The first chapter of this thesis introduces the fundamental concepts governing the design and synthesis of supramolecular complexes. By illustrating the synthesis of several coordination cages reported in the literature, the principles underlying the construction of coordination cages by subcomponent self-assembly are elucidated. Ionic liquids are then proposed as solvents for cage systems; general methods for the preparation and synthesis of these solvents are described. The second chapter explores the use of ionic liquids as solvents for existing coordination cages. Potential methods of characterising these cages in ionic liquids are discussed; cages are demonstrated to be stable and capable of encapsulating guests in these ionic environments; and systems in which cages have good solubility in ionic liquids are designed. Building upon these observations, a triphasic sorting system is presented such that each of three different host-guest complexes are soluble in only one of three immiscible liquid phases. In contrast to the static triphasic system described in the second chapter, the third chapter explores directed phase transfer of coordination cages and their cargos from water, across a phase interface, and into an ionic liquid phase. The host-guest complex can then be recycled from the ionic liquid layer back into water after several additional steps. Furthermore, phase transfer of cationic cages is used to separate a mixture of cationic and anionic host-guest complexes. In the fourth chapter, fully reversible phase transfer of coordination cages is developed. Using anion exchange to modulate the solubility of three different cationic cages, reversible transport between water and ethyl acetate is demonstrated. Sequential phase transfer can also be achieved such that, from a mixture of cubic (+16) and tetrahedral (+8) cages, the cubic cage transfers from water to ethyl acetate before the tetrahedral cage. This process is fully reversible; upon the addition of a hydrophilic anion, the tetrahedral cage returns from ethyl acetate to water before the cubic cage.

Ce travail de thèse a pour objet la synthèse, la caractérisation et l’étude des propriétés de complexation de cages moléculaires riches en électrons, préparées selon une stratégie d’auto-assemblage dirigé par des métaux, ainsi que l’étude de leur aptitude à complexer ou libérer un substrat à l’aide d’un stimulus redox.Une présentation de la stratégie d’auto-assemblage dirigé par des métaux et de son efficacité pour l’élaboration de structures tridimensionnelles est d’abord proposée.Ce projet repose sur un travail préalable de synthèse de ligands riches en électrons, dérivés de l’unité tétrathiafulvalène (TTF) ou de son dérivé à système-pi étendu (ex TTF), motif dont les propriétés de donneurs pi sont bien établies. Plusieurs ligands tétra-topique sont ainsi été préparés et caractérisés.Les auto-assemblages discrets correspondant ont été obtenus par réaction avec divers complexes métalliques, donnant naissance à des cavités variées,contrôlées en termes de forme et de taille. Ces édifices ont été caractérisés par RMN (dont DOSY),spectrométrie de masse, le cas échéant par diffraction des rayons-X et leurs propriétés électrochimiques ont été étudiées par voltammétrie cyclique. Leur capacité à complexer des invités neutres ou ioniques a également été mise en évidence. Enfin, exploitant les caractéristiques géométriques et électroniques remarquables des dérivés à base ex TTF, l’aptitude de l’une des cages correspondantes à contrôler réversiblement le processus de libération/complexation d’un invité par oxydation/réduction chimique, a pu être démontrée. / This work is related to the synthesis and the characterization of electron-rich molecular cages, which are generated through a coordination-driven selfassembly strategy, as well as to the study of their ability to complex or release a substrate using a redox stimulus. A presentation of the metal-driven self-assembly methodology and of the corresponding efficiency in the preparation of three-dimensional structures is first proposed. This project is based on preliminary efforts in the design and the synthesis of electron-rich ligands, which are derived from the tetrathiafulvalene unit (TTF) or its piextended derivative (exTTF), whose pi-donating properties are well-established. Several tetratopic ligands were prepared and characterized. The corresponding discrete self-assemblies were obtained by reaction with various metal complexes, giving rise to various cavities whose shapes and sizes can be triggered. These structures were characterized by NMR (including DOSY), mass spectrometry, X-ray diffraction in some cases. Their electrochemical properties were studied by cyclic voltammetry. Their good binding properties for various neutral and ionic guests were also shown. Finally, exploiting the remarkable geometric and electronic features of exTTF derivatives, the ability of one of the corresponding cages to trigger reversibly the release/complexation process of a guest upon chemical oxidation/reduction, could be demonstrated

