The challenges in modern biological imaging applications are two-fold: (i) to develop better methods of imaging, and (ii) develop dyes that are suitable for these methods. This dissertation deals with the design and synthesis of dyes mainly by modification of known dyes to make them suitable for modern biological applications. Towards this aim, novel ways of derivatizing BODIPY dyes are explored. One method involves extending the conjugation via phenyl acetylene units, pushing fluorescence wavelengths near 600 nm. A different approach deals with C-H functionalization of BODIPY in which the fluors are functionalized with acrylate units, extending their fluorescence to the red. The BODIPY dyes developed are then incorporated in through-bond energy transfer cassettes. We examine the factors affecting energy transfer efficiencies by synthesizing analogs of the cassettes and also studying the electrochemical behavior of the donor and acceptor parts. The concept of through-bond energy transfer is incorporated into conjugated polymers by random incorporation of BODIPY dyes into polyfluorenes. The ideal ratio of fluorene to BODIPY parts was found to be 4:1. The BODIPY doping agents result in dispersed emissions when excited the polyfluorene polymers. Concurrently, the polyfluorene backbone acts as an energy harvester for the BODIPY dyes, in effect increasing their molar absorptivities. Finally the use of BODIPY dyes as photodynamic therapeutic agents was examined. We found that BODIPY dyes are efficient at producing reactive oxygen species when halogens are attached directly on the BODIPY core. Furthermore, the mechanism of cell death by using such agents was elucidated. Attachment of the most promising agent to polyglutamic acid is done to promote the EPR effect. Lastly we develop a potentially new type of PDT agent that absorbs strongly above 800 nm, permitting its use in deep tissue PDT.

The derivatives of boradiazaindacene (BODIPY) are highly fluorescent dyes which have quantum yields near 1.0. These dyes that have exceptional spectral and photophysical stability as compared to other fluorescent groups are used for several different applications. The fluorescent sensor molecules for the detection of cations with PET (photoinduced-electron transfer) mechanism in general have been obtained by the differentiation of the BODIPY core. The extension of conjugation over the pyrrole ring shifts the absorption and emission at longer wavelength. Moreover, it is seen that red emission occurs from an ICT (intramolecular-charge transfer) state. iii In this study, we designed and synthesized an unsymetrically substituted BODIPY dye series, carrying a cation-sensitive phenylazacrown ether group conjugated to the core, and investigated the ion sensing properties of these compounds. Both aza-crown derivatives displayed selectivity towards Ca(II).

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Over the past several decades the phenomenon of luminescence (divided into fluorescence and phosphorescence) has received great attention in the field of biological science. This quest has motivated scientists for a variety of applications, including fluorescence imaging. Fluorescence microscopy techniques that provide unique advantages, such as high spatial resolution and superior sensitivity, have been regarded as attractive tools in biophotonics. With the progress of ultrafast laser sources, two-photon absorption (2PA), in which a molecule absorbs two photons simultaneously, has opened possibilities of using it for various applications. Two-photon fluorescence microscopy (2PFM), which affords deeper tissue penetration and excellent three-dimensional (3D) images, is now being widely employed for bioimaging. This dissertation focuses on the design, synthesis, and photophysical characterization of new fluorophores, as well as desirable applications. Chapter 1 gives an account of a brief introduction of luminescence and 2PA, as well as their utilities in biological applications. In chapter 2, a series of new BODIPY derivatives are presented along with their comprehensive linear and nonlinear characteristics. They exhibited excellent photophysical properties including large extinction coefficients, high fluorescence quantum yields, good photostability, and reasonable two-photon absorption cross sections. Two promising compounds were further evaluated as NIR fluorescent probes in one-photon and two-photon fluorescence imaging. Chapter 3 provides the design, synthesis, and photophysical characterization of two BODIPY dyes. In order to assess the potential of using the dye as a fluorescent probe, Lysotracker Red, a commercial lysosomal marker, was investigated for comparison purposes. The results indicate that figure of merit of both compounds were three orders of magnitude higher than that of Lysotracker Red. With an eye towards applications, one of the compounds was encapsulated in silica-based nanoparticles for in vitro and ex vivo one-photon and two-photon fluorescence imaging, in which the surface of the nanoparticle was modified with RGD peptides for specific targeting. The nanoprobe exhibited good biocompatibility and highly selective RGD-mediated uptake in ?V?3 integrin-overexpressing cancers, while maintaining efficient fluorescence quantum yield and high photostability. In chapter 4, the synthesis and photophysical properties of a novel photosensitizer with heavy atoms (halogen) were presented. The dye exhibited low fluorescence quantum yield, resulting in high singlet oxygen generation quantum yield. In vitro photodynamic studies demonstrated that photosensitization of the agent can induce cellular damage, subsequently leading to cell death by a necrotic cell death mechanism, supporting the therapeutic potential of using the agent for photodynamic therapy.

