Le sujet de thèse concerne l’immunothérapie induite par des glycolipides synthétiques dont le chef de file est le KRN7000. Ce composé montre une activité à stimuler le système immunitaire renforçant l’action antitumorale. Cependant, comme la plupart des principes actifs, le KRN 7000 n’est pas spécifique des cellules tumorales. Pour pallier ce manque de spécificité, nous avons envisagé de coupler des glycolipides à un agent ciblant des cellules tumorales selon deux approches. La première a consisté à lier de manière covalente l’agent ciblant au glycolipide via un espaceur, ce qui a permis d’évaluer si le greffage de cet immunostimulant sur l’agent ciblant ne perturberait pas la reconnaissance par le récepteur membranaire. Concernant la seconde approche, une étude préliminaire reposant sur le relargage du KRN7000 a été abordé en préparant une prodrogue du glycolipide. Un autre problème du KRN7000 est qu’il n’est pas sélectif vis-à-vis de deux voies d’activation du système immunitaire. Pour pallier ce problème, la synthèse de nouveaux analogues C-glycosidiques d’alpha-galactosylcéramides plus stables et plus sélectifs de la voie Th1 a été envisagée. La stratégie de synthèse met en œuvre une cycloaddition 1,3-dipolaire entre un C-vinyl glycoside et une nitrone. Dans un premier temps, une étude méthodologique de cette réaction a d’abord été réalisée. Dans un deuxième temps, la fonctionnalisation du cycle isoxazolidine puis son ouverture devrait permettre d’accéder aux analogues ciblés. / This PhD work concerns glycolipid-induced activation of immune system with KRN7000 as lead compound. This latter has shown its ability to stimulate NKT cells which are T cells of the immune system resulting in potent antitumor activity. However, like lots of drugs, KRN7000 is not specific for tumor cells. To tackle this lack of specificity, we plan to graft glycolipids to a targeting agent for tumor cells following two approaches. The aim of the first one was to bind covalently the glycolipid to the targeting agent in order to determine the effect of the glycolipid grafting onto the targeting agent on the recognition by the membrane receptor. Regarding the second approach, a preliminary study based on the KRN7000 release was performed by synthesizing a glycolipid prodrug. Another drawback of the KRN7000 is the lack of selectivity towards two ways of activation of the immune system. In order to favor the Th1 immune response, the synthesis of new C-glycosidic analogues of alpha-galactosylceramides was implemented. The synthetic strategy has involved a 1,3-dipolar cycloaddition between a C-vinyl glycoside and a nitrone. First, a methodologic study about this reaction was performed. Then functionalization of the obtained isoxazolidine ring and the N-O bond cleavage should lead to the expected original analogs.

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Carbohydrates play important roles in biological processes. Their function is closely related to their conformation. In this thesis, conformational studies of carbohydrates by NMR spectroscopy and molecular dynamics computer simulations are described. The first two papers discuss the anomalous solubility of β-cyclodextrin compared to other cyclodextrins. Time correlation functions revealed flexibility in all cyclodextrins. Molecular dynamics computer simulations showed that the glycosidic linkages were rather rigid and the flexibility was suggested to be macrocyclic. From spatial distribution functions β-cyclodextrin was found to have greater ability to order the surrounding water than the other cyclodextrins. Paper III deals with some of the difficulties of conformational studies. In Paper IV, a new method, Additative Potential Maximum Entropy, APME, is applied to a disaccharide. Conformational distribution functions are derived from NOEs, J-couplings and residual dipolar couplings and calculated from computer simulations. All distribution functions were found to be in good agreement. In papers V and VI oligosaccharides from human milk are studied. Residual dipolar coupling, J-couplings and cross relaxation rates were measured by NMR spectroscopy and molecular dynamics computer simulations were carried out. Both oligosaccharides showed high flexibility for the β-D-GlcpNAc-(1→3)-β-D-Galp linkage.

<p>In this work, I develop computational and visual tools for analyzing and manipulating the backbone of macromolecules, and I demonstrate that these tools support building better structures than currently done. These visualization and analysis tools belong to an "Intelligence Amplification" (IA) tradition (rather than complete Artificial Intelligence (AI) automation), empowering users to improve structures.</p><p>Proteins and nucleic acids are among the most important molecules in biology, mediating the majority of biochemical processes that comprise a living organism. Therefore, these macromolecules are important targets, both for basic research to improve understanding of how life works, and for medical research as possible drug targets. </p><p>The function of these macromolecules is largely determined by their 3D structure. Although these macromolecules are chemically fairly simple, made up of linear sequences of a few possible subunits, they physically fold into complex, compact structures. Overall, structural biology aims to determine the general relationship between sequence and structure of these macromolecules, through determination of the positions of the atoms within individual macromolecules. </p><p>Because it is currently impossible to directly see the position of atoms in a molecule, all structural determination techniques, including X-ray crystallography, NMR, and homology modeling, result in an interpreted <italic>model</italic> of a structure. Nearly all of these models contain mistakes, in which atoms are fit in incorrect or impossible positions. These mistakes, especially at a functionally-important location in a structure, can mislead both basic and medical research, making it critical for structural biologists to build the highest quality models possible. </p><p>This document details how my dissertation work enables the building of better macromolecular structure models. This work follows an iterative development cycle, where visual analysis of models spurs development of better tools, which in turn improves the analysis. First, I describe how my analysis of protein loops from X-ray crystal structures reveals that the traditional definition of loop endpoints is too restrictive. Second, I create a protein backbone analysis and modeling tool, using a new peptide-centric division system. I show how this tool makes it easier to study protein loops, and also how it improves an algorithm for calculating core protein models from NMR residual dipolar coupling (RDC) data. Third, I describe how 3D visualization of RDCs in their structural context improves understanding of RDCs and validates NMR models in a novel way. Fourth, I describe how local quality analysis can diagnose problems in homology models. Fifth, I demonstrate that local quality analysis can be successfully used in conjunction with model rebuilding software to correct errors in low resolution structures. The various tools and software packages I created during the course of my work are freely available and have already made a positive impact on structures being generated by the community.</p><p>Archive versions of several of these software packages (JiffiLoop, RDCvis, and KiNG) should be included with this document; current versions can be downloaded from http://kinemage.biochem.duke.edu.</p> / Dissertation

In this thesis the entanglement properties of atom-atom, atom-photon, and photon-photon are investigated. The recent developments of quantum computation as well as quantum information and communication have attracted much interest in the generation of these entanglements in the laboratory. To generate atom-photon entanglement, I discuss a model system in the cavity QED setup. By using a four-level atom and two resonant cavity modes, we can generate atom-photon entanglement almost deterministically. An extension of the above model to a six-level atom and again two resonant cavity modes can generate entangled photon pairs by appropriately adjusting system parameters. I then investigate the atom-atom entanglement in a 1D harmonic trap. I show the dependence of the pair entanglement on the scattering length and temperature, as well as the particle symmetry requirement (bosons or fermions). Among many peculiar properties in a 1D system, we briefly discuss the Fermi-Bose duality". While the entanglement properties of a single-channel model have recently been obtained for 1D and 3D systems, I thus study the entanglement of a multi-channel process in a cylindrical harmonic trap. I discuss the dependence of entanglement on the trap geometry. Finally I present detailed studies of the spin mixing between two Rb87 atoms in a single lattice site. The topic is emphasized on various motional state approximations and dipolar effect. Various motional state approximations can cause up to 20% error to experimental data. I also find that the dipolar interaction can lead to an experimentally observable frequency shift in a cylindrical harmonic trap with very large aspect ratio. The spin mixing of spin-2 manifold has also been discussed.

Acyl phosphonates are interesting precursors for the synthesis of biologically active compounds. In the first part, the acyl phosphonates are synthesized starting from the corresponding acyl chloride. The acyl chlorides are converted into acyl phosphonates by using trialkylphosphites. The reaction of acyl phosphonates with aldehydes in the presence of proline furnished not the suggested aldol products via proline catalyzed aldol reaction but bicyclic products via one pot tricomponent 1,3-dipolar cycloaddition reaction. The formation of the bicyclic compound was suggested as followed / The formation of iminium salt of proline with aldehyde followed by decarboxylation furnished azomethine. The 1,3-dipolar cycloaddition of the formed azomethine with carbonyl group of acyl phosphonate afforded substituted hexahydro pyrrolo oxazole structures. 1,3-Dipolar cycloaddition forms the basis of the most preparatively useful procedures for the synthesis of five-membered heterocycles. One example is the 1,3-dipolar cycloaddition of azomethine ylides (from imines) and alkenes, which allows the stereoselective synthesis of pyrrolidines or proline derivatives.

ABSTRACT DEVELOPMENT OF NEW SYNTHETIC METHODOLOGIES FOR ISOQUINOLONE AND ISOINDOLINONE DERIVATIVES M&uuml / jde, Berk M.Sc., Department of Chemistry Supervisor: Prof. Dr. Metin Balci July 2010, 146 pages Due to the wide range of physiological activities, heterocycles containing nitrogen and oxygen have always attracted the interest of chemists. The objective of this research is to develop new synthetic routes to the synthesis of isoquinolone and isoindolinone derivatives starting from 2-(2-carboxyethyl)benzoic acid and homophthalic acid, respectively. The half ester produced from 2-(2-carboxyethyl)benzoic acid was an important key compound for the synthesis of new isoquinolone derivatives which are expected to be biologically active. The corresponding acyl azides and isocyanates were generatedwhich might be used as a precursors to construct a variety of isoquinolone derivatives. Transformation of acyl azides into urea derivatives followed by ring-closure under the basic conditions provided isoquinolones. Bromo- and methoxyhomophthalic acid derivatives were synthesized to increase in variety of isoindolinone derivative. Then corresponding anhydrides were generated to further reactions for synthesis of isoindolinone derivatives. Surprisingly, tetrazolinone derivatives are also formed by 1,3 dipolar cycloaddition. Whole products were conscientiously purified and characterized. In addition, the similar methodology which was used for the synthesis of isoquinolone derivatives, was applied to 2-(carboxymethyl)furan-3-carboxylic acid to synthesize new nitrogen and oxygen containing heterocycles.

A novel application of the Pauson-Khand reaction was applied to the synthesis of a series of bridged azatricyclic piperazines. This method represents the first application of the Pauson-Khand reaction to synthesize azabridged scaffolds. The ubiquity of bridged azabicyclic ring systems in biologically active natural product skeletons has provided the synthetic chemist with a wealth of opportunity for development over the last century. To this day, the development of new methodologies to tackle these structurally challenging systems remains at the forefront of synthetic chemistry. During our efforts to achieve a total synthesis of the stemofoline alkaloids, we have thus far developed a novel and scalable synthetic strategy to access the fully functionalized caged azatricyclic core of these challenging alkaloids. The overall synthetic strategy we have implemented began with the commercially available and affordable 2-deoxy-D-ribose as a chiral starting material. Furthermore, we have developed a novel 1,3-dipole cascade cycloaddition, which was successfully employed as the key step in the construction of the bridged azatricyclic core of the stemofoline alkaloids. / text

This dissertation contains four chapters with advances relevant to the fields of nanoparticle synthesis and nanoparticle self-assembly: a review of nanoparticle self-assembly, or “colloidal polymers”; dumbbell heterostructured nanorod synthesis; dipolar matchstick heterostructured nanorod synthesis; and self-assembly of dipolar matchsticks to form colloidal polymers. These chapters are followed by appendices containing supporting data for chapters two through four. The first chapter is a review summarizing current research involving the 1-D assembly of nanocrystals to form “colloidal polymers.” One of the major goals of materials chemistry is to synthesize hierarchical materials with precise controlled particle ordering covering all length scales of interest (termed, the “bottom up” approach). Recent advances in the synthesis of inorganic colloids have enabled the construction of complex morphologies for particles in the range of 1 – 100 nm. The next level of structural order is to control the structure of assemblies formed from these materials. Linear nanoparticle assemblies are particularly challenging to achieve due to the need to impart functionality to colloids such that (typically) only two sites are active per particle. An emerging idea in the literature which addresses this challenge is to consider linear assemblies of inorganic nanoparticles as colloidal analogs to traditional polymers. This conceptual framework has enabled the formation of linear assemblies having controlled composition (to form segmented and statistical copolymers), architecture (linear, branched, cyclic), and degree of polymerization (chain length). However, this emerging field of synthesizing colloidal polymers has not yet been reviewed in terms of methods to control fundamental polymer parameters. Therefore, linear nanoparticle assembly is reviewed in chapter 1 by applying concepts from traditional polymer science to nanoparticle assembly. The emphasis of chapter 1 is on controlling degree of polymerization, architecture, and composition for colloidal polymers, and seminal examples are highlighted which control these parameters. The second chapter is centered on a novel methodology to install ferromagnetic cobalt domains onto core@shell, “CdSe@CdS” nanorods. While the structures synthesized in this work were novel, the key advance from this work was the development of a methodology to separate nanorod activation from deposition of ferromagnetic cobalt domains onto semiconductor nanorods. As synthesized CdSe@CdS nanorods are passivated with strongly binding phosphonic acid ligands, and these ligands prevent direct deposition of many materials (such as cobalt). Synthetic methods must therefore modify nanorod surfaces prior to deposition of additional nanoparticle domains (tips). Previous synthetic methods for the deposition of magnetic domains onto nanorod termini typically combined activation of nanorod termini and metal deposition into a single synthetic step. While these previous reports were successful in achieving tipped nanorods, the coupling of these two reactions required matching the kinetics of nanorod activation and decomposition/reduction of metal precursors in order to achieve the desired heterostructure morphology. However, the presence of ligands used for nanorod activation can also affect the rate of metal precursor decomposition/reduction and the propensity of the metal to form free nanoparticles through homogeneous nucleation. Thus, simultaneous nanorod activation and metal deposition hinders modification of these syntheses to obtain differing heterostructured morphologies. In the work presented in chapter 2, we chemically activate nanorod termini towards cobalt deposition in a separate chemical step from deposition of metallic cobalt nanoparticle domains. First, reductive platinum deposition conditions were utilized to activate nanorod termini towards the deposition of cobalt domains, which were deposited in a subsequent reaction step. Then, the kinetics of nanorod activation during platinum deposition were tracked, and the platinum-tipped nanorod morphologies were correlated with the results of subsequent cobalt deposition reactions. Ultimately, controlled placement of cobalt domains onto one or both nanorod termini was demonstrated based on the degree of activation during platinum deposition. Cobalt nanoparticle tips were then selectively oxidized to form CoₓOy-tipped nanorods, which were a novel class of p-n type nanomaterials achieved over a total of five synthetic steps. Relevant supporting details for the synthesis of these dumbbell tipped nanorods are provided in Appendix A. The third chapter describes the synthesis of CoNP-tipped nanorods with a single, strongly dipolar, ferromagnetic CoNP-tip per nanorod. The key synthetic advance was the ability to activate a single terminus per nanorod without activation of lateral nanorod facets, which was vital in achieving these larger, dipolar, cobalt tips (rather than lateral decoration of cobalt onto nanorod lateral facets). These dipolar “matchstick” CoNP-tipped nanorods then spontaneously formed linear assemblies carrying nanorod side chains as pendant functionality. Activation of CdSe@CdS nanorods was found to occur through the deposition of small (< 2 nm) PtNP-tips which were not readily observable by standard characterization techniques. The finding that small (< 2 nm) PtNP-tips altered nanorod reactivity towards cobalt deposition emphasized the effect of subtle changes to nanorod surface chemistry. Relevant supporting details for the synthesis of these dipolar matchstick tipped nanorods are provided in appendix B. The fourth chapter is centered on the self-assembly of dipolar matchstick cobalt-tipped nanorods to form colloidal (co)polymers reminiscent of traditional bottlebrush polymers, with controlled composition and phase behavior on carbon surfaces. Similar to earlier findings in traditional polymer science, nanorod side chain length was found to significantly impact surface assembly of these colloidal analogs of bottlebrush copolymers, which provided a useful parameter for affecting surface wetting and phase behavior of nanoparticle thin films. This work was also the first demonstration of colloidal copolymers from the dipolar assembly of magnetic nanoparticles, where both segmented and statistical copolymer compositions were achieved. We then demonstrated, for the first time, that a colloidal copolymer with segmented composition can form a mesoscopic phase separated morphology which is similar to that observed for traditional block copolymers. This key advance opens the possibility of controlling structural ordering over still longer length scales by the development of methods to control phase separated morphologies in a manner similar to traditional block copolymers. Relevant supporting details for the synthesis and assembly of these colloidal bottlebrush polymers are provided in appendix C.