This thesis discusses progress made towards assembling molecular building blocks in the presence of our molecular host of choice, cucurbit[8]uril (CB[8]). Our studies on the self-assembly of synthetic and biological components in water bridge overlapping conceptsand techniques drawn from the fields of synthetic organic chemistry, supramolecular self-assembly, and applied NMR techniques. Chapter 1 introduces the reader to chemical complexity, and how supramolecular chemistshave advanced in their capability of assembling more complex molecular architectures. The discussion focusses particularly on self-assembly carried out in the aqueousphase, and how, like in biology, molecular design of the building blocks become criticalin enabling non-covalent assembly to occur in this dynamic, and relatively competitiveenvironment. The cucurbit[n]uril family of molecular hosts are then introduced with anoverview of their modes of binding, and affinities towards typical guests. Finally, a practicalintroduction to NMR methods gaining prominence in supramolecular chemistry ispresented. In particular, the use of diffusion NMR, a key tool for probing the solutiondynamics of molecular assemblies, is highlighted. Chapter 2 details work carried out on the CB[8]-mediated self-assembly of supramolecularblock copolymers from polymeric, and small molecule building blocks. Here, endgroup-functionalised polymer guests were shown to assemble with small molecule ditopicguests in the presence of CB[8] to form block copolymers. Copolymers of various molecularweights were assembled, and the supramolecular complexes were studied usingsolution viscometry and diffusion NMR. This study represented the first use of diffusionNMR for probing the assembly of polymeric guests with CB[8].Chapter 3 describes the self-assembly of CB[8] with complementary ditopic guests. Highmolecular weight supramolecular polymers are known to form through the step-growthassembly of complementary ditopic building blocks. Here we sought to probe CB[8]?sability to drive supramolecular polymerisation. Solution viscometry, ESI-MS, and diffusionNMR were used to investigate the self-assembly process, which indicated that cyclicoligomers had formed. The relatively low solubility of CB[8] in water was thought to bea major limitation to polymer formation in this instance. Important observations relating to the effect of salts on the solution viscosities and stabilitiesof the complexes, are also discussed. Chapter 4 places emphasis on the synthetic methods employed towards preparing multivalentguests for CB[8] binding studies. Our synthetic guests were based on watersolubleoligomers of ethylene glycol. A bidirectional elongation route is presented foraccessing higher molecular weight, and monodisperse ethylene glycol oligomers (n = 12)in suitable purity. Chapter 5 describes the assembly of protein-polymer conjugates, and the versatility ofdiffusion NMR as a means to probe the assembly process. Here, end group-functionalisedpoly(ethylene glycol) guests were appended to bovine serum albumin (BSA) through amixed chemical ligation-self assembly protocol. The NMR studies conducted are emphasisedhere, which served to complement other characterisation methods used thatare reported elsewhere. Chapter 6 discusses ongoing work on lipid-based guests, and the resulting liposome assembliesformed. Head group-functionalised phospholipid guests, and cholesterol-basedguests were synthesised. Phospholipid guests were obtained through an enzymatic route,a novelty in our group. Dye-encapsulated liposomes were then assembled, purified, andcharacterised by fluorescence microscopy. Finally, we sought to optimise lipid formulationsto enhance liposome stability, towards conducting molecular recognition studies inthe presence of CB[8].Chapter 7 then closes the thesis with concluding remarks that summarise the describedresearch, while highlighting points of note.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22661号 / 工博第4745号 / 新制||工||1741(附属図書館) / 京都大学大学院工学研究科高分子化学専攻 / (主査)教授 山子 茂, 教授 田中 一生, 教授 村田 靖次郎 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

This dissertation investigates non-covalent macromolecular chemistry using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) based techniques. The included studies reveal the impact of molecular structure on conformation and binding energetics. Supramolecules that might be too heavy to be dissociated in single collision-induced dissociation (CID) were dissociated using sustained off-resonance collision induced dissociation (SORI-CID) techniques. Relative binding energies and thresholds were evaluated for various macromolecular host-guest systems. Besides the non-covalent binding energies, conformation characterization was undertaken by a novel method to determine collision cross sectional areas using FTICR (CRAFTI, and multi-CRAFTI), initially developed by the Dearden lab. The systems chosen for further understanding of macromolecular interactions include calixarene-alkali metal complexes, cucurbit[5]uril-alkali halide complexes and cryptand-alkali metal complexes. The results were found to be consistent with expected behavior, and strongly correlated with predictions from computations. Size- and shape selectivity, as well as host-guest polarizability, are the main factors that govern the non-covalent macromolecular interactions that control complex conformation and dissociation. The results demonstrate the ability of FTICR to simultaneously determine binding energy, structure and conformation, which are the most important aspects for determination of comprehensive molecular characterization.

