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Single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) constitute important sources of genetic variation which provide insight into disease aetiology and idiosyncratic differences in drug response. The analysis of such genetic variation relies upon the generation of allele-specific products, typically by enzymatic extension or the hybridization of allele-specific DNA probes. Herein, a distinct enzyme-free, dynamic chemistry-based method of producing allele-specific products for genotyping was developed. The approach was initially demonstrated in model systems using synthetic DNA, which was used as a template in a base-filling reductive amination reaction on a PNA backbone. The templated dynamic reaction between a free secondary amine at a ‘blank’ position on the PNA strand and four aldehyde-modified nucleobases drove selective formation of the ‘correct’ iminium intermediate according to Watson-Crick base-pairing rules. In a blind trial, the method was extended to genotype twelve cystic fibrosis patients for two mutations (one SNP and one indel) linked to this disease. Enzyme-free dynamic chemistry thus permitted successful genotyping in both singleplex and duplex formats, demonstrating the application of dynamic chemistry as a distinct method of allelediscrimination with certain advantages over those reported previously. The application of this method as a tool for the discovery of non-natural nucleobases with improved properties for antisense and genotyping applications was also investigated. Furthermore, progress was made towards the use of dynamic chemistry as a means of full nucleic acid sequence analysis, through the templated sequence-selective extension of PNA probes by reductive amination.

This  thesis  is  divided  into  four  parts,  all  centered  around  Constitutional Dynamic  Chemistry  (CDC)  and  Dynamic  Kinetic  Resolution  (DKR)  using biocatalysts for selective transformations, and their applications in screening of bioactive compounds, organic synthesis, and enzyme classification.    In  part  one,  an  introduction  to  CDC  and  DKR  is  presented,  illustrating  the basic  concepts,  practical  considerations  and  potential  applications  of  such dynamic systems, thus providing the background information for the studies in the following chapters.   In part two, Dynamic Systemic Resolution (DSR), a concept based on CDC is exemplified.  With  enzyme-catalyzed  transformations  as  external  selection pressure,  optimal  structures  can  be  selected  and  amplified  from  the  system. This  concept  is  expanded  to  various  types  of  dynamic  systems  containing single, double cascade/parallel, and multiple reversible reactions. In addition, the  substrate  selectivity  and  catalytic  promiscuity  of  target  enzymes  are  also investigated.   In   part   three,   DKR   protocols   using   reversible   reactions   for   substrate racemizations  are  illustrated.  Biocatalysts  are  here  employed  for  asymmetric transformations,  resulting  in  efficient  synthetic  pathways  for  enantioenriched organic compounds.   Part  four  demonstrates  two  unique  applications  of  CDC:  one  resulting  in enzyme  classification  by  use  of  pattern  recognition  methodology;  the  other involving  enzyme  self-inhibition  through  in  situ  transformation  of  stealth inhibitors employing the catalytic activity of the target enzyme. / <p>QC 20130614</p>

Le domaine de la chimie supramoléculaire met en oeuvre des systèmes chimiques complexes formés de composants moléculaires assemblés par des forces intermoléculaires non covalentes dans le but de créer des procédés fonctionnels. La chimie dynamique, fondée sur la constitution de composants réversibles ouvre la voie à la chimie adaptative, où la diversité constitutionnelle d’un système s’organise par sélection sous l’action d’agents externes. Dans l’élaboration de systèmes complexes, l’interconnectivité structurelle entre les différentes molécules peut être représentée de manière schématique par un réseau dynamique constitutionnel. L’utilisation de réseaux de pyridyl-hydrazones et des pyridyl-acylhydrazones met en évidence leurs adaptations orthogonales à des stimuli externes par métallosélection et par photosélection grâce aux dynamiques constitutionnelles, conformationnelles et configurationnelles de ces molécules. Ainsi, une réponse constitutionnelle du système est apportée à un changement d’informations conformationnelles et configurationnelles. Ces systèmes dynamiques permettent aussi la formation de matériaux adaptatifs, et la réalisation de séparations de phases et de modulations de pH photoinduites. / The field of supramolecular chemistry implements complex chemical systems formed from molecular components assembled by non covalent intermolecular forces to generate functional processes. Thedynamic chemistry, based on the ability of supramolecular species to exchange their constituents, gives access to an adaptative chemistry, where the constitutional diversity of a system self-organizesby selection in response to external factors. In the progress towards systems presenting higher levels of complexity, the set of dynamically interconverting constituents of a constitutional dynamic libraryforms a constitutional dynamic network, which can be represented in a schematic way by a weighted graph. The use of pyridyl-hydrazones and pyridyl-acylhydrazones networks allows for orthogonaladaptation to external stimuli by metalloselection and photoselection due to the dynamic properties of constitution, conformation and configuration of these molecules. A constitutional response is expressed by conformational and configurational information changes. These dynamic systems afford also the formation of adaptative materials, and the realization of photoinduced phase separation and pH modulation.

This thesis is divided into three parts, revolving around the developments of dynamic systems utilized in dynamic kinetic resolution (DKR) and constitutional dynamic chemistry (CDC). The first section gives an introduction to constitutional dynamics, the core concept of this thesis. Constitutional dynamics can be tuned through reversible interactions. Then, the basic principles of constitutional dynamics in DKR and CDC are discussed, along with their applications. The second section explores the asymmetric synthesis of oxazolidinone derivatives using lipase catalysis through kinetic resolution (KR) and dynamic kinetic resolution. In the first example, synthetic protocol to enantioenriched 5-phenyloxazolidin-2-ones is described, where a kinetically controlled carbamation is followed by lipase-catalyzed cyclization. In contrast to the 5-substituted species, the synthesis of 3-phenyloxazolidin-2-one derivatives could be achieved through lipase-catalyzed cascade O- and N- alkoxycarbonylations in one pot. Furthermore, this KR system could be coupled to a ruthenium-catalyzed racemization process of 1,2-aminoalcohols, thus providing an efficient DKR methodology for asymmetric transformations. The third section focuses on dynamic systems built through reversible covalent reactions. In the first example, a selective gelation process is described, and employed to resolve dynamic imine systems consisting of gelator candidates.  In the second example, reversible reactions with aldehyde enamines are presented, including enamine formation and exchange reactions. In particular, Bi(III) and Sc(III) were discovered to accelerate the enamine exchange reactions by 50-400 times, in which the equilibria could be reached within hours. The last example describes reversible nitroaldol reactions in aqueous media, where rapid and efficient equilibration was identified for selected structures in neutral phosphate buffer. / <p>QC 20150911</p>

The research work reported in the thesis deals with the development of dynamic covalent systems and their applications in evaluation and screening of protein-ligands and enzyme inhibitors, as well as in synthetic methodologies. The thesis is divided into four parts as described below. In part one, synthetic methodologies to access 3-functionalized phthalides and 3-thioisoindolinones using the concept of cascade reactions are demonstrated. Efficient syntheses of the target products are designed and performed in one-pot process under mild reaction conditions.  In part two, phosphine-catalyzed disulfide metathesis for the generation of dynamic carbohydrate system in aqueous solution is demonstrated. In the presence of biological target (Concanavalin A), the optimal dynamic ligand is successfully identified in situ by the 1H STD-NMR spectroscopy. In part three, lipase-catalyzed resolutions of dynamic reversible systems using reversible cyanohydrin and hemithioacetal reactions in one-pot processes are demonstrated. The dynamic systems are generated under thermodynamic control in organic solution and subsequently resolved by lipase-mediated resolution under kinetic control. The resolution processes resulted in the lipase-selected substrates with high structural and stereochemical specificities. In the last part, dynamic fragment-based strategy is presented using β-galactosidase as a model target enzyme. Based on our previous study, the best dynamic inhibitor of β-galactosidase was identified using 1H STD-NMR technique from dynamic hemithioacetal systems. The structure of the dynamic inhibitor is tailored by fragment linking and optimization processes. The designed inhibitor structures are then synthesized and tested for inhibition activities against β-galactosidase. / QC 20110526

This work deals with the design and synthesis of building blocks, usable for creating dynamic polymers based on the reversible formation of hemiacetals bond. Next part is focused on the study of the formation of hemiacetal between polyfunctional alcohols and trifluoromethylketones via NMR spectroscopy. Key words: constitutional dynamic chemistry, hemiacetals, trifluoromethylketones, diols and polyols

In the adaptation to the oxidative environment on earth, metals played a crucial role for the evolution of life. The presence of metals also allowed access to advanced functions due to their unique coordination sphere and reactivity. This thesis focused on exploiting these unique properties for further development of the field of dynamic chemistry – a field in which adaptation plays a central role as well. The first part of the thesis aimed to create a better understanding of multivalent effects in carbohydrate-lectin interactions. By reversible ligand coordination to zinc ions one of the nanoplatforms, the Borromean rings, could be selectively obtained. After carbohydrate functionalization the binding events were monitored by quartz crystal microbalance technology and compared to glycosylated fullerenes and dodecaamide cages. Overall, this investigation indicated that statistical and polyelectrolyte effects play a considerable role in the observed multivalent effects. The second part of the thesis aimed to design and synthesize a new catalyst for application in aqueous olefin metathesis. This afforded a ruthenium based catalyst that was applied in the self- and cross-metathesis of highly functionalized substrates, such as carbohydrates. In addition, it was shown that addition of a small amount of acetic acid prevented undesired double bond isomerization. The last part of the thesis aimed to explore new methods to discover transition metal catalysts. Dynamic exchange of directing groups generated a pool of potential substrates for C-H activation. Combining this pool of substrates with a pool of potential catalysts resulted in amplification of a reactive substrate/metal combination. By iterative deconvolution in combination with mass spectrometry, this “intermediate” could be identified from the mixture, proving applicability of this alternative approach to catalyst discovery. / <p>QC 20170809</p>

Vinylene-linked two-dimensional conjugated covalent organic frameworks (V-2D-COFs), belonging to the class of two-dimensional conjugated polymers, have attracted increasing attention due to their extended π-conjugation over the 2D backbones associated with high chemical stability. The Knoevenagel polycondensation has been demonstrated as a robust synthetic method to provide cyano (CN)-substituted V-2D-COFs with unique optoelectronic, magnetic, and redox properties. Despite the successful synthesis, it remains elusive for the relevant polymerization mechanism, which leads to relatively low crystallinity and poor reproducibility. In this work, we demonstrate the novel synthesis of CN-substituted V-2D-COFs via the combination of Knoevenagel polycondensation and water-assisted dynamic Michael-addition-elimination, abbreviated as KMAE polymerization. The existence of C=C bond exchange between two diphenylacrylonitriles (M1 and M6) is firstly confirmed via in situ high-temperature NMR spectroscopy study of model reactions. Notably, the intermediate M4 synthesized via Michael-addition can proceed the Michael-elimination quantitatively, leading to an efficient C=C bond exchange, unambiguously confirming the dynamic nature of Michael-addition-elimination. Furthermore, the addition of water can significantly promote the reaction rate of Michael-addition-elimination for highly efficient C=C bond exchange within 5 mins. As a result, the KMAE polymerization provides a highly efficient strategy for the synthesis of CN-substituted V-2D-COFs with high crystallinity, as demonstrated by four examples of V-2D-COF-TFPB-PDAN, V-2D-COF-TFPT-PDAN, V-2D-COF-TFPB-BDAN, and V-2D-COF-HATN-BDAN, based on the simulated and experimental powder X-ray diffraction (PXRD) patterns as well as N2-adsorption–desorption measurements. Moreover, high-resolution transmission electron microscopy (HR-TEM) analysis shows crystalline domain sizes ranging from 20 to 100 nm for the newly synthesized V-2D-COFs.

Chimie dynamique: reconnaissance de nucléobases par des récepteurs synthétiques et isomérie cis-trans d'hydrazones acylées.Ce travail traite du développement des systèmes moléculaires qui peuvent s'adapter à l'addition de substances qui agissent comme un gabarit. Cette approche permet d'isoler une espèce majeure à partir d'un mélange de composés par le biais de la chimie combinatoire dynamique (CCD). La première partie de ma thèse de doctorat inclus l'utilisation d'un ADN simple brin (ADNsb) comme un gabarit pour le transfert d'information par auto-assemblage de récepteurs sans avoir besoin d'enzyme. De nouveaux récepteurs de l'adénine et de la guanine (pinces A et G) solubles dans l'eau ont été conçues dans ce but. Une approche utilisant la résonance magnétique nucléaire (RMN) a été utilisée pour déterminer l'affinité de liaison comme preuve d'une reconnaissance spécifique et efficace. Une évaluation dans l'eau par dichroïsme circulaire (CD) et mesure de la température de fusion par UV (Tm) a été réalisée. Cela a permis de tester respectivement la capacité d'auto-assemblage entre les pinces et un modèle ADNsb, et la force du processus de coopérativité. La deuxième partie de ce travail est axée sur le tri spontanné de motifs pyridine acylhydrazone et sur les configurations intéressantes qu'ils adoptent. Nous avons étudié la synthèse d'une série de motifs pyridine acylhydrazone: dimère, trimères et pentamères. Des études RMN ont permis d'évaluer les changements dans l'équilibre configurationnel cis / trans de ces systèmes dynamiques. Les études ont montré que l'équilibre attendu est biaise la cis acylhydrazone pyridine isomère a été observée par diffraction des rayons X. / Dynamic chemistry: nucleobase recognition by synthetic receptors and cis-trans acylhydrazone isomerism. This work deals with the development of molecular systems which can adapt upon the addition of substances that act as templates. This approach enables one major species to be identified from a mixture of compounds through the use of dynamic combinatorial chemistry (DCC). The first part of my PhD included the use of a single stranded DNA (ssDNA) as a template for information transfer via the self-assembly of receptors without the need for enzymes. New water soluble adenine and guanine receptors (A and G clamps) were designed and synthesised for this purpose. Nuclear magnetic resonance (NMR) titration studies were carried out to calculate the binding affinity and as a proof of specific and efficient recognition. An assessment in water via circular dichroism (CD) and UV temperature melting (Tm) studies was carried out. This tested the ability for self-assembly between the clamps and a ssDNA template and the strength of the cooperative process respectively. The second part of my PhD focused on the self-sorting of acylhydrazone pyridine motifs and the interesting configurations they adopt. The feasibility to synthesise these acylhydrazone pyridine motifs (dimer, trimers and pentamers) was investigated. X-ray and NMR studies showed that the equilibrium was found to be biased in an unusual way, and the cis acylhydrazone pyridine isomer was observed.