A enzima cruzaína, expressada durante todo o ciclo de vida do parasita Trypanosoma cruzi (T. cruzi), é a principal cisteíno protease desse parasita e,vem se apresentando como elemento promissor para o tratamento da doença de Chagas. Neste trabalho, sintetizamos uma série de dipeptidilnitrilas que apresentam atividade sobre a enzima cruzaína em concentrações baixo-micromolar. Esses compostos apresentam também atividade diante do parasita T. cruzi, sendo prototípico o composto 9, um dos mais potentes, capaz de inibir a enzima com IC50 de 1.89 ± 0.11 µM (pIC50 = 5.7) e, uma vez em face do parasita, IC50 de 2.7 ± 0.3 µM (pIC50 = 5.6). O composto 9 é mais potente que o fármaco benzonidazol (BZ), que foi usado como controle nos ensaios bioquímicos das nossas moléculas; o BZ apresentou pIC50 = 4.6. Os compostos 9 e 7 apresentam estrutura similar, mas exibiram diferenças significantes nos ensaios diante do T. cruzi. Eles foram rotulados mediante a incorporação de fluoróforos da família dos borodipirrometenos (Bodipy) e, finalmente, monitorados mediante microscopia confocal para identificar processos biológicos específicos ou alguma resposta celular in vitro nas moléculas. / The Cruzaíne enzyme, a cysteine protease expressed throughout the life cycle of the parasite Trypanosoma cruzi (T. cruzi), is the main cysteine protease of this parasite and has been presented as a promising target for the treatment of Chagas\' disease. In this work, we have synthesized a series of dipeptidylnitriles that have activity against the enzyme cruzaína in low-micromolar concentrations. These compounds also present activity against the parasite T. cruzi, the prototypical compound being one of our most potent compounds, which inhibits the enzyme with IC50 of 1.89 89 ± ± 0.11 µM (pIC50 pIC50 = = 5.7), and against the parasite IC50 of 2.7 7 ± ± 0.3 3 µM (pIC50 pIC50 = = 5.6), compound 9 is more potent than the drug Benzonidazole (BZ) which was used as a control in the biochemical assays of these molecules, this (BZ) had pIC50 pIC50 = = 4.6. Compounds 09 and 07 have a similar structure but showed a significant difference in the assays against the T. cruzi parasite, these two compounds were labelled by the incorporation of borodipyrromethene family fluorophores (Bodipy) and finally, they were monitored by microscopy confocal, to identify specific biological processes or some cellular response in vitro to these molecules.

Cette thèse s’inscrit dans le développement et l’évaluation de nouvelles plateformesmoléculaires pour une application en imagerie optique par fluorescence. Nous avons cherché àdévelopper de nouveaux outils multifonctionnels et modifiables à façon. Cette approche estnécessaire car l’introduction d’un fluorophore peut fortement influencer les propriétés ducomposé final. Cela signifie que l’introduction du fluorophore sur l’agent sélectionné doit avoirêtre réalisé dès le départ. Pour cela deux axes principaux ont été étudiés; le premier consiste àutiliser des BODIPY pour le développement d’agents thérapeutiques traçables pour uneapplication principalement in vitro; le deuxième cible sur la conception de plateformes à based’AzaBODIPY compatibles avec l’imagerie in vivo.Dans la première partie deux fluorophores à base de 3,5-dichloro-BODIPY ont été identifiéscomme plateformes prometteurs. Ils ont été fonctionnalisés sélectivement par un agent or(I)-phosphine, un thiosucre et un phosphonium afin de pouvoir étudier l’influence du positionnementde chaque substituant sur les propriétés finales. Nous avons pu démontrer qu’unefonctionnalisation sélective et spécifique est possible avec ces substituants fragiles ; cela nous apermis de développer 12 agents théranostiques à base d’or(I). Les propriétés photophysiques etbiologiques ont ensuite été évaluées; pour cela nous avons déterminé leurs propriétés antiprolifératives (3 lignés cellulaires), la balance hydrophile, l’accumulation d’or dans les cellules etla localisation des composés des composés par microscopie confocale. Cette stratégie deplateforme multifonctionnelle nous a permis de développer un panel de composés traçables ayantdes activités mixtes ainsi que des distributions cellulaires distinctes. Cette étude a permisl’identification et la sélection de trois ou quatre composés qui feront l’objet d’une étudeapprofondie.Dans la deuxième partie de cette thèse nous avons développé des plateformes multifonctionnellescompatibles avec l’imagerie in vivo; pour cela nous avons poursuivi deux approches différentes.La première était l’utilisation de 1,7-di(phenol)3,5-di(phenyl)-azaBODIPY, suivi par safonctionnalisation sur les groupements OH afin de développer un traceur bioconjugablefluorescent dans le proche infrarouge (NIR-I). Malheureusement ce traceur possède despropriétés optiques très défavorables. Nous avons alors développé une approche innovante baséesur la fonctionnalisation de l’atome de bore. En s’appuyant sur cette approche deux traceursfortement fluorescents dans le proche infrarouge et solubles dans l’eau ont été développés. Cesfluorophores ont été conjugués sur un anticorps innovateur afin de permettre l’imagerie optiquedu ligand PD-L1. Les traceurs se sont montrés stables pour au moins 48h dans le plasma murin etpossèdent de très bonnes propriétés optiques. Comme preuve de concept nous avons conduitune étude préclinique in vivo. Cette étude a montré que les traceurs sont fortement fluorescents(NIR-I) et ne possèdent pas de toxicité imminente.La méthodologie développée pendant cette thèse présente un grand potentiel pour des étudesallant plus loin et des futures applications ; il est possible d’appliquer les principes et outilsdéveloppés sur d’autre fluorophores ; la méthodologie permet une fonctionnalisation très richeavec une grande variété de substituants d’intérêt. Son utilisation n’est pas limitée aux applicationsbiologiques, biochimiques et médicinales. / The objective of this thesis was the development and evaluation of new molecular platformsfor optical fluorescence imaging applications. This work sought to develop new tools that caneasily be modified and adapted to the specific needs of the intended use. This is required asthe fluorophore will influence the final properties and should thus be incorporated beforestructural optimization of the selected agent rather than at the very end. Two main axes wereexplored; the use of BODIPYs for the development of trackable therapeutic agents that areprimarily intended for in vitro applications and the use of azaBODIPYs for the design of an invivo compatible fluorescent platform.In the first part two fluorophores on the basis of a 3,5-dichloro-BODIPY were identified aspromising platforms. These platform molecules were selectively functionalized using a gold(I)-phosphine moiety, a thiosugar and a phosphonium to explore their selective functionalizationand investigate the influence of each substitutents position on the final properties. Weshowed that a site-specific, selective functionalization with these fragile substituents ispossible and developed 12 gold(I)-bearing therapeutic agents. We evaluated thephotophysical properties of all obtained compounds which was followed by a characterizationof their biological properties (antiproliferative properties on 3 cancer cell lines, lipophilicbalance and cellular gold accumulation as well as fluorescence imaging on 3 cell lines for upto 24h). We succeeded in developing a panel of closely related trackable compounds thatdisplay mixed activity in cells and distinct cellular localization. This investigation permitted theselection of three to four hits that will be studied further.In the second part we developed an in vivo-compatible multifunctional platform following twostrategies: the first was the use of 1,7-di(phenol)-3,5-di(phenyl)-azaBODIPY and thefunctionalization of the hydroxy groups for the development of a bioconjugable NIR-I probe.Unfortunately the developed probe displayed very unfavourable optical properties; wetherefore developed a new strategy that is entirely based on the functionalization of the boronatom. Using this approach we successfully synthesized 2 watersoluble, strongly fluorescent(NIR-I) molecular platforms that were conjugated to an innovative antibody to image the PD-L1 ligand. The developed probes displayed excellent optical properties, are stable for at least48h in mice plasma and were validated in a preclinical study on mice. The developed probesdisplayed strong fluorescence in vivo and showed no acute toxicity.The developed methodology shows great potential for further investigations and futurestudies; it can be transposed onto other closely related fluorophores and permits versatilefunctionalization with a large variety of compounds of interest. Its use is thus not limited tobiological, biochemical and medical applications.

Analogues structuraux des porphyrines et des Salens, des ligands de type dipyrrométhène bis-phénol ont été étudiés dans notre groupe, notamment sous forme de complexes pour la catalyse d'oxydation. L'activité catalytique de ces complexes étant faible, il a été proposé de remplacer les phénols par des triazoles. L'objet de cette thèse était d'étudier et de valoriser une nouvelle famille de ligands dipyrrométhène bis-triazole.Plusieurs voies de synthèse ont d'abord été étudiées et optimisées pour accéder à ces nouveaux ligands. Nous nous sommes attachés ensuite à valoriser ces nouveaux ligands selon plusieurs axes.Un de ces ligands a été testé en reconnaissance d'anions, ainsi que les dérivés monotriazolium et bis-triazolium. Les triazoliums ont également permis l'accès à des métallocomplexes carbéniques, qui ont été étudiés.Par ailleurs, les métallocomplexes des dipyrrométhène bis-triazole ont été préparés et caractérisés, y compris par électrochimie. Des essais d'utilisation en oxydation ont été entrepris. Enfin, la synthèse de BODIPYs® liposolubles et hydrosolubles a été réalisée. Les propriétés optiques ont été mesurées puis ces dérivés fluorescents ont été testés pour le marquage fluorescent de cellules HeLa / Known as structural analogues of porphyrins and Salens, dipyrromethene bis-phenol-type ligands have been studied in our group, especially as complexes for oxidation catalysis. Due to the poor catalytic activity of these complexes, it has been proposed to replace the phenol moieties with triazoles. The purpose of this thesis was to study and develop a new family of dipyrromethene bis-triazole ligands.Several synthetic routes were first investigated and optimized to reach these new ligands. We then have endeavoured to add value to these new ligands along several lines.The ligand has been tested in anion recognition, as well as monotriazolium and bis-triazolium derivatives. The triazoliums also allowed access to carbene metallocomplexes that were studied.Furthermore, dipyrromethene bis-triazole metallocomplexes were prepared and characterized, notably by electrochemistry. Oxidation catalysis tests were undertaken.Finally, the synthesis of liposoluble and hydrosoluble BODIPYs® was performed. Their optical properties were measured and these fluorescent derivatives were tested for the fluorescent labeling of HeLa cells

La mélatonine est une neurohormone synthétisée au niveau de la glande pinéale durant la période nocturne chez l'ensemble des mammifères. Les sécrétions de cette hormone circulante par voie sanguine permette à tout système doté de récepteurs mélatoninergiques (MT1, MT2) de transmettre l'information de photopériode entrainant ainsi une adaptation aux périodes jour/nuit. La mélatonine est impliquée dans de nombreuses fonctions biologiques mais aussi dans diverses pathologies du système nerveux central tel que les troubles du rythmes circadien, l'anxiété, la dépression… A l'heure actuelle, il existe de nombreux ligands affins des ces récepteurs, cependant le manque de marqueurs sélectifs ralentit les recherches associées (pharmacologie). Partant de ce constat, nous avons conçu et synthétisé, selon deux approches différentes, des ligands fluorescents utilisant comme squelette de base, la structure de la mélatonine et certains analogues. Dans une première approche dite conventionnelle, les ligands mélatoninergiques sont associés à un fluorophore organique au moyen d'un bras espaceur et dans une seconde approche plus novatrice, le noyau indolique du ligand endogène est fusionné avec un pyrrole par analogie avec les fluorophores de types BODIPYs ®, puis dans une troisième partie, dérivée de la précédente, la mélatonine est fonctionnaliser par un hétérocycle azoté capable de chélater un atome de bore. Les évaluations pharmacologiques de ces composés ont montré de bonnes affinités de l'ordre du nanomolaire pour les récepteurs MT1 et MT2. Les études photophysiques ont confirmé la fluorescence induite par les fluorophores dans l'approche conventionnelle, et ont surtout montré l'existence de fluorescence par simple modification structurale de la mélatonine endogène. Les tests d'imagerie cellulaire ont également permis de valider ces méthodologies. / Melatonin is a main neurohormone synthesized in the pineal gland during the night in all mammals. Secretions of the blood circulating hormone through any system endowed melatoninergic receptors (MT1, MT2) transmit information leading to photoperiod and adaptation of the day / night periods. Melatonin is involved in many biological functions but also in various diseases of the central nervous system such as circadian rhythm disorders, anxiety, depression... Actually, there are many affinity receptors ligands, however, research on the pharmacology and the functionality of melatonin receptors suffers from the lack of selective probes for these two receptors. In order to overcome this scientific obstacle, we designed and synthesized fluorescent melatonin ligands according two different approaches. In a first conventional approach the melatoninergic ligands are tagged with an organic fluorophore via a linker. In a second approach more innovative, the indole ring of the endogenous ligand is fused with a pyrrole in order to obtain a structural analogy with the fluorophores BODIPYs types. In a third series derived from the previous one, melatonin is functionalized with a aza-heterocycle able to chelate a boron atom. Pharmacological evaluations of these compounds have shown nanomolar affinity for the receptors. Photophysical studies confirmed the fluorescence induced by the fluorescent dye in the conventional approach, and induced by simple melatonin structural modifications in the orthers. Preliminary cell imaging have also validated the methodologies.

Au cours de cette thèse, des dyades chromophoriques à base d’oligoprolines ont été développées afin d’étudier les transferts d’énergies au sein de système hélicoïdaux. L’étude préliminaire de ces dyades n’a pas permis d’obtenir l’étude de transfert d’énergie souhaitée. La présence conjointe de deux conformères, ainsi que des problèmes de pureté, semblent en être la cause. C’est pourquoi dans un second temps, plusieurs modèles d’oligoprolines ayant une conformation largement majoritaire ont été conçus. Basés sur un blocage de conformation via des effets stériques cumulés, les modèles présentés conservent une unique conformation dans des solvants favorisant les deux types d’hélice. Pour finir, une propagation de la conformation a été étudiée à partir des composés modèles afin de créer une dyade chromophorique induite. L’étude photo-physique de celle-ci permet d’en étudier le transfert d’énergie. / During this thesis, chromophoric dyads based on oligoprolines have been developed in order to studyEnergy transfer within helical systems. Preliminary studies of these dyads were unsuccessful to study thedesired energy transfer. The presence of two conformers and purity problems seems to be responsible. This iswhy, in a second step, several oligoproline models with a major conformation were designed. Based on aconformation induction via cumulative steric effects, the models presented maintain a unique conformation insolvents favoring both types of helices. Finally, a propagation of the conformation will be studied based on themodel compounds in order to create an induced chromophoric dyad. The photo-physical study show anefficient energy transfer.

Organic solar cell (OSC) has been an active research field over the past decades, due to their intrinsic advantages, such as low consumption of materials and energy, the applicability on flexible substrates and the degradability of the organic components. Compared with the solution processing technology using polymers as electron donor materials, small molecule vacuum deposition is regarded as a promising fabrication method, avoiding the use of toxic aromatic solvents and guaranteeing constant batch-to-batch performance. Moreover, it is much easier to realize multi-junction tandem solar cells (TSCs) by thermal deposition, and the leading power conversion efficiency (PCE) of 13.2% was achieved using three different absorbers by vacuum deposition (“Heliatek sets new organic photovoltaic world record efficiency of 13.2%” 2016). In this dissertation, novel electron donor materials are synthesized based on the molecular skeleton of a famous chromophore, boron dipyrromethene (BODIPY), and chemical modifications are carried out to tune the intense absorption bands of these dyes to near infrared (NIR, λ>750,nm) region. Efficient small molecule NIR absorbers are highly required for TSCs, because they can construct a complementary absorption over the visible and NIR spectral region in cooperation with a wide bandgap material. Three β-fused aza-BODIPY molecules with heterocyclic substituents on α-positions are prepared using organolithium reagents and phthalonitrile as the starting materials. The organolithium reagents, namely N-methylpyrrole, N-methylindole and 2-trimethylsilylthiophene, are used instead of commonly used Grignard reagents. Moreover, three corresponding aza-BODIPY derivatives are obtained by replacing one fluorine atom in the BF_{2} moiety by a cyano group. UV-vis absorption spectra reveal that all these materials are strong NIR absorbers, and their abortion in solid state cover a wide range from 600 to 1000,nm. OSCs with these aza-BODIPY donors give a best PCE of 3.0%, which is a reasonable value for the NIR devices with the maximum and the onset of the EQE spectrum around 850 and 950,nm respectively. A series of furan-fused BODIPYs with a electron withdrawing CF_{3} group on the meso-C are synthesized, and the photophysical/electrochemical properties can be tuned easily by the electronic properties of the substituents on the peripheral aromatic rings. The most promising candidate gives a high PCE of 6.1% in a single junction OSC with a J_{sc} of 13.3,mA/cm^{2}, a V_{oc} of 0.73,V, and a FF of 62.7%. A serial connected TSC is fabricated using this BODIPY as the low bandgap donor and a “green” donor, and its EQE spectrum covers a wide range from 400 to 900,nm. The PCE reaches 9.9% with a J_{sc} of 9.9,mA/cm^{2}, a V_{oc} of 1.70,V, and a FF of 59.0%. Based on the general structure of furan-fused BODIPY, alkyl or fluorinated alkyl substituents with larger volume is introduced on either peripheral aromatic rings or the meso-C. The variations that caused by these substituents on the photophysical and electrochemical properties are negligible. The investigations on the OSCs demonstrate that the introduction of these alkyl chain substituents have positive influence on the PCE values, which benefit mainly from the increased photocurrent. However, there is no positive relationship between the device performance and the volume of the alkyl chain substituents. BODIPY molecules have been demonstrated as efficient and promising NIR electron donor materials for vacuum-deposited OSCs. Taking advantages of facile molecular modification, oustanding photophysical behaviors and tunable electrochemical properties, this series of dyes are also intereting for other semiconductor devices.