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In this study, we extend the rigidity and resonance of benzobisthiazo- le for the application as second-order nonlinear optics. A novel nonlinear optical polyimide (NLO-PI) containing side-chained benzobisthiazole- based chromophore has been synthesized. A hydroxyl- containing PI (PHI) was first prepared using direct thermal imidization of 2,4-diaminophenol dihydrochloride and 4,4¡¦-(hexafluoroisopropylidene)diphthalic anhydride; the benzobisthiazole-based chromophore was then prepared using 2,5-diamino- 1,4-benzenedithiol dihydrochloride as the starting monomer. The final NLO-PI was obtained by the Mitsunobu reaction via ether linkage between PHI and the chromophore. This ether linkage is expected to provide chain flexibility for better orientation under electric field during poling. Formation of benzobisthiazole-based chromophore and the corresponding NLO-PI was evidenced by FTIR and UV-vis spectra. TGA and TMA reveal a thermal decomposition temperature and a glass transition temperature as high as 576 and 324oC, respectively. The electrooptic coefficient of the NLO-PI at a wavelength of 630nm was found to be r33 = 6.62 pm/V.

Le cadre général de cette thèse est une étude théorique par chimie quantique et dynamique moléculaire de la relation entre la structure et la fluorescence des protéines fluorescentes, en particulier, de la protéine fluorescente jaune (YFP). Dans cette protéine l'énergie de transition électronique est réduite par rapport à celle de la protéine fluorescente verte (GFP) en raison de l'empilement π entre le chromophore (la partie qui peut absorber et émetre de la lumiere visible au cœur de la protéine) et une tyrosine. Cet effet constitue la base de son utilité au laboratoire (transfert d'énergie par résonance «FRET» avec d’autres protéines). Ce travail comporte deux parties. D’une part, nous avons cherché à déterminer si un champ de force classique (ff99 de la suite AMBER) permet de représenter l’effet de π -stacking sur la dynamique à l’état excité. Pour cela nous avons effectué une série de calculs CASPT2 sur une grille de points. La conclusion est que la différence entre les surfaces d’énergie d’interaction résultant du champ de force et des calculs de chimie quantique CASPT2 ne semblent pas déterminante pour les propriétés de fluorescences.D’autre part, nous avons utilisé un modèle développé dans le groupe ThéoSim pour décrire le déclin à partir d’une série de dynamique (300ns) utilisant un champ de force classique. Cette méthode conduit à déterminer des paramètres en principe transférables d’une protéine fluorescente à une autre. Nous avons comparé la GFP et l’YFP. Cette approche ouvre la voie à une méthode rapide pour des propriétés de fluorescences pour de nouvelles protéines fluorescentes. Une prochaine étape serait d'améliorée la description du déclin radiatif utilisée dans ce modèle. / The general framework of this PhD is a theoretical study by quantum chemistry and molecular dynamics of the relationship between the structure and the fluorescence properties of fluorescent proteins, particulary, of the yellow fluorescent protein (YFP). In this protein, the electron transition energy is reduced with respect to that of the green fluorescent protein (GFP) as a result of a π stacking between the chromophore (the part that absorbs and emits visible light in the protein) and a tyrosine . This effect is the basis of the usefulness of YFP in the laboratory (resonance energy transfer "FRET" with other proteins).This study has two parts. First, we have tried to determine if a classical force field (ff99 of the AMBER suite) can represent the effect of π stacking on the dynamics in the excited state. For this goal, we performed a series of CASPT2 calculations on a grid of points. The conclusion is that the difference between the interaction energy surfaces resulting from the force field and the CASPT2 calculations does not seem decisive for the fluorescence properties. Second, we used a model developed in the ThéoSim group to extract the fluorescence decay time from a series of dynamics (300ns) using a classical force field. This method leads to the determination of parameters in principle transferable across fluorescent protein. We compared GFP and YFP. This approach opens the way to a fast method for determining fluorescence properties for new fluorescent proteins. A next step would be to improve the description of radiative decay used in this model.

Reported in Chapter 2 of this thesis is the reliable and tolerant synthesis of a small library of pyrazole and triazole heterocycles. This synthesis was achieved in two steps in good yields from the reaction of acetophenone and benzamide derivatives with dimethyl formamide-dimethyl acetal followed by a cyclization with hydrazine. Also reported is the synthesis and characterization of their corresponding scorpionate ligands. Preliminary co ordination chemistry was done with a variety of lanthanide metals and was studied by standard spectroscopic methods as well as variable temperature 1H NMR, which revealed that Curie-Weiss behaviour was followed for these complexes in solution. An X-ray crystal structure of a nine co-ordinate ytterbium metal centre with eight nitrogen atom (four pyrazole, four pyridine) donors and one chloride atom was obtained, which may have been a product of decomposition during crystal growth. The bond lengths of this structure were compared with other lanthanide complexes of similar structural motifs. This comparison supported the theory of decomposition as the pyridine nitrogen atom-ytterbium bond lengths were longer than the average ytterbium-nitrogen atom bond length. Reported in Chapter 4 of this thesis is the synthesis and partial characterization of a new organic dye named perinaphthindigo. Perinaphthindigo was synthesized with adapted iv Baeyer-Drewson reaction conditions for the synthesis of indigo which involved the treatment of 1,8-nitronaphthaldehyde with acetone under basic conditions, and was found to be an intense green colour in solution. Perinaphthindigo was produced in poor yields, so efforts were undertaken to improve the yields through an alternative two-step synthesis, first between 1,8-nitronaphthaldehyde and nitromethane in a Henry reaction followed by oxidative coupling. The synthesis of perinaphindigo was adapted so as to structurally modify the final compound, either through incorporation of solubilizing tert-butyl groups or bromine atoms for future cross-coupling chemistry. The brominated derivatives of perinaphthindigo were also synthesized in low yields so cross-coupling conditions were scanned on model precursor compounds. The brominated perinaphthindigo compounds were found to have a bathochromically shifted absorbance maximum from the parent perinaphthindigo. This bathochromic shift was more pronounced in our compounds than in the comparison of indigo and 6.6’-dibromoindigo which indicates our compounds are more sensitive to perturbation by substitution. Reported in Chapter 5 of this thesis is the study of the acid and base chemistry of Nindigo, a previously reported compound. The treatment of Nindigo with a series of strong acids led to an interesting “protoisomerization”, or trans to cis isomerization of the central olefin, with ultimate structural determination through X-ray crystallographic methods. This isomerization was studied through absorbance stopped-flow methods which identified a probable pathway of the isomerization through a neutral, cis species. The investigation of neutral Nindigo was undertaken to attempt to identify two peaks which are red-shifted from the π-to-π transition at 586 nm. These two peaks appear at 657 nm and 741 nm and are present in all solvents. The preparative acid chemistry allowed us to assign the first red shifted peak at 657 nm to the cationic species. Aggregation studies showed concentration dependent behaviour of the ratio between the peaks at 586 nm and 657 nm with little effect on the species at 741 nm. In order to probe whether an autoionization process was occurring, variable temperature NMR and UV-Vis experiments were performed which did not provide a definitive answer to the species at 741 nm. / Graduate

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Fluorescent proteins (FPs) are extremely valuable biochemical markers which have found a wide range of applications in cellular and molecular biology research. The monomeric variants of red fluorescent proteins (RFPs), known as mFruits, have been especially valuable for in vivo applications in mammalian cell imaging. Fluorescent proteins consist of a chromophore caged in the beta-barrel protein scaffold. The photophysical properties of an FP is determined by its chromophore structure and its interactions with the protein barrel. Application of hydrostatic pressure on FPs results in the modification of the chromophore environment which allows a systematic study of the role of the protein-chromophore interactions on photophysical properties of FPs. Using Molecular Dynamics (MD) computer simulations, I investigated the pressure induced structural changes in the monomeric variants mCherry, mStrawberry, and Citrine. The results explain the molecular basis for experimentally observed pressure responses among FP variants. It is found that the barrel flexibility, hydrogen bonding interactions and chromophore planarity of the FPs can be correlated to their contrasting photophysical properties at vaious pressures. I also investigated the oxygen diffusion pathways in mOrange and mOrange2 which exhibit marked differences in oxygen sensitivities as well as photostability. Such computational identifications of structural changes and oxygen diffusion pathways are important in guiding mutagenesis efforts to design fluorescent proteins with improved photophysical properties.

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Une série de bisthiényléthènes (BTE), chromophores photochromes, à différents ponts éthène centraux a été synthétisée. Jusque là, la conception rationnelle des BTE a reposé sur la nature des substituants des groupes latéraux. Dans notre travail, nous avons étudié l'influence de l'aromaticité du pont sur les propriétés photochromes. De plus, alors que les cycles à cinq atomes sont le plus souvent utilisés, nous avons introduit des cycles à six atomes au niveau de ce pont. Dans le Chapitre 1, les définitions principales liées au photochromisme, ainsi que des exemples, sont donnés. Le Chapitre 2 est dédié au BTTE, un BTE à pont benzobisthiadiazole, doté d'excellentes propriétés photochromes. Sa fluorescence peut être modulée par solvato- et photochromisme. c-BTTE, l'isomère fermé, a une excellente stabilité dans divers solvants et à l'état solide. Il ne présente pas de retour thermique typique des BTE à pont cyclique à six atomes. Le Chapitre 3 est consacré à des composés comportant des ponts de divers degrés d'aromaticité (BTE-NA, BTA et BTTA). Leur fluorescence peut être modulée par solvato- et photochromisme. Une faible aromaticité peut être corrélée à une irréversibilité thermique, comme illustré par le cas du BTTA à pont benzobisthiadiazole. De plus, la faible barrière énergétique entre les conformations parallèle et anti-parallèle et la grande différence d'absorption entre isomères conduisent à une conversion totale de BTTA à c-BTTA. Des molécules à pont benzothiadiazole, conçues pour la complexation et la commutation de propriétés optiques non linéaires, ont été obtenues (Chapitres 4 et 5). Cependant, pour l'instant, les propriétés visées n'ont pas été mises en évidence. / A series of photochromic bisthienylethenes (BTE) chromophores with different central ethene bridges were synthesized. Up to date, the rational design of BTE have been mainly carried out on the side aryl groups. In our work, the influence of the aromaticity of the central ethene bridge on the photochromic properties was studied. Moreover, unlike in the literature where most of BTE have a five-membered ring bridge, six-membered ring bridges were used. In Chapter 1, examples of photochromes are given, along with the main definitions. Chapter 2 deals with BTTE, a BTE with a benzobisthiadiazole bridge and with excellent photochromic properties. c-BTTE, the closed isomer, exhibits excellent thermal stability in various solvents and in the solid state. Its fluorescence can be modulated by solvato- and photochromism. It eliminates the usual bias of thermal back reaction, typical of BTE with a six-membered ring ethene bridge. Chapter 3 is devoted to compounds with bridges having different aromaticities (BTE-NA, BTA and BTTA). Their fluorescence can be modulated by solvato- and photochromism. The relation between aromaticity and thermal stability was established: the low aromaticity of the central ethene bridge with benzobisthiadiazole unit leads to a thermal irreversibility for BTTA, and the small energy barrier between the parallel and anti-parallel conformers and the great difference in absorption between BTTA and c-BTTA allow the full conversion from BTTA to c-BTTA. Molecules with a benzothiadiazole bridge, designed for complexation and for switchable nonlinear optical properties were prepared (Chapters 4 and 5). However, the targeted properties were not evidenced up to now.