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.

This dissertation investigates the preparation and electrochemical studies on a series of novel redox active hybrid dendrimers. The author also describes cucurbit[8]uril (CB8) mediated dendrimer self-assembly and their size selection by applying external electrochemical stimulus. In addition to this, a series of redox active, carboxylic acid terminated dendrimers were deposited onto indium tin oxide (ITO) surfaces. The surface interactions between the dendrimers and the metal oxides were characterized by electrochemical, spectroscopic, and atomic force microscopic methods. Additionally, the author describes molecular recognition behavior studies between several redox active guests and cucurbit[7]uril (CB7) in non-aqueous media. Furthermore, the author also describes the preparation and electronic communication studies on a series of bisferrocenylamino triazine derivatives. Three chapters of this dissertation deal with dendrimer applications in several different topics. A general introduction to dendrimers is given in Chapter I, including a short history, dendrimer structural features, synthetic methodologies, and also including their general applications on several different topics. Chapter II describes the preparation and characterization of a series of novel redox active hybrid dendrimers. These dendrimers consist of a ferrocenylamino nucleus and two series of popular dendrons (Fréchet and Newkome type). Interestingly, the microenvironment surrounding the redox residues is finely adjustable by varying the size of these two types of dendrons. Chapter III describes the molecular recognition studies with selected redox active guests and the macrocyclic host CB7 in non-aqueous media. The extremely strong host-guest interaction between CB7 and ferrocenylmethyl-trimethylammonium (FA) in aqueous media experiences a substantial thermodynamic stability loss when transferred to non-aqueous media. In stark contrast to this, the binding behavior between CB7 and the dicationic guest methyl viologen (MV) exhibits less sensitivity to environmental variation. Furthermore, the electrochemical studies were performed under non-aqueous media. In general, host CB7 encapsulation of these redox active guests in non-aqueous media induces different electrochemical behavior compared to that of aqueous media. For instance, the cyclic voltammetric response of CB7 encapsulated FA in DMSO exhibit substantial cathodic potential shift, which is opposite to the behavior in aqueous media. Chapter IV describes CB8 mediated dendrimer self-assembly. A new series of pi-donor containing Newkome type dendrimers were synthesized. These pi-donor containing dendrimers are found to form stable ternary charge transfer complexes with another series of pi-acceptor (viologen) containing dendrimers. Furthermore, one electron reduction of the viologen residue disrupts the charge transfer complexes and leads to the assembly of viologen radical cation dimmers. And, thus, may result in substantial size selection between these two types of dendrimer assemblies. Chapter V describes the exploration of a series of redox active dendrimers bearing multiple carboxylic acids as surface anchoring groups to attach onto the optical transparent semiconductor material ITO coated glass surfaces. The dendrimer derivatized ITO slides were further prepared as working electrodes, and the subsequent electrochemical studies revealed that these dendrimers strongly adsorb onto ITO surfaces. Especially, the ITO electrodes treated with the second generation dendrimer exhibit rather stable electrochemical behavior. The surface coverages of ITO electrodes treated with dendrimers were estimated by current integration. Atomic force microscopic studies provided insights on surface topographical variation before and after the dendrimer deposition. Infrared spectroscopic studies further revealed the chemical interactions between dendrimer carboxylic acid groups and the metal oxide surfaces. Chapter VI describes the preparation of a series of triazine based bisferrocenylamino derivatives. Variable 1H-NMR and 13C-NMR spectroscopic studies clearly indicate that these bisferrocenylamino triazine derivatives exhibit rotamerization phenomena. And, the rotamer coalescence temperatures are mediated by the third substituent group. The X-ray crystallographic analyses disclose the partial double bond character between the amino nitrogen and the triazine carbon, which reveal the structural proof behind the rotamerization phenomena. Furthermore, electrochemical experiments are performed under two sets of experimental conditions. No electronic communication is observed when using the traditional tetrabultylammonium hexafluorophosphate (TBAPF6) as supporting electrolyte. In stark contrast to this, electronic communication between the bisferrocenyl residues is observed when using tetrabultylammonium tetrakis(pentafluorophenyl)borate (TBAB(C6F5)4) as supporting electrolyte. Surprisingly, the electronic communication strength can be mediated by a third substituent group. Computational studies provide insights into the molecular geometry and electronic structure of the mixed valence species. By combining the supporting electrolyte dependant electronic communication behavior, near-IR spectroscopic studies and the computational results, we conclude that, the electronic communication between the bisferrocenyl residues in these investigated triazine derivatives occurs through space metal-metal interactions.

