Abstract: Owing to the light-induced switching between their trans- and cis-isomers, azobenzenes display a wide range of applications including stimuli-responsive polymers, acid-base indicators, colorful systems, liquid crystals, and bio-medicals. In the past decades, much research on azobenzenes has been carried out and they have become a growing research topic. Particularly, the synthetic methodology of azobenzene derivatives has become mature. However, a general synthetic method of furnishing the bis- and tris-azobenzene compounds in one step is still lacking, and the study of bis-azobenzene is nearly blank including the solution properties and applications. In this thesis, we focus on the design, and preparation of bis-, tris- and small cyclic azobenzene derivatives; followed by a further investigation of their properties in solution. We also explore the preparation and applications of azobenzene-based stimuli-responsive polymeric materials. The first chapter describes an efficient strategy for the synthesis of bis- and tris-azobenzene derivatives. In this synthetic pathway, the bis- and tris-azobenzenes could be obtained in one pot, together with mono-azobenzene side products. By modifying the reaction conditions, the yields of the azobenzene compounds were mainly dependent on the substituents on the phenols and diazonium salts, and the molar ratio of starting materials. Compared with the unsubstituted aniline, the use of anilines with electron-withdrawing groups, leading to electron-deficient diazonium salts, favors the formation of mono-azobenzenes, rather than bis-azobenzenes. Whereas, anilines with electron-donating groups are not efficient during the first step leading to the formation of mono-azobenzene and thus favor the generation of bis-azobenzenes. Large amounts of anilines (over two-fold and three-fold excess), are the best choice to obtain bis- and tris-azobenzenes in good yields. In Chapter 2, we describe a novel method for the cyclization of mono- and bis-azobenzenes without ultraviolet light to form seven-membered heterocycles. The starting materials contain ortho-fluoro atom and ortho-phenol groups on the phenyl rings of the azobenzene systems. The role of the fluoro substituent is twofold. It promotes the stability of the cis-form of the azobenzene and it acts as a leaving group when its carbon atom neighbor is attacked by the phenolate. The nature of solvents was found to have a pronounced effect on the spontaneous cyclization reaction by stabilizing the  intermediate complex. The cyclization rate could be accelerated under the UV irradiation and by using more polar solvents. Due to the competing keto-enol tautomerizations and cyclizations, we observed complicated changes in UV-vis absorption and color of solutions over time. It was revealed that, for ortho-hydroxyl azobenzenes with ortho-fluorine atom in polar solvents, the trans-to-cis isomerization and cyclization happened under daylight, and keto-enol tautomerization occurred in the dark. In Chapter 3, we studied a class of novel dual-responsive (photo- and thermo-) copolymers by modifying Poly(N-isopropylacrylamide) (PNIPAM) with bis-azobenzene moieties. The copolymers were prepared from a free radical copolymerization of N-isopropylacrylamide (NIPAM) and bis-azobenzenes bearing electron-donating or electron-accepting substituents. It was found that bis-azobenzene moieties could influence the cloud point of aqueous copolymer solution due to the photoisomerization of bis-azobenzenes and the conformation of polymer chain upon the photoreactions. Varying substituents on bis-azobenzene moieties, the copolymer solutions displayed an opposite cloud point shift after the photoreactions of the chromophores. When the substituents on azobenzene have push-pull feature, the polymer chains prefer aggregation after UV irradiation, which decreases the cloud point. By contrast, the cloud point shifts to higher temperature upon UV light irradiation when the bis-azobenzenes bears the donors, which is caused by cis-isomer being more hydrophilic than the trans-isomer. However, the effect of photoisomerization of azobenzene on the cloud point shift appears to be greater on PNIPAM containing mono-azobenzene pendent groups. / En raison de la commutation induite par la lumière entre leurs isomères trans et cis, les azobenzènes affichent une gamme étendue d'applications. On y retrouve des polymères sensibles aux stimuli, des indicateurs acido-basiques, des systèmes colorés, des cristaux liquides et des matériaux aux applications biomédicales. Dans les dernières décennies, de nombreuses recherches sur les azobenzènes ont été menées et ils sont devenues un sujet de plus en plus important. En particulier, la méthodologie de synthèse des dérivés d'azobenzène est devenue mature. Cependant, une méthode synthétique générale pour l’obtention des composés bis- et tris-azobenzène en une seule étape est encore manquante, et l'étude du bis-azobenzène est presque vierge, y compris les propriétés et les applications en solution. Dans cette thèse, nous nous concentrons sur la conception et la préparation de bis-, tris- et de petits dérivés cycliques de l'azobenzène. Ce premier volet est suivi d'une étude plus poussée de leurs propriétés en solution. Nous explorons également la préparation et l'application de matériaux polymères d'azobenzène, réagissant à plusieurs stimulations. Le premier chapitre décrit une stratégie efficace pour la synthèse des dérivés bis- et tris-azobenzène. Dans cette voie de synthèse, les bis- et tris-azobenzènes peuvent être obtenus dans un pot réactionnel, avec des produits secondaires mono-azobenzène. En modifiant les conditions de réaction, les rendements des composés azobenzène dépendent principalement des substituants sur les phénols et les sels de diazonium, et du rapport molaire des produits de départ. Par rapport à l'aniline non substituée, l'utilisation d'anilines avec des groupes électroattracteurs, conduisant à des sels de diazonium déficients en électrons, favorise la formation de monoazobenzènes plutôt que de bis-azobenzènes. En revanche, les anilines à groupements donneurs d'électrons ne sont pas efficaces au cours de la première étape conduisant à la formation de monoazobenzènes et favorisent ainsi la génération de bis-azobenzènes. De grandes quantités d'anilines (excès de plus de deux et trois fois) sont le meilleur choix pour obtenir des bis- et tris-azobenzènes avec de bons rendements. Dans le chapitre 2, nous décrivons une nouvelle méthode de cyclisation des mono- et bis-azobenzènes, sans lumière ultraviolette, pour former des hétérocycles à sept chaînons. Les produits de départ contiennent des groupes ortho-fluoro et orthophénol sur les cycles phényle des systèmes azobenzène. Le rôle du substituant fluoro est double. Il favorise la stabilité de la forme cis de l'azobenzène et agit comme un groupe partant lorsque son atome de carbone voisin est attaqué par le phénolate. La nature des solvants s'est avérée avoir un effet prononcé sur la réaction de cyclisation spontanée en stabilisant le complexe intermédiaire . La vitesse de cyclisation peut être accélérée sous l'irradiation UV et en utilisant des solvants plus polaires. En raison des tautomérisations céto-énol et des cyclisations en compétition, nous avons observé que l’évolution des spectres d'absorption UV-vis et de la couleur des solutions au fil du temps était compliqué. Il a été révélé que, pour les ortho-hydroxyl azobenzènes avec un atome d'ortho-fluor dans les solvants polaires, l'isomérisation et la cyclisation trans-cis se produisaient à la lumière du jour et que la tautomérisation céto-énol se produisait dans l'obscurité. Dans le chapitre 3, nous avons étudié une classe de nouveaux copolymères biosensibles (photo- et thermo-) en modifiant le poly(N-isopropylacrylamide) (PNIPAM) avec des portions bis-azobenzène. Les copolymères ont été préparés à partir d'une copolymérisation radicalaire de N-isopropylacrylamide (NIPAM) et de bis-azobenzènes portant des substituants donneurs ou accepteurs d'électrons. Il a été constaté que les fragments bis-azobenzène pouvaient influencer le point de trouble de la solution aqueuse de copolymère en raison de la photoisomérisation des bis-azobenzènes et de la conformation de la chaîne polymère lors des photoréactions. En changeant les substituants sur les fragments bis-azobenzène, les solutions de copolymères présentaient un décalage du point de trouble opposé après les photoréactions des chromophores. Lorsque les substituants sur l'azobenzène ont une influence «push-pull», les chaînes polymères préfèrent l'agrégation après l'irradiation UV, ce qui diminue le point de trouble. En revanche, le point de trouble passe à une température plus élevée lors de l'irradiation par la lumière UV lorsque les bis-azobenzènes portent des donneurs, ce qui est dû au fait que l'isomère cis est plus hydrophile que l'isomère trans. Cependant, l'effet de la photo-isomérisation de l'azobenzène sur le décalage du point de trouble semble être plus important sur les groupes pendants mono-azobenzène contenant du PNIPAM.

Chloroperoxidase (CPO) is a potential biocatalyst for use in asymmetric synthesis. The mechanisms of CPO catalysis are therefore of interest. The halogenation reaction, one of several chemical reactions that CPO catalyzes, is not fully understood and is the subject of this dissertation. The mechanism by which CPO catalyzes halogenation is disputed. It has been postulated that halogenation of substrates occurs at the active site. Alternatively, it has been proposed that hypochlorous acid, produced at the active site via oxidation of chloride, is released prior to reaction, so that halogenation occurs in solution. The free-solution mechanism is supported by the observation that halogenation of most substrates often occurs non-stereospecifically. On the other hand, the enzyme-bound mechanism is supported by the observation that some large substrates undergo halogenation stereospecifically. The major purpose of this research is to compare chlorination of the substrate beta-cyclopentanedione in the two environments. One study was of the reaction with limited hydration because such a level of hydration is typical of the active site. For this work, a purely quantum mechanical approach was used. To model the aqueous environment, the limited hydration environment approach is not appropriate. Instead, reaction precursor conformations were obtained from a solvated molecular dynamics simulation, and reaction of potentially reactive molecular encounters was modeled with a hybrid quantum mechanical/molecular mechanical approach. Extensive work developing parameters for small molecules was pre-requisite for the molecular dynamics simulation. It is observed that a limited and optimized (active-site-like) hydration environment leads to a lower energetic barrier than the fully solvated model representative of the aqueous environment at room temperature, suggesting that the stable water network near the active site is likely to facilitate the chlorination mechanism. The influence of the solvent environment on the reaction barrier is critical. It is observed that stabilization of the catalytic water by other solvent molecules lowers the barrier for keto-enol tautomerization. Placement of water molecules is more important than the number of water molecules in such studies. The fully-solvated model demonstrates that reaction proceeds when the instantaneous dynamical water environment is close to optimal for stabilizing the transition state.

Ab initio Hartree-Fock and density functional theory calculations were carried out to investigate the structures, energies, and vibrational spectra of indole and two of its hydrogen migration tautomers. The calculated results of indole are in good agreement with experiments. Rotational constants and infrared spectral features of 2H-indole and 3H-indole are predicted to assist future experimental identification of the two tautomers. Transition states of unimolecular isomerization among the three tautomers are also optimized and activation barriers of the isomerization reactions evaluated. The results indicate that unimolecular indole → 3H-indole proceeds via 2H-indole with an activation barrier of 51 kcal/mol.

PixD (Slr1694) ist ein Photorezeptor, der den sensors of blue light using FAD (BLUF) Proteinen zugeordnet wurde. Die Übertragung des Stimulus auf das Apoprotein erfolgt in dieser Proteinfamilie über eine Neuordnung des Wasserstoffbrückennetzwerkes um den Kofaktor, in das die strikt konservierten Reste Tyrosin-8 (Y8), Glutamin-50 (Q50) und möglicherweise das semi-konservierte Tryptophan-91 (W91) involviert sind. Ziel dieser Arbeit war es, weitere Hinweise auf die Wasserstoffbrückenkonfiguration der Flavinbindetasche in Dunkel- und Lichtzustand zu erhalten, um eine bessere Vorstellung von der Stabilisierung des Lichtzustandes zu bekommen und mögliche Wege der Signaltransduktion an die Proteinoberfläche einzugrenzen. Die Ergebnisse weisen darauf hin, dass sich lichtaktivierte Interaktionsänderungen zwischen Apoprotein und Chromophor auf die Neubildung einer Wasserstoffbrücke zum Flavin C4-Carbonyl beschränken. In Übereinstimmung zu früheren Analysen liegt das Q50 im Dunkelzustand in seiner Amid-Form vor. Sein Seitenkettencarbonyl ist im Lichtzustand vermutlich zu Y8 ausgerichtet, wobei Hinweise auf eine Amid-Imidsäure-Tautomerisierung des Glutamins in PixD gefunden wurden. Eine selektive Isotopenmarkierung des Tryptophan-91 zeigte Anzeichen für eine Verlängerung des β5-Stranges, die wahrscheinlich ein zentrales Element der Signalweiterleitung an die Proteinoberfläche darstellt. Möglicherweise erstreckt sich das Wasserstoffbrückennetzwerk dabei bis in die über dem beta5-Strang liegende alpha-Helix. Wird es gestört, scheint das Proteininnere für Imidazol zugänglich gemacht zu werden, wo es die Aktivierungsenergie für die Rückkehr in den Dunkelzustand beeinflusst. Auch Substitutionen des H73 im gegenüberliegenden Eckstrang des beta-Faltblattes beeinflussten die Geschwindigkeit der Dunkelrelaxation von PixD. Sie veränderten die IR-Absorption gegenüber dem Wildtyp jedoch nicht und unterstützen die Theorie einer Protonenleitung über das benachbarte H72. / The photoreceptor PixD (Slr1694) belongs to the sensors of blue light using FAD (BLUF) protein family. These photoreceptors propagate the signal by a rearrangement of hydrogen bonds surrounding the cofactor, involving the highly conserved residues tyrosine-8 (Y8), glutamine 50 (Q50) and perhaps the semi-conserved tryptophan-91 (W91). One aim of the presented work was to gain a deeper insight into the hydrogen bond configuration of the flavin binding pocket in the light and dark state conformations. Thereby, knowledge of the stabilization mechanisms for the light state and the signal propagation to the protein surface could be acquired. The results indicate a restriction of light induced changes in hydrogen bonding of the flavin to its C4 carbonyl. In agreement with former studies, the Q50 forms the amide isomer in the dark state. Its side chain carbonyl group most likely points towards Y8 in the active protein. Besides, the results support an amide-imidic acid-tautomerization of Q50 in PixD. A selective isotope labeling of the tryptophan-91 localized at the beginning of an edge strand of the beta sheet indicates an elongation of the secondary structure that may represent a central element of the signal propagation to the protein surface. The secondary structure is possibly connected with an alpha helix located above the beta5 strand by hydrogen bonds. A disturbance of this interaction probably allows the base catalyst imidazole to enter the protein core. Substitutions of H73 in the opposing edge beta strand changed the rate of the PixD dark relaxation as well. However, they had no visible effect on the infrared absorbance compared to the wild type and hence support a putative involvement of the neighbouring H72 in proton transfer reactions.

A detailed understanding of natural photosynthesis provides inspiration for the development of sustainable and renewable energy sources, i.e. a technology that is capable of converting solar energy directly into chemical fuels. This concept is called artificial photosynthesis. The work described in this thesis contains contributions to the development of artificial photosynthesis in two separate areas. The first one relates to light harvesting with a focus on the question of how electronic properties of photosensitizers can be tuned to allow for efficient photo-induced electron transfer processes. The study is based on a series of bis(tridentate)ruthenium(II) polypyridyl complexes, the geometric properties of which make them highly appealing for the construction of linear donor-photosensitizer-acceptor arrangements for efficient vectorial photo-induced electron transfer reactions. The chromophores possess remarkably long lived 3MLCT excited states and it is shown that their excited-state oxidation strength can be altered by variations of the ligand scaffold over a remarkably large range of 900 mV. The second area of relevance to natural and artificial photosynthesis that is discussed in this thesis relates to the coupled movement of protons and electrons. The delicate interplay between these two charged particles regulates thermodynamic and kinetic aspects in many key elementary steps of natural photosynthesis, and further studies are needed to fully understand this concept. The studies are based on redox active phenols with intramolecular hydrogen bonds to quinolines. The compounds thus bear a strong resemblance to the tyrosine/histidine couple in photosystem II, i.e. the water-plastoquinone oxidoreductase enzyme in photosynthesis. The design of the biomimetic models is such that the distance between the proton donor and acceptor is varied, enabling studies on the effect the proton transfer distance has on the rate of proton-coupled electron transfer reactions. The results of the studies have implications for the development of artificial photosynthesis, in particular in connection with redox leveling, charge accumulation, as well as electron and proton transfer. In addition to these two contributions, the excited-state dynamics of the intramolecular hydrogen-bonded phenols was investigated, thereby revealing design principles for technological applications based on excited-state intramolecular proton transfer and photoinduced tautomerization.

Despite comprehensive studies addressing the chemical kinetics of butanol isomers, relevant uncertainties associated with the emissions of relevant pollutants persists. Also, a lack of chemistry knowledge of processes designed to produce biofuels limits their implementation at industrial scales. Therefore, the first objective of this thesis was to use cutting-edge kinetic theories to calculate rate constants of propen-2-ol, 1-pronenol, and vinyl alcohol keto-enol tautomerizations, which account for the production of the harmful carbonyl species. The second objective was to use the predictive capabilities of dynamic theories to reveal new chemistry of syngas oxy-combustion in supercritical CO2 and complexities of the zeolite dealumination, two processes involved in coal and biomass conversion. Rate constants computations considered transition state theory with variational effects, tunneling correction, and multistructural torsional anharmonicity. The study also included pressure effects by using and improving the system-specific quantum Rice-Ramsperger-Kassel/modified strong collision model. The atomistic simulations used ReaxFF force fields in hydrogen/oxygen/carbon monoxide/ carbon dioxide mixtures to represent the syngas system and an MFI zeolite with different water loading to model the dealumination. The results show that the studied assisted tautomerizations have much lower energy barriers than the unimolecular process. However, the “catalytic” effect is efficient only if the partner molecule is at high concentrations. Pressure effects are pronounced in the chemically activated tautomerizations, and the improved algorithm to compute pressure-dependent rate constants overcomes the initial difficulties associated with its application to C3 or larger molecules at temperatures above 800-1000 K. Reactive molecular dynamics simulations revealed the role of CO2 as an initiator in the syngas oxy-combustion and a new step involving the formation of formic acid. Those simulations for the zeolite dealumination process also showed that proton transfer, framework flexibility, and aluminum dislodging mediated by silicon reactions are complex dynamic phenomena determining the process. These aspects complement the dealumination theory uncovered so far and establish new paths in the study of water-zeolite interactions. Overall, the rate constants computed in this work reduce relevant uncertainties in the chemical kinetic mechanisms of alcohol oxidation, and the molecular dynamics simulations broaden the chemical knowledge of processes aimed at the utilization of alternative energy resources.

5-aminolevulinic acid (5-ALA) and derivatives thereof are widely usedprodrugs in treatment of pre-malignant skin diseases of the cancer treatmentmethod photodynamic therapy (PDT). The target molecule in 5-ALAPDTis protoporphyrin IX (PpIX), which is synthesized endogenously from5-ALA via the heme pathway in the cell. This thesis is focused on 5-ALA,which is studied in different perspectives and with a variety of computationalmethods. The structural and energetic properties of 5-ALA, itsmethyl-, ethyl- and hexyl esters, four different 5-ALA enols, and hydrated5-ALA have been investigated using Quantum Mechanical (QM) first principlesdensity functional theory (DFT) calculations. 5-ALA is found to bemore stable than its isomers and the hydrolysations of the esters are morespontaneous for longer 5-ALA ester chains than shorter. The keto-enoltautomerization mechanism of 5-ALA has been studied, and a self-catalysismechanism has been proposed to be the most probable. Molecular Dynamics(MD) simulations of a lipid bilayer have been performed to study themembrane permeability of 5-ALA and its esters. The methyl ester of 5-ALAwas found to have the highest permeability constant (PMe-5-ALA = 52.8 cm/s).The mechanism of the two heme pathway enzymes; Porphobilinogen synthase(PBGS) and Uroporphyrinogen III decarboxylase (UROD), have beenstudied by DFT calculations and QM/MM methodology. The rate-limitingstep is found to have a barrier of 19.4 kcal/mol for PBGS and 13.7kcal/mol for the first decarboxylation step in UROD. Generally, the resultsare in good agreement with experimental results available to date.