Dissertations / Theses on the topic 'Molecular self-assembly on silicon'

Grâce à leur propriétés uniques, les nanofils d'InAs et de Bi1-xSbx sont important pour les domaines de la nanoélectronique et de l'informatique quantique. Alors que la mobilité électronique de l'InAs est intéressante pour les nanoélectroniques; l'aspect isolant topologique du Bi1-xSbx peut être utilisé pour la réalisation de Qubits basés sur les fermions de Majorana. Dans les deux cas, l'amélioration de la qualité du matériau est obligatoire et ceci est l'objectif principal cette thèse ou` nous étudions l'intégration des nanofils InAs sur silicium (compatibles CMOS) et où nous développons un nouvel isolant topologique nanométrique: le Bi1-xSbx. Pour une compatibilité CMOS complète, la croissance d'InAs sur Silicium nécessite d'être auto- catalysée, entièrement verticale et uniforme sans dépasser la limite thermique de 450 ° C. Ces normes CMOS, combineés à la différence de paramètre de maille entre l'InAs et le silicium, ont empêché l'intégration de nanofils InAs pour les dispositifs nanoélectroniques. Dans cette thèse, deux nouvelles préparations de surface du Si ont été étudiées impliquant des traitements Hydrogène in situ et conduisant à la croissance verticale et auto-catalysée de nanofils InAs compatible avec les limitations CMOS. Les différents mécanismes de croissance résultant de ces préparations de surface sont discutés en détail et un passage du mécanisme Vapor-Solid (VS) au mécanisme Vapor- Liquid-Solid (VLS) est rapporté. Les rapports d'aspect très élevé des nanofils d'InAs sont obtenus en condition VLS: jusqu'à 50 nm de diamètre et 3 microns de longueur. D'autre part, le Bi1-xSbx est le premier isolant topologique 3D confirmé expérimentalement. Dans ces nouveaux matériaux, la présence d'états surfacique conducteurs, entourant le coeur isolant, peut héberger les fermions de Majorana utilisés comme Qubits. Cependant, la composition du Bi1-xSbx doit être comprise entre 0,08 et 0,24 pour que le matériau se comporte comme un isolant topologique. Nous rapportons pour la première fois la croissance de nanofils Bi1-xSbx sans défaut et à composition contrôlée sur Si. Différentes morphologies sont obtenues, y compris des nanofils, des nanorubans et des nanoflakes. Leur diamètre peut être de 20 nm pour plus de 10 microns de long, ce qui en fait des candidats idéaux pour des dispositifs quantiques. Le rôle clé du flux Bi, du flux de Sb et de la température de croissance sur la densité, la composition et la géométrie des structures à l'échelle nanométrique est étudié et discuté en détail
InAs and Bi1-xSbx nanowires with their distinct material properites hold promises for nanoelec- tronics and quantum computing. While the high electron mobility of InAs is interesting for na- noelectronics applications, the 3D topological insulator behaviour of Bi1-xSbx can be used for the realization of Majorana Fermions based qubit devices. In both the cases improving the quality of the nanoscale material is mandatory and is the primary goal of the thesis, where we study CMOS compatible InAs nanowire integration on Silicon and where we develop a new nanoscale topological insulator. For a full CMOS compatiblity, the growth of InAs on Silicon requires to be self-catalyzed, fully vertical and uniform without crossing the thermal budge of 450 °C. These CMOS standards, combined with the high lattice mismatch of InAs with Silicon, prevented the integration of InAs nanowires for nanoelectronics devices. In this thesis, two new surface preparations of the Silicon were studied involving in-situ Hydrogen gas and in-situ Hydrogen plasma treatments and leading to the growth of fully vertical and self-catalyzed InAs nanowires compatible with the CMOS limitations. The different growth mechanisms resulting from these surface preparations are discussed in detail and a switch from Vapor-Solid (VS) to Vapor- Liquid-Solid (VLS) mechanism is reported. Very high aspect ratio InAs nanowires are obtained in VLS condition: upto 50 nm in diameter and 3 microns in length. On the other hand, Bi1-xSbx is the first experimentally confirmed 3D topololgical insulator. In this new material, the presence of robust 2D conducting states, surrounding the 3D insulating bulk can be engineered to host Majorana fermions used as Qubits. However, the compostion of Bi1-xSbx should be in the range of 0.08 to 0.24 for the material to behave as a topological insula- tor. We report growth of defect free and composition controlled Bi1-xSbx nanowires on Si for the first time. Different nanoscale morphologies are obtained including nanowires, nanoribbons and nanoflakes. Their diameter can be 20 nm thick for more than 10 microns in length, making them ideal candidates for quantum devices. The key role of the Bi flux, the Sb flux and the growth tem- perature on the density, the composition and the geometry of nanoscale structures is investigated and discussed in detail

Silicon nanocrystal’s (SiNCs) size dependent optical properties and nontoxic nature portend potential applications across a broad range of industries. With any of these applications, a thorough understanding of SiNC photophysics is desirable to tune their optical properties while optimizing quantum yield. However, a detailed understanding of the photoluminescence (PL) from SiNCs is convoluted by the complexity of the decay mechanisms, including a stretched-exponential relaxation and the presence of both nanosecond and microsecond decays.

In this dissertation, a brief history of semiconductor nanocrystals is given, leading up to the first discovery of room temperature PL in SiNCs. This is then followed by an introduction to the various nanocrystal synthetic schemes and a discussion of quantum dot photophysics in general. Three different studies on the PL from SiNCs are then presented. In the first study, the stretched nature of the time dependent PL is analyzed via chromatically-resolved and full-spectrum PL decay measurements. The second study analyzes the size dependence of the bimodal PL decay, where the amplitude of the nanosecond and microsecond decay are related to nanocrystal size, while the third project analyzes the temperature and microstructure dependencies of the PL from SiNC solids.

After an indepth look at the PL from SiNCs, this report examines preliminary results of SiNC and silver nanocrystal self-assembly. When compared to metal and metal chalcogenide nanoparticles, there is a dearth of literature on the self-assembly of SiNCs. To understand these phenomena, we analyze the size dependent ability of SiNCs to form a ‘superlattice’ and compare this with silver nanocrystals. Although the results on self-assembly are still somewhat preliminary, it appears that factors such as SiNC concentration and size dispersity play a key role in SiNC self-assembly, while suggesting intrinsic differences between the self-assembly of SiNCs and silver nanocrystals.

Finally, at the end of this dissertation, a corollary project is presented on the computational analysis of fluorescent silver nanoclusters (AgNCs). Due to their small size and non-toxic nature, AgNCs are an ideal fluorophore for biological systems, yet there is a limited understanding of their photophysics, which is the focus of this part of the dissertation.

Silicon nanocrystal?s (SiNCs) size dependent optical properties and nontoxic nature portend potential applications across a broad range of industries. With any of these applications, a thorough understanding of SiNC photophysics is desirable to tune their optical properties while optimizing quantum yield. However, a detailed understanding of the photoluminescence (PL) from SiNCs is convoluted by the complexity of the decay mechanisms, including a stretched-exponential relaxation and the presence of both nanosecond and microsecond decays. In this dissertation, a brief history of semiconductor nanocrystals is given, leading up to the first discovery of room temperature PL in SiNCs. This is then followed by an introduction to the various nanocrystal synthetic schemes and a discussion of quantum dot photophysics in general. Three different studies on the PL from SiNCs are then presented. In the first study, the stretched nature of the time dependent PL is analyzed via chromatically-resolved and full-spectrum PL decay measurements. The second study analyzes the size dependence of the bimodal PL decay, where the amplitude of the nanosecond and microsecond decay are related to nanocrystal size, while the third project analyzes the temperature and microstructure dependencies of the PL from SiNC solids. After an indepth look at the PL from SiNCs, this report examines preliminary results of SiNC and silver nanocrystal self-assembly. When compared to metal and metal chalcogenide nanoparticles, there is a dearth of literature on the self-assembly of SiNCs. To understand these phenomena, we analyze the size dependent ability of SiNCs to form a ?superlattice? and compare this with silver nanocrystals. Although the results on self-assembly are still somewhat preliminary, it appears that factors such as SiNC concentration and size dispersity play a key role in SiNC self-assembly, while suggesting intrinsic differences between the self-assembly of SiNCs and silver nanocrystals. Finally, at the end of this dissertation, a corollary project is presented on the computational analysis of fluorescent silver nanoclusters (AgNCs). Due to their small size and non-toxic nature, AgNCs are an ideal fluorophore for biological systems, yet there is a limited understanding of their photophysics, which is the focus of this part of the dissertation.
NSF CBET-1133135
NSF CBET-1603445
DOE DE-FG36-08G088160

Au cours de ce travail nous avons étudié la réalisation de couches moléculaires d’accroche terminées amine. Sur l’oxyde de silicium l’aminopropyletriméthoxysilane (APTMS) a été déposé à partir d’une solution, et via une méthode originale par voie sèche qui nous a permis de mettre en évidence les temps caractéristiques de greffage et d’organisation de la couche d’APTMS. Sur l’or, les monocouches d’aminoéthanethiol (AET) et d’aminothiophénol (ATP) ont été réalisées à partir d’une solution. Nous avons ensuite étudié les aspects structuraux et cinétiques du greffage des fullerènes C60 sur de telles couches d’accroche, constituées de terminaisons amines soit sur toute la surface soit en des zones isolées (couches binaires). Les techniques de spectroscopie UV-Visible, IRTF, Raman, et XPS ont permis d’observer le greffage des C60 sur les couches aminées. La spectroscopie Raman en mode exalté (SERS) a mis en lumière que les molécules d’ATP étaient plus inclinées après le greffage à reflux des C60. Les analyses des diverses couches à l’échelle moléculaire ont été menées par microscopie à sondes locales (AFM, STM), et les mesures électriques réalisées sur or à l’aide de la pointe STM ont montré le caractère isolant de la couche d’accroche seule et un gap proche de celui du C60 après greffage des fullerènes. Elles ont également mis en évidence que le C60 était greffé sélectivement sur les zones terminées amines des couches d’accroche binaires. Enfin, une application potentielle des couches de C60 étant les mémoires moléculaires, les propriétés électriques des diverses couches réalisées ont été mesurées à l’aide de contacts électriques évaporés
In this work we studied the preparation of sticking amine- terminated molecular layers. On silicon dioxide, 3-aminopropyltrimethoxysilane (APTMS) was de- posited from a solution, and using an original dry method that allowed us to determine time constants of APTMS layer grafting and organization. On gold surfaces, monolayers of aminoethanethiol (AET) and aminothiophenol (ATP) molecules were prepared from a solution. Then, we studied structural and kinetic aspects of ullerene C60 grafting on such sticking layers, terminated by amines either all over the surface or on isolated areas (binary layers). UV-visible, FTIR, Raman and XPS spectroscopy techniques enabled to observe that C60 was grafted on the amine-terminated layers. Exalted Raman spec- troscopy (SERS) revealed ATP molecules were more tilted after C60 grafting under reflux. Analyses of all the layers were made at a molecular level by local probe microscopy (AFM, STM), and electrical measurements performed on gold using the STM tip showed the in- sulating nature of the sticking layer whereas a gap close to that of C60 appeared after grafting of fullerenes. They also highlighted that C60 was selectively grafted on amine- terminated zones within binary sticking layers. At last, one of potential applications of C60 layers being molecular memory cells, electrical properties of the various studied layers were measured through evaporated electrical contact pads

Thesis: S.M., Massachusetts Institute of Technology, Department of Materials Science and Engineering, 2019
Cataloged from PDF version of thesis.
Includes bibliographical references.
The block copolymer (BCP) self-assembly has garnered significant interest due to its ability to generate periodic nanostructures with a variety of morphologies. Compared to diblock copolymers that have been extensively studied to form the conventional morphologies such as spheres, cylinders, and lamellae depending on the block volume fraction, more complex polymer architectures are expected to offer additional degrees of freedom and a wider range of structures. Solvent vapor annealing (SVA) using a continuous gas flow system allows a precise control over the annealing condition, which can capture intermediate morphologies including perforated lamellae and gyroids and can create unique nanostructures that have not been observed in diblock copolymers. Combining with self-consistent field theory (SCFT) modeling and in situ grazing-incidence small-angle X-ray scattering (GISAXS) measurement, the phase behavior of advanced polymer architectures can be revealed in details.
Here, the self-assembly behavior of silicon-containing triblock copolymer and terpolymers in multi-layered films under SVA is presented. Using both experimental and SCFT approaches, the phase behavior of poly(stryrene-b-dimethylsiloxane-b-styrene) (PS-b-PDMS-b-PS or SDS32) thin films was investigated as a function of the as-cast film thickness and the ratio of two different solvent vapors, toluene and heptane. In comparison with diblock PS-b-PDMS with same molecular weight, the SDS32 offers a simple route to produce a diversity of well-ordered bilayer structures with smaller feature sizes, including the formation of bilayer perforated lamellae over a large process window. In addition, the morphological evolution of core-shell cylinder-forming triblock terpolymers during SVA was monitored in situ using GISAXS. A reversible order-order phase transformation between spheres and cylinders occurred during the annealing process.
One of the final morphologies consisted of the regions of in-plane cylinders, with the majority of the film comprising vertical core-shell cylinders passing through perforated lamellae of poly 1,1-dimethyl silacyclobutane (PDMSB).
by Sangho Lee.
S.M.
S.M. Massachusetts Institute of Technology, Department of Materials Science and Engineering

In this thesis, we investigate the mechanisms driving the self-assembly of peptides and proteins using computational and theoretical tools, always validating our results with experimental measures when possible. In the first part, Chapters 2-5, we focus on the Aβ system, a peptide whose aggregation is intimately linked with the development of Alzheimer's Disease. We begin by simulating the major alloforms of the peptide, Aβ_40 and Aβ_42, demonstrating that the two populate similar disordered ensembles and matching experimental data. Next we investigate how disordered Aβ_42 monomers interact with each other, finding that oligomerisation into amorphous aggregates is driven largely by hydrophobic, non-specific forces. We then move on to probing the aggregation of Aβ_42 into amyloid structures using a native-centric coarse-grained model, and explain the results with a novel Markov state analysis from which we are able to extract structural, kinetic and thermodynamic information on elongation reactions. Finally, we probe the interactions of Aβ_42 monomers with Aβ_42 fibrillar surfaces using a specially designed enhanced sampling scheme, which allows us to obtain enthalpy-driven binding thermodynamics consistent with experiments and to propose major polar binding modes. In the second part of the thesis, Chapters 6 and 7, we model the aggregation of two other self-assembling systems, viruses and a truncated form of the molecular chaperone Hsp70. We first develop a data analysis platform to extract information on the microscopic mechanisms of viral capsid self-assembly from experimental data, synthesising the results from several different systems to draw general evolutionary conclusions about the assembly mechanism. Finally, we model the oligomerisation of Hsp70 thermodynamically and kinetically, showing that its self-assembly is a highly cooperative reaction that is under strong structural constraints.

The work presented is a continuation of the study of a homologous series of tetrabutylammonium perfluoroalkylcarboxylate surfactants in water. These systems showed phase behaviour uncharacteristic of ionic perfluorocarbon surfactant systems in that they exhibit a clouding phenomenon with increasing temperature. This behaviour was ascribed to the tight association of the large, hydrophobic counterions with the poiar head group region. In this study a series of perfluorocarbon surfactants have been synthesised in which the hycirophobicity of the counterion is varied. The counterion is W (CH2CH2CH2CH3)(CH3) 41 whilst the surfactant ion remains unchanged throughout the series as periluorodecanoate. The number of butyl chains. 'n' controls the hydrophobicity of the counterion and, in these experiments, n = 4, 2, 1 and 0. The phase diagrams and the detailed phase structures have been investigated using optical polarising microscopy, 2H NMR spectroscopy and small angle x-ray scattering. As n decreases, the phase diagrams change, recovering the "generic" phase behaviour more usual for a perfluorocarbon surfactant - water system. X-ray measurements show that in the n = 4 (tetrabutylammonium perfluorodecanoate) system, all the phases (both liquid crystalline and non-liquid crystalline) have uniform mean interfacial curvature. The phases observed are L 1 (vesicles), L. and L 2. With decreasing counterion hydrophobicity, the population of counterions associated with the interface decreases, introducing greater curvature into the system. The mean curvature of the phase structures also becomes nonuniform. For n = 0 (tetramethylammonium perfluorodecarioate) no classical mesophases are observed. Much of the liquid crystalline region is taken up with a random mesh intermediate phase, Mh 1 (0) and an extensive rhombohedral mesh intermediate phase, Mh1 (R3 m). Phase behaviour intermediate between the two extremes is observed at n = 1 (butyltrimethylammonium perfluorodecanoate). In this system, the clouding phenomenon is not observed but there is a two phase region of L 1 + L. at low concentration and high temperatures. The phase structures also possess uniform mean curvature. In keeping with the less hydrophobic systems, the L. phase is less temperature sensitive at high concentrations. This work has shown that the but'l groups of the counterion are, in part, responsible for the unusual phase behaviour observed in the TBA surfactants. The hydrophobic nature of the counterion has a major impact on the structures formed even at high dilution. This nature probably drives the counterion to the interface which affects the type of mesophase formed at higher concentrations and also determines its stability with respect to temperature and concentration.

Advances in molecular engineering have enabled the formation of increasingly sophisticated molecular systems. Use of DNA and other biomolecules has proven a particularly powerful tool for nanotechnology, with their unique chemistry allowing the synthesis of self-assembling nanoscale devices with complex structures and functionalities. The ability to integrate such constructs with solid state electronic devices would be of great value for the development of these technologies into practical devices. In this project, a method was developed allowing the specific targeted alignment and binding of single molecules to sites on nano-patterned metal electrodes, relying on the highly specific molecular recognition capabilities of DNA. The patterning method utilised self-assembled monolayers of I-mercapto11- undecanol as a molecular resist, which could be removed via reductive electrochemical desorption of the gold-thiol bond. This allowed the patterning of thiolated DNA probes on selected electrodes in an array. A DNA strand with sticky ends complementary to the surface probes can then specifically bind to the surface, bridging between sites where this enables the simultaneous hybridisation of both its single stranded regions. The surface binding and hybridisation of thiolated DNA oligonucleotides was tested using a colorimetric surface staining technique and the quality of monolayers was investigated using several methods. These trials informed the development of DNA-coated surfaces resistant to non-specific binding. The electrochemical desorption of SAMs was then investigated as a means for the high-resolution patterning of surfaces. Employing these techniques, the specific bridging of gold electrodes separated. by 70nm with 330 basepair DNA strands was demonstrated. Additionally, the selective thermal melt ing of different DNA probes and the ligation of surface-bound DNA constructs were examined as further methods of controlling the specificity of the assembly reaction.

Amyloids are highly ordered cross-Greek lowercase letter beta] sheet aggregates that are associated with many diseases such as Alzheimer's, type II diabetes and prion diseases. Recently a progress has been made in structure elucidation, environmental effects and thermodynamic properties of amyloid aggregates. However, detailed understanding of how mutation, packing polymorphism and small organic molecules influence amyloid structure and dynamics is still lacking. Atomistic modeling of these phenomena with molecular dynamics (MD) simulations holds a great promise to bridge this gap. This Thesis describes the results of MD simulations, which provide insight into the effects of mutation, packing polymorphism and molecular inhibitors on amyloid peptides aggregation. Chapter 1 discusses the structure of amyloid peptides, diseases associated with amyloid aggregation, mechanism of aggregation and strategies to treat amyloid diseases. Chapter 2 describes the basic principles of molecular dynamic simulation and methods of trajectory analysis used in the Thesis. Chapter 3 presents the results of the study of several all-atom molecular dynamics simulations with explicit solvent, starting from the crystalline fragments of two to ten monomers each. Three different hexapeptides and their analogs produced with single glycine replacement were investigated to study the structural stability, aggregation behavior and thermodynamics of the amyloid oligomers. Chapter 4 presents multiple molecular dynamics (MD) simulation of a pair polymorphic form of five short segments of amyloid peptide. Chapter 5 describes MD study of single-layer oligomers of the full-length insulin with a goal to identify the structural elements that are important for insulin amyloid stability, and to suggest single glycine mutants that may improve formulation.; Chapter 6 presents the investigation of the mechanism of the interaction of polyphenols molecules with the protofibrils formed by an amyloidogenic hexapeptide fragment (VQIVYK) of Tau peptide by molecular dynamics simulations in explicit solvent. We analyzed the trajectories of the large (7x4) aggregate with and without the polyphenols. Our MD simulations for both the short and full length amyloids revealed adding strands enhances the internal stability of wildtype aggregates. The degree of structural similarity between the oligomers in simulation and the fibril models constructed based on experimental data may explain why adding oligomers shortens the experimentally observed nucleation lag phase of amyloid aggregation. The MM-PBSA free energy calculation revealed nonpolar components of the free energy is more favorable while electrostatic solvation is unfavorable for the sheet to sheet interaction. This explains the acceleration of aggregation by adding nonpolar co-solvents (methanol, trifluoroethanol, and hexafluoroisopropanol). Free energy decomposition shows residues situated at the interface were found to make favorable contribution to the peptide-peptide association. The results from the simulations might provide both the valuable insight for amyloid aggregation as well as assist in inhibitor design efforts. First, the simulation of the single glycine mutants at the steric zipper of the short segments of various pathological peptides indicates the intersheet steric zipper is important for amyloid stability. Mutation of the side chains at the dry steric zipper disrupts the sheet to sheet packing, making the aggregation unstable. Thus, designing new peptidomimetic inhibitors able to prevent the fibril formation based on the steric zipper motif of the oligomers, similar to the ones examined in this study may become a viable therapeutic strategy.; The various steric zipper microcrystal structures of short amyloid segments could be used as a template to design aggregation inhibitor that can block growth of the aggregates. Modification of the steric zipper structure (structure based design) with a single amino acid changes, shuffling the sequences, N- methylation of peptide amide bonds to suppress hydrogen bonding ability of NH groups or replacement with D amino acid sequence that interact with the parent steric zipper could be used in computational search for the new inhibitors. Second, the polyphenols were found to interact with performed oligomer through hydrogen bonding and induce conformational change creating an altered aggregate. The conformational change disrupts the intermolecular amyloid contact remodeling the amyloid aggregate. The recently reported microcrystal structure of short segments of amyloid peptides with small organic molecules could serve as a pharamcophore for virtual screening of aggregation inhibitor using combined docking and MD simulation with possible enhancement of lead enrichment. Finally, our MD simulation of short segments of amyloids with steric zipper polymorphism showed the stability depends on both sequence and packing arrangements. The hydrophilic polar GNNQQNY and NNQNTF with interface containing large polar and/or aromatic side chains (Q/N) are more stable than steric zipper interfaces made of small or hydrophobic residues (SSTNVG, VQIVYK, and MVGGVV). The larger sheet to sheet interface of the dry steric zipper through polar Q/N rich side chains was found to holds the sheets together better than non Q/N rich short amyloid segments. The packing polymorphism could influence the structure based design of aggregation inhibitor and a combination of different aggregation inhibitors might be required to bind to various morphologic forms of the amyloid peptides.
ID: 030646234; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Thesis (Ph.D.)--University of Central Florida, 2011.; Includes bibliographical references.
Ph.D.
Doctorate
Chemistry
Sciences
Chemistry

Thesis (Ph. D.)--University of Oregon, 2006.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 173-182). Also available for download via the World Wide Web; free to University of Oregon users.

A new route to molecular self-assembly using a simple acid-base hydrolytic approach on silica based surfaces, is reported in this thesis. Based on this methodology, a number of compounds containing terminal groups with acidic protons, such as alcohols, thiols, carboxylic acids, and terminal alkynes, can be easily deposited on silica surfaces. The quality of the thin films was monitored by contact angle goniometry, ellipsometry, XPS, FTIR-ATR and UV-Vis absorption spectroscopies. The deposition conditions were optimized to produce ordered and densely packed mono- and multilayers. Using the two-step process, self-assembled monolayers (SAMs) of a variety of long chain alcohols containing terminal alkyl, phenyl and acetylene groups on silica surfaces were successfully prepared. The newly formed monolayers were found to be relatively ordered and densely packed. They showed comparable stabilities to OTS/SiO 2 at ambient and high temperatures, and upon treatment with acids and bases. A layer-by-layer construction methodology, based on acid-base hydrolysis of aminosilanes and dihydroxy terminated molecules containing rigid-rod type and alkyldiacetylene backbones, led to multilayers with higher stability under various conditions compared to monolayers. The thin film assemblies were subjected to topochemical polymerization, and upon UV-Vis exposure, the formation of a blue film was observed.
Using the acid-base hydrolytic chemistry approach, silica surfaces functionalized with Sn-NEt2 groups can be easily modified using a number of terminal alkyne molecules with varied backbones. SAMs of a variety of rigid-rod alkynes on silica surfaces were successfully prepared. The pi-pi interactions in the molecules lead to ordered and densely packed thin film structures with a surface coverage of 2--7 molecules/100 A 2. The thin film assembly with diacetylene backbone was also subjected to topochemical polymerization, and upon UV-Vis exposure, the formation of a blue film was observed. Furthermore, a layer-by-layer construction methodology using aminostannanes and dialkyne terminated molecules containing alkyl or aromatic type backbone led to multilayered structures on silica surfaces without increasing disorder in the thin films with the increase in number of layers. The acetylene groups in the thin film assemblies were found to coordinate with cobalt carbonyl, corroborated by the observation of lambdamax at 277 nm.

In this thesis, the phase behavior in water of a technical grade diglycerol-based surfactant (C41V) and a group of dyes (Quinaldine Red, Pyronin Y, N-Alkylthiacarbocyanines, Oxacarbocyanines, Pinacyanol and Alcian Blue) was studied. Several experimental techniques such as polarized optical microscopy, small and wide X-ray scattering, dynamic light scattering, UV-Vis and NMR spectroscopy, were used to characterize the different phases and get insight into the molecular self- assembly behavior. The phase diagram of the water/C41V system is characterized by a wide region at temperatures lower than 70 ºC in which an inverse hexagonal liquid crystal (H2) coexists with excess water. The H2 phase could be successfully dispersed in water in the form of nanoparticles (hexosomes). A hydrophobic drug (Ketoprofen) was encapsulated in the hexosomes and its release to a receptor solution showed a non-Fickian diffusion profile. Excess of glycerol and surfactants with higher degree of esterification were separated from C41V. It was found that glycerol causes phase segregation at high C41V concentrations. The spontaneous curvature of the surfactant system can be tuned by mixing the purified C41V with the surfactants with higher degree of esterification. Structural characterization of dyes in water reveals that the molecules stack in columnar aggregates, which increase in size with concentration. At relatively high concentrations (ca. > 30 wt%) Quinaldine Red and Pyronin Y form a Nematic chromonic liquid crystal composed by columns with unimolecular cross-section. Additionally, at higher concentrations, Quinaldine Red forms a chromonic rectangular phase, which indicates that the columns cross-section is anisotropic. UV-Vis spectroscopy suggests that N-Alkylthiacarbocyanines stack face to face. The dimer model was used to fit the UV-Vis spectra and to estimate the dimeric constant and the intermolecular dissociation. The intermolecular interactions increase with the alkyl chain length (from 19.2 kBT to 20.5 kBT) suggesting that not only aromatic p-p interactions but also the hydrophobic effect contribute to the aggregation process. From small angle X-ray scattering measurements it can be inferred that the molecular columns are hollow. By applying the exciton theory to the UV-Vis spectra of Oxacarbocyanines it was found that the stacking angle of these dyes is around 54.7 º. It was also found that the molecular interactions can also be tuned by varying the carbon atoms in the poly- methine spacer of cyanine dyes. Alcian Blue showed evidence of stacking in aqueous solution, however, due to the poor solubility of this dye in water no liquid crystal was formed; nevertheless, Alcian blue solubility increases at acidic pH and liquid crystals can be formed. Cyanine dye aggregates were used as templates for silica synthesis by a sol-gel reaction. Silica nanofibers with high surface area (i.e. 230 m2/g) and hierarchical arranged mesopores were obtained. Furthermore, silica nanofibers were used as hard templates to produce carbon materials. The resulting templated carbon nanofibers were used as functional materials in energy storage and sensing applications. Carbon nanofibers showed superior performance as double layer capacitors (capacitance values of ca. 3000 F/g) and presented potential as sensing materials for aromatic compounds, especially pyridine.
En las últimas décadas, el auto-ensamblaje molecular ha ganado importancia debido a su potencial tecnológico. El estudio de nuevas moléculas con capacidad de formar agregados funcionales es un área de investigación relevante en la ciencia de materiales. Los tensioactivos son los ejemplos más representativos de moléculas auto-ensambladas. Los tensioactivos están formados por una cadena hidrocarbonada (hidrófoba) y un grupo polar (hidrófilo). Los tensioactivos se auto- agregan en solución debido a segregación entre el solvente y las cadenas hidrofóbicas formando un amplio rango de nanoestructuras, desde micelas esféricas hasta cristales líquidos. No obstante, el auto-ensamblaje molecular no es una propiedad que está restringida a los tensioactivos. Algunas moléculas planas y aromáticas, como las llamadas cromónicas, pueden también auto-organizarse en solución. Las propiedades de las moléculas cromónicas son diferentes de aquellas mostradas por los tensioactivos. El estudio de las propiedades de auto-agregación de las moléculas cromónicas está restringida a unos pocos sistemas. Es por eso que se conoce muy poco sobre la relación entre su estructura molecular y su comportamiento de auto-agregación en solución. Los nanomateriales han sido una de las áreas de mayor enfoque científico y tecnológico de los últimos años debido a que estos presentan propiedades únicas. Estas propiedades dependen en gran medida de la composición química, tamaño y morfología, es por eso que controlar estos parámetros es fundamental. Principalmente hay dos metodologías de síntesis de nanomateriales: aquellas que parten de un material en el estado masivo (“bulk”) para obtener unidades más pequeñas (“top- down”) y aquellas que consisten en partir de átomos y moléculas para construir nanomateriales (“bottom-up”). La metodología “bottom-up” produce estructuras estables y robustas; adicionalmente es económico, versátil y fácil. Entre los métodos de bottom-up quizás los que están más ampliamente estudiados son aquellos que utilizan auto-agregados (especialmente tensioactivos) en solución como plantillas. En este caso la morfología y tamaño del material final están determinados por el tipo de agregado utilizado. Desde un punto de vista industrial, se prefiere el uso de tensioactivos de grado técnico (disponibles comercialmente) debido a que son más económicos; no obstante, las propiedades de auto-ensamblaje de tensioactivos pueden cambiar por la presencia de impurezas y es por ello que el estudio del efecto de dichas impurezas es relevante. Por otra parte, es de interés el uso de otro tipo de agregados con morfologías distintas a aquellas presentadas por sistemas tensioactivos. A este respecto, las moléculas cromónicas son atractivas ya que poseen propiedades ópticas que, combinadas con materiales inorgánicos, pueden usarse en un amplio rango de aplicaciones. En este contexto, el objetivo principal de este trabajo de tesis es el de estudiar y caracterizar el comportamiento de auto-ensamblaje molecular de tensioactivos de grado comercial y moléculas cromónicas en medio acuoso y utilizar estos agregados para sintetizar nanomateriales funcionales. Para ello el plan de trabajo se dividió en tres partes: * Estudio del comportamiento fásico de las moléculas seleccionadas en medio acuoso. * Preparación de materiales usando los agregados identificados en el estudio del comportamiento fásico como plantillas. * Estudio de las posibles aplicaciones de los materiales preparados en liberación controlada de fármacos, almacenaje de energía y tecnología de sensores. Se determinó el comportamiento fásico mediante determinación de diagramas de fase en función de la concentración y temperatura de los distintos compuestos elegidos. Los límites de las distintas fases se determinaron mediante microscopia de luz polarizada (POM) con control de temperatura. La estructura de los agregados se caracterizó por técnicas de dispersión de radiación, tales como dispersión de rayos X a ángulo pequeño (SAXS/WAXS) y dispersión dinámica de luz (DLS). Para los tensioactivos derivados de di-glicerol poli-isostearatos, se demostró que el di-glicerol mono-isostearato (C41V) en medio acuoso se autoagrega formando estructuras de cristal líquido hexagonal inverso (H2). Este cristal líquido H2 se dispersó en agua mediante distintos métodos formando los denominados ‘’hexosomas’’. El método de evaporación de solvente proporcionó los mejores resultados, obteniéndose tamaños de hexosomas más pequeños y con baja polidispersidad. Se encapsuló en los hexosomas obtenidos un fármaco hidrófobo (ketoprofeno)se estudió su liberación a un medio gastrointestinal simulado. Estos estudios pusieron de manifiesto que puede controlarse la difusión del fármaco a una solución receptora. Adicionalmente los hexosomas formados por C41V se degradan en condiciones gastro-intestinales, lo cual evita que estos se acumulen en los órganos corporales. El glicerol y los tensioactivos con grados de esterificación más altos presentes en C41V se separaron y se estudió la influencia de las impurezas en el comportamiento fásico del tensioactivo. Se encontró que el glicerol produce una segregación de fases a altas concentraciones de C41V. Adicionalmente se demostró que variando la cantidad de tensioactivo con mayor grado de esterificación en C41V se pueden obtener distintos cristales líquidos en coexistencia con un exceso de agua. En los sistemas acuosos de colorantes estudiados, se evidenció que todas las moléculas seleccionadas (Quinaldine red, Pyronin Y, Tiacarbocianinas, Oxacarbocianinas, Alcian Blue) se auto-agregan formando columnas moleculares apiladas cara-a-cara. Estas columnas crecen a medida que la concentración del colorante aumenta. A concentraciones suficientemente altas se forma una fase cristal líquido nemático (Fase N) y una fase de cristal líquido hexagonal (Fase M). En el sistema de agua/Quinaldine Red se identificó una estructura a concentraciones altas en la cual las columnas moleculares están ordenadas en una estructura rectangular. Los estudios con las Tiacarbocianinas y Oxacarbocianinas pusieron de manifiesto que las fuerzas inter-moleculares se pueden modular cambiando el tamaño de cadena de las cadenas alquílicas laterales o la cadena de metinos que separa los grupos aromáticos. Los estudios con Alcian Blue muestran que este colorante se auto-agrega en solución, pero se disocia poco en agua por lo cual no forma cristales líquidos. Alcian Blue en medio acido forma cristales líquidos debido que su disociación aumenta al disminuir el pH. Los agregados de los colorantes se han utilizado como plantillas para sintetizar nano-fibras de sílice con una nano-estructura determinada y una elevada superficie específica (230 m2/g). Los materiales derivados se han estudiado mediante diferentes técnicas tales como SEM, SAXS y adsorción/desorción de gases. Las nano-fibras de sílice se usaron como plantillas para obtener fibras de carbono Se exploraron aplicaciones de las fibras de carbono obtenidas en súper-capacitores mediante técnicas electroquímicas y se encontró que los materiales muestran un excelente rendimiento (capacitancias de hasta 300 F/g). Adicionalmente se estudió el uso de las fibras de carbono como sensores de vapores orgánicos, obteniéndose una alta sensibilidad respecto a compuestos aromáticos.

Aquesta tesis doctoral està dividida en dues parts. La primera part de la tesi inclou el disseny, la síntesi i caracterització d’una sèrie de receptors trimèrics de porfirines així com l’estudi de la formació de complexes d’inclusió amb ful•lerens (C60, C70, C84, Sc3N@C80), nanotubs de carboni (CNT) i bucky onions. L’objectiu principal d’aquest primer bloc és la preparació de receptors de porfirines capaços de formar, de manera selectiva o preferent, complexos d’inclusió amb ful•lerens grans (>C84) així com carbon nano onions (CNOs) i nanotubs de carboni (CNT). En la segona part de la tesi, es detalla la síntesi i estudi de un monòmer piramidal amb estructura central de CTV quiral connectada a llargues cadenes alquíliques a través d’enllaços d’urea. L’objectiu principal d’aquest segon bloc és la preparació d’un monòmer de CTV capaç d’ampliar tal quiralitat del monòmer a l’estructura supramolecular. Per tal de promoure aquest comportament, els monòmers van ser previstos de urees que degut a la seva habilitat per establir ponts d’hidrogen d’especificitat i direccionalitat alta promourien la formació d’una hèlix macroscòpica.
Esta tesis doctoral está dividida en dos partes. La primera parte de la tesis incluye el diseño, síntesis y caracterización de una serie de receptores trimericos de porfirinas así como el estudio de la formación de complejos de inclusión con fulerenos (C60, C70, C84, Sc3N@C80), nanotubos de carbono (CNT) y bucky onions. El objetivo principal de este primer bloque es la preparación de los receptores de porfirinas capaces de formar de manera selectiva o preferente, complejos de inclusión con fulerenos grandes (>C84) así como carbon nano onions (CNOs) y nanotubos de carbono (CNT). En la segunda parte de la tesi se detalla la síntesis y estudio de un monómero piramidal con estructura central de CTV quiral conectada a largas cadenas alquílicas a través de enlaces tipo urea. El objetivo principal de este segundo bloque es la preparación de un monómero capaz de ampliar tal quiralidad a la estructura supramolecular. Para promover tal comportamiento, los monómeros son provistos de ureas que debido a su habilidad para establecer puentes de hidrogeno de alta especificidad y direcctionalidad promoverian la formación de una hélice macroscópica.
This thesis is divided in two different parts. The first part includes the design, synthesis and characterization of a series of porphyrin trimeric receptors as well as the study of the inclusion complex formation with fullerenes (C60, C70, C84, Sc3N@C80), carbon nanotubes (CNT) and bucky onions. The main objective of this first bloc is the preparation of porphyrin-based receptors able to selectively encapsulate big fullerenes (>C84) as well as carbon nano onions (CNOs) and carbonnanotubes (CNT). The second part of the thesis deals with the synthesis and studies of a chiral pyramidic monomer bearing a CTV central core connected to long alkyl chains through urea type linkers. The objective of this second block would be the preparation of a CTV-monomer able to transfer the chirality from the CTV central core to the supramolecular column. To promote such behavior, the monomers are provided with urea moieties that due to their high specificity and directionality would promote de formation of the macroscopic helix.

Ce mémoire décrit la synthèse d’hôtes organiques et organométalliques contenant des motifs riches en électrons, particulièrement le tétrathiafulvalène (TTF), pour la complexation supramoléculaire de fullerènes C60 et C70. Le chapitre 1 est une revue de la littérature qui présente les notions de cavitant, de métallocavitant et des hôtes supramoléculaires. Le chapitre 2 présente les méthodes de caractérisation utilisées dans ce travail. Le chapitre 3 est consacré à une nouvelle méthode de synthèse de pinces moléculaires et des récepteurs tripodaux contenant l’unité riche en électrons (TTF). Les pinces triazoles ont été préparées par chimie « clic » entre l'azoture -TTF et des dérivés benzéniques disubstitués en position 1 et 3 par un acétylène. La réaction de l'azoture-TTF et des 1,3, 5-benzènes trisubstitués a donné des récepteurs tripodaux. L'affinité des hôtes avec les fullerènes C60 et C70 a été étudiée par la méthode optique spectroscopique UV-vis dans quatre solvants différents. La constante d’association la plus élevée a été calculée pour l’hôte 4 dans le chlorobenzène. Cependant, le récepteur tripodal n'a pas montré une affinité importante envers les fullerènes. Le chapitre 4 est consacré à la synthèse des nouveaux metallocavitands de zirconium TTF- Zr3 préparés par la méthode d’agrégation. Un seul hôte a été isolé et caractérisé par la méthode spectroscopique. Dans ce chapitre, nous présentons l'étude des interactions supramoléculaires avec les fullerènes en surveillant la réponse UV-vis à l’addition d’une quantité croissante de fullerènes à la solution contenant l’hôte. Le chapitre 5 décrit la synthèse de nouveaux metallocavitants de Zr3 à partir de la réaction de dichlorure de zirconocène sur l'acide carboxylique. Quatre metallocavitants de Zr3 ont été préparés. Les structures cristallographiques, les propriétés photophysiques et leurs utilisations potentielles en tant que matériaux émissifs bleus ont été présentées. Le chapitre 6 est séparé en trois sections. La première section décrit la synthèse et l’affinité de metallocavitant de tantale (V) avec les fullerènes. La deuxième section illustre la tentative de synthèse d’une librairie de Zr3 en utilisant la réaction de couplage croisée. Enfin, la dernière section présente la synthèse du nouveau metallocavitant de Ta3Carbox obtenu par la méthode d’agrégation à partir de la réaction de Cp*TaMe4 avec de l'acide 4 - iodobenzoïque. La structure est étudiée par rayons X.
This thesis described the synthesis of organic and organometallic hosts containing electron rich units in particularly tetrathiafulvalene (TFF) to bind fullerenes C60 and C70. Chapter two illustrates the different analysis techniques used in this thesis. Chapter three described new method for the synthesis of tweezers-like TTF and tripodal TTF molecules in addition to their binding affinity towards fullerenes C60 and C70. The tweezers-like TTF were prepared by click chemistry from azide-TTF and 1,3 substituted benzene. Similarly, the reaction of azide-TTF and 1,3, 5 substituted benzene yielded the tripodal-TTF receptor. The affinity toward fullerenes C60 and C70 were studied in four different solvents. The highest binding constant was calculated for host 4 in chlorobenzene toward fullerene C70. Moreover, solvent dependant behavior was observed with the studied host. However, the tripodal receptor did not showed significant affintity towards fullerenes. Chapter four described the synthesis of new TTF-Zr3 metallocavitand by coordination method; two hosts were isolated and characterized. In this chapter we present the binding study toward fullerenes by monitoring the UV-vis response to increasing amount of fullerenes added to the solution of the host. Chapter five described the synthesis of new Zr3 metallocavitand in one pot reaction from the reaction of zirconocene dichloride with carboxylic acid in aqueous media. Four Zr3 metallocavitand were prepared and the crystallography was presented in addition to the photophysical properties and their potential uses as blue emissive materials. The last chapter is separated into three sections. The first section described our early work on tantalum (V) metallocavitand in addition to their hosting capability toward fullerenes. The second section illustrate the tentative has been committed to the design and synthesis of Zr3 library using cross-coupling reaction in addition to the synthesis of extended Zr3-cinnamate metallocavitand. Lastly, the last section illustrates the synthesis of new Ta3-Carbox achieved by aggregation method from reaction of Cp*TaMe4 with 4-iodobenzoic acid. The single X-ray structure revealed a new structure with trimetallic core comparable to the core observed for tantalum metallocavitand.

Les virus sont connus pour infecter toutes les classes d’organismes vivants sur Terre, qu’elles soient végétales ou animales. Les virions consistent en un génome d'acide nucléique protégé par une enveloppe protéique unique ou multicouche appelée capside et, dans certains cas, par une enveloppe de lipides. La capside virale est généralement composée de centaines ou de milliers de protéines formant des structures ordonnées. La moitié des virus connus présentent une symétrie icosaédrique, les autres étant hélicoïdaux, prolats ou de structure irrégulière complexe. Récemment, les particules virales ont attiré une attention croissante en raison de leur structure extrêmement régulière et de leur utilisation potentielle pour la fabrication de nanostructures ayant diverses fonctions. Par conséquent, la compréhension des mécanismes d'assemblage sous-jacents à la production de particules virales est non seulement utile au développement d'inhibiteurs à des fins thérapeutiques, mais elle devrait également ouvrir de nouvelles voies pour l'auto-assemblage de matériaux supramoléculaires complexes. À ce jour, de nombreuses études expérimentales et théoriques sur l'assemblage de virus ont été effectuées. Des recherches expérimentales ont permis d'obtenir de nombreuses informations sur l'assemblage du virus, y compris les conditions appropriées requises pour l'assemblage et les voies cinétiques. En combinant ces informations et méthodes théoriques, une première compréhension du mécanisme d'assemblage des virus a été élaborée. Cependant, les informations provenant uniquement d'expériences ne peuvent donner une image complète, en particulier à l'échelle microscopique. Par conséquent, dans cette thèse, nous avons utilisé des simulations informatiques, y compris des techniques de Monte Carlo et de la dynamique moléculaire, pour sonder l’assemblage du virus, dans l’espoir de mieux comprendre les mécanismes moléculaires en jeu
Viruses are known for infecting all classes of living organisms on Earth, whether vegetal or animal. Virions consist of a nucleic acid genome protected by a single or multilayered protein shell called capsid, and in some cases by an envelope of lipids. The viral capsid is generally made of hundreds or thousands of proteins forming ordered structures. Half of all known viruses exhibit an icosahedral symmetry, the rest being helical, prolate or having a complex irregular structure. Recently, viral particles have attracted an increasing attention due to their extremely regular structure and their potential use for fabricating nanostructures with various functions. Therefore, understanding the assembly mechanisms underlying the production of viral particles is not only helpful to the development of inhibitors for therapeutic purpose, but it should also open new routes for the self-assembly of complex supramolecular materials. To date, numerous experimental and theoretical investigations on virus assembly have been performed. Through experimental investigations, a lot of information have been obtained on virus assembly, including the proper conditions required for the assembly and the kinetic pathways. Combining those information and theoretical methods, an initial understanding of the assembly mechanism of viruses has been worked out. However, information coming purely from experiments cannot give the whole picture, in particular at a microscopic scale. Therefore, in this thesis, we employed computer simulations, including Monte Carlo and molecular dynamics techniques, to probe the assembly of virus, with the expectation to gain new insights into the molecular mechanisms at play

Ce travail de thèse est consacré à l’étude d’auto-assemblages de molécules organiques π-conjuguées par microscopie à effet tunnel (STM)sous ultra-vide sur une surface de silicium dopée bore. Le manuscrit est constitué de cinq chapitres : dans le premier chapitre, nous présentons un état de l’art des assemblages organiques sur les surfaces métalliques et sur les semi-conducteurs. Le chapitre deux décrit le dispositif expérimental utilisé au cours de cette thèse. Il présente également le substrat de Si(111)-B et fournit les concepts théoriques associés à la microscopie à effet tunnel. Le troisième chapitre décrit en détail les réseaux supramoléculaires obtenus à partir d’une molécule aromatique halogénée de symétrieC2. L’adsorption de 4,4"-dibromo-p-terphényle conduit à la formation de deux types de structures compactes (l’une en bande et l’autre en chevron) stables à température ambiante et commensurables avec la surface. Nous montrons que ces architectures sont pilotées conjointement par la liaison hydrogène, la liaison halogène et du π -stacking. Le quatrième chapitre étudie l’influence du nombre de cycles aromatiques sur la géométrie et la périodicité d’auto-assemblages obtenus sur Si (111) -B. Pour cela, nous avons synthétisé deux molécules organiques composées d’une partie centrale aromatique et de deux chaînes latérales (O-(CH2)9-CH3). La partie centrale est constituée respectivement de trois ou cinq cycles phényles terminées par des groupements cyano. Nous nous sommes également intéressés à l’influence des groupements terminaux sur l’organisation du réseau. Nous montrons que l’effet des groupements cyano sur les interactions "molécule/molécule" et sur les interactions "molécule/surface" est négligeable. A partir des travaux obtenus dans le chapitre 4, nous concluons notre manuscrit en présentant des réseaux supramoléculaires de molécules dipolaires. Ces réseaux forment des lignes de dipôles. Nous montrons que sur de petites échelles les molécules favorisent un alignement de leurs moments dipolaires
This work is dedicated to the investigation under ultra high vacuum of _-conjugated molecule on a silicon surface by means of scanningtunneling microscopy (STM). The manuscript consists of five chapters.In the first chapter, we present a state-of-the-art of organic assembly on metal and semiconductor.Chapter two describes the experimental setup using during thesis. It also shows Si(111)-B substrate and gives theoretical conceptsassociated with the scanning tunneling microscopy.The third chapter describes in detail the supramolecular network obtained from an aromatic halogenated molecule with C2 symmetry. Theadsorption of 4,4"-dibromo-p-terphenyl leads to the formation of two kinds of compacts structures (a stripe structure and a herringbonestructure). The formed networks are stable at room temperature and commensurable with the surface. These architectures are promotedby hydrogen bond, halogen bond and _-stacking.Chapter four studies influence of benzene ring number on the geometry and the periodicity of self-assemblies on Si(111)-B. To do that,we have synthesis two organics molecules composed of an aromatic central part and two laterals chains (O-(CH2)9-CH3). The centralpart is composed of respectively three or five phenyl ring ended by cyano groups. We are also interested to the terminal groups effecton the network organisation. We show that the cyano groups effect on the "molecule/molecule" interaction and the "molecule/surface"interaction are negligible. Basis of the work conducted on the chapter four, we conclude our manuscript by presenting supramolecularsnetworks of dipolar molecule. These networks form dipole lines. We show that on small scale the molecules promote an alignment of theirdipolar moments

Self-assembling molecules are central to a plethora of processes found in nature, biotechnology and even disease. The importance of the non-covalent interaction of monomers to the formation of fibrillar assemblies is evident in the repeated use of this mechanism throughout nature, from essential cellular processes such as the formation of the cytoskeleton to the production of silk. Further, it has been recognised in the last two decades that a self-assembly mechanism, that is the formation of amyloid, underpins the pathology of protein misfolding diseases; it is therefore essential to dissect these mechanisms. Despite recent technological and model system developments, self-assembling molecules remain challenging to investigate. Using combined structural and biophysical characterisations of penta- and hexa-peptide self-assembling model systems these investigations shed further light on the structure of amyloid-like fibrils. The elucidation of the structures of these fibrillar systems not only has implications for disease but also makes them well placed for consideration for biotechnological applications. In reflecting upon how cross-ß structural architectures can be organised in the fibrillar state, a molecular and supramolecular model of fibrils formed by a fragment of !-synuclein is reported. The fibrils are found to consist of a novel and elaborate cross-ß architecture that leads to a helical supramolecular assembly spanning length scales previously unobserved for such a system. Where self-assembly is a useful route to supramolecular structure formation, the use of low molecular weight gelator (LMWG) peptides to create fibrillar structures with defined material properties is also explored. The complex link between molecular structure, self-assembled architecture, fibril formation, fibril interaction and ultimately bulk material properties is described. It is found that the determinants of self-assembly are distinct from the determinants of gelation and so future LMWG design will have to consider both individually. This work presents methodological advances in the characterisation of self-assembled structures. The investigations presented here have relevance for disease related processes but also to the technological use of these systems as materials. Finally, this work emphasises the beauty of the extravagant, yet elegant connection between molecular interaction and supramolecular selfassembly.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2007.
Includes bibliographical references.
Molecular self-assembly describes the assembly of molecular components into complex, supramolecular structures governed by weak, non-covalent interactions. In recent years, molecular self-assembly has been used extensively as a means of creating materials and devices with well-controlled, nanometer-scale architectural features. In this thesis, molecular self-assembly is used as a tool for the fabrication of both gene and drug delivery systems which, by virtue of their well-controlled architectural features, possess advantageous properties relative to traditional materials used in these applications. The first part of this thesis describes the solution-phase self-assembly of a new family of linear-dendritic "hybrid" polymers with plasmid DNA for applications in gene therapy. It begins with an overview of the design of next-generation, non-viral gene delivery systems and continues through the synthesis and validation of hybrid polymer systems, which possess modular functionalities for DNA binding, endosomal escape, steric stabilization, and tissue targeting. This part of the thesis concludes with applications of these systems to two areas of clinical interest: DNA vaccination and tumor targeted gene therapy.
(cont.) The second part of this thesis describes the directed self-assembly of polymeric thin films which are capable of degrading in response to either passive or active stimuli to release their contents. It begins with a description of passive release thin films which degrade by basic hydrolysis to release precise quantities of model drug compounds. These systems can be engineered to release their contents on time scales ranging from hours to weeks and can also be designed to release multiple drugs either in series or in parallel. Later, field-activated thin films which release their contents in response to an external, electrical stimulus are described and characterized in detail. Together, these approaches combine rapid and inexpensive processing, the ability to conformally coat any surface regardless of composition, size, or shape, and the ability to release multi-drug or multi-dose schedules, and as such they may find applications in a range of areas.
by Kris Cameron Wood.
Ph.D.

In dieser Dissertation wird die Selbstorganisation von pi-konjugierten (makro)molekularen Architekturen durch Chemisorption oder Physisorption in hochgeordnete supramolekulare nanoskopische und mikroskopische Strukturen auf festen Trägern untersucht. Ihre Struktur und Dynamik wurden auf molekularer Skala hauptsächlich mit Rastersondenmikroskopien, insbesondere mit Rastertunnel- und Rasterkraftmikroskopie, untersucht. Dies erlaubte die Charakterisierung einer Reihe von Phänomenen, die sowohl an Fest-Flüssig-Grenzflächen auftreten, wie beispielsweise die Dynamik der einzelnen molekularen Nanostäbchen (Ostwald Reifung) und die Fraktionierung steifer Polymerstäbchen durch Physisorption an der Grafitoberfläche aus der Lösung heraus, als auch in trockenen Filmen vorkommen wie die Selbstorganisation steifer Polymerstäbchen zu Nanobändern mit molekularen Querschnitten, die sich epitaktisch auf Oberflächen orientieren lassen und auch die Ausbildung gestapelter Architekturen von diskförmigen Molekülen. Außerdem wurden die elektronischen Eigenschaften der untersuchten Systeme mit Hilfe von Photoelektronenspektroskopie charakterisiert. Die entwickelten Nanostrukturen sind nicht nur für Nanokonstruktionen auf festen Oberflächen von Interesse, sondern besitzen auch Eigenschaften, die sie für Anwendungen in einer zukünftigen molekularen Elektronik prädestiniert, etwa für den Aufbau molekularer Drähte.
In this thesis the self-assembly of pi-conjugated (macro)molecular architectures, either through chemisorption or via physisorption, into highly ordered supramolecular nanoscopic and microscopic structures has been studied. On solid substrates structure and dynamics has been investigated on the molecular scale making use primarily of Scanning Probe Microscopies, in particular Scanning Tunneling Microscopy and Scanning Force Microscopy. This allowed to characterize a variety of phenomena occurring both at the solid-liquid interface, such as the dynamics of the single molecular nanorods (known as Ostwald ripening), the fractionation of a solution of rigid-rod polymers upon physisorption on graphite; and in dry films, i.e. the self-assembly of rigid-rod polymers into nanoribbons with molecular cross sections which can be epitaxially oriented at surfaces and the formation ordered layered architectures of disc-like molecules. In addition the electronic properties of the investigated moieties have been studied by means of Photoelectron Spectroscopies. The nanostructures that have been developed are not only of interest for nanoconstructions on solid surfaces, but also exhibit properties that render them candidates for applications in the field of molecular electronics, in particular for building molecular nanowire devices.

Metallosupramolecular self-assembly has fast expanded as a field due to the possibility for relatively facile construction of large assemblies through reversible non-covalent interactions, compared to their more synthetically challenging covalent counterparts. Not least, it provides a fast and often quantitative route to the construction of three-dimensional structures with a cavity. These internal spaces have been shown to be effective for a variety of applications, including but not limited to catalysis, drug delivery, use as a noncovalent protecting group, a separations material etc. Thermodynamic processes, with the inherent advantages of atom efficient, high-yielding reactions, usually control these systems. However this can also be a double-edged sword, with these systems susceptible to changes to specific ambient conditions, and are thus often not kinetically stable. Herein, we report the expansion of a method utilising the one electron oxidation of high spin d7 cobalt(II) to low spin d6 cobalt(III) as a molecular locking mechanism as part of the assembly process. This allows for the formation of species under thermodynamic control in the CoII manifold, with the kinetic stability of these assemblies in the oxidised CoIII and has been used to synthesise a variety of tetrahedra and helicates with a series of bis-bidentate N,N’-chelate ligands, which have shown to be stable away from their thermodynamically preferred conditions for long periods of time. These containers can be made both water and organic soluble via counteranion exchange, and a series of guests have been shown to bind in the tetrahedral species. Alongside on going biological viability tests, these guests show promise for a variety of applications including fluorescent tagging and radio-diagnostic agents. Novel switching methods have also been demonstrated for transformations between these species going both energetically down and up hill.

Biology can achieve phenomenal information storage/processing capabilities from just four hydrogen bonding molecules. The orthogonal self-sorting of these four hydrogen bonding motifs is achieved alongside the hydrophobic collapse of the DNA backbone. Orthogonal self-sorting without the aid of a polymer backbone is dicult to achieve, as shown by the minimal examples of self-sorting hydrogen bonding motifs available in the literature. This thesis describes the design, synthesis and binding studies of molecules that are capable of orthogonal self-sorting, without a preorganising backbone and begins to use them in a signalling cascade. In Chapter 2 ureidoimidazole, a conformer independent triple hydrogen-bond array, is introduced. Studies were carried out to investigate what effect, if any, preorganisation using intramolecular hydrogen bonding had on the binding affnity of triply hydrogen bonded complexes. Chapter 3 investigates another factor that can effect the binding affnity of complexes,the remote substituent effect. Two series of complementary molecules were synthesised so that they contained a variety of electron donating/withdrawing groups and the effect that these had on the binding affnity of the complex was measured. Chapter 4 describes a novel quadruple hydrogen-bond array, which was designed to interact strongly with its complementary partner. It was found that a combination of effects (differences in geometry and undesired conformers being favoured) lead to a low binding affnity being observed. Chapter 5 begins to investigate non-linear arrays, however none of those proposed were able to form heterodimers. Therefore a self-sorting system was assembled using a triple and quadruple hydrogen-bonded array. High fidelity interactions were achieved, even though it was possible to form undesired complexes. These undesired molecular interactions were exploited in Chapter 5, where a signalling cascade is described. Careful planning of the order in which to add the molecules can give different routes in which to achieve the self-sorting system, each with it's own fidelity trace. A photolabile tag was introduced to one of the molecules so that a photosensitive system could be achieved.

Inspired by the performance and evolutionarily-optimised natural molecular machines that carry out all the essential tasks contributing to the molecular basis of life, chemists aim towards fabricating synthetic molecular machines that mimic biological nanodevices. The use of rotaxanes as a prototype for molecular machines has emerged as a result of their ability to undergo translational motion between two or more co-conformations. Although biological machines are capable of complex and intricate functions, their inherent stability and operational conditions are restricted to in vivo. Synthetic systems offer a limitless number of building blocks and a range of interactions to be manipulated. Transition metal-ligand interactions are utilised as one strategy to control the directional movement of submolecular components in artificial machines due to their well-defined geometric requirements and significant strength. This thesis presents new externally addressable and switchable molecular elements for transition metal complexed-molecular machines involving an acid-base switch. The proton input that induces changes to cyclometallated platinum complexes can be exploited to control exchange between different coordination modes. The development of the pH-switchable metal-ligand motif for the stimuli-responsive platinum-complexed molecular shuttle has also been explored. The metal-directed self-assembly of tubular complexes were studied in order to develop self-assembled rotaxanes. A series of metal building blocks was explored to extend the scope for a tube self-assembly.

Thesis (Ph.D.)--University of Delaware, 2006.
Principal faculty advisors: Eric W. Kaler, College of Engineering; and Abraham M. Lenhoff, Dept. of Chemical Engineering. Includes bibliographical references.

Supramolecular chemistry, the domain of chemistry ‘beyond the molecule’, is finding increasing application in a diverse range of scientific fields. A key concept in this field, termed molecular self-assembly, has important applications ranging from nanotechnology to medicine, and refers to the intermolecular assembly of individual molecules via non-covalent forces, most importantly hydrogen bonding and π-π stacking interactions. Specifically, this thesis considers the self-assembling arrangements of synthetic pyrimidine-based heterocyclic systems, which present guanine/cytosine DDA/AAD hydrogen bonding motifs. Characterisation of such systems is well documented in the liquid phase, but there exists a general paucity of solid-state analytical data for such materials. Owing to the inherent difficulty in crystallising these systems, typically due to disordered alkyl and aryl sidechains, high-resolution 1H MAS NMR is uniquely placed to elucidate hydrogen bonding arrangements in these systems, given the sensitivity of the 1H chemical shift to its local atomic environment. For cases where single-crystal X-ray structures can be obtained, a so-called NMR crystallographic approach can be used to complement the existing single-crystal X-ray data. By comparison of GIPAW calculated 1H chemical shielding parameters to experimentally observed chemical shifts and, more specifically, through comparison of calculated shielding values for the full crystal versus the isolated molecule, an analysis of the strength of non-covalent phenomenon present in a given system can be presented. This thesis applies fast MAS 1H detected 2D NMR methods to a range of structural problems concerning pyrimidine-based synthetic organic molecules. Specifically,1H – 1H DQ/SQ MAS, 14N – 1H HMQC and 1H – 13C techniques, such as the refocused INEPT and well-known CP MAS methods, are used, where applicable, in conjunction with GIPAW calculated NMR parameters to provide a comprehensive study of the solid-state packing arrangements of a series of guanine/cytosine synthetic derivatives which exhibit a diverse range of self-assembling architectures, including helical and stacking trimeric motifs. It is shown that, for crystalline compounds, confirmation of chemical shift assignments via the GIPAW method can be used to infer the structure of related systems for which diffraction data is not available, through comparison of the observed experimental NMR data. In addition, it is demonstrated that, for a series of pyrimidine and pyridopyrimidine intermediates which form non-crystalline powdered solids, high-resolution 1H MAS NMR methods can be applied alone to elucidate likely hydrogen bonding motifs in the absence of crystallographic data, thereby allowing the observer to speculate on likely modes of self-assembly in the solid state. Interestingly, this study involves the relatively novel investigation (by means of solid-state NMR) of aldehyde and, in particular, oxime containing organic molecules, for which (in the case of the latter functional group) no published 1H MAS NMR studies have been presented at the time of writing. Finally, in collaboration with the spectrometer company JEOL, it is shown that a selective saturation pulse can be employed to supress excessive t1 noise in two-dimensional 1 H MAS NMR spectra, at fast MAS frequencies. To demonstrate this effect, the intense methyl resonance of a synthetic nucleoside derivative is suppressed, whilst reduced spin diffusion rates at higher MAS frequencies ensure that the effect on nearby spins is minimised.

A significant number of RNA viruses assemble their protein containers and genomic material simultaneously. Here the implications of this protein-RNA co-assembly are investigated using an extended version of a model first proposed by Adam Zlotnick in 1994 (Zlotnick, 1994). The inspirations for this extended model are the cases of bacteriophage MS2 and the STMV virus, viruses that have been well characterised experimentally. Example pathways of RNA virus assembly have been enumerated and kinetic simulations have been run on these networks. The results show the most likely pathways of virus assembly and the concentrations of the intermediates. This work will also demonstrate how kinetic traps may be avoided when proteins are able to bind RNA during assembly. Additionally modelled are DNA cages, which are three-dimensional shapes made from double-helical DNA molecules. Such cages have been seen within viruses but may also be constructed artificially. This model has been used to produce energetically optimised designs for icosidodecahedron-shaped DNA cages.

This thesis focuses on the characterisation of supramolecular structures containing p-sulfonatocalix[ n]arenes (where n=4,5,6,8) with suitable guest molecules and lanthanide metal cations. The characterisation is based primarily on X-ray diffraction but high-resolution NMR techniques have also been used to identify p-sulfonatocalix[4]arene/crown ether complexation in the solution phase. Notably, remarkable control can be achieved over the formation and geometries of nano-metre scale spheroids or tubules containing p-sulfonatocalix[4]arene via guest selection. Chapter 1 gives a short overview of supramolecular chemistry, molecular recognition and the history and synthesis of calixarenes. The supramolecular chemistry of the p-sulfonatocalx[n]tilarenes and a selection of interesting and recently reported nano-metre scale multi-component supramolecular architectures are also reviewed. Chapter 2 describes the pH dependent formation of a number of molecular capsule and bi-layer supramolecular architectures based on p-sulfonatocalix[4]arene, (di)aza-functionalised guest species and lanthanide metals. Chapter 3 describes the formation of several bi-layer structures based on p-sulfonatocalix[4]arene and lanthanide, metals. Incorporation of different lanthanide metal salts changed the resulting structures by either inclusion or exclusion of the anions in the supramolecular architectures. Chapter 4 describes a series of Diffusion Ordered Spectroscopy experiments that were performed in collaboration with Dr. Julie Fisher at the University of Leeds. The experiments were based on calixarene/crown ether systems and the results showed 1: 1 host-guest complexation in solution with a series of charged species. Chapter 5 describes the formation of Russian doll complexes and the design and control over nanometre scale spheroidal arrays composed of p-sulfonatocalix[4]arene. Chapters 6 and 7 describe the formation of novel supramolecular complexes that are based on the p-sulfonatocalix[5,6,8]arenes. The resulting supramolecular architectures include unprecedented bis-molecular capsules, coordination polymer chains and 3-D networks.

The structural pathway from a single molecule to clustering through to nucleation during a crystallisation process is not fully understood. As such the solution state structure, nucleation kinetics and phase transformation kinetics of p-Aminobenzoic (PABA) acid are probed using a combination of in-situ crystallisation characterisation techniques and nucleation kinetic analysis methods. The solubility of alpha PABA is measured in a number of solvents where van’t Hoff analysis shows that solute-solute interactions are probable in all solvents. Solution state FTIR studies reveal the presence of a distribution of solvated monomer and carboxylic acid dimer species in acetonitrile solutions. This provides a link between solution state structural synthons and the carboxylic acid dimer structural synthon of the alpha PABA solid phase. Isothermal nucleation kinetic analysis reveals that calculated interfacial tension, γeff, values are found to be low for an organic material; where γeff values are 0.85 – 1.31 mJ/m2 in ethanol and 2.36 – 2.60 mJ/m2 in water. Due to this the critical cluster sizes are in the region of 0.48 – 1.98 nm. Poly-thermal kinetic analysis reveals a nucleation mechanism change from instantaneous to progressive as a function of decreasing solubility in ethanol, acetonitrile and water. This is caused by an increase in attachment frequency due to decreasing de-solvation free energy of PABA found from molecular dynamics simulations, this in combination with increasing γeff causes the thermodynamic component of the nucleation rate to become limiting. Isothermal and poly-thermal X-ray scattering studies of PABA nucleation reveal the formation of large liquid-like clusters of PABA, >40nm, in the under-saturated state. These Nano-scale assemblies increase in size and structural ordering, indicated by an increase in fractal dimensionality from 1 – 2 as a function of driving force. The Guinier region of the high q structures is found to increase from Rg = 0.46nm to 0.53 nm which indicates a population of monomers and dimers of PABA in the supersaturated state. This was confirmed as the carboxylic acid dimer structure from form factor fitting of known structural synthons of the alpha phase. In-situ XRD studies of the polymorphic phase transformation of the beta-alpha phase, indicates that the dissolution and growth processes are consistent with zero order nucleation kinetics and first and zero order kinetics respectively with the latter seemingly temperature dependant. UV/Vis analysis in combination with the XRD data reveal the transformation is a dissolution controlled process explained by particle morphology. The transformation temperature was also estimated from the growth and dissolution rate constants as 22.8 – 23.6 °C.

Gold (Au) implantation in silicon (Si) has been a topic of great interest from both fundamental and applied perspectives. Ion implantation is a versatile technique due to its ability to form surface-embedded nanoparticles that provide better adhesion. Also, being an integral part of the substrate lattice, the nanoclusters produced by ion implantation are free from impurities and their size distribution can be controlled by carefully optimizing the beam parameters. During our experiments to produce nanoclusters of Au on Si for use as seeds for the growth of nanowires, we stumbled across an unusual pattern formation process under specific conditions. This unique self-assembly process is observed only within a critical threshold implantation fluence and above a threshold annealing temperature. Fabrication of ordered arrays of metal nanoparticles on Si substrates is of significance for both fundamental science associated with low-dimensional physics and technical app lications. The application of functional nanostructures strongly depends on their assembly in ordered one- or two- dimensional arrangements. These arrangements may play an important role in fabricating ordered arrays of semiconductor/oxide nanowires.This thesis discusses a systematic study performed to understand the temperature and time dependent nucleation, growth of Au nanoclusters and evolution of the self-assembled patterns. A growth model is proposed to show the re-crystallization behaviour of Au supersaturated amorphous silicon (a-Si) on Si substrate. The observed self-assembled periodic patterns of Au nanoclusters bear resemblance to the Liesegang ring structures prevalent in some chemical reaction-diffusion systems. Based on this systematic study of the growth and morphology of Au nanoclusters, a tentative growth mechanism has been proposed for the formation mechanism of this unusual self-assembled pattern. The pattern formation of this non-equilibrium process is expected to originate due to instabilities of the three scales of Au nanoclusters at elevated temperatures. The kinetics of pattern formation from a supersaturated solid solution (a-Si/Au alloy) is demonstrated using numerical solutions obtained by a two-dimensional growth model, which takes into account the nucleation, diffusion and the aggregation process. The numerical solution of the diffusion equations appear to be in good agreement with the experimental results.

The aim of this dissertation is to investigate self-assembled structures and the phase diagram of amphiphilic molecules of diverse geometric shapes using a number of different computer simulation methods. The semi-realistic coarse-grained model, used extensively for simulation of polymers and surfactant molecules, is adopted in an off-lattice approach to study how the geometric structure of amphiphiles affects the aggregation properties. The results of simulations show that the model system behavior is consistent with theoretical predictions, experiments and lattice simulation models. We demonstrate that by modifying the geometry of the molecules, self-assembled aggregates are altered in a way close to theoretical predictions. In several two and three dimensional off-lattice Brownian Dynamics simulations, the influence of the shape of the amphiphilic molecules on the size and form of the aggregates is studied systematically. Model phospholipid molecules, with two hydrophobic chains connected to one hydrophilic head group, are simulated and the formation of stable bilayers is observed. In addition, (practically very important) mixtures of amphiphiles with diverse structures are studied under different mixing ratios and molecular structures. We find that in several systems, with Poisson distributed chain lengths, the effect on the aggregation distribution is negligible compared to that of the pure amphiphilic system with the mean length of the Poisson distribution. The phase diagrams of different amphiphilic molecular structures are investigated in separate simulations by employing the Gibbs Ensemble Monte Carlo method with an implemented configurational-bias technique. The computer simulations of the above mentioned amphiphilic systems are done in an area where physics, biology and chemistry are closely connected and advances in applications require the use of new theoretical, experimental and simulation methods for a better understanding of their self-assembling properties. Obtained simulation results demonstrate the connection between the structure of amphiphilic molecules and the properties of their thermodynamically stable aggregates and thus build a foundation for many applications of the remarkable phenomena of amphiphilic self-assembly in the area of nanotechnology.
Ph.D.
Department of Physics
Arts and Sciences
Physics