Supramolecular copolymers have become of increasing interest in recent years for the search of new materials with tunable properties. In particular, metallo-supramolecular block copolymers have seen important progresses since the last five years. In this thesis, a library of metallo-supramolecular amphiphilic block copolymers containing a hydrophilic block, linked to a hydrophobic block, through a metal-ligand complex has been investigated. The micelles formed in water from these copolymers were characterized by AFM and TEM and exhibited a different behavior compared to their covalent counterpart. Furthermore, a novel strategy to control the formation of amphiphilic brushes from metallo-supramolecular block copolymers has been developed. Starting from a heteroleptic block copolymer, the initial low molecular weight counterions were exchanged for polymeric ones, leading to the formation of complex architectures. Another part of this thesis is dedicated to the use of metal-ligand interactions located at the extremity of micelles. Since ligands are located at the extremity of the coronal chains, they are available for complexation with metal ions. The effect of the addition of various metal ions to this system was studied in the dilute regime by dynamic light scattering, and different situations have been observed depending on the metal-to-ligand ratio and to the nature of the metal ions. In more concentrated solutions, a second hierarchical level is reached leading to the formation of a micellar gel, due to the formation of intermicellar bridges. Rheological measurements revealed that the characteristic behavior of those gels critically depends on the added metal ions. Finally, the self-assembly of a metallo-supramolecular block copolymer in thin films was investigated. Due to the presence of the charged complex at the junction of the two blocks, this copolymer could be considered as a triblock with a highly immiscible block that effects the orientation of the cylindrical microdomains and the lateral ordering.

Notre thèse consiste en l’étude des relations entre la morphologie microscopique et les propriétés optoélectroniques de films minces de matériaux organiques pi-conjugués. En particulier, nous avons porté notre attention sur des oligomères, polymères et copolymères pi-conjugués à base de thiophène et/ou de fluorène, particulièrement intéressants pour des applications dans des dispositifs optiques et électroniques « plastiques ». Nous avons montré que l’assemblage des molécules peut mener à des (nano)structures de taille et de forme spécifiques, par exemple des structures fibrillaires (unidimensionnelles), des plaquettes (bidimensionnelles), ou des agrégats non-texturés, en fonction de l’architecture moléculaire, du solvant et du substrat utilisés dans la préparation des films minces. La modélisation moléculaire nous a permis d’une part de proposer des modèles d’assemblages de molécules au sein des différentes structures, et d’autre part de mieux comprendre l’importance des interactions molécule-molécule et molécule-surface. Nous avons ainsi pu établir les relations entre l’ordre structural au sein de ces dépôts minces et les propriétés optiques et électroniques, en étudiant notamment la photoluminescence à l’état solide ou le transport de charges dans des transistors à effet de champ. Nous avons également eu recours à des techniques de lithographie "douce" pour contrôler l’assemblage des molécules conjuguées, ce qui a permis d’améliorer les performances des dispositifs électroniques. Globalement, les résultats obtenus apportent une meilleure compréhension des relations entre l’organisation des molécules conjuguées à l’état solide et les propriétés optoélectroniques des matériaux conjugués semiconducteurs.

