The study of topologically complex molecules is necessary to better understand the knotted architectures that abound within Nature and are vital in the functioning of DNA and proteins. Metal based template strategies have played a key role in the successful synthesis of a number of interwoven structures constructed from small molecule building blocks, however novel methodology is crucial for the expansion of this fascinating field of chemistry. The strategy of linking the ends of a cyclic helicate has been developed within the Leigh group and applied with great success to the synthesis of the first molecular pentafoil knot. This thesis presents the application of this strategy to the high yielding synthesis of a molecular Solomon link. In depth studies of the self-assembly of a pentafoil knot and self-sorting reactions are also presented, offering insights into the nontrivial self-assembly of these topologically complex molecules.

This thesis presents a modular palladium(II) template-directed synthetic strategy towards mechanically interlocked polymacrocyclic architectures, such as a Borromean link and linear [n]-catenanes. Central to the synthetic strategy is the use of the Huisgen-Meldal-Sharpless Cu(I)-catalysed 1,3-cycloaddition of azides to terminal alkynes (CuAAC) as a ring-closure procedure between complementary pairs of building blocks. The amalgamation of the palladium(II) [3+1]-template and CuAAC reaction is without methodological precedent and represents both an efficient and versatile procedure for the construction of interlocked architectures. Thematically, this thesis consists of three parts arranged in chronological order. Beginning with the synthesis towards a Borromean link, where the first successful palladium(II) template-directed double CuAAC ring-closure is documented. This is followed by the application of the “double-click” strategy to form a [3]catenane - the first such structure generated using metal ions other than Cu(I). Finally, the development of a modular CuAAC building block library is described, which was used to construct a [2]catenane and [3]catenane as well as later developments towards higher oligocatenanes.

The template synthesis of rotaxanes and catenanes has allowed a detailed study of their intrinsically novel and interesting properties. A key strategy has been the deployment of transition metal ions with their well-defined coordination geometries allowing high-yielding and facile preparation of interlocked architectures. Knowledge of how to exploit the coordination sphere of metal ions and the design of ligands for the creation of intermediates that are pre-disposed to undergo ‘stoppering’ or ‘clipping’ has been a crucial requirement for this approach. This Thesis is in three parts describing the use of three dimensional, two dimensional and one dimensional coordination geometries in the synthesis of interlocked architectures. Firstly, the octahedral coordination geometry of cobalt(III) was utilized to organize dianionic pyridine-2,6-dicarboxamido ligands in a mutually orthogonal arrangement such that ring closing metathesis macrocyclizations gave access to interlocked or entwined products. A ‘figure-of-eight’ complex was obtained from a double macrocyclizations, whereas a catenate was accessed through a single macrocyclization. The topology of the isomers was proved by X-ray crystallography. An analogous [2]rotaxane was synthesized and the interlocked nature of the rotaxane demonstrated by 1H NMR spectroscopy and mass spectrometry. Secondly, an “active” metal template strategy, in which the metal ion plays a dual role – acting to both organize ligands and catalyze mechanical bond formation – allowed rotaxanes be constructed using the square planar coordination geometry and Lewis acidic nature of a palladium(II) complex. The interlocked nature of the rotaxane was proved by X-ray crystallography, demonstrating that a nitrile group present in the thread acted as a “station” for the Pd(II)-macrocycle. This observation led to the construction of a two “station” degenerate molecular shuttle in which the dynamics of translocation were controlled by reagent addition and observed by 1H NMR techniques. Lastly, the linear coordination geometry of gold(I) was successfully used as a template for construction of rotaxanes and catenanes via a ‘clipping’ strategy. The linear coordination geometry and the interlocked nature of the gold(I)-catenate was proved by X-ray crystallography, the rotaxane architecture was proved by 1H NMR spectroscopy and mass spectrometry. Chapters Two, Three and Four are in the form of articles that have been published in peer-reviewed journals, and are reproduced, in their published format, in the Appendix. No attempt has been made to rewrite the published work; as a consequence the numbering of compounds, whilst consistent within each Chapter, is not consistent throughout this Thesis. Another consequence is that the many failed synthetic routes have been left out. I hope the reader will forgive these omissions as well as the slight repetition that occurs in the introduction and bibliography of each chapter. Additionally, preceding each Chapter is a brief synopsis that places the work in context and acknowledges the contributions of my fellow researchers.

The construction of mechanically interlocked molecules has been the subject of decades of research. The efficiency of strategies for preparing these molecules has increased continuously. In recent years, the transition metal templation strategy has played quite a remarkable role in the synthesis of entwined or mechanically bonded structures due to the metals’ diverse coordination chemistry and ability to chelate ligands. In the early stages of this method’s development, the metal ions were used as integral part of the scaffold for such components as rings and stoppers to generate the interlocked structures. In newly developed active metal templation strategies, metal ions are used to promote covalent bond forming reactions while simultaneously acting as structural supports. In this thesis, three main aspects are expanded for the discussion of the application of metal template strategies. First of all, the newly developed strategy - active metal template - will be described and exemplified using the Huisgen-Meldal-Fokin Cu(I)- catalyzed 1,3-cycloaddition of azides with terminal alkynes (the CuAAC “click” reaction), the Cu(I)-mediated Cadiot-Chodkiewicz heterocoupling of an alkyne halide with a terminal alkyne, and the Ni(II)-catalyzed Csp3-Csp3 homocoupling reaction. Secondly, the thesis discusses the use of these strategies to obtain several hard-to-access structures, including the first high-yielding doubly threaded [3]rotaxanes, heterocircuitcatenanes and the one pot synthesis of homocircuit-catenanes, and the smallest molecular trefoil knot prepared to date. Lastly, as an extension of the metal temptation strategy, the final chapter of this thesis will discuss the assembly of inorganic metal-organic catenanes by metal coordination.

<div>Segmented material systems have been shown to provide advantages over monolithic materials including the potential for combinations of properties such as strength, toughness, and ductility that are not otherwise attainable. One such class of segmented system is that of topologically interlocked material (TIM) systems. These are material systems consisting of one or more repeating unit blocks assembled in a planar configuration. When coupled with a bounding frame, this plate-like structure can withstand transverse loads without the use of adhesive or fasteners between blocks.</div><div><br></div><div>One method of generating TIM systems is to start with a 2D tiling and project each edge of the tiles at alternating angles from the tile normal. This work examines 18 unique configurations of TIM systems generated from the Archimedean and the Laves tilings. These systems are constructed as segmented plates having approximately the same number of building blocks and with equivalent overall dimensions so that the effect of the segmentation patterns on the load response of the TIM system can be investigated. Finite element models were utilized to simulate both displacement controlled loading and body force loading of each configuration with various coefficients of friction. The load responses were recorded and the characteristics of chirality and reciprocity of the load response were observed.</div><div><br></div><div>The TIM system configurations in this study resulted in a wide variety of performance. Their range of properties is presented, and a mechanism for strength in a TIM system is postulated. The findings of this work enable the material design space to be expanded by facilitating the creation of material systems with a greater range of properties than is possible with monolithic materials.</div>

This thesis describes the synthesis of interlocked anion host systems which exploit hydrogen bonding, halogen bonding, and lanthanide-coordination for anion recognition and sensing in aqueous solution. Chapter 1 introduces the field of anion supramolecular chemistry, with particular focus on areas of particular relevance to this thesis, namely anion recognition and sensing, anion templation and the synthesis of interlocked structures. Chapter 2 describes the synthesis of hydrogen bonding rotaxane and catenane hosts for recognising and sensing oxoanions in aqueous solvent media. The novel use of nitrate anion templation for the synthesis of interlocked molecules is reported, and the unprecedented selective recognition of nitrate in aqueous solvent media is demonstrated. Chapter 3 details the preparation of water soluble permethylated β-cyclodextrin-stoppered rotaxane hosts that utilise halogen bonding and hydrogen bonding interactions to bind anions in pure water. The first thermodynamic investigation into halogen bonding in water is reported, and the relative capabilities of halogen and hydrogen bonding for anion recognition in water are compared. Chapter 4 investigates the incorporation of lanthanide cations into rotaxane hosts for optical anion sensing. The seminal use of lanthanide cation templation for interlocked molecule synthesis is described, before anion templation approaches towards the synthesis of lanthanide-based rotaxanes are discussed. The luminescence anion sensing capabilities of these interlocked hosts are investigated. Chapter 5 describes the experimental procedures used in this work, and details the characterisation of compounds presented in Chapters 2–4. Chapter 6 summarises the conclusions of this thesis.

In contrast to the classic ‘passive template’ approach, an ‘active-metal’ template strategy involves a metal centre which acts as both a template and the catalyst for covalent bond formation in the construction of mechanically interlocked architectures. The crucial formation of a covalent bond between two ‘half-threads’ is promoted by the catalyst and directed through the cavity of the macrocycle by the catalyst’s coordination requirements. The main attractive features of such a synthetic approach are the efficiency (as one step is required instead of two), the rapid assembly of inaccessible structures, the possibility of ‘traceless’ assemblies, the versatility, the possibility to use catalytic amount of the metal template and to provide mechanistic insight. This novel concept was successfully introduced by our group and applied to a wide range of well-known transition metal-catalysed reactions. The thesis will present several examples of active-metal template reactions for the synthesis of interlocked architectures, including Cu(I)-catalysed alkyne-azide cycloaddition (CuAAC popularised as the click reaction), Pd(II)-catalysed alkyne homocouplings Pd(II)-catalysed oxidative Heck cross-couplings and Lewis acids mediated Diels-Alder reactions.

Cette thèse est dédiée à la conception de synthons entrelacés pour la préparation efficace de machines moléculaires pH-sensible de type rotaxane et de rotaxanes dénués de site de reconnaissance. Bien que la stratégie dirigée par l’effet « template » ait été employée très fréquemment et avec succès à ce jour, elle ne mène dans la plupart des cas qu’à des composés entrelacés qui contiennent les sites d’interactions nécessaires à la reconnaissance préalable des éléments moléculaires à assembler. Pour remédier à cette limitation, une nouvelle voie d’accès directe utilisant des synthons entrelacées pour la préparation de machines moléculaires de type rotaxanes et de rotaxanes dénués de site d’interaction fort a été étudié. Dans un premier temps, des « briques moléculaires » [2]rotaxanes isolables, bien qu’activées, ont été obtenus par une stratégie de glissement. Dans le but de les convertir aisément en machines moléculaires, les paramètres cinétiques et thermodynamiques relatifs au processus d’entrelacement ont été déterminés et ont permis de juger de l’importance de la nature et de l’orientation des pseudo-bouchons sur la cinétique d’entrelacement, ainsi que du rôle primordial du degré de liberté conformationnel de l’axe moléculaire sur la vitesse de formation des rotaxanes. Par la suite, les synthons entrelacées activés sous forme d’ester actif (ester de NHS isolable) sont utilisées dans la préparation de différentes machines moléculaires possédant une station moléculaire principale ammonium et une station moléculaire secondaire triazolium ou amide (secondaire ou tertiaire). D’autres synthons entrelacés qui différent par l’orientation du motif NHS sont utilisé comme transporteurs d’éther couronne pour permettre la préparation de rotaxanes dénués de site d’interaction fort. Enfin, dans la continuité des travaux réalisés au laboratoire sur le contrôle de la conformation chaise d’un mannosyl par une machinerie moléculaire, de nouvelles navettes pH-sensible de type glyco[2]rotaxanes contenant toutes une station moléculaire principale anilinium, et qui différent des machines précédentes par la deuxième station pyridinium, ont été obtenus et étudiés. / This thesis is dedicated to the synthesis of interlocked synthons for the efficient preparation of pH-sensitive rotaxane molecular machines and rotaxanes devoid of recognition site. Although the strategy directed by the "template" effect has been used very frequently and successfully so far, in most cases it only leads to interlocked compounds that contain the interaction sites necessary for prior recognition molecular elements to assemble. To overcome this limitation, a new direct access using interlocked synthons for the preparation of molecular machines of the rotaxane and rotaxane type devoid of strong interaction sites has been studied. Firstly, isolable [2]rotaxane "building block", although activated, were obtained by a slipping strategy. In order to easily convert them into molecular machines, the kinetic and thermodynamic parameters relating to the slipping process were determined and made it possible to judge the importance of the nature and orientation of the pseudo-stopper on the kinetics of slipping, as well as the primordial role of the degree of conformational freedom of the molecular axis on the speed of formation of rotaxanes. Subsequently, the activated ester (NHS isolatable ester) interlocked synthon are used in the preparation of different molecular machines having a main ammonium molecular station and a secondary molecular triazolium or amide station (secondary or tertiary). Other interlocked synthons that differ in the orientation of the NHS motif are used as crown ether transporters to enable the preparation of rotaxanes devoid strong interaction sites. Finally, in the continuity of the work carried out in the laboratory on the control of the chair conformation of a mannosyl by a molecular machinery, new pH-sensitive shuttles of glyco[2]rotaxane containing a main molecular station anilinium, and which different previous machines by the second station pyridinium, were obtained and studied.

Les structures autobloquantes sont des assemblages de blocs disposés périodiquement. La géométrie des blocs etles frottements entre blocs ainsi que la compression appliquée aux bords de l'assemblage jouent un rôle centraldans la cohésion de l'ensemble de l'assemblage. Des expériences d'indentation ont été menées pour étudier la réponse mécanique de matériaux autobloquants constitués de cubes en alumine et de blocs ostéomorphes enpolymère. Ces résultats ont été reproduits en utilisant deux méthodes numériques : la méthode des éléments finiset la méthode des éléments discrets utilisant un code dédié. Différentes variables de conception ont pu être étudiées par simulations numériques et les expériences nous ont permis de connaître la réponse d'un assemblage endommagé. De nouveaux assemblages à structure hierarchique ont été proposés et testés ouvrant de nouvellesperspectives. / Interlocked materials are periodic paving of elementary blocks. The cohesion is insured by the boundary conditions applied on the edge of the assembly as well as the topology of the blocks and the friction between the blocks.Experiments were performed to study the mechanical response of interlocked assemblies built with cubes in alumina and osteomophic blocs in polymer. Those results have been reproduced using two numerical methods: the finite element method and the discret element method with the help of a dedicated code. Differents design parameters have been studied with numerical methods and experiments allowed us to know the response of a dammage assembly. New assemblies having a hierachical structure were proposed and tested opening new perspectives.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24663号 / 農博第2546号 / 新制||農||1098(附属図書館) / 学位論文||R5||N5444(農学部図書室) / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 杉山 淳司, 教授 藤井 義久, 教授 仲村 匡司 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM