization of the transition state of the reactivation. QM/MM simulations of the reactivation with classical reactivator 2-PAM, as well as two non-pyridinium reactivators, were performed. It was shown that Glu202, a residue near the catalytic triad of AChE, needs to be protonated for the reactivation to occur. Those simulations also showed that the reactivator can be deprotonated in the active site of AChE by His447. Non-pyridinium reactivator were found to have a greater nucleophilicity than 2-PAM and, for one of them, to be easily deprotonated in the active site. Our results indicate that the capacity of a reactivator to be deprotonated in the active site of the enzyme is more important than its nucleophilicity. Finally, a proton relay mechanism was identified through QM/MM and EVB simulations. It involves two glutamate residues, Glu450 and Glu452, positioned behind the active site. The potential for these two residues to be transiently protonated and thus involved in a proton relay was confirmed by CpHMD simulations. This proton relay mechanism relies on the N-protonation of an amide which is a novel mechanism.

Tobacco smoke particulate matter (PM) is a complex mixture of condensed organic compounds, with about 5 to 10% water. Its general properties are similar in some respects to that of atmospheric organic aerosol PM and thus provides a useful surrogate when studying atmospheric PM. Due to its ability to undergo acid-base chemistry, nicotine is of particular interest in the tobacco smoke system. The gas/particle partitioning of nicotine depends on the protonation state of nicotine in the particles, so the distribution of nicotine between these phases provides a means of understanding the acid-base balance in the tobacco smoke system. The goal of this work is to develop an acid-base balance for mainstream tobacco smoke that accounts for the extent of protonation of nicotine. Samples of extracted smoke particulate matter from seven brands of cigarettes were analyzed by ion chromatography (IC) and titration by both acid (HCl) and base (lithium phenoxide) for comparison with nicotine data collected by colleagues. IC analysis was used to quantify tracers of known acidic and basic species in tobacco smoke. Anion tracers for acids included: glycolate, acetate, formate, lactate, chloride, nitrite, sulfate, and nitrate. The cation tracers for base were ammonium, sodium, and potassium. The tobacco smoke extracts were also analyzed after acidification by the HCl titrant for changes in ammonia and organic acid concentrations to determine whether "bound" forms of these compounds were present in the PM. The titration data provided total concentrations of weak acid and bases in the samples. This titration data was compared with the concentrations of the tracers for weak acids and bases (along with the quantification of total nicotine by colleagues) to determine whether the IC analyses were accounting for all of the important species. The results of this comparison show that these analyses missed relevant species in the tobacco smoke system. As tobacco smoke PM is a complex organic mixture, the ability of acid species to protonate nicotine will be different than in aqueous media. The acidic species of interest were assumed to be either strong or weak, with the strong species assumed to be fully ionized after protonation of nicotine. Some portion of the weak acid species could then protonate any available nicotine. An electroneutrality equation (ENE) was developed for the tobacco smoke PM and populated using the IC data and the nicotine data obtained by colleagues. Using this ENE, the extent ionization of the weak acids species (α1A) and the net reaction constant for the protonation of nicotine by these weak acids (K*) was estimated. However, interpretation of the results were complicated by the underrepresentation of the pertinent weak acid species in our IC analyses. This study concluded that further work is needed to identify the missing weak acid and base species to obtain a better representation of the acid-base balance in tobacco smoke PM and to understand the ability of these weak acid species to protonate nicotine.

Choline oxidase catalyzes the oxidation of choline to glycine betaine. This reaction is of considerable medical and biotechnological applications, because the accumulation of glycine betaine in the cytoplasm of many plants and human pathogens enables them to counteract hyperosmotic environments. In this respect, the study of choline oxidase has potential for the development of a therapeutic agent that can specifically inhibit the formation of glycine betaine, and therefore render pathogens more susceptible to conventional treatment. The study of choline oxidase has also potential for the improvement of the stress resistance of plant by introducing an efficient biosynthetic pathway for glycine betaine in genetically engineered economically relevant crop plant. In this study, codA gene encoding for choline oxidase was cloned. The cloned gene was then used to express and purify the wild-type enzyme as well as to prepare selected mutant forms of choline oxidase. In all cases, the resulting enzymes were purified to high levels, allowing for detailed characterizations. The biophysical and biochemical analyses of choline oxidase variants in which the positively charged residue close to the flavin N(1) locus (His466) was removed (H466A) or reversed (H466D) suggest that in choline oxidase, His466 modulates the electrophilicity of the bound flavin and the polarity of the active site, and contributes to the flavinylation process of the covalently bound FAD as well as to the stabilization of the negative charges in the active site. Biochemical, structural, and mechanistic relevant properties of selected flavoproteins with special attention to flavoprotein oxidases, as well as the biotechnological and medical relevance of choline oxidase, are presented in Chapter I. Chapter II summarizes all the experimental techniques used in this study. Chapter III-VII illustrate my studies on choline oxidase, including cloning, expression, purification and preliminary characterizations (Chapter III), spectroscopic and steady state kinetics (Chapter IV), the catalytic roles of His466 and the effects of reversing the protein positive charge close to the flavin N(1) locus (Chapter V and VI), and the roles of His310 with a special attention to its involvement in a proton-transfer network (Chapter VII). Chapter VIII presents a general discussion of the data presented.

The enzymatic oxidation of choline to glycine betaine is of interest because organisms accumulate glycine betaine intracellularly in response to stress conditions, as such it is of potential interest for the genetic engineering of crops that do not naturally possess efficient pathways for the synthesis of glycine betaine, and for the potential development of drugs that target the glycine betaine biosynthetic pathway in human pathogens. To date, one of the best characterized enzymes belonging to this pathway is the flavin-dependent choline oxidase from Arthrobacter globiformis. In this enzyme, choline oxidation proceeds through two reductive half-reactions and two oxidative half-reactions. In each of the reductive half-reactions the FAD cofactor is reduced to the anionic hydroquinone form (2 e- reduced) which is followed by an oxidative half-reaction where the reduced FAD cofactor is reoxidized by molecular oxygen with formation and release of hydrogen peroxide. In this dissertation the roles of selected residues, namely histidine at position 310, valine at position 464 and serine at position 101, that do not directly participate in catalysis in the reaction catalyzed by choline oxidase have been elucidated. The effects on the overall reaction kinetics of these residues in the protein matrix were investigated by a combination of steady state kinetics, rapid kinetics, pH, mutagenesis, substrate deuterium and solvent isotope effects, viscosity effects as well as X-ray crystallography. A comparison of the kinetic data obtained for the variant enzymes to previous data obtained for wild-type choline oxidase are consistent with the valine residue at position 464 being important for the oxidative half-reaction as well as the positioning of the catalytic groups in the active site of the enzyme. The kinetic data obtained for the serine at position 101 shows that serine 101 is important for both the reductive and oxidative half-reactions. Finally, the kinetic data for histidine at position 310 suggest that this residue is essential for both the reductive and oxidative half-reactions.

The photochemistry of several novel photoacids was addressed experimentally and theorectically. Initial studies focused on the excited-state proton transfer (ESPT) of several chiral phtoacids and explored the effects of chirality on ESPT; subsequent studies examined photochemistry and photophysics of "super" photoacid N-methyl-6-hydroxyquinolinium (MHQ). In the initial studies, no enantioselectivity was observed from the chiral photoacids to various chiral proton acceptors. In the later studies examining ESPT in MHQ both experimentally and theoretically, the excited-state acidity constant of the photoacid was determined to be an unprecedented -7, making it the strongest photoacid reported in the literature to-date. Consideration was then given to applications of the novel photoacid including its properties as a photoinitiator in cationic polymerizations and as a photochemical probe in gas-expanded liquids and in the Nafion membrane. In the course of these studies, an interesting fluorescence quenching effect was observed that became the subject of some exploratory studies that suggest a nucleophilic quenching mechanism.

Oxygenated volatile organic compounds ((O)VOCs) contribute to ozone formation, affect the oxidising capacity of the troposphere and are sources of growth, and in some cases formation, of aerosols. It is therefore important to identify and quantify sources of (O)VOCs in the troposphere. In the late 1990s a unique technique for quantification of organic trace gas species, proton transfer reaction mass spectrometry (PTR-MS) was developed. PTR-MS potentially offers rapid response and high sensitivity without the need for sample pre-concentration. Concentrations can be derived from the PTR-MS either by calibration or can be calculated from measured ion count rates and kinetic considerations. In this work, the methodology of PTR-MS application is critically assessed. The uncertainties and inaccuracies associated with each parameter employed in the calculation of concentrations are reviewed. This includes a critical appraisal of models for the calculation of the collisional rate constant currently applied in the field of PTR-MS. The use of a model to account for the effects of the electric field, available in the literature but not previously applied to the PTR-MS, is advocated. Collisional rate constants employing each of the models discussed have been calculated for the reactions of H3O+ with over 400 molecules for PTR-MS. In PTR-MS it cannot be assumed that the product ion occurs only at the protonated non-dissociated mass. Few product distributions obtained from PTR-MS are cited in the literature, and even then the reaction chamber conditions (pressure, temperature and electric field strength) are not always specified. A large volume of product distributions for trace gases with H3O+ in select ion flow tube mass spectrometry (SIFT) exists in the literature and is reviewed. In SIFT, no electric field is applied to the reaction chamber and the extent and even nature of fragmentation can differ in PTR-MS. In addition to the application of an electric field, the energy in the reaction chamber can be increased by increasing the temperature or by variation of the reagent ion. In this work, the increase in energy via the three methods is approximated to enable a comparison of product distributions. The review of product distributions in PTR-MS, select ion flow drift tube mass spectrometry (SIFDT), variable temperature select ion flow tube mass spectrometry (VT-SIFT), SIFT, proton transfer reaction time of flight mass spectrometry (PTR-TOF-MS), proton transfer reaction ion trap mass spectrometry (PTR-ITMS) and electron ionisation mass spectrometry (EI-MS) is used alongside thermodynamic considerations to collate a list of potential contributors to a range of mass to charge ratios (m/z) in the PTR-MS. The need for further measurements of product distributions as a function of temperature, pressure and electric field strength for a wider range of (O)VOCs is highlighted. This enables dissociation to be better used as a tool for compound identification rather than being considered a hindrance. The collation of likely product distributions is applied to identify possible contributors to m/z observed during PTR-MS measurements of emission from cattle slurry. Field measurements were made during fertilisation of a grassland site south of Edinburgh in 2004 and 2005 and in laboratory-based measurements in 2006. Contextual reasoning, previous measurements and isotope ratios are used to narrow the list of possible contributors. Large concentrations of m/z cautiously identified as alcohols followed by a latter peak in carboxylic acids were observed during laboratory measurements. Increases in the corresponding m/z were also observed during the fertilisations. Other tentatively identified compounds emitted included phenol, methyl phenol, trimethylamine, and various sulphur containing compounds.