In recent years, the aim of supramolecular syntheses is not only the creation of particular structures but also the introduction of specific functions in these supramolecules. The present work describes the use of the ionic self-assembly (ISA) route to generate nanostructured materials with integrated functionality. Since the ISA strategy has proved to be a facile method for the production of liquid-crystalline materials, we investigated the phase behaviour, physical properties and function of a variety of ISA materials comprising a perylene derivative as the employed oligoelectrolyte. Functionality was introduced into the materials through the use of functional surfactants. <br><br> In order to meet the requirements to produce functional ISA materials through the use of functional surfactants, we designed and synthesized pyrrole-derived monomers as surfactant building blocks. Owing to the presence of the pyrrole moiety, these surfactants are not only polymerizable but are also potentially conductive when polymerized. We adopted single-tailed and double-tailed N-substituted pyrrole monomers as target molecules. Since routine characterization analysis of the double-tailed pyrrole-containing surfactant indicated very interesting, complex phase behaviour, a comprehensive investigation of its interfacial properties and mesophase behavior was conducted. The synthesized pyrrole-derived surfactants were then employed in the synthesis of ISA complexes. The self-assembled materials were characterized and subsequently polymerized by both chemical and electrochemical methods. The changes in the structure and properties of the materials caused by the in-situ polymerization were addressed.<br><br> In the second part of this work, the motif investigated was a property rather than a function. Since chiral superstructures have obtained much attention during the last few years, we investigated the possibility of chiral ISA materials through the use of chiral surfactants. Thus, the work involved synthesis of novel chiral surfactants and their incorporation in ISA materials with the aim of obtaining ionically self-assembled chiral superstructures. <br><br> The results and insights presented here suggest that the presented synthesis strategy can be easily extended to incorporate any kind of charged tectonic unit with desired optical, electrical, or magnetic properties into supramolecular assemblies for practical applications. / Supramolekulare Chemie zielt auf den Aufbau großer Moleküle und neuer Materialien aus kleineren Einheiten. Durch supramolekulare Wechselwirkungen d.h. nicht-kovalente Bindungen, können definierte Ordnungen von Molekülverbänden in Größen von mehreren 100 Mikrometern hergestellt werden. Diese Wechselwirkungen und die daraus resultierenden Anordnungen von Molekülen bestimmen die für Anwendungen relevanten makroskopischen Materialeigenschaften. <br><br> Es gibt viele verschiedene Wechselwirkungen, die in der Supramolekularen Chemie angewendet werden können. Eine davon ist die ionische Wechselwirkung, die in dieser Arbeit als Triebkraft für die Herstellung supramolekularer Materialien verwendet wird. Diese Strategie wurde vor kurzem ISA (Ionic-Self-Assembly, d.h. Ionische Selbsorganisation) genannt. <br><br> Die vorliegende Arbeit beschäftigt sich mit der Herstellung funktioneller Nanomaterialen durch die Anwendung der ISA-Strategie. Da sich die ISA-Strategie als einfache Methode für die Produktion von Flüssigkristallen herausstellte, untersuchten wir die Eigenschaften vieler ISA-Materialen, die einen Farbstoffbaustein integriert haben. Die Funktion der Materialien wurde hierbei durch die Verwendung funktioneller Tenside geschaffen. Um die Anforderungen für die Produktion funktioneller ISA-Materialen durch die Nutzung funktioneller Tenside sicherzustellen, wurden Pyrrol-Monomere als Tenside hergestellt. Durch die Pyrrol-Einheiten sind die Tenside polymerisierbar und zeigen danach Potential für Leitfähigkeit. <br><br> Es wurden Pyrrol-Tenside sowohl mit Einzel- als auch mit Doppelketten synthetisiert. Da die Standardcharakterisierung des Doppelketten-Tensids ein interessantes Phasenverhalten zeigte, wurden umfassende Untersuchungen der Grenzflächeneigenschaften und des mesophasen Verhaltens durchgeführt. Beide Tenside wurden dann in der Produktion von ISA-Materialien verwendet. Die hergestellten Materialen wurden charakterisiert und konnten durch die Pyrrol-Einheit sowohl chemisch als auch elektrochemisch polymerisiert werden. Die aus dieser Polymerisierung resultierenden Änderungen der Eigenschaften, Struktur und Function der Materialen wurden ebenfalls untersucht. <br><br> Der zweite Teil dieser Arbeit klärt Nutzungsmöglichkeiten chiraler Tenside für die Herstellung chiraler ISA-Strukturen. Obwohl Chiralität keine eigentliche Funktion sondern eine Eigenschaft ist, haben chirale Strukturen in den letzten Jahren viel Aufmerksamkeit bekommen. Deshalb wurden, mit dem Ziel chirale ISA-Strukturen zu erhalten, neue chirale Tenside hergestellt und diese als Bausteine in ISA-Materialien benutzt.<br><br> Die mit dieser Arbeit gewonnenen Ergebnisse und neuen Einsichten zeigen, dass die ISA-Strategie leicht erweitert werden kann, um jede Art von Bausteine zu integrieren. Dadurch können nanostukturierte Materialien mit gewünschten spezifischen optischen, elektrischen oder elektromagnetischen Eigenschaften für praktische Anwendungen geschaffen werden.

