Chemical modification of cellulose has been of growing interest, owing to the abundance and processing challenges of natural cellulose. To date, etherification and esterification are the most effective strategies to modify physicochemical properties of cellulose and append new functionalities. However, they typically require relatively harsh conditions, thus limiting introduction of new functional groups. An alternative strategy to synthesize novel cellulose derivatives is to append a good leaving group to cellulose backbone, followed by nucleophilic substitution reaction. Though tosylation and bromination of cellulose are frequently used, they have drawbacks such as chemo- and regioselectivity issues, high cost, and difficulty in purification. We have successfully developed a method to chemo- and regioselectively chlorinate cellulose esters using MsCl. Compared to bromination of cellulose typically used, this chlorination method has many advantages, including low cost of reagents and ease of separation. The chlorinated cellulose esters are useful intermediates for appending new functionalities by displacement reactions. We have synthesized a library of cellulose ester derivatives by this chlorination/nucleophilic substitution strategy, including cationic and anionic cellulose ester derivatives. These cellulose ester derivatives possess great potentialiii for various applications, including amorphous solid dispersion, tight junction opening, anionic drug delivery, and gas separation membranes. / MS

No / Phosphonium tosylates have been investigated as solvents for the Diels¿Alder reactions of isoprene with methyl acrylate, but-3-en-2-one and acrylonitrile. The reactions with oxygen-containing dienophiles showed high regioselectivity. Graphic

Epoxide hydrolase I from Solanum tuberosum (StEH1) and isolated variants thereof has been studied for mapping structure-function relationships with the ultimate goal of being able to in silico predict modifications needed for a certain activity or selectivity. To solve this, directed evoultion using CASTing and an ISM approach was applied to improve selectivity towards either of the enantiomeric product diols from (2,3-epoxypropyl)benzene (1). A set of variants showing a range of activites and selectivities was isolated and characterized to show that both enantio- and regioselectivity was changed thus the enrichment in product purity was not solely due to kinetic resolution but also enantioconvergence. Chosen library residues do also influence selectivity and activity for other structurally similar epoxides styrene oxide (2), trans-2-methyl styrene oxide (3) and trans-stilbene oxide (5), despite these not being selected for.    The isolated hits were used to study varying selectivity and activity with different epoxides. The complex kinetic behaviour observed was combined with X-ray crystallization and QM/MM studies, powerful tools in trying to explain structure-function relationships. Crystal structures were solved for all isolated variants adding accuracy to the EVB calculations and the theoretical models did successfully reproduce experimental data for activities and selectivities in most cases for 2 and 5.  Major findings from calculations were that regioselectivity is not always determined in the alkylation step and for smaller and more flexible epoxides additional binding modes are possible, complicating predictions and the reaction scheme further. Involved residues for the catalytic mechanism were confirmed and a highly conserved histidine was found to have major influence on activity thus suggesting an expansion of the catalytic triad to also include H104. Docking of 1 into the active site of the solved crystal structures was performed in an attempt to rationalize regioselectivity from binding. This was indeed successful and an additional binding mode was identified, involving F33 and F189, both residues targeted for engineering. For biocatalytic purpose the enzyme were was successfully immobilized on alumina oxide membranes to function in a two-step biocatalytic reaction with immobilized alcoholdehydrogenase A from Rhodococcus ruber, producing 2-hydroxyacetophenone from racemic 2.

<p>Molecular modelling strategies for evaluation of enzyme selectivity wereinvestigated with a focus on principles of how molecular interactionscould be evaluated to provide information about selectivity. Althoughmolecular modelling provides tools for evaluation of geometrical andenergy features of molecular systems, no general strategies for evaluationof enzyme selectivity exist. Geometrical analyses can be based uponinspection and reasoning about molecular interactions, which provide aneasily accessible way to gain information, but suffer from the risk of biasput in by the modeller. They can also be based on geometrical features ofmolecular interactions such as bond lengths and hydrogen-bond formation.Energy analyses are appealing for their modeller independenceand for the possibility to predict not only stereopreference, but also itsmagnitude.In this thesis, four examples of enantio- or regioselective serinehydrolase-catalysed reaction systems are presented together with developedmodelling protocols for explanation, prediction or enhancement ofselectivity. Geometrical as well as energy-based methodology were used,and provided an understanding of the structural basis of enzymeselectivity. In total, the protocols were successful in making qualitative explanationsand predictions of stereoselectivity, although quantitative determinationswere not achieved.</p>

Recent years have seen tremendous developments in methods for computational modeling of (bio-) molecular systems. Ever larger reactive systems are being studied with high accuracy approaches, and high-level QM/MM calculations are being routinely performed. However, applying high-accuracy methods to large biological systems is computationally expensive and becomes problematic when conformational sampling is needed. To address this challenge, classical force field based approaches such as free energy perturbation (FEP) and empirical valence bond calculations (EVB) have been employed in this work. Specifically: Force-field independent metal parameters have been developed for a range of alkaline earth and transition metal ions, which successfully reproduce experimental solvation free energies, metal-oxygen distances, and coordination numbers. These are valuable for the computational study of biological systems. Experimental studies have shown that the epoxide hydrolase from Solanum tuberosum (StEH1) is not only an enantioselective enzyme, but for smaller substrates, displays enantioconvergent behavior. For StEH1, two detailed studies, involving combined experimental and computational efforts have been performed: We first used trans-stilbene oxide to establish the basic reaction mechanism of this enzyme. Importantly, a highly conserved and earlier ignored histidine was identified to be important for catalysis. Following from this, EVB and experiment have been used to investigate the enantioconvergence of the StEH1-catalyzed hydrolysis of styrene oxide. This combined approach involved wildtype StEH1 and an engineered enzyme variant, and established a molecular understanding of enantioconvergent behavior of StEH1. A novel framework was developed for the Computer-Aided Directed Evolution of Enzymes (CADEE), in order to be able to quickly prepare, simulate, and analyze hundreds of enzyme variants. CADEE’s easy applicability is demonstrated in the form of an educational example. In conclusion, classical approaches are a computationally economical means to achieve extensive conformational sampling. Using the EVB approach has enabled me to obtain a molecular understanding of complex enzymatic systems. I have also increased the reach of the EVB approach, through the implementation of CADEE, which enables efficient and highly parallel in silico testing of hundreds-to-thousands of individual enzyme variants.

Desde sua descoberta, os reagentes organometálicos tem sido amplamente utilizados em estudos metodológicos para preparação de novas substâncias orgânicas e na síntese de moléculas bioativas. De maneira geral, a escolha pelo uso de determinado reagente organometálico envolve o conhecimento de sua natureza química bem como de sua reatividade. Assim, o objetivo deste trabalho foi investigar a reatividade de novos reagentes mistos de magnésio e de lítio na funcionalização de 2-oxazolinas e dioxinonas, que são importantes intermediários na síntese de substâncias bioativas. No caso das 2-oxazolinas, embora as reações de troca iodo-magnésio nos substratos iodados não tenham levado aos resultados esperados, um estudo complementar, envolvendo a base TMPMgCl.LiCl, levou ao desenvolvimento de uma nova metodologia de funcionalização de halofenil-2-oxazolinas. Neste estudo, após a etapa de metalação, os reagentes organometálicos puderam ser reagidos com diferentes eletrófilos, levando aos produtos em bons rendimentos. Além disso, após uma etapa de transmetalação com cloreto de zinco, os intermediários puderam ser arilados através de reações de acoplamento cruzado. De forma similar, na sequência do trabalho, a funcionalização de uma série de piridino-oxazolinas com TMPMgCl.LiCl foi também avaliada, levando aos produtos desejados com um interessante controle da quimio- e da regiosseletividade. Na etapa final do projeto, foi realizado um estudo sobre a funcionalização de dioxinonas, que são importantes precursores da síntese de produtos naturais. Nestes estudos, a dibase mista de lítio-magnésio TMP2Mg.2LiCl levaram aos produtos ortofuncionalizados com grande seletividade. O sucesso desta metodologia nos motivou a realizar também investigações preliminares sobre a síntese de um análogo da caramboxina, um produto natural de grande interesse farmacológico / Since their discovery, organometallic reagents have been widely used in methodological studies aiming the preparation of new organic compounds and in the synthesis of bioactive molecules. In general, the choice by the use of certain organometallic reagent involves the knowledge of their chemical nature as well as their reactivity. Thus, the objective of this study was to investigate the reactivity of new mixed magnesium-lithium reagents in the functionalization of 2-oxazolines and dioxinones, which are important intermediates in the synthesis of bioactive substances. In the case of the 2-oxazolines, though the iodinemagnesium exchange reactions in iodinated substrates have not led to the expected results, an additional study involving the base TMPMgCl.LiCl led to the development of a new methodology for functionalization halophenyl-2- oxazolines. In this study, after the metalation step, the organometallic reagents could be reacted with various electrophiles, leading to the desired products in good yields. Furthermore, after a transmetalation step with zinc chloride, intermediates could be arylated via cross-coupling reactions. Similarly, the functionalization of a series of pyridine-oxazolines with TMPMgCl.LiCl was evaluated and led to the desired products in an interesting control chemo- and regioselectivity. In the final stage of the project, studies on the functionalization of dioxinones, that are important precursors in the synthesis of natural products, were conducted. In these studies, the mixed lithium-magnesium dibase TMP2MgCl.LiCl was used leading to the orhto-functionalized products with high selectivity. The success of this approach led us to perform preliminary investigations on the synthesis of an analogue of caramboxin, a natural product of great pharmacological interest

The kinetic mechanism of an α/β hydrolase fold epoxide hydrolase from potato, StEH1, has been studied with the aims of explaining the underlying causes for enantio- and regioselectivity, both being important for product purity. Further effort has been laid upon understanding the causes of a hysteretic behavior discovered in the measurements leading to Paper I. The enantioselectivity was investigated with substrates differing only in substituent size at one carbon of the oxirane ring structure. In catalysis with trans-stilbene oxide and styrene oxide, enantioselectivity is the result of differences in alkylation rates. In pre-steady state measurement with trans-2-methylstyrene oxide (2-MeSO), a rate-limiting step involving slow transitions, referred to as hysteresis, was discovered. With this substrate enantioselectivity is proposed to be a consequence of the catalytic rate of (1R,2R)-enantiomer being more influenced by the hysteretic behavior than was the rate of the other enantiomer. In steady-state measurements with (1R,2R)-2-MeSO, at different temperatures and pH, hysteretic cooperativity was displayed. It can be concluded that this behavior is dependent on the relationship between kcat and the rate of transition between two Michaelis complexes. From the differences in pH dependence of kcat/KM in formation of the two diols resulting from low regioselectivity in catalysis of (1R,2R)-2-MeSO, it is suggested that hysteresis is a result of the substrates placed in different conformational modes within the active site cavity. Regioselectivity is proposed to be the result of specific interactions between the catalytically important Tyr and the substrate, with a link between KM-values and degree of regioselectivity. Furthermore, the hysteretic kinetic model proposed can explain hysteresis, cooperativity and regioselectivity resulting from StEH1 catalyzed hydrolysis of (1R,2R)-2-MeSO.

Cette thèse décrit dans un premier temps la synthèse entièrement régiosélective de phtalocyanines tétra-(endo-alcoxy)-fonctionnalisées puis la formation de leurs complexes avec des ions métalliques. Dans un second temps sont étudiées leurs propriétés magnétiques, l'induction de mésophases colonnaires dans des gammes de températures convenables et avec des tailles modérées de substituants, ainsi que leur utilisation dans des diodes organiques. L'approche synthétique à suivre est la cyclo-tétramérisation de 3-(2-alkylalcoxy)-phtalonitriles suivie de la coordination d'un ion métallique. La symétrisation des chaînes aliphatiques dans le précurseur 3-alcoxy-phtalonitrile, en allant de 2 butyloctyl à 2-pentylheptyl, maintient la régiosélectivité et le mésomorphisme, tandis que les courtes chaînes 2-butylhexyl mènent à la formation d'un mélange de phtalocyanines régioisomères et à une plus grande tentance à la crystallisation. La combinaison de températures de clarification raisonnables avec un empilement colonnaire à température ambiante et avec une proportion assez importante de centres conjurés au sein de la masse moléculaire rend les deux premières séries de matériaux, c'est-à-dire MPc(OCH2CHBuHex)4, and MPc(OCH2CHPent2)4, potentiellement utiles comme transporteurs de charges uniformément orientables dans des dispositifs électroniques organiques. Nous démontrons que ces matériaux phtalocyanines tétra-α-alcoxy-substitués, représentés par H2Pc(OCH2CHBuHex)4, NiPc(OCH2CHBuHex)4 et CuPc(OCH2CHBuHex)4, mènent à des performances originales des dispositifs quand ils sont utilisés comme couche active organique dans des structures simples de diode ITO/PEDOT :PSS/PC/Al. Un redressement prononcé du courant est obtenu dans des diodes malgré l’alignement planaire prépondérant des colonnes dans les couches. Le ligand Pc tétra-α-alcoxy-substitué très soluble donne des molécules-aimants mononucléaires originales par coordination avec MnIII et DyIII. Remarquablement, l’isomère de symétrie C4h du complexe sandwich octa-alcoxy se forme sélectivement grâce aux subsistants encombrants sur les deux cycles Pc. / This thesis describes the fully regioselective synthesis of symmetric all-endo tetra-alkoxy-functionalized phthalocyanines and their metal ion complexes accompanied by induction of columnar mesophases in convenient temperature ranges at moderate substituent sizes, as well as their use in organic diodes and the study of their magnetic properties. The synthetic approach to follow is lithium-induced macrocyclization of 3-(2-alkylalkoxy)-phthalonitriles prior to transition meatl ion insertion. Symmetrization of the aliphatic chains in the 3-alkoxy-phthalonitrile precursor from 2-butylocytyl to 2-pentylheptyl maintains both the regioisomeric mixture during the cyclo-tetramerization and to a somewhat greater tendency to crystallization. The combination of attainable clearing temperatures with room temperature columnar stacking and with a relatively high content of conjugated core within the molecular mass makes the first two series of materials, i.e. MPc(OCH2CHBuHex)4, and MPc(OCH2CHPent2)4, potentially useful as uniformly orientable charge transposters in organic electronic devices. We establish that these tetra-α-alkoxy substituted phthalocyanine materials, as exemplified with H2Pc(OCH2CHBuHex)4, NiPc(OCH2CHBuHex)4 and CuPc(OCH2CHBuHex)4, lead to original device performances when applied as an active organic layer in simple ITO/PEDOT:PSS/PC/Al diode structures. A pronounced current rectification of the diodes is obtained despite the preponderantly planar alignment of the columns in the films. The highly soluble tetra-α-alkoxy-substituted Pc ligand, when combined with MnIII and DyIII, gives rise to original mononuclear single molecule magnets. Remarkably, the C4h-symmetric isomer of the octa-alkoxy double decker complex is formed selectively due of presence of the bulky substituents on both Pc rings.

Les flavonoïdes sont des composés poly-hydroxylés d’origine végétale, connus pour leurs vertus pour la santé. Afin d’obtenir des dérivés plus stables et solubles dans des formulations hydrophobes tout en conservant les activités biologiques des molécules d’origine, une solution consiste à acyler ces composés de manière régiosélective. Ceci peut être accompli en utilisant des lipases comme catalyseurs, en milieu organique. Grand nombre d’études expérimentales sur ces bioprocédés sont disponibles, mais aucune d’entre elles n’apporte d’explication, au niveau moléculaire, de la sélectivité de ces réactions d’acylation. Le but de cette étude est d’appliquer différents outils de simulation moléculaire pour mieux comprendre, au niveau moléculaire, les propriétés de sélectivité de l’acétylation de trois flavonoïdes (quercétine et ses dérivés glycosylés isoquercitrine et rutine), en utilisant les lipases CALB et PCL. D’abord, des simulations de docking ont été appliquées, afin d’obtenir les positions et les orientations les plus probables des flavonoïdes dans la cavité des lipases préalablement acétylées. Ensuite, des simulations de dynamique moléculaire ont été exécutées sur les complexes obtenus par docking, afin d’étudier stabilité structurale des complexes sur une période de temps et notamment la stabilité des interactions enzyme-substrats. Enfin, des simulations basées sur une approche de chimie quantique (DFT) ont été appliquées pour évaluer la réactivité chimique des flavonoïdes dockées dans les complexes. Les premières tendances observées aux cours des simulations ont présenté une bonne corrélation avec les résultats expérimentaux d’acétylation. Globalement, les résultats obtenus ont montré que la sélectivité de ces réactions dépend de l’orientation des substrats (flavonoïde et acétate) dans la cavité catalytique de la lipase, des interactions intermoléculaires stabilisant ces substrats et de la réactivité chimique intrinsèque des groupements OH des flavonoïdes se situant à proximité des résidus catalytiques / Flavonoids are plant-produced polyhydroxylated compounds, well-known for their beneficial health effects. In order to obtain more stable and soluble derivatives for incorporation in hydrophobic formulations without damaging the biological activities of the native molecules, a solution consists to perform a regioselective acylation of these molecules. This can be accomplished by using lipase biocatalysts, in organic media. Several experimental studies dealing with such processes are available, but none of them give any explanation, at the molecular level, for the regioselectivity of such reactions. This study aimed to apply different molecular modelling tools in order to better understand, at the molecular level, the selectivity properties of the acetylation of three flavonoids (quercetin and its glycosylated derivatives isoquercitrin and rutin), by using the lipases CALB and PCL. Firstly, docking simulations were applied, in order to obtain the most probable positions and orientations of the flavonoids in the cavities of acetylated lipases. Then, molecular dynamics simulations were performed, aiming to study the structural stability of the complexes upon a period of time and specially the stability of the enzyme-substrates interactions. Finally, quantum chemical simulations (DFT) were applied to evaluate the chemical reactivity of the flavonoids as docked in the complexes. The trends observed during the simulations were well correlated with previous experimental results on the acetylation reaction of these flavonoids. Overall, the results showed that the selectivity in such reactions depends upon the substrates (flavonoid and acetate) orientations in the enzyme catalytic cavity, the intermolecular interactions that stabilize these substrates and the intrinsic chemical reactivity of the flavonoids OH groups reaching the catalytic residues

Une étude synthétique de la koumine par une stratégie basée sur une étape de désymétrisation a permis de développer, par un résultat inattendu, une fragmentation de 1,3-cyclohexanediones en lactones. Suite à ce résultat, une étude méthodologique a été réalisée en partant de différentes dicétones substituées pour synthétiser des lactones indoliques, ainsi que déterminer la régiosélectivité et la diastéréosélectivité. Finalement, la synthèse totale de la goniomitine a été éffectuée en utilisant cette méthode de fragmentation. / A synthetic study of koumine by a strategy based on a desymmetrization step led, through an unexpected result, to the development of a fragmentation of 1,3-cyclohexanediones into lactones. Following this result, a methodological study was carried out starting from different substituted diketones to synthesize indolic lactones, as well as to determine regioselectivity and diastereoselectivity. Finally, the total synthesis of goniomitine was performed using this fragmentation method.