Systems chemistry is an emerging field of chemistry that studies complex mixtures of molecules that give rise to emergent properties that are not always predictable when studying the components of the mixtures in isolation. A systems chemistry approach has been adopted in fields such as self-assembly and self-sorting, where the dynamic recognition of complementary binding motifs to organize molecules is the central focus. Supramolecular systems are assembled through reversible, non-covalent interactions. The reversibility of supramolecular systems makes them dynamic. Understanding the dynamic nature of complex systems will allow for a bottom-up approach to the rational design of complex mixtures, such as kinetically trapped self-sorting systems. The first objective of this work was to understand the effects the identity and concentration of biologically relevant metal cations have on a the mechanism of binding and rate of kinetics of a cucurbit[7]uril (CB[7])-guest complex. Metal cations are frequently added to cucurbit[n]uril (CB[n]) systems. While metal cations are known to decrease the overall equilibrium constant of a CB[n]-guest complex, there has not been much consideration about how different metal cations can affect the CB[n]-guest binding mechanism beyond introducing competitive equilibria. Kinetic studies of the interactions between CB[7] and 1-(2-naphthyl)-ethylammonium (NpH+) in the presence of Ca2+ and Na+ were investigated. It was found that the binding mechanism between NpH+ and CB[7] was the formation of an exclusion complex and an inclusion complex. An exclusion complex is the formation of a complex where the cationic ammonium group of the guest associates to the carbonyl lined portals of CB[7], while the aromatic group remains exposed to the surrounding; while an inclusion complex is formed when the aromatic group of the guest enters the hydrophobic cavity of CB[7]. By increasing the metal cation concentrations, the exclusion complex was seen to disappear from the overall kinetics. When Ca2+ cations were used instead of Na+ cations, a Ca2+ cation capped inclusion complex was formed. The Ca2+ cation capped inclusion complex was found to have a lower dissociation rate constant than the uncapped complex between NpH+ and CB[7]. The second objective of this work was to understand how the structure of guest molecules effected the kinetic time scale of reaction with CB[7]. The kinetics between CB[7] and three different aromatic dications were measured to understand the structural features that influence the change in kinetic time scales: methyl viologen (MV2+), benzidine (Bn2+) and 2,7’-dimethyl-diazapyrenium (MDAP2+). It was found that moving the cationic charges further apart slowed down the kinetics from the sub millisecond time scale (MV2+) to the millisecond time scale (Bn2+); further, it was found that adding rigidity and width to the molecule (MDAP2+) slowed down the kinetics onto the minute time scale. The final objective of this work was to use the understanding of complexity gained in the metal cation project and the guest design for kinetic time scales project to rationally design a kinetically-trapped self-sorting system. The equilibrium constants and time scale of kinetics between a ditopic guest molecule and three host molecules (CB[6], CB[7] and β-CD) were determined to investigate the feasibility of the kinetically-trapped self-sorting system. Due to the complexity introduced by metal cations discovered earlier, β-cyclodextrin (β-CD) was used to modulate the concentration of guest that could be bound by CB[n]s. As a concentration modulator the requirements of β-CD were that the kinetics must be faster than the millisecond time scale and the equilibrium constant with the guest must be much lower than the equilibrium constants between the guest and CB[n]s. CB[6] was proposed as a thermodynamic sink due to its slow kinetics for complex formation with benzyl ammonium. The requirements for the guest complexation with CB[6] were that the kinetics had to be on the minute to hour time scale and the equilibrium constant with the guest had to be the highest of the three host molecules. CB[7] was chosen as the kinetic trap of the self-sorting system. The requirements for the CB[7] complex were that the kinetics had to be on the millisecond to second time scale and the equilibrium constant needed to be lower than the equilibrium constant of the guest@CB[6] complex, but higher than the guest@β-CD complex. The kinetic and thermodynamic requirements between the guest molecule and CB[7], and between the guest molecule and β-CD were met. The kinetics between CB[6] and the guest molecule were on the hour time scale, meaning the kinetic requirement was met, however, the equilibrium constant was found to be lower than the equilibrium constant between the guest molecule and CB[7]. The results in this work showed that the rational design of kinetically-trapping self-sorting systems is possible, but some modifications to the structure of the guest molecule is required to make this self-sorting system work. / Graduate / 2021-06-05

