This work describes an investigation into the solution-phase binding of anionic guests by bimacrocyclic lanthanide complexes. It outlines the preparation of different classes of complexes bearing two metallic domains, and the effects of association on both the complex and the guest. Chapter one provides a cursory introduction to the fundamental properties of the lanthanides with a focus on luminescence. A brief literature review is given on the use of emissive lanthanide probes for the sensing of analytes. Chapter two concerns the preparation and properties of a series of binuclear complexes in which the two centres are linked with a short spacer group, with the aim of selectively sequestering small anions such as the halides in solution. The concept of luminescence titration will be introduced and then used to assess the binding parameters of a selection of guests. Chapter three describes a related class of ditopic lanthanide complexes in which the two metal centres are separated by a semi-rigid butyne linking group. Luminescence studies are again used to evaluate the binding constants of homologous series of dianions to ascertain how the size, geometry and functionalization of the anionic guest impacts on binding. Chapter four explores the coordination of phosphate species and assesses the ability to bind biologically significant phosphates of some of the complexes from Chapter 3. Chapter five details an investigation into the effects on guest-selectivity of further lengthening the linking unit which separates the two macrocyclic binding domains. Chapter six summarises the work done throughout the thesis and draws some overarching conclusions, as well as highlighting areas for further study. Chapter seven describes the experimental procedures.

L’objectif de cette thèse était d’obtenir des nanocylindres de Janus, particules présentant deux faces différentes, parchimie supramoléculaire. De telles particules seraient très intéressantes comme stabilisant d’émulsions mais sont trèsdifficiles à synthétiser. Notre idée a consisté à utiliser des systèmes auto-associatifs de type bisurée et trisurée, capablesde s’organiser en solution en structures cylindriques par le biais de liaisons hydrogène directionnelles. En décorant cesfonctions de deux bras polymères incompatibles, des propriétés de Janus sont attendues.Tout d’abord, l’étude de l’auto-association en solution de bisurées et trisurées décorées de deux bras polyisobutylène(PIB) identiques a montré que la formation de longs cylindres nécessitait des motifs trisurées s’associant assez fortementpour contrebalancer la gêne stérique des bras PIB. Pour des trisurées décorées de deux bras polystyrène (PS), il estnécessaire de synthétiser des bras PS très courts pour former des cylindres anisotropes, ce qui a été possible en ayantrecours à la polymérisation radicalaire contrôlée.Les résultats précédents ont permis d’identifier une trisurée décorée par un bras PIB et un bras PS court comme candidatidéal à l’élaboration de nanocylindres de Janus. La synthèse d’une telle molécule a été mise au point. Son organisation ensolution a été étudiée par diffusion de lumière, révélant que la taille des objets est principalement contrôlée par les brasPS encombrants. Bien que l’incompatibilité forte entre le PS et le PIB, vérifiée en masse, laisse espérer leur ségrégationde phase en solution, le caractère Janus des particules reste une perspective essentielle de ce travail. / The goal of this thesis was to obtain Janus self assembled nanocylinders. These particles present two different faces andwould be very interesting as emulsion stabilizers but are very difficult to synthesize. Our idea was to use self assemblingsystems based on bisureas and trisureas. These systems are able to self-assemble in solution into cylindrical structuresthrough directional hydrogen bonds. Decorating them by two incompatible polymer arms should lead to Janus properties.First, the study of the self-assembly in solution of bisureas and trisureas decorated by two identical polyisobutylene (PIB)arms has demonstrated that the formation of long cylinders required trisureas, able to develop strong enough hydrogenbonds to counterbalance the steric hindrance of the PIB arms. Trisureas decorated by two identical polystyrene (PS) armsrequired the synthesis of very short PS arms in order to form anisotropic cylinders. This could be achieved usingcontrolled radical polymerization.The previous results allowed the identification of a trisurea decorated by one PIB arm and one short PS arm as idealcandidate for the elaboration of Janus nanocylinders. The synthesis of such a molecule was developed. Its self-assemblyin solution was studied by light scattering, revealing that the size of the objects was mainly controlled by the bulky PSarms. Although the strong incompatibility between PS and PIB, which was evidenced in the bulk, gives hope that thesepolymers will phase segregate in solution, the Janus character of these particles remains an essential outlook of thiswork.

In this thesis, density functional theory is employed in the study of two kinds of systems that can be considered to be biomimetic in their own ways. First, three binuclear metal complexes, synthesized by the group of Prof. Ebbe Nordlander, have been investigated. The complexes are designed to resemble the active sites of phosphatase enzymes and have been examined in complexes where either two Zn(II) ions or one Fe(III) and one Mn(II) ion are bound. These dinuclear compounds were studied as catalysts for the hydrolysis of bis(2,4-dinitrophenyl) phosphate and the transesterification of 2-hydroxypropyl p-nitrophenyl phosphate, which are model systems for the same reactions occurring in DNA or RNA. It was found that the two reactions take place in similar ways: a hydroxide ion that is terminally bound to one of the metal centers acts either as a nucleophile in the hydrolysis reaction or as a base in the transesterification. The leaving groups depart in an effectively concerted manner, and the formed catalyst-product complexes are predicted to be the resting states of the catalytic cycles. The rate-determining free energy barriers are identified from the catalyst-product complex in one catalytic cycle to the transition state of nucleophilic attack in the next. Another type of biomimetic modeling is made with an aim of imitating the conceptual features of selective binding of guests and screening them from solute-solvent interactions. Such features are found in so-called nanocontainers, and this thesis is concerned with studies of two capsules synthesized by the group of Prof. Julius Rebek, Jr. First, the cycloaddition of phenyl acetylene and phenyl azide has experimentally been observed to be accelerated in the presence of a capsule. Computational studies were herein performed on this system, and a previously unrecognized structure of the capsule is discovered. Two main factors are then identified as sources of the rate acceleration compared to the uncatalyzed reaction, namely the reduction of the entropic component and the selective destabilization of the reactant supercomplex over the transition state. In the second capsule study, the alkane binding trends of a water-soluble cavitand was studied. It is found that implicit solvation models fail severely in reproducing the experimental equilibrium observed between binding of n-decane by the cavitand monomer and encapsulation in the capsule dimer. A mixed explicit/implicit solvation protocol is developed to better quantify the effect of hydrating the cavitand, and a simple correction to the hydration free energy of a single water molecule is proposed to remedy this. The resulting scheme is used to predict new hydration free energies of the cavitand complexes, resulting in significant improvement vis-à-vis experiments. The computational results presented in this thesis show the usefulness of the quantum chemical calculations to develop understanding of experimental trends observed for substrate binding and catalysis. In particular, the methodology is shown to be versatile enough such that experimental observations can be reproduced for such diverse systems as studied herein. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.</p>

Le travail qui est décrit dans ce manuscrit de thèse traite de la chimie des superbases de type proazaphosphatranes, systèmes phosphorés bicycliques très utilisés en catalyse. L’objectif des investigations qui ont été menées à été d’ouvrir de nouvelles voies d’applications de ces catalyseurs. Afin de satisfaire cet objectif, plusieurs stratégies ont été envisagées. D’une part par la mise en confinement de la structure proazaphosphatrane et l’étude de l’influence de ce confinement sur la réactivité intrinsèque du proazaphosphatrane, et d’autre part par la catalyse en conditions bi-phasiques, que ce soit à l’interface entre une phase liquide et un solide ou entre deux phases liquides non-miscibles. Les recherches se sont orientées dans un premier temps sur la synthèse et la caractérisation complète d’un proazaphosphatrane supramoléculaire, obtenu par la fonctionnalisation par un proazaphosphatrane de la cavité supramoléculaire d’un récepteur macrobicyclique. Les séparations semi-préparatives des deux énantiomères d’un intermédiaire et de la molécule phosphorée finale ont également été réalisées, séparations qui ont permis de réaliser l’attribution des configurations absolues des deux structures macrobicycliques. La synthèse d’une famille de catalyseurs de type proazaphosphatrane supportés sur silice mésoporeuse a ensuite été réalisée, suivie de sa caractérisation texturale et structurale par les procédés physico-chimiques habituels, et enfin de sa mise en application dans des réactions d’intérêts de la synthèse organique. En dernier lieu, l’exploitation de la forme acide conjuguée des proazaphosphatranes, dite forme azaphosphatrane, dans des réactions de catalyse par transfert de phase a été entreprise. Il a ainsi put être démontré leur activité en tant qu’agent de transfert dans le cadre de quatre réactions significatives de la catalyse par transfert de phase en version racémique. Ce travail de thèse s’est finalement terminé par une ouverture vers la catalyse par transfert de phase en version asymétrique, par le biais de l’utilisation d’azaphosphatranes chiraux énantiopurs. / The work described in this PhD thesis deals with the chemistry of proazaphosphatrane-type superbases, which are highly reactive bicyclic phosphorous systems largely applied in catalysis. The main goal of these investigations was to devise new applications for their use in catalysis. In this way, several strategies were followed, with an emphasis on their molecular confinement and use in interfacial catalytic systems. In the first part, the manuscript describes the synthesis and characterisation of a supramolecular proazaphosphatrane obtained via the enclosing of a proazaphosphatrane moiety in a hemicryptophane-type macrobicyclic cavity. In parallel, the semi-preparative scale resolution of two macrobicyclic intermediates allowed us to assign their absolute configurations. In the second part, the synthesis and characterisation of a new class of superbases supported on mesoporous silica was achieved. The synthesis was followed by their application in base-catalysed organic reactions. The last part reports the use of their conjugate acids, or azaphosphatranes, in phase transfer catalysis. Their usefulness as achiral phase transfer agents in four relevant reactions was thus determined. The thesis ends with an introduction into asymmetric phase transfer catalysis, using enantiopure azaphosphatranes.

La presente tesis doctoral titulada ¿Supramolecular and heterosupramolecular chemistry in controlled release and molecular recognition processes¿ está centrada en los dos aspectos principales de la química supramolecular que han experimentado un gran auge en los últimos años: el reconocimiento molecular y los procesos de liberación controlada. En particular la primera parte de la tesis se focaliza en el diseño y síntesis de moléculas orgánicas que pueden ser empleados cómo sensores para especies aniónicas y neutras. El paradigma seleccionado para los procesos de reconocimiento molecular fue la aproximación del dosimetro químico. Esta aproximación presenta ventajas con respecto a los otros dos métodos de determinación de aniones (desplazamiento y unidad coordinanteunidad indicadora), cómo, por ejemplo, la posibilidad de determinar los analitos en disolución acuosa. Así se sintetizaron dos sensores selectivos, uno para el anión fluoruro (F-) y el otro para glutatión (GSH). El sensor selectivo para la determinación de F- está basado en un colorante azoico funcionalizado, en su ¿OH fenólico, cómo silileter. Esta molécula presenta una banda de absroción muy intensa centrada a 350 nm que, después de la adición de F- , sufre un efecto hipocrómico significativo y un desplazamiento batocromico ligero (de ca. 10 nm), mientras aparece una nueva banda a 470 nm, determinando un cambio de incoloro a amarillorojo. Para obtener un sensor selectivo para GSH se sintetizó una sonda químico basado en una sal de 2,6-difenilpirilio. Sucesivamente se preparó una disolución de este compuesto en agua/CTAB, que se caracterizaba por un intenso color azul. En este caso, la adición de GSH produce una disminución significativa de la banda del visible, acompañada por la consecuente decoloración. Además la adicón de GSH induce la aparición de Resumen vi una intensa banda de emisión centrada a 485 nm (después de la irradiación a 350 nm). La segunda parte de esta tesis doctoral se basa en el diseño y síntesis de nuevos sistemas híbridos orgánicos-inorgánicos para procesos de liberación controlada en ambiente celular. Estos materiales híbridos se componen en general, de dos unidades: una matriz inorgánica mesoporosa de base silícea, capaz de almacenar moléculas orgánicas (colorantes, farmacos...) y un compuesto orgánico anclado covalentemente a la superficie externa del soporte inorgánico mesoporoso, que actúa cómo puerta molecular. La aplicación de un estímulo externo puede modificar la conformación de la puerta molecular permitiendo o bien impidiendo la difusión de la carga almacenada en los mesoporos hacía el exterior (disolución o citoplasma). El primer sistema sintetizado y estudiado se compone de una matriz inorgánica mesoporosa (MCM-41), cargada con el colorante Ru(bipy)3 2+ y funcionalizada en la superficie con un oligoetilen glicol mediante un grupo ester. La adición de la enzima esterasa determinaba la hidrólisis del grupo ester y la consecuente reducción del tamaño de la puerta molecular, acompañada por la liberación del colorante previamente cargado. Otro sistema de liberación preparado consiste en el uso de la misma matriz MCM-41 nanoscópica y el mismo colorante Ru(bipy)3 2+, pero se funcionalizó la superficie con una puerta molecular fotolabil. La irradiación en el maximo de absorción de la puerta molecular inducía la fotodegradación de la misma y la consecuente liberación del colorante. Un tercer ejemplo de sistema de liberación consiste en una puerta molecular caracterizada por la presencia de dos grupos funcionales hidrolizables con enzimas diferentes: grupos urea y amida. vii El material final, caracterizado por la presencia del mismo esqueleto inorgánico, y cargado con Ru(bipy)3 2+, era capaz de liberar selectivamente cantidades distintas de colorante, dependiendo del enzima empleado. Así se podían conseguir dos tipos de perfiles de liberación: uno muy rápido y poco intenso y otro más lento pero mucho mas intenso. Finalmente se sintetizó un material híbrido siempre basado en la misma matriz de MCM- 41, cargado con rodamina-B y funcionalizado en la superficie con galactooligosacáridos. Con este material se podía conseguir una liberación controlada del colorante selectivamente en células senescentes, debido a que estas sobreexpresan el enzima ß-galactosidasa que es capaz de hidrolizar los galactooligosacáridos. / Agostini, A. (2013). Supramolecular and heterosupramolecar chemistry in controlled release and molecular recognition processes [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/29397 / TESIS

Les travaux de cette thèse intitulée « Associations supramoléculaires des Complexes de clusters métalliques avec les cyclodextrines : Des interactions en solution à la conception de systèmes mixtes Clusters-polyoxométallates » portent sur l’encapsulation de clusters octaédriques par des oligosaccharides cycliques appelés cyclodextrines. La première partie de ce travail concerne l’étude en solution aqueuse du comportement de clusters de rhénium cationiques [Re6Q8(H2O)6]2+ (avec Q = S ou Se) ou anioniques du type [Re6Q8(CN)6]4- (avec Q = S, Se ou Te) vis-à-vis de cyclodextrines de type α, β et γ. Les études menées en solution au moyen de la RMN de 1H montrent que les clusters aquo cationique [Re6Q8(CN)6]4- interagissent très faiblement avec la cyclodextrine γ (noté γ -CD) alors que la diffraction des rayons X révèle que ces systèmes cristallisés contiennent l’adduit supramoléculaire de type hôte-invité de stoichiométrie 1:1 {[Re6Q8(H2O)6]@g-CD}2+ sans que l’analyse structurale ne révèle d’intéractions attractives significatives entre le cluster et le macrocycle. L’étude des dérivés anioniques cyano [Re6Q8(CN)6]4- (Q = S, Se ou Te) a permis d’établir les critères favorisant les interactions de type hôte-invité. Les études en solution montrent que pour ces systèmes cluster-CD, les interactions supramoléculaires peuvent être classés selon l’ordre α-CD < β-CD < γ-CD. Cependant, la nature du ligand chalcogénure (Q = S, Se, Te) a aussi une influence déterminante dans le processus de reconnaissance supramoléculaire en suivant le classement suivant S < Se < Te. Les études RMN 1H, 77Se et 125Te complétées par la détermination par ITC des grandeurs thermodynamiques associées au processus de reconnaissance hôte-invité. Ces études révèlent dans tous les cas que le processus de reconnaissance est très largement favorisé d’un point de vue enthalpique alors que la contribution entropique est toujours défavorable. Cette signature thermodynamique peut être reliée au comportement chaotrope de ces ions en solution. Les études structurales menées par diffraction des rayons X ont dans tout les cas montrées des associations supramoléculaires qui peuvent différer subtilement selon la nature du cluster et le type de cyclodextrine. Enfin, des études électrochimiques confirment les résultats précédents et mettent davantage en lumière le rôle déterminant de la charge ionique sur la stabilité des agrégats supramoléculaires.Ces complexes de rhénium ont été engagés dans des associations inédites avec des polyoxométallates. L’idée sous jacente de cette étude repose sur la création de système « push-pull » inorganiques associant une unité riche en électrons (le cluster) avec unité pauvre en électrons (le POM). Plusieurs structures sont décrites avec l’ion de Dawson [P2W18O62]6- ou un POM géant dérivé des bleus de molybdène. Elles démontrent le rôle déterminant de la cyclodextrine dans le processus d’interaction qui permet d’associer des anions cluster-POM. Ces composés apparaissent comme de très bon candidats pour l’élaboration de phases nanostructurées à base d’oxychalcogénures métalliques.Dans une dernière partie, les travaux ont été étendus aux clusters {M6X8Cl6}2- ( avec M = Mo ou W et X = Br ou I). Bien que certains d’entre eux présentent des propriétés remarquables de luminescence, leur faible résistance à l’hydrolyse en milieu aqueux limite considérablement leur utilisation pour des applications biomédicales. Ce travail réalisé au moyen de la RMN de 35Cl et UV-vis montre que les associations supramoléculaires de type hôte-invité permet de stabiliser de façon spectaculaire ces clusters. Des études préliminaires de cytotoxicité et de photothérapie dynamique (PDT) menées sur certains de ces systèmes cluster-CD montrent des résultats encourageant qui augurent de belles perspectives pour l’avenir. / In this work, we report in first part the detailed study of the interaction of rhenium cluster complexes [{Re6Q8}(H2O)6]2+ and [{Re6Q8}(CN)6]4–/3– (Q = S, Se, Te) with cyclodextrins (α, β and γ). Upon dissolving the reagents in water and then evaporating the solution or diffusion of ethanol vapors into the solution, crystalline products were obtained which crystallized as fragments without the formation of host-guest compounds (α-CD and Q = Se, Te ) or inclusion compounds with weak interactions with the primary or secondary face of CD (β-CD and all complexes, γ-CD / α-CD and Q = S), or very tightly coupled inclusion compounds involving the secondary face of CD (γ- CD and Q = Se, Te), which was confirmed by XRD. Moreover, similar behavior was found in aqueous solutions using a wide range of methods such as NMR spectroscopy (both from the host and the guest side), ITC, mass spectrometry, etc. Also, it was demonstrated that the inclusion cyclodextrins strongly affects the properties of cluster complexes, especially redox and luminescent. All data obtained by solution methods lead to the identification of two main factors of interaction with the CD, namely: (1) size-matching of host and guest, (2) the chaotropic nature of the guest. The chaotropic effect (the water structure breaking) of the complexes makes a significant contribution to the formation of inclusion compounds, however, when size-matching is additionally observed, the interaction becomes even stronger. The chaotropic effect was also confirmed by studying two complexes with different charges. Thus, an increase in the chaotropic effect without changing the size of the complex led to an increase in the binding constants with γ-CD by approximately 1000 times.In the second part, we have demonstrated that the inclusion compounds of rhenium cluster complexes with cyclodextrin can be combined with other functional inorganic compounds - polyoxometalates. In such three-component systems, cyclodextrin plays the role of a binding agent. In the case of a logical combination of oppositely charged cationic cluster complexes and a Dawson-type anion, the system is mainly formed due to the strong bond between the POM and the CD, since cluster interacts very weakly with CD. On the other hand, ions of the same charge (anionic cluster and anionic POM) can also form three-component systems, which are mainly based on inclusion of cluster into CD. Moreover, inclusion compounds can participate in the formation of nanoscale supramolecular ensembles with a nano-wheel {Mo154}, which exist both in solid state and in aqueous solution.In the last part, it was demonstrated that, using the supramolecular approach, it is possible to stabilize molybdenum and tungsten cluster complexes with low hydrolytic stability in aqueous solutions. For the first time, water-soluble Na2[{M6X8}Cl6] complexes (M = Mo, W, X = Br, I) were obtained and the kinetics of substitution of terminal ligands in water was studied in detail. Adding γ-CD to the system leads to the formation of strong inclusion compounds in a 1:2 ratio with the participation of the secondary face of cyclodextrin. Moreover, inclusion in γ-CD significantly reduces the rate of substitution of terminal ligands and allows us to obtain solutions that are stable for at least several months. The obtained compounds possess the best photophysical characteristics of luminescence in aqueous solutions among molybdenum and tungsten cluster complexes. Also, inclusion in the CD allowed us to study for the first time the redox properties of complexes in water. In conclusion, it was demonstrated that such systems have the lowest cytotoxicity, which makes them promising for further studies for use in biology and medicine.

Le développement d'architectures moléculaires enchevêtrées (rotaxanes) est un sujet d'actualité en chimie supramoléculaire. Cette thèse examine la synthèse multi-étape de sous-unités de rotaxanes, notamment de composants macrocycliques électroactifs, et leur assemblage dans des structures moléculaires imbriquées. De nouveaux cycles à 31 et 35 chaînons à liaison hydrogène comprenant un motif récepteur bis (2,6-diamidopyridine) et une unité électroactive, à savoir du ferrocène ou de la triphénylamine, ont été synthétisés. Ces macrocycles ont été analysés par voltampérométrie cyclique, analyse par diffraction des rayons X sur cristal unique, ainsi que par spectroscopie RMN et spectrométrie de masse. Les interactions hôte-invité avec un acide complémentaire 5,5’-diéthylbarbiturique (Barbital) en tant qu’invité modèle ont également été étudiées par titrage spectroscopique par absorption électronique et RMN 1H. Les affinités de liaison étaient corrélées à la structure moléculaire. Des approches pour former des [2]rotaxanes, notamment en utilisant une réaction de matrice métallique active, où l'ion métallique joue le double rôle de matrice et de catalyseur, sont décrites. En particulier, les réactions de couplage de Huisgen ainsi que de Glaser catalysées au cuivre(I) ont été utilisées avec des bouchons de volumes variés. Dans une deuxième approche complémentaire de type "attache" de la formation de rotaxane, l'anneau électroactif a été formé directement entourant le composant de filetage servant de modèle. Cette méthodologie a permis d'obtenir deux [2] rotaxanes inédits via une réaction de "clipping" à cinq composants assistée par matrice, l'un des rotaxanes intégrant deux unités de ferrocène, tandis que l'autre comprenait deux unités de type triphénylamine. Les études de diffraction des rayons X sur cristal unique ont confirmé le caractère imbriqué des assemblages. / Development of interlocked molecular ring-on-thread architectures (rotaxanes) represents a central current topic in supramolecular chemistry. This thesis considers the multi-step synthesis of rotaxane subcomponents, notably electroactive macrocyclic components, and their assembly into interlocked molecular structures. Novel hydrogen-bonding 31- and 35-member rings comprising a bis(2,6-diamidopyridine) receptor motif and an electroactive unit, namely ferrocene or triphenylamine, were synthesized. These macrocycles were analyzed by cyclic voltammetry, single crystal X-ray diffraction analysis, as well as NMR spectroscopy and mass spectrometry. Host-guest interactions with a complementary 5,5’-diethylbarbituric acid (Barbital) as model guest were also studied by electronic absorption and 1H-NMR spectroscopic titrations. Binding affinities were correlated to molecular structure. Approaches to form 2rotaxanes, notably by employing an active metal template reaction, where the metal ion plays the dual role of template and catalyst, are described. In particular, the copper(I)-catalyzed Huisgen as well as Glaser coupling reactions were employed with a variety of bulky stopper groups. In a second complementary “clipping”-type approach to rotaxane formation, the electroactive ring was directly formed encircling the templating thread component. This methodology yielded two further novel [2]rotaxanes via a template-assisted five-component clipping reaction, one rotaxane integrating two ferrocene units while the other comprised two triphenylamine-like units. Single crystal X-ray diffraction studies confirmed the interlocked nature of the assemblies.

No description available.

<p>  </p> <p>DNA nanotechnology has rendered programmable, bottom-up self-assembly of nanostructures in various morphology, versatile functionalization, and atomic level precision over the last forty years. DNA nanostructures are usually assembled in solution by the thermodynamic process in a specific solution. In recent years, DNA two-dimensional (2D) structures on the surface have been widely applied in semiconductors, electronic devices, and biomedical studies. My research mainly focused on novel DNA nanostructures assembly on the surface and their applications. I have developed an equilibrium-enabled flexibly curved DNA homopolymer. I have further developed a novel method to determine the interhelical angle of DNA secondary structure by DNA 2D-array.</p> <p>In this thesis, I have envisioned a strategy to prepare DNA linear polymers with flexible curvature and further assembled them into spiral or concentric rings on the surface. In DNA double crossover-like (DXL) homopolymers, an aromatic chemical group was introduced to the 3'-end in each strand. The planar group could stack into the DNA homopolymer, which increases the length on one side of the DXL polymer and further bend the structure by uneven-length stress. Moreover, the stacking in is under the equilibrium with flipping out, endowing the dynamic change and flexibility to the curvature of the DNA homopolymer, which could be a benefit in the surface-assisted construction of spirals or concentric rings.</p> <p>With the appropriate design, DNA could be self-assembled on the surface into 2D crystals in a certain periodicity. Such a structure could be applied in nucleic acid secondary structure determination as a crystallography-like method. In this work, I have successfully incorporated the 10-23 DNAzyme, a common-used RNA-cleavage DNA sequence into DNA 2D arrays. In the brick-wall-like DNA 2D arrays, the repeating distance determined the interhelical angle of the 10-23 DNAzyme flanks. By 2D fast Fourier transform (FFT), this repeating distance could be measured and calibrated, following the deduction of the target angle. This approach had been validated with well-known DNA secondary structures. </p>

Rewritable photochrome-based 3D optical data storage requires photochromic molecules with high two-photon absorption (2PA) cross sections. Currently, the low value of two-photon absorption cross sections of existing photochromes makes them unsuitable for practical application in 3D data storage. Worldwide attempts to increase the cross section of photochromic molecules by altering the chemical structure have yielded poor results. In this work, two ways to increase the two-photon absorption cross sections of photochromes were investigated. In the first method, partial success demonstrated by extending the conjugation of a photochromic molecule, a high two-photon absorption cross section of the closed form isomer and high photoconversion to the closed form were realized. At the same time, a decrease in photoswitching quantum yield and low photoconversion to open form was observed. A discussion is provided to explain the results, suggesting that the proposed method of extending the conjugation may not solve the problem. For this reason a new method for effective two-photon absorption cross section enhancement of photochromes was proposed. As a proof of principle, a new two-photon absorbing dye with a hydrogen bonding moiety was synthesized and used for the formation of supramolecular structures with a photochromic compound. Theoretical reasoning and experimental demonstration of energy transfer from the dye to the photochrome under one and two-photon excitation confirmed the practical value of the method. The effects of a 2PA dye on the photochromic properties of a diarylethene were investigated using a model compound to simplify data analysis. Formation of supramolecular structures was revealed using ¹H NMR spectroscopic methods. The model compound, having the same hydrogen bonding moiety as 2PA dye, has been demonstrated to bind with photochrome molecules at very low concentrations. Photochromic properties of 2,3-bis(2,4,5-trimethyl-3-thienyl)maleimide, including conversions at the photostationary state, extinction coefficients, photoisomerization reaction rates and quantum yields, were shown to be affected by hydrogen bonding with the model compound - 2,6-bis-(acetamido)pyridine. The extent of this change was determined and discussed, demonstrating a balanced supramolecular strategy to modulate photochemical and photophysical properties of this important class of photochromic material.