This thesis examines the design, synthesis and biological applications of a series of inhibitors which incorporate an azobenzene photoswitch, a peptidyl backbone and a trifluoromethyl ketone warhead. The photoswitch can be isomerised by irradiation with UV or visible light and has been employed to modulate the reactivity of the enzyme. Chapter one gives a brief outline of some of the important areas related to this work. Examples of previously utilised photoswitches as well as some background on serine protease and the uses of fluorine in medicine has been covered. Chapter two outlines the synthesis of the key trifluoromethyl carbinol 2.6 by two different methods. The condensation of a fluorinated aldehyde with a nitroalkane affords an α-nitro trifluoromethyl carbinol which can be reduced to give the desired amine 2.6. Treatment of oxazolones with trifluoroacetic anhydride via a modified Dakin-West reaction gives trifluoromethyl ketones which can be reduced to give trifluoromethyl carbinols. Chapter three investigate the synthesis of substituted stilbenes and phenanthrenes as alternative molecular switches to azobenzenes. Molecular modelling of phenanthrenes suggests they may be suitable mimics of E-azobenzenes. Chapter four outlines the synthesis of a series of mono and disubstituted azobenzenes by direct sulfonation of azobenzene or by condensation of nitroso arenes with aryl amines. The switches incorporate one or two peptidyl residues designed to improve specificity towards the enzyme. Chapter five examines the photoisomerisation of eight potential inhibitors by irradiating with UV or visible light. Irradiation with UV light enriches the sample to give 78-93 % of the Z-isomer. Irradiation with visible light gave photostationary states with 14-21 % Z-isomer. Ambient photostationary states are ca. 22 % Z-isomer. Chapter six looks at the testing of five trifluoromethyl ketones as potential inhibitors ofα-chymotrypsin. The inhibitors vary in substituents, substitution patterns and chain length. The inhibitors were tested at both ambient and Z-enriched photostationary states and were found to exhibit slow binding kinetics. In all cases the Z-enriched inhibitor solution was at least 3-fold more potent than the ambient solution. Chapter seven is an experimental chapter and outlines the synthesis of the compounds prepared in this thesis.

This thesis examines the design, synthesis and biological applications of a series of inhibitors which incorporate an azobenzene photoswitch, a peptidyl backbone and a trifluoromethyl ketone warhead. The photoswitch can be isomerised by irradiation with UV or visible light and has been employed to modulate the reactivity of the enzyme. Chapter one gives a brief outline of some of the important areas related to this work. Examples of previously utilised photoswitches as well as some background on serine protease and the uses of fluorine in medicine has been covered. Chapter two outlines the synthesis of the key trifluoromethyl carbinol 2.6 by two different methods. The condensation of a fluorinated aldehyde with a nitroalkane affords an α-nitro trifluoromethyl carbinol which can be reduced to give the desired amine 2.6. Treatment of oxazolones with trifluoroacetic anhydride via a modified Dakin-West reaction gives trifluoromethyl ketones which can be reduced to give trifluoromethyl carbinols. Chapter three investigate the synthesis of substituted stilbenes and phenanthrenes as alternative molecular switches to azobenzenes. Molecular modelling of phenanthrenes suggests they may be suitable mimics of E-azobenzenes. Chapter four outlines the synthesis of a series of mono and disubstituted azobenzenes by direct sulfonation of azobenzene or by condensation of nitroso arenes with aryl amines. The switches incorporate one or two peptidyl residues designed to improve specificity towards the enzyme. Chapter five examines the photoisomerisation of eight potential inhibitors by irradiating with UV or visible light. Irradiation with UV light enriches the sample to give 78-93 % of the Z-isomer. Irradiation with visible light gave photostationary states with 14-21 % Z-isomer. Ambient photostationary states are ca. 22 % Z-isomer. Chapter six looks at the testing of five trifluoromethyl ketones as potential inhibitors ofα-chymotrypsin. The inhibitors vary in substituents, substitution patterns and chain length. The inhibitors were tested at both ambient and Z-enriched photostationary states and were found to exhibit slow binding kinetics. In all cases the Z-enriched inhibitor solution was at least 3-fold more potent than the ambient solution. Chapter seven is an experimental chapter and outlines the synthesis of the compounds prepared in this thesis.

L’objectif de cette thèse a été axé sur le développement des systèmes capable de répondre à des stimuli externes, basés sur des unités photochromiques. Le but d’une telle quête est d’augmenter la complexité des dispositifs et des machines moléculaires synthétiques. Avec l’objectif de développer des dispositifs et des machines artificiels plus complexes, nous avons réalisé de systèmes comprenant de multiples interrupteurs moléculaires. En vue de la réalisation de cette thèse, des nouveaux systèmes multi-photochromiques, où hybrides photochrome/nanomatériaux contenant des fragments azobenzène, diaryléthène ou spiropyrane ont été réalisés et étudiés. D’abord, on s’est focalisés sur des systèmes multi-azobenzènes capables de subir de grands réarrangements géométriques lors de la photoisomérisation, ils pourraient être utilisés à l'avenir comme éléments constitutifs des matériaux host-guest ou metal-organic frameworks contrôlables par des stimuli lumineux. Dans un second exemple, des commutateurs photochromiques de type dithiényléthène ont été utilisés pour déclencher l'émission d'une porphyrine. Cette dyade à montré une modulation réversible de son émission, affichant un contraste particulièrement élevé. Comme dernier exemple, un dérivé de spiropyrane a été combiné avec des nanoparticules d’or anisotropes. En induisant l'isomérisation de l’interrupteur moléculaire dans les dispersions colloïdales des nanorods d’or en liquide, nous avons visualisé une grande variation du spectre d'extinction des colloïdes, dépendante de la longueur d’onde du mode LSPR et du recouvrement spectrale avec le photoswitch. / The aim of this thesis has been to develop systems capable of responding to external stimuli, based on photochromic units. The goal of such a quest is to increase the complexity of devices and synthetic molecular machines. With the goal of developing more complex artificial devices and machines, we have realised systems containing multiple molecular switches. For the realisation of this thesis, new multi-photochromic systems, or photochromes/nanomaterials hybrids containing azobenzene, diarylethene or spiropyran moieties have been realised and studied. Firstly, we focused on multi-azobenzene systems capable of undergoing large geometric rearrangements during photoisomerisation, as they may be used in the future as constituent elements of host-guest or metal-organic frameworks controllable by luminous stimuli. In a second example, dithienylethene-type photochromic switches have been used to trigger the emission of a porphyrin. This dyad exhibited a reversible modulation of its emission, displaying a particularly highly contrasted response. As a final example, a spiropyran derivative has been combined with anisotropic gold nanoparticles. By inducing the isomerisation of the molecular switch in the AuNR colloidal liquid dispersions, we visualised a large variation of the colloid extinction spectrum, dependent on the LSPR mode wavelength and the spectral overlap with the photoswitch.

Nucleic acids, such as DNA, play an essential role in all known forms of life; however, despite their fundamental importance, there is still a significant lack of understanding surrounding their functional behaviour. This thesis explores the structure and dynamics of DNA by employing methods based on fluorescence and through the use of computational calculations. Time-resolved fluorescence experiments have been performed on dinucleotides containing 2-aminopurine (2AP) in various alcohol-water mixtures. 2AP, a fluorescent analogue of the nucleobase adenine, has been used extensively to investigate nucleic acids because of its ability to be incorporated into their structures with minimal perturbation and its high sensitivity to its local environment. Direct solvent effects on 2AP were established through measurements on the free fluorophore. Analysis of the complex fluorescence decays associated with the dinucleotides was challenging but has provided insight into their conformational dynamics. Solvent polarity was found to play a significant role in determining both photophysical and conformational properties in these systems. The complicated fluorescence decay of 2AP in nucleic acids highlights the need for accurate and unbiased analysis methods. Various time-resolved fluorescence analysis methods, including iterative reconvolution and the exponential series method, have been investigated with real and simulated data to obtain an overview of their benefits and limitations. The main outcome of the evaluation is that no single method is preferred in all situations and there is likely to be value in using a combination when there is ambiguity in the interpretation of the results. Regardless of the analysis technique used, the parameterised description of the observed fluorescence decay is meaningless if the underlying physical model is unrealistic. The advance of computational methods has provided a new means to rigorously test the viability of proposed models. Calculations have been performed at the M06-2X/6-31+G(d) level of theory to investigate the stability of 2AP-containing dinucleotides in conformations similar to those observed in the double-helical structure of DNA. The results help to explain the similarity of the time-resolved fluorescence behaviour of 2AP in dinucleotide and DNA systems but also bring to light subtle differences that could perhaps account for experimental discrepancies. The recent emergence of advanced optical microscopy techniques has offered the prospect of being able to directly visualise nucleic acid structure at the nanoscale but, unfortunately, limitations of existing labelling methods have hindered delivery of this potential. To address this issue, a novel strategy has been used to introduce reversible fluorescence photoswitching into DNA at high label density. Photophysical studies have implicated aggregation and energy-transfer as possible quenching mechanisms in this system, which could be detrimental to its future application. The reliability of fluorescence photoswitching was investigated at ensemble and single-molecule level and by performing optical lock-in detection imaging. These developments lay the foundations for improved and sequence-specific super-resolution microscopy of DNA, which could offer new insights into the 3D nanoscale structure of this remarkable biopolymer. In summary, the work presented in this thesis outlines important observations and developments that have been made in the study of the structure and dynamics of nucleic acids.

This work aimed at studying biophysical properties of two membrane proteins, one of potential nanotechnological use, bacteriorhodopsin, and one potential drug target, the NTS1 neurotensin receptor, at the single molecule scale. Bacteriorhodopsin (BR) is the only protein in the purple membrane (PM) of the halophilic organism Halobacterium salinarium. It is a light-driven proton pump converting light into a transmembrane proton gradient through isomerization of its retinal chromophore. Its stability, as well as its photoactivity remaining in dry protein layers, has made BR an attractive material for biomolecular devices. Numerous studies have been published on this topic; however, they have all used BR within the PM, on relatively large (µm-wide) surfaces. Here, conducting-probe atomic force microscopy (C-AFM) analysis was performed after removing most of the membrane lipids. For the first time, it was shown that the molecular conductance of BR can be reversibly photoswitched with predictable wavelength sensitivity. Intimate and robust coupling to gold electrodes was achieved by using a strategically engineered cysteine which, combined with partial delipidation, generated protein trimers homogenously orientated on the surface. Numerous controls using biophysical (SPR, ellipsometry, Kelvin-probe AFM) and chemical (photocurrent, cyclic voltammetry) techniques confirmed the wavelength specificity of the photoswitch, the anchoring role of the mutation and the homogenous orientation of the protein on the gold surface. Neurotensin is a brain and gastrointestinal 13 amino acid peptide acting as a neuromodulator in the central nervous system and as a hormone in the periphery. Its wide range of biological activities is primarily mediated through its binding to the neurotensin type 1 receptor (NTS1). NTS1 expressed in E.coli was purified and inserted into 100 nm brain polar lipid liposomes in a conformation which retained its ligand-binding capabilities. Initial AFM characterisation was performed as a prelude for ligand-receptor interaction studies, including high resolution imaging, force spectroscopy and solid state NMR approaches.

Optical modulation of the physical properties of materials is important for future development of optical memories and switches, optoelectronics, and smart surfaces. Incorporation of an optically bistable photochromic compound into an electronically bifunctional material is a promising strategy for a development of photoswitchable materials. Photochromic spirooxazine ligands undergo light-induced ring-opening and closure between the closed-spirooxazine (SO) and open-photomerocynanine (PMC) forms. The structural reorganization leads to accompanying changes in electronic structure which can lead to a change in the oxidation/reduction potentials and spin state of a bound metal center. Changes in the ligand field about a metal center in turn can lead to “non-classical” photoinduced magnetic (PIM) effects. The “non-classical” PIM effect is an effect that occurs through ligand-centered processes via the metal center, rather than direct excitation at the metal center. The structural change of the photochromic compounds also results in a change in the frontier orbital energies and donor-acceptor character, which may lead to optically-gated charge-transfer and energy-transfer processes. In this dissertation, the structural factors that govern thermal relaxation of spirooxazines, as optical control units, was investigated toward controlling the photostationary states of this important class of photochromes. The electronic structure of the PMC form of azahomoadamantyl-based spirooxazines was found to control the thermal coloration/decoloration rates of photochromic spirooxazines. A significant charge-separated character of the PMC form was correlated with the slow thermal coloration/decoloration rates in spirooxazines. This concept was then extended to an investigation of the effect of Lewis-acidic metal complexation. Solution study of the charge-separated character of the PMC form via metal complexation of the photochromic spirooxazines supported the correlation between the charge-separated character of the PMC form and the rate of the thermal coloration/decoloration. The studies provide a potential pathway for modulating PMC thermal relaxation rates through optimization of the structure of the spirooxazines and metal complexation. The studies were then extended to an investigation of the photomodulation of charge-transfer processes in cobalt multinuclear clusters by photoisomerization of photochromic spirooxazines. Incorporation of optically bistable phenanthroline-spirooxazine ligands into a magnetically bistable cobalt-dioxolene valence tautomeric cluster resulted in large magnetic moments in the solid and solution states. This study suggests that the redox-isomeric behavior of the cobalt dioxolenes can be coupled to isomerization of the photochromic ligand in the solution state when the π-acceptor ability of the photochromic ligands align with the direction of charge transfer of the cobalt dioxolene components. The potential of these cobalt multinuclear clusters to enhance the relaxivity of water in MRI for biological imaging was investigated. A cobalt tetranuclear cluster was prepared and found to exhibit high magnetic moments in solution at room temperature, and large relaxivities relative to commercially available gadolinium based MRI contrast agents. Lastly, the photomodulation of ionic doping of graphene organic field-effect transistors (OFETs) by photochromic spirooxazines was investigated. The electron donor or acceptor nature of the photochromic isomers modulates the direction and magnitude of ionic doping of graphene, and in turn the gate voltages of graphene OFETs, leading to optical modulation of OFET gate voltages for data processing and memory technologies. / Graduate / 2020-02-08

Avec les progrès de l'informatique, la quantité de données crée et échangée augmente exponentiellement. Le stockage de l'information doit évoluer pour être plus performant, et les matériaux actuels atteignent leur limite. Une évolution technologique est nécessaire. Une des réponses possibles se trouve dans les polymères de coordinations photo-commutables, dont la propriété de bi-stabilité permettrait d'obtenir des densités de stockage et des vitesses de lecture/écriture jamais atteintes. Afin d'utiliser ces matériaux, leur mise en forme, et particulièrement leur réduction en taille, est nécessaire, mais accomplir cette mise en forme sans affecter la propriété de commutation est ardu. Dans ce travail, nous proposons une mise en forme contrôlée à base de silice mésoporeuse pour obtenir des nanoparticules de composés de coordination possédant des propriétés intéressantes pour des applications. Spécifiquement, Ce travail a pour objectifs de (i) réduire en taille les composés fonctionnels, (ii) étudier la propriété à l'échelle du nanomètre, (iii) utiliser les possibilités de notre voie de synthèse pour comprendre l'effet de la mise en forme et (iv) aller vers de nouvelles propriétés causées par la mise en forme. Nous espérons ainsi poser une base solide pour l'étude de ces composés fonctionnels à l'échelle du nanomètre. / With the raise of information technology, the amount of data created and exchanged increases drastically. Information storage must evolve to be more and more efficient, but the current materials used are reaching their peak. A technological evolution is needed. One of the possible answers is found with the photo-switchable coordination polymers, which property would allow us to attain storage density as well as addressing times never seen before. In order to use these materials, their processing, and especially their size reduction, is the key. However, successfully processing these without impacting the switching property is not an easy task. In this work, we propose a perfectly controlled processing based on mesoporous silica for the synthesis of nanoparticles of potentially applicative coordination compounds. To be specific, our work intends to (i) reduce the size of functional compounds, (ii) study the property at the nanoscale, (iii) use the possibilities of our synthesis to understand the effect of processing on the property and (iv) obtain new properties, caused by the processing. We therefore hope to lay a solid basis for the nanoscale study of these functional compounds.

Le stockage optique de l’information et l’imagerie à super-résolution sont des champs d’application dont les besoins en matériaux et en molécules photocommutables sont grandissants. Une des approches consiste à associer au sein d’une même structure moléculaire des photochromes et des fluorophores au sein de laquelle des transferts d’énergie résonants sont possibles. La combinaison des propriétés photophysiques des deux types d’entités conduit à la photocommutation de fluorescence recherchée. Pour concevoir de tels systèmes, nous avons basé notre approche sur le concept de click chemistry qui permet d’avoir une grande flexibilité du point de vue synthétique. Ainsi, en utilisant des plateformes moléculaires comme les dérivés de sucres et la β-cyclodextrine, nous avons synthétisé de nombreuses architectures multichromophoriques. En variant le ratio entre le nombre de photochromes (DAE) et de fluorophores (DCM) au sein d’une même molécule, nous avons pu progresser dans la compréhension des relations entre les structures et les propriétés photophysiques de ces systèmes, impliquant des transferts d’énergie multiples entre les différentes entités. Cette démarche nous a permis, d’une part, d’appréhender les effets d’extinction non-linéaire de fluorescence, et d’autre part, de découvrir l’effet d’hystérèse photocontrôlable résultant de la compétition entre les transferts d’énergie et les réactions photochromes. / The fields of optical data storage and super-resolution imaging are in expansion and attract an increasing demand on photoswitchable materials and molecules. One approach consists in associating photochromic and fluorophores units in the same molecular structure, allowing resonant energy transfer processes. The combination of the photophysical properties of the two units leads to the expected fluorescence photoswitching. To design such systems, we based our approach on the click chemistry concept which offers a great flexibility in terms of synthesis pathways. Thus, using molecular platforms such as sugar derivatives and β-cyclodextrin, we have synthesized many multichromophoric architectures. By varying the ratio between photochromic (DAE) and fluorophore (DCM) units in the same molecule, we improved our comprehension of the structure-properties relationships, involving multiple energy transfers between the different entities. This allowed us, first, to understand the effects of non-linear fluorescence quenching, and secondly, to discover the light-controlled hysteresis effect resulting from the competition between energy transfers and photochromic reactions.

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