The structures of endohedral complexes of the polyhedral oligomeric silsesquioxane (POSS) cage molecule (HSiO 3/2) 12, with both D 2d and D 6h starting cage symmetries, containing the atomic or ionic species: Li 0, Li +, Li -, Na 0, Na +, Na -, K 0, K +, K -, F -, Cl -, Br -, He, Ne, Ar were optimized by density functional theory using B3LYP and the 6-311G(d,p) and 6-311 ++G(2d,2p) basis sets. The exohedral Li +, Na +, K +, K -, F -, Cl -, Br -, He, Ne, Ar complexes, were also optimized. The properties of these complexes depend on the nature of the species encapsulated in, or bound to, the (HSiO 3/2) 12 cage. Noble gas (He, Ne and Ar) encapsulation in (HSiO 3/2) 12 has almost no effect on the cage geometry. Alkali metal cation encapsulation, in contrast, exhibits attractive interactions with cage oxygen atoms, leading to cage shrinkage. Halide ion encapsulation expands the cage. The endohedral X@(HSiO 3/2) 12 (X = Li +, Na +, K +, F -, Cl -, Br -, He and Ne) complexes form exothermically from the isolated species. The very low ionization potentials of endohedral Li 0, Na 0, K 0 complexes suggest that they behave like "superalkalis". Several endohedral complexes with small guests appear to be viable synthetic targets. The D 2d symmetry of the empty cage was the minimum energy structure in accord with experiment. An exohedral fluoride penetrates the D 6h cage to form the endohedral complex without a barrier.

Convergent and divergent strategies for the synthesis of viologen dendrimers with 1,3,5-tri-methylene branching units are presented. The synthesis of 3,5-bis(hydroxymethyl) benzyl bromide was optimized. The analysis of the crystal structure of 1-[3,5-bis(hydroxymethyl)benzyl]-4-(pyridin-4-yl) pyridinium hexafluorophosphate together with PM3 calculations opens an avenue to judge the structure and conformation of benzylic viologen dendrimers. In order to study chemical trigger induced conformational changes, viologen dendrimers were spin-labeled via a divergent approach. 1-(2,4-dinitrophenyl)-4-(pyridin-4-yl)pyridinium hexafluorophosphate was used as the end group to yield an activated dendrimer of the respective generation. The corresponding dendrimers were spin-labeled by reacting the active functionality with 4-amino TEMPO. The products were characterized by ESR (spin-label efficiency) and conventional cyclic voltammetry. Dynamic ESR studies are planned. New trimethylene-dipyridinium dendrimers were synthesized via a divergent approach using 4-tert-butylbenzyl group as the peripheral group. These dendrimers are well soluble in DMF or DMSO as PF6 salts and they act as a host for anthraquinone-2,6-disulfonate (AQDS). They can be stoichiometrically titrated with AQDS as shown by 1H-NMR, DOSY and cyclic voltammetry. Upon loading them with AQDS, the dendrimers undergo first a contraction, they reach a minimum hydrodynamic radius for complete charge compensation and they re-open when overcharging takes place. The contraction is supported by MM+ calculations. Upon stepwise loading of G2 (42 positive charges) with AQDS (2 negative charges), the first 3 molar equivalents (6 neg. charges) occupy the innermost dendrimer shell (consisting of 6 pos. charges), the next 6 equivalents (12 neg. charges) occupy the middle shell (12 pos. charges) and the last 12 equivalents AQDS (24 neg. charges) occupy the outermost shell of the dendrimer (24 pos. charges), as supported by 1H-NMR titrations yielding the magic equivalent numbers of 3, 9=3+6, and 21=3+6+12. Such stepwise radial complexations again in DMSO were further demonstrated using other molecular guests (mono-, di- and trianionic) as well as with on purpose synthesized viologen dendrimers. α,ω-dibromoalkanes were bifunctionalized in two steps to yield alkyl phosphonates with pyridinium, trimethylenedipyridinium, bipyridinium or a sulfonate at their ω end. These compounds were used as surface modifiers to build biomimetic membranes on the pore walls of mesoporous TiO2. Host-guest interaction studies with on purpose synthesized viologen compounds have been performed in collaboration.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第18234号 / 工博第3826号 / 新制||工||1586(附属図書館) / 31092 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 北川 進, 教授 松田 建児, 教授 濵地 格 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第18298号 / 工博第3890号 / 新制||工||1597(附属図書館) / 31156 / 京都大学大学院工学研究科高分子化学専攻 / (主査)教授 山子 茂, 教授 中條 善樹, 教授 村田 靖次郎 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM