The work presented in this dissertation attempts to form an understanding of the importance of polymer connectivity and nanoparticle shape and curvature on the formation of non-covalent interactions between polymer and nanoparticles by monitoring the dispersion of nanoparticles in copolymers containing functionalities that can form non-covalent interactions with carbon nanoparticles. The first portion of this study is to gain a fundamental understanding of the role of electron donating/withdrawing moieties on the dispersion of the fullerenes in copolymers. UV- Vis spectroscopy and x-ray diffraction were used to quantify the miscibility limit of C60 fullerene with the incorporation of electron donor-acceptor interactions (EDA) between the polymer and fullerene. The miscibility and dispersion of the nanoparticles in a polymer matrix are interpreted to indicate the extent of intermolecular interactions, in this case non-covalent EDA interactions. Experimental data indicate that the presence of a minority of interacting functional groups within the polymer chains leads to an optimum interaction between polymer and fullerene. This is further affirmed by density functional theory (DFT) calculations that specify the binding energy between interacting monomers and fullerenes. The second portion focuses on the impact of sample preparation on the dispersion of graphene nanocomposites. Visualization and transparency are used to quantify the dispersion of graphene in the polymer matrix. In addition, differential scanning Calorimetry (DSC) also provides insight into the efficiency of the preparation process in forming a homogeneous sample, where rapid precipitation and solvent evaporation are studied. Examining the change in glass transition temperature, Tg, with nanoparticle addition also provides insight into the level of interaction and dispersion in the graphene nanocomposites. The approach of utilizing non-covalent interactions to enhance the dispersion of polymer nanocomposites is realized by varying the functional group in the copolymer chains, while the impact of nanoparticle shape is also examined. The optimum enhancement of dispersion is interpreted in terms of the improvement of interaction between polymer and nanocomposites. This interpretation leads to the conclusion that chain connectivity and the ability of the polymer to conform to the nanoparticle shape are two important factors that govern the formation of non-covalent interactions in polymer nanocomposites.

Unconventional non-covalent interactions such as halogen, chalcogen, and tetrel bonds are gaining interest in several domains including but not limited to drug design, as well as novel catalyst design. Non-covalent interactions are known as weak forces of interactions when they are considered on an individual basis, but on a molecular basis, these effects become important such that their prevalence can be seen in the construction of large biomolecules like proteins, DNA and RNA. In this work, the fundamental aspects of these interactions are looked upon using ab initio and Density Functional Theory (DFT). An essential aspect of chalcogen bonds involving Sulfur as donor atom with nitrogen, oxygen and π-system as electron sources was examined. These bonds are strong with binding energy that varies from a minimum of 3 kcal/mol in some π-system to 19 kcal/mol in primary amine systems. Decomposition of the total interaction energy reveals that the induction energy constitutes more than half of the total interaction energy. The shortness and strength of some of the chalcogen bond interactions suggest these interactions may in some cases be described as weak covalent bonds. A comparative study of π-hole tetrel bonding with σ-hole halogen bonds in complexes of XCN (X = F, Cl, Br, I) and ammonia shows that the π-hole geometry if favored for X = F, and the σ-hole structure is preferred for the heavier halogens. Also, the potential use of these non-covalent interactions in organic catalysis was explored. The energy barrier of the Aza-Diels-Alder reaction is substantially lowered by the introduction of an imidazolium catalyst with either a Hydrogen or halogen (X) atom in the 2-position.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20938号 / 理博第4390号 / 新制||理||1631(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 三木 邦夫, 教授 杉山 弘, 教授 秋山 芳展 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Le fondaparinux (Arixtra®), anticoagulant de la classe des pentasaccharides de synthèse, est le premier inhibiteur d'origine synthétique, spécifique et indirect du facteur Xa de la coagulation. Il résulte de la synthèse chimique de l'unité pentasaccharidique des héparines, capable de se lier à l'antithrombine, une protéine endogène, inhibitrice de la coagulation. Cependant, son utilisation reste limitée par son administration uniquement possible par voie parentérale.L'objectif de ce travail de thèse est de développer une forme orale du fondaparinux en l'associant à un dérivé squalénique. Le squalène, terpénoïde naturel précurseur de la synthèse du cholestérol, possède une très bonne absorption orale (supérieure à 60 %). Dans ce contexte, deux stratégies d'association ont été développées: la première consistant à associer par liaison covalente le fondaparinux à un dérivé squalénique selon le concept de la « squalénisation » et la deuxième à associer par interactions non covalentes le fondaparinux à un dérivé squalénique cationique.Les travaux expérimentaux ont montré que la première stratégie était délicate à mettre en œuvre en raison d'une part de la difficulté à synthétiser un bioconjugué fondaparinux-squalène et d'autre part de la perte de l'activité anticoagulante du fondaparinux. En raison de ces obstacles, le concept de la « squalénisation » n'est pas adapté à ce type de molécule active. En revanche, la deuxième stratégie s'est montrée très prometteuse. Elle a consisté à formuler des nanoparticules par association non covalente du fondaparinux, chargé négativement, à un dérivé squalénique cationique. Cette approche a permis de mettre en évidence l’excellente capacité d'auto-assemblage en milieu aqueux de ces deux composés, liée à l’établissement de deux types d’interactions, électrostatiques et hydrophobes (entre les molécules de squalène). L'absorption orale du fondaparinux a été considérablement augmentée grâce à ce nouveau système nanoparticulaire. Cette nouvelle approche à base de squalène a ainsi montré son efficacité dans l'amélioration de l'administration orale du fondaparinux et pourrait représenter un système thérapeutique potentiel dans le traitement des maladies thromboemboliques. / Since its introduction in the market in 2002, fondaparinux (Arixtra®) is a drug of choice in the anticoagulant therapy. Its structure corresponds to the heparin pentasaccharide sequence that mediates its interaction with the natural plasma inhibitor of coagulation, antithrombin. However, like heparin, its application is limited due its unique administration by parenteral route. The aim of this project is to develop an efficient oral delivery system for fondaparinux by association with a squalene derivative. Squalene, a natural precursor of cholesterol in sterol biosynthesis, is well-known for its excellent oral absorption (i.e. more than 60 %). In this context, two strategies were investigated. The first consisted in achieving a covalent coupling between fondaparinux and a squalene derivative according to the concept of “squalenoylation”. The second was to associate fondaparinux to a cationic squalenoyl derivative by non-covalent association.Experimental work showed that the first strategy was delicate to implement due to the difficulty to synthesize a fondaparinux-squalene bioconjugate and, the loss of the anticoagulant properties of fondaparinux. Because of these obstacles, the concept of "squalenoylation" was not suitable for this type of active molecule. In contrast, the second strategy has been very promising. It consisted in the formulation of a nanoparticulate delivery system by ion-pairing of fondaparinux and a cationic squalenoyl derivative. This approach permitted to highlight the self-assembly of these two compounds in water as monodisperse nanoparticles thanks to electrostatic and hydrophobic interactions. Furthermore, the oral absorption of fondaparinux was significantly increased with this new nanoparticulate system. This new squalene-based approach has shown its effectiveness in improving the oral administration of fondaparinux and could be a potential delivery system in the treatment of thromboembolic diseases.

Non-covalent bonds are an important class of intermolecular interactions, which result in the ordering of atoms and molecules on the supramolecular scale. One such type of interaction is brought about by the bond formation between a region of positive electrostatic potential (σ-hole) interacts and a Lewis base. Previously, the halogen bond has been extensively studied as an example of a σ-hole interaction, where the halogen atom acts as the bond donor. Similarly, carbon, and the other tetrel elements can participate in σ-hole bonds. This thesis explores the nature of the carbon tetrel bond through the use of computational chemistry and solid state nuclear magnetic resonance (NMR) spectroscopy. The results of calculations of interaction energies and NMR parameters are reported for a series of model compounds exhibiting tetrel bonding from a methyl carbon to the oxygen and nitrogen atoms in a range of functional groups. The ¹³C chemical shift (𝛿iso) and the ¹ᶜ𝐽(¹³C,¹⁷O/¹⁵N) coupling across the tetrel bond are recorded as a function of geometry. The sensitivity of the NMR parameters to the non-covalent interaction is demonstrated via an increase in 𝛿iso and in |¹ᶜ𝐽(¹³C,¹⁷O/¹⁵N)| as the tetrel bond strengthens. There is no direct correlation between the NMR trends and the interaction energy curves; the energy minimum does not appear to correspond to a maximum or minimum chemical shift or J-coupling value. Gauge-including projector-augmented wave density functional theory (DFT) calculations of 𝛿iso are reported for crystals which exhibit tetrel bonding in the solid state. Experimental 𝛿iso values for sarcosine, betaine and caffeine and their tetrel-bonded salts generally corroborate the computational findings. This work offers new insights into tetrel bonding and facilitates the incorporation of tetrel bonds as restraints in NMR crystallographic structure refinement.

The majority of drugs are small organic molecules, so-called ligands, that influence biochemical processes by interacting with proteins. The understanding of how and why they interact and form complexes is therefore a key component for elucidating the mechanism of action of drugs. The research presented in this thesis is based on studies of acetylcholinesterase (AChE). AChE is an essential enzyme with the important function of terminating neurotransmission at cholinergic synapses. AChE is also the target of a range of biologically active molecules including drugs, pesticides, and poisons. Due to the molecular and the functional characteristics of the enzyme, it offers both challenges and possibilities for investigating protein-ligand interactions. In the thesis, complexes between AChE and drug-like ligands have been studied in detail by a combination of experimental techniques and theoretical methods. The studies provided insight into the non-covalent interactions formed between AChE and ligands, where non-classical CH∙∙∙Y hydrogen bonds (Y = O or arene) were found to be common and important. The non-classical hydrogen bonds were characterized by density functional theory calculations that revealed features that may provide unexplored possibilities in for example structure-based design. Moreover, the study of two enantiomeric inhibitors of AChE provided important insight into the structural basis of enthalpy-entropy compensation. As part of the research, available computational methods have been evaluated and new approaches have been developed. This resulted in a methodology that allowed detailed analysis of the AChE-ligand complexes. Moreover, the methodology also proved to be a useful tool in the refinement of X-ray crystallographic data. This was demonstrated by the determination of a prereaction conformation of the complex between the nerve-agent antidote HI-6 and AChE inhibited by the nerve agent sarin. The structure of the ternary complex constitutes an important contribution of relevance for the design of new and improved drugs for treatment of nerve-agent poisoning. The research presented in the thesis has contributed to the knowledge of AChE and also has implications for drug discovery and the understanding of biochemical processes in general.

The connection of molecular monomers through non-covalent interaction (e.g. hydrogen bonding, π-π interaction, coordination bonding) enables the formation of supramolecular polymers. The major advantage of these bonds is their reversibility and consequently their ability to self-assembly or to disconnect depending on given conditions. This thesis examines the self-assembly through quadruple hydrogen bonding, which is strong and the resulting structures stable. Ureidopyrimidinon A and aromatic amines were always used as the starting compound for the preparation of monofunctional and bifunctional ureidopyrimidinones.

L’objectif de ce travail de thèse était la préparation et la caractérisation des hétéropolyanions anhydres sur supports oxydes par la stratégie de chimie organométallique de surface. Les acides anhydres H3PMo12O40 et H3PW12O40 ont été préparés sur silice partiellement déshydroxylée. Cette réaction conduit à une interaction ionique par protonation des silanols de surface. La réactivité de ces hétéropolyacides anhydres en présence d’alkylsilanes a été étudiée en milieu homogène et a conduit à la formation d’espèces silylées cationiques [Et2MeSi+]3[HPA3-] et au dégagement d’hydrogène. Cette réactivité a ensuite été appliquée en milieu hétérogène en fonctionnalisant la surface de la silice par des groupements [(≡SiO)SiMe2H] et a conduit à la formation d’une espèce de surface polyoxometalate liée de manière covalente au support. L’introduction de fonction chloroalkylsilane à la surface de la silice [(≡SiO)SiMeCl2] et [(≡SiO)2SiMeCl] a également permis de former des liaisons covalentes Si Support-O-M HPA. Par ailleurs, Par ailleurs, l’activation du méthane a été observée sur tous les solides HPA/SiO2 à travers le dégagement de CO2, H2O, H2. L’activation C-H a lieu sur ces systèmes même à basse température et les données obtenues suggèrent la formation d’une espèce méthoxy de surface par réaction des protons acides avec le méthane / The aim of this work was the preparation and characterization of anhydrous heteropolyanions on oxide supports using surface organometallic chemistry approach. Anhydrous H3PMo12O40 and H3PW12O40 were prepared on partially dehydroxylated silica. This reaction led to an ionic interaction by protonation of surface silanols. The reactivity of these heteropoly compounds with alkylsilanes was studied in homogeneous conditions and led to the formation of cationic silicon species [Et2MeSi+]3[HPA3-] and release of hydrogen. This reactivity was then applied in heterogeneous conditions by introduction of silane groups [(≡SiO)SiMe2H] at the silica surface and led to the formation of a surface polyoxometalate species covalently bonded to the support. The introduction of chloroalkylsilane groups [(≡SiO)SiMeCl2] and [(≡SiO)2SiMeCl] has also enabled the formation of covalent bonds Si Support-O-M HPA. In addition, methane activation was observed on all HPA/SiO2 solids through the releases of CO2, H2O, H2. The C-H activation takes place on these systems even at low temperature and obtained data suggest the formation of a methoxy surface species by reaction of stronf acidic protons with methane

Mass spectrometry has in recent years been established as the standard method for protein identification and characterization in proteomics with excellent intrinsic sensitivity and specificity. Fourier transform ion cyclotron resonance is the mass spectrometric technique that provides the highest resolving power and mass accuracy, increasing the amount of information that can be obtained from complex samples. This thesis concerns how useful information on proteins of interest can be extracted from mass spectrometric data on different levels of protein structure and how to obtain this data experimentally. It was shown that it is possible to analyze complex mixtures of protein tryptic digests by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and identify abundant proteins by peptide mass fingerprinting. Coupling on-line methods such as liquid chromatography and capillary electrophoresis increased the number of proteins that could be identified in human body fluids. Protein identification was also improved by novel statistical methods utilizing prediction of chromatographic behavior and the non-randomness of enzymatic digestion. To identify proteins by short sequence tags, electron capture dissociation was implemented, improved and finally coupled on-line to liquid chromatography for the first time. The combined techniques can be used to sequence large proteins de novo or to localize and characterize any labile post-translational modification. New computer algorithms for the automated analysis of isotope exchange mass spectra were developed to facilitate the study of protein structural dynamics. The non-covalent interaction between HIV-inhibitory peptides and the oligomerization of amyloid β-peptides were investigated, reporting several new findings with possible relevance for development of anti-HIV drug therapies and understanding of fundamental mechanisms in Alzheimer’s disease.

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