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.

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.

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19744号 / 工博第4199号 / 新制||工||1648(附属図書館) / 32780 / 京都大学大学院工学研究科高分子化学専攻 / (主査)教授 中條 善樹, 教授 赤木 和夫, 教授 松原 誠二郎 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

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The thesis work described herein explores two avenues of post-functionalization of conjugated polymers using ‘click’ chemistry. The first avenue utilizes the Strain-Promoted Alkyne-Azide Cycloaddition (SPAAC) and the second an Inverse Electron-Demand Diels-Alder (IEDDA). In the first part of this thesis, various azide moieties were SPAAC ‘clicked’ onto a dibenzocyclooctyne-containing polymer, such as small molecules like para-phenyl-nitroazide, as well as larger azide-terminated chains like polystyrene and polyethylene glycol. Host-guest chemistry and self-healing organogels were also explored. The synthesis of each component, including the cyclooctyne diamine monomer, dialdehyde comonomer, resulting polymer, various azide moieties, as well as the SPAAC click reactions, are all described in detail along with extensive characterization. Similarly, the second part of this thesis involved the synthesis and characterization of several components, including the tetrazine monomer, fluorene comonomer, resulting polymer, and various TCO derivatives for the post-polymerization IEDDA ‘click’ reactions onto the backbone. Some of the click reactions described include small molecule TCO derivatives, polymeric PEG TCO, and a difunctional linker to generate a crosslinked foam. / Conjugated polymers attract significant attention due to their interesting optoelectronic and physical properties. Over the past few decades, tremendous effort has been devoted to expanding the structural diversity and applications of this class of macromolecules. The pursuit of structural variability of conjugated polymers has resulted in a broad range of research to understand their structure-property relationships via functionalization. This functionalization is crucial for tailoring performance in any given application. Thus, the ability to synthesize a library of homologous polymers would prove very useful. Efficiency is of utmost importance when creating a library of homologous conjugated polymers, as the faster a library can by synthesized, the sooner said polymers can be screened for any desirable properties. Such an approach requires a post-polymerization functionalization strategy, whereby a progenitor polymer undergoes efficient reactions at each repeat unit of the backbone. The work presented in this thesis involves synthesizing a reactive conjugated polymer scaffold, followed by efficiently post-polymerization functionalization via “click” chemistry. Two elegant click reactions are described in this work; the Strain-Promoted Alkyne-Azide Cycloaddition (SPAAC) and Inverse Electron-Demand Diels-Alder (IEDDA). The SPAAC reaction allowed for rapid functionalization of triazole moieties on a dibenzocyclooctyne-containing polymer backbone, creating a small polymer library with a consistent degree of polymerization (DP). Grafting with polystyrene and polyethylene glycol azide-terminated polymers allowed the efficient syntheses of a series of graft-co-polymers with Mn values up to 800 kDa and varying solubilities. Secondly, The IEDDA reaction was applied to a poly(tetrazine-co-fluorene) conjugated polymer, which resulted in the rapid and quantitative functionalization of the polymer backbone with trans-cyclooctene derivatives. These reactive conjugated polymers were explored in a variety of applications, including supramolecular chemistry and gel formation. / Thesis / Doctor of Philosophy (PhD) / Conjugated polymers are a class of macromolecular materials that attract significant attention due to their interesting behaviors and properties. Under certain conditions, these polymers even display conductivities like that of metals. As such, they show promise in applications such as organic solar cells, chemical sensors, organic light-emitting diodes, and supercapacitors. Over the past few decades, tremendous effort has been devoted to expanding on the types of conjugated polymers as well as their structural diversity. This, of course, has resulted in polymers that exhibit vastly different behaviours depending on what they are made of. As certain applications (e.g.: solar cells) require polymers with very specific properties, being able to ‘tune’ a conjugated polymer to ‘match’ a required property would be extremely useful. This tuning of polymer properties can be successfully accomplished by attaching different structures onto the polymer chain by utilizing a reaction known as ‘post-polymerization functionalization’. In doing so, a starting reactive polymer can be transformed into an entirely different polymer with specific chemical properties and behaviors. The work presented in this thesis involves synthesizing two types of conjugated polymers and attaching various structures onto their backbones to yield different properties. The synthesis, characterization, and potential applications of said polymers are described herein.

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