Le monoxyde d’azote (NO), dont le rôle biologique a été découvert à la fin du 20ème siècle, est impliqué dans la régulation de nombreux processus à l’échelle de la cellule et de l’organisme. Sa biosynthèse est réalisée par les enzymes NO synthases (NOS), et met en jeu la liaison de NADPH à leur domaine réductase suivie d’une série de transfert d’électrons vers leur domaine oxygénase, où la formation de NO se produit par oxydation de la L-arginine. En s’inspirant de mimes photo-activables de NADPH précédemment décrits dans la littérature, appelés nano-déclencheurs (NT, de l’anglais nanotriggers), induisant la production de NO par illumination, nous avons conçu et synthétisé de nouvelles générations de composés potentiellement capables d’initier l’activité catalytique de NOS sous irradiation. Ils comportent une unité de reconnaissance de NOS dérivée de l’adénosine et une unité chromophorique de type diaminophényl butadiène, liées entre elles par un groupement triazole. Ces structures modulables, facilement assemblées par chimie « click » ont permis la préparation d’une librairie de nano-déclencheurs, dont les propriétés photophysiques et la stabilité dans des conditions physiologiques ont été évaluées. Ces nouvelles générations de composés offrent des perspectives intéressantes pour le contrôle de processus biologiques par la lumière. / Nitric oxide (NO), whose biological role has been discovered in the late 20th century, is involved in the regulation of many processes in cell and organism. Its biosynthesis is carried out by enzymes named nitric oxide synthases (NOS) and involves NADPH binding to their reductase domain followed by a series of electron transfers to their oxygenase domain, where the formation of NO takes place by oxidation of L-arginine. Inspired by photoactivatable NADPH mimics called nano-triggers (NT), previously described in the literature, able to produce NO upon illumination, we designed and synthesized new generations of compounds potentially capable of initiating the catalytic activity of NOS under irradiation. They contain a recognition unit for NOS derived from adenosine and a diaminophenyl butadiene chromophoric moiety, linked together by a triazole group. These modular structures, easily assembled by "click" chemistry allowed the preparation of a library of nano-triggers, whose photophysical properties and stability under physiological conditions were evaluated. These new generations of compounds offer interesting perspectives for the control of biological processes by light.

For inorganic semiconductors such as silicon, crystalline order leads to bands in the electronic structure which give rise to drastic differences with respect to disordered materials. Distinct band features lead to photo-effect, and the band structure can be tuned to optimize the performance of the photovoltaic (PV) device. An example is the presence of an indirect band gap. For organic semiconductors, such effects are typically precluded, since most organic materials employed are disordered, which hampers their characterization and theoretical analysis. The inspiration for this thesis came from the very first evidence of an indirect band gap exhibited by highly ordered and crystalline porphyrin-based surface-mounted metal-organic framework (PP-based SURMOF) material [J. Liu et al. Angew. Chem. Int. Ed. 2015, 54, 7441]. The presence of an indirect band gap should in principle result in suppressed charge recombination and efficient charge separations which would significantly enhance the PV device performance. However, the energy gain from the electronic band dispersion in the reported Pd-PP-Zn-SURMOF is far too low (≈5 meV) and results in a very low photocurrent generation (efficiency 0.2%), which is certainly not sufficient for the application. Another noticeable shortcoming is the weakly absorbing Q-bands of the employed PP chromophore (Pd-metal containing porphyrinoid, Pd-PP) in the visible region of the solar spectrum. Nevertheless, this novel research has highlighted the potential to improve the photophysical properties of PP-based SURMOFs by (i) introducing various functional groups or metal ions to the PP-core and (ii) controlling the PP-stacking behavior in layered materials. To overcome the posed shortcomings of the PP-MOF prototype PV material and to exploit the potential of PP-based SURMOFs, we have employed the following approach to increase the light absorption and the electronic band dispersion. Firstly, we proposed a computationally feasible simplified time-dependent approach to investigate the light absorption properties of PP derivatives or related PP-containing materials. Secondly, we predicted the light absorption properties of multi-functionalized PPs (i.e. tuning the weakly absorbing Q-bands), thus allowing us to identify different PP linkers with different light absorption properties, allowing to bridge the so-called green gap. Finally, we incorporated the most promising PP linkers for the construction of SURMOFs and applied state-of-the-art DFT methods in various approximations to optimize the PP-stacking behavior to achieve the desired photophysical properties. Besides PPs, we have extended our investigations to phthalocyanines (PCs) as alternative individual SURMOF building blocks, because they do not only exhibit structural robustness and stability but also possess enhanced absorption in the visible and the near IR spectral regions in comparison to PPs. Hence, the exploitation of PCs could enrich the library of SURMOFs with the desired optical quality.

Time Dependent Density Functional Theory offers a good accuracy/computational cost ratio among different methods used to predict the electronic structure for molecules of practical interest. The Coupled Electronic Oscillator (CEO) formalism was recently shown to accurately predict Nonlinear Optical (NLO) properties of organic chromophores when combined with Time Dependent Density Functional Theory. Unfortunately, CEO does not lend itself easily to interpretation of the structure activity relationships of chromophores. On the other hand, the Sum Over States formalism in combination with semiempirical wavefunction methods has been used in the past for the design of simplified essential states models. These models can be applied to optimization of NLO properties of interest for applications. Unfortunately, TD-DFT can not be combined directly with SOS because state-to-state transition dipoles are not defined in the linear response TD approach. In this work, a second order CEO approach to TD-DFT is simplified so that properties of double excited states and state-to-state transition dipoles may be expressed through the combination of linear response properties. This approach is termed the a posteriori Tamm-Dancoff approximation (ATDA), and validated against high-level wavefunction theory methods. Sum over States (SOS) and related Two-Photon Transition Matrix formalism are then used to predict Two-Photon Absorption (2PA) profiles and anisotropy, as well as Second Harmonic Generation (SHG) properties. Numerical results for several conjugated molecules are in excellent agreement with CEO and finite field calculations, and reproduce experimental measurements well.

No description available.

Unlike canonical phytochromes, the GAF domain of cyanobacteriochromes (CBCRs) can bind bilins autonomously and is sufficient for functional photocycles. Despite the astonishing spectral diversity of CBCRs, the GAF1 domain of the three-GAF-domain photoreceptor all2699 from the cyanobacterium Nostoc 7120 is the only CBCR-GAF known that converts from a red-absorbing (Pr) dark state to a far-red-absorbing (Pfr) photoproduct, analogous to the more conservative phytochromes. Here we report a solid-state NMR spectroscopic study of all2699g1 in its Pr state. Conclusive NMR evidence unveils a particular stereochemical heterogeneity at the tetrahedral C31 atom, whereas the crystal structure shows exclusively the R-stereochemistry at this chiral center. Additional NMR experiments were performed on a construct comprising the GAF1 and GAF2 domains of all2699, showing a greater precision in the chromophore–protein interactions in the GAF1-2 construct. A 3D Pr structural model of the all2699g1-2 construct predicts a tongue-like region extending from the GAF2 domain (akin to canonical phytochromes) in the direction of the chromophore, shielding it from the solvent. In addition, this stabilizing element allows exclusively the R-stereochemistry for the chromophore-protein linkage. Site-directed mutagenesis performed on three conserved motifs in the hairpin-like tip confirms the interaction of the tongue region with the GAF1-bound chromophor

La polyvalence de la réaction de couplage-croisé C-N a été explorée pour la synthèse de deux nouvelles classes de ligands: (i) des ligands bidentates neutres de type N^N et (ii) des ligands tridentates neutres de type N^N^N. Ces classes de ligands contiennent des N-hétérocycles aromatiques saturés qui sont couplés avec hexahydropyrimidopyrimidine (hpp). Les ligands forment de cycles à six chaînons sur la coordination du centre Ru(II). Ce fait est avantageux pour améliorer les propriétés photophysiques des complexes de polypyridyl de Ru(II). Les complexes de Ru(II) avec des ligands bidentés ont des émissions qui dépendent de la basicité relative des N-hétérocycles. Bien que ces complexes sont électrochimiquement et photophysiquement attrayant, le problème de la stereopurité ne peut être évité. Une conception soigneuse du type de ligand nous permet de synthétiser un ligand bis-bidentate qui est utile pour surmonter le problème de stereopurité. En raison de la spécialité du ligand bis-bidentate, son complexe diruthénium(II,II) présente une grande diastéréosélectivité sans séparation chirale. Alors que l'unité de hpp agit comme un nucléophile dans le mécanisme de C-N réaction de couplage croisé, il peut également agir en tant que groupe partant, lorsqu'il est activé avec un complexe de monoruthenium. Les complexes achiraux de Ru(II) avec les ligands tridentés présentent des meilleures propriétés photophysiques en comparason avec les prototypes [Ru(tpy)2]2+ (tpy = 2,2′: 6′, 2′′-terpyridine). L’introduction de deux unités de hpp dans les ligands tridentates rend le complexe de Ru(II) en tant que ‘absorbeur noir’ et comme ‘NIR émetteur’ (NIR = de l’anglais, Near Infra-Red). Cet effet est une conséquence d'une meilleure géométrie de coordination octaédrique autour de l'ion Ru(II) et de la forte donation sigma des unités hpp. Les complexes du Re(I) avec des ligands tridentates présentent un comportement redox intéressant et ils émettent dans le bleu. L'oxydation quasi-réversible du métal est contrôlée par la donation sigma des fragments hpp, tandis que la réduction du ligand est régie par la nature électronique du motif N-hétérocycle central du ligand lui-même. Cette thèse presente également l'auto-assemblage des métal-chromophores comme ‘métallo-ligands’ pour former des espèces supramoléculaires discretes utilisant des complexes neutres. Les synthèses et propriétés des métaux-chromophores précités et les supramolécules sont discutées. / The versatility of C-N cross coupling reactions has been explored for the synthesis of two novel classes of ligands : (i) neutral bidentate N^N ligands and (ii) neutral tridentate N^N^N ligands. Both classes of ligands contain saturated aromatic N-heterocycles coupled with the unsaturated hexahydropyrimidopyrimidine (hpp) unit. The ligands form six-membered chelate rings upon coordination to a Ru(II) center. This fact is advantageous to improve the photophysical properties of Ru(II)-polypyridyl complexes. Ru(II) complexes of bidentate ligands can act as red-emitters. The red-emission is dependent on the relative basicity of the N-heterocycles. While these complexes are electrochemically and photophysically appealing, the problem of stereopurity can not be avoided. Careful ligand design affords bis-bidentate ligand that is useful to overcome the problem of stereopurity. Due to the speciality of this bis-bidentate ligand, its diruthenium(II,II) complex exhibits high diastereoselectivity without any chiral separation. While the hpp unit acts as a nucleophile in the mechanism of C-N cross coupling reaction, it can also act as a leaving group when activated as a monoruthenium complex. Achiral Ru(II) complexes of the tridentate ligands display improved photophysical properties over the prototype complex [Ru(tpy)2]2+ (tpy = 2,2’:6’,2’’-terpyridine). Introduction of two hpp units in the tridentate ligands renders the Ru(II) complex into a ‘black absorber’ and a ‘NIR emitter’ (NIR = Near Infra-Red). This fact is a consequence of better octahedral geometry around the Ru(II) ion and strong sigma-donation from the hpp units. The blue-emitting Re(I) complexes of the tridentate ligands also exhibit interesting redox behavior. The metal-based quasi-reversible oxidation is controlled by the sigma-donation from the hpp moieties, while the ligand-based reduction is governed by the electronic nature of the central N-heterocycle of the same ligand moiety. This thesis also incorporates self-assembly of metal-chromophores as ‘metallo-ligands’ to form discrete supramolecular species using neutral metal-complexes. The syntheses and properties of the aforesaid metal-chromophores and the supramolecules are discussed.

Our understanding of the folding of membrane proteins lags behind that of soluble proteins due to the challenges posed by the exposure of hydrophobic regions during in vitro chemical denaturation and refolding experiments. While different folding models are accepted for soluble proteins, only the two-stage model and the long-range interactions model have been proposed so far for helical membrane proteins. To address our knowledge gap on how different membrane proteins traverse their folding landscapes, Chapter 2 investigates the structural features of SDS-denatured states and the kinetics for reversible unfolding of sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis. pSRII is difficult to denature, and only SDS can dislodge the retinal chromophore without rapid aggregation. Even in 30% SDS (0.998 $\mathit{\Chi}_{SDS}$), pSRII retains the equivalent of six out of seven transmembrane helices, while the retinal binding pocket is disrupted, with transmembrane residues becoming more solvent-exposed. Folding of pSRII from an SDS-denatured state harbouring a covalently-bound retinal chromophore shows deviations from an apparent two-state behaviour. SDS denaturation to form the sensory opsin apo-protein is reversible. This chapter establishes pSRII as a new model protein which is suitable for membrane protein folding studies and has a unique folding mechanism that differs from those of bacteriorhodopsin and bovine rhodopsin. In Chapter 3, SDS-denatured pSRII, acid-denatured pSRII and sensory opsin obtained by hydroxylamine-mediated bleaching of pSRII were characterised by solution state NMR. 1D $^1$H and $^{19}$F NMR were first used to characterise global changes in backbone amide protons and tryptophan side-chains. Residue-specific changes in backbone amide chemical shifts and peak intensities in 2D [$^1$H,$^{15}$N]-correlation spectra were analysed. While only small changes in the chemical environment of backbone amides were detected, changes in backbone amide dynamics were identified as an important feature of SDS- and acid-denatured pSRII and sensory opsin. $^{15}$N relaxation experiments were performed to study the backbone amide dynamics of SDS-denatured pSRII, reflecting motions on different timescales, including fast fluctuations of NH bond vectors on the ps-ns timescale and the lack of exchange contributions on the µs timescale. These studies shed insight on differences in the unfolding pathways under different denaturing conditions and the crucial role of the retinal chromophore in governing the structural integrity and dynamics of the pSRII helical bundle. Hydrogen bonds play fundamental roles in stabilising protein secondary and tertiary structure, and regulating protein function. Successful detection of hydrogen bonds in denatured states and during protein folding would contribute towards our understanding on the unfolding and folding pathways of the protein. Previous studies have demonstrated residue-specific detection of stable and transient hydrogen bonds in small globular proteins by measuring $^1{\it J}_{NH}$ scalar coupling constants using NMR. In Chapter 4, different methods for measuring $^1{\it J}_{NH}$ scalar coupling were explored using RalA, a small GTPase with a mixed alpha/beta fold, as proof-of-concept. Detection of hydrogen bonds was then attempted with OmpX, a beta-barrel membrane protein, both in its folded state in DPC micelles and in the urea-denatured state. While $^1{\it J}_{NH}$ measurement holds promise for studying hydrogen bond formation, further optimisation of NMR experiments and utilisation of perdeuterated samples are required to improve the precision of such measurements in large detergent-membrane protein complexes. Naturally occurring split inteins can mediate spontaneous trans-splicing both in vivo and in vitro. Previous studies have demonstrated successful assembly of proteorhodopsin from two separate fragments consisting of helices A-B and helices C-G via a splicing site in the BC loop. To complement the in vitro unfolding/folding studies, pSRII assembly in vivo was attempted by introducing a splicing site in the loop region of the beta-hairpin constituting the BC loop of pSRII. The expression conditions for the N- and C-terminal pSRII-intein segments were optimised, and the two segments co-expressed. However, the native chromophore was not observed. Further optimisation is required for successful in vivo trans-splicing of pSRII and application of this approach towards understanding the roles of helices and loops in the folding of pSRII.

Die Arbeit untersucht den Anregungsenergietransfer in supramolekularen Phäophorbid-a-Komplexen. Das P4- und das P16-Molekül bestehen aus vier bzw. sechzehn Phäophorbid-a-Molekülen. Die Komplexe werden in explizitem Lösungsmittel im Rahmen einer gemischt quanten-klassischen Methode untersucht. Klassische Molekulardynamik-Simulationen werden durchgeführt. Die zeitabhängige Schrödingergleichung wird gelöst, der entsprechende Hamiltonoperator hängt parametrisch von den Kernkoordinaten ab. Es wird eine Methode vorgestellt, die die Berechnung des Schwingungsbeitrags der Koordinatenabhängigkeit in harmonischer Näherung ermöglicht. Die Qualität der Methode wird bewiesen. Es werden drei verschiedene Ansätze benutzt, um das Zeitverhalten des Anregungsenergietransfers innerhalb der Chromophorkomplexe zu charakterisieren. Es werden zunächst Transferraten berechnet und entsprechende Ratengleichungen gelöst. Desweiteren werden gemittelte zeitabhängige Populationen aus der Lösung der Schrödingergleichung bestimmt. Zudem wird die Zeitskala des Anregungsenergietransfers aus der Anisotropie erhalten. Die Berechnung der Anisotropie beruht auf der Lösung einer Schrödingergleichung, welche das elektromagnetischen Feldes explizit enthält. Für alle drei Ansätze ergibt sich die gleiche Dynamik des Anregungsenergietransfers. Es werden zudem lineare und transiente Spektren der Qy-Banden der Chromophorkomplexe berechnet. Für ein einzelnes Phäophorbid-a-Molekül in Ethanol werden zusätzlich die Qx-Bande und die Schwingungsprogression bestimmt. Außerdem wird die lineare Absorption von Phäophorbid a und P16 neben einem Gold-Nanopartikel untersucht, die erwartete Verstärkung des Absorptionssignals durch die Präsenz des Nanoteilchens wird gezeigt. Abschließend wird eine neue Methode vorgestellt, die es erlaubt, die abstands- und orientierungsabhängige Abschirmung der exzitonischen Kopplung parametrisch in die gemischt quanten-klassische Methode zu integrieren. / This thesis investigates the excitation energy transfer in pheophorbide a complexes. The P4 and the P16 molecule consist of four and sixteen pheophorbide a molecules, respectively. The complexes in explicit ethanol solution are investigated utilizing a mixed quantum-classical methodology. Classical molecular dynamics simulations are carried out. The time-dependent Schrödinger equation is solved for a Hamiltonian that depends parametrically on the classical nuclear coordinates. In this thesis a method is introduced which allows the computation of the vibrational contribution in harmonic approximation. The high quality of the method is proven. Three different ansatzes were utilized to compute the time development of the excitation energy transfer within the chromophore complexes. The expansion coefficients that result from the solution of the time-dependent Schrödinger equation are utilized to compute averaged time-dependent populations. Also, the expansion coefficients are used to compute excitation energy transfer rates in second order of the excitonic coupling. Thirdly, the time scale of the excitation energy transfer is derived from the delay-time dependent transient anisotropy. In order to compute the anisotropy, the electromagnetic field is included directly in the Hamiltonian of the system. The excitation energy transfer dynamics is exactly the same for the three approaches. In addition, linear and transient spectra of the chromophor complexes Qy band are computed. For a single pheophorbide a in ethanol, the Qx band and the vibrational progression are calculated. Furthermore, the linear absorption of pheophorbide a and P16 next to a gold nanoparticle is studied. The amplification of the molecular absorption signal due to the presence of the nanoparticle is shown. Finally, a new method is introduced to treat distance and conformation dependent screening of the excitonic coupling parametrically within a mixed quantum-classical description.

The global lighting source energy consumption accounts for about 22% of the total electricity generated. New high-efficiency solid-state light sources are needed to reduce the ever increasing demand for energy. Single-phased emitter-based composed of transparent conducting oxides (TCOs) nanocrystals and fluorescent dyes can potentially revolutionize the typical composition of phosphors, the processing technology founded on the binding of dye acceptors on the surface of nanocrystals, and the configurations of the light-emitting diodes (LEDs) and electroluminescence devices. The hybrid white-light-emitting nanomaterial is based on the expanded spectral range of the donor-acceptor pair (DAP) emission originated from the γ-gallium oxide nanocrystals via Förster resonance energy transfer (FRET) to the surface-anchored fluorescent dyes. The emission of the nanocrystals and the sensitized emission of the chromophore act in sync as an internal relaxation upon the excitation of the γ–gallium oxide nanocrystals. It extends the lifetime of the secondary fluorescent dye chromophore and the internal relaxation within this hybrid complex act as a sign for a quasi single chromophore. The model system of white-light-emitting nanostructure system developed based on this technology is the γ–gallium oxide nanocrystals-Rhodamine B lactone (RBL) hybrid complex. The sufficient energy transfer efficiency of 31.51% within this system allowed for the generation of white-light emission with the CIE coordinates of (0.3328, 0.3380) at 5483 K. The relative electronic energy differences of the individual components within the hybrid systems based on theoretical computation suggested that the luminance of the nanocomposite comprised of RBL is dominantly mediated by FRET. The production of white-light-emitting diode (WLED) based on this technology have been demonstrated by solution deposition of the hybrid nanomaterials to the commercially available ultraviolet (UV) LED due to the versatility and chemical compatibility of the developed phosphors.

Gegenstand der vorliegenden Arbeit ist die Synthese und Charakterisierung neuer chromophorer Catecholderivate mit ausgeprägten push-pull-pi-Systemen. Die solvatochromen Eigenschaften dieser Verbindungen werden in Abhängigkeit der Wasserstoffbrückenbindungsdonor- und -akzeptorfähigkeit sowie Lösungsmitteldipolarität diskutiert. Mit entsprechenden methoxy- und dimethoxyfunktionalisierten Catecholderivaten ist es möglich, vergleichende Struktur-Eigenschaftsbeziehungen aufzustellen. Durch Untersuchungen zu den Wechselwirkungen der chromophoren Catechole mit Schwermetallionen kann gezeigt werden, dass die synthetisierten Verbindungen als Sensoren eingesetzt werden können. In der vorliegenden Arbeit wird des Weiteren die Adsorption der Catecholderivate an Metalloxide beschrieben. Mit Farbstoffen sensibilisierte Oberflächen stellen derzeit ein interessantes Forschunggebiet dar. Ferner wird über die Umsetzung der Catecholderivate mit Trialkoxysilanen zu zwitterionischen, spirozyklischen, pentakoordinierten lambda5Si-Silicaten sowie mit Tetraalkoxysilanen zu dianionischen, hexakoordinierten lambda6Si-Silicaten berichtet. Besonderes Augenmerk lag dabei auf UV/vis-spektroskopischen Untersuchungen.