Imagine if you could combine the power and capabilities ofan entire laboratory in the palm of your hand. Advances inmicrofluidic chip technology promise to integrate andminiaturize multiple lab processes into a single palm-sizeddevice. The advantages of these lab-on-a-chip devices,sometimes also referred to as micro total analysis systems(µTAS), compared with conventional bench-scale systems arenumerous and wide ranging and include: less reagentconsumption, low manufacturing costs, increased performance,faster analysis, high sample throughput, integration andautomation possibilities, and disposability. However,microfluidic devices also present challenges such as theinterfacing to the macro world and detection limits. In this thesis the focus has been to develop novel discretemicrofluidic components for biotechnology and organic chemicalapplications with the goal to integrate them to formlab-on-chips. A flow-through filter-chamber device has beendesigned, manufactured and evaluated for chemical analysis onbeads. Passive liquid handling has been integrated on the chipin the form of hydrophobic valves at the inlet channels. Anarray format has also been developed to allow parallel analysisof multiple samples. The filter-chamber functions well forsingle nucleotide analysis using pyrosequencing. Initialevaluations on catalyst screening in the filter-chamber devicehas been performed. The suitability of valve-less micropumps for biochemicalapplications is presented. Fluids encountered in variousbiochemical methods, including living cells, that areproblematic for other micropumps have been pumped with goodperformance. This thesis also introduces expandablemicrospheres as a novel component in microfluidics includingapplications such as one-shot valves, micropositioning andsurface enlargement. A novel technique for bead immobilization in microfluidicdevices based on surface chemistry is presented in this thesis.Beads for both biochemical assays and organic chemistry havebeen self-sorted and self-assembled in line patterns as narrowas 5 µm on both structured and unstructured substrates.This method will greatly facilitate the generation of screeningplatforms, for example. To develop a microfluidic device for catalysis-on-chip,ligands for asymmetric catalysis have successfully beenimmobilized in silicon channels by consecutive microcontactprinting, which is a novel technique presented in thisthesis. <b>Keywords:</b>microfluidics, beads, microspheres, silicon,filter-chamber, flow-through, bead trapping, DRIE, passivevalves, fluorocarbon, microfluidic array, adhesive bonding,valve-less micropump, microcontact printing, PDMS,self-assembly, self-sorting, DNA, SNP, pyrosequencing,allele-specific extension, expandable microspheres, catalysis,chiral ligand, monolayer, miniaturization, lab-on-a-chip,µTAS.

Today, the dominating way of patterning nanosystems is by irradiation-based lithography (e-beam, DUV, EUV, and ions). Compared to the other irradiations, ion tracks created by swift heavy ions in matter give the highest contrast, and its inelastic scattering facilitate minute widening and high aspect ratios (up to several thousands). Combining this with high resolution masks it may have potential as lithography technology for nanotechnology. Even if this ‘ion track lithography’ would not give a higher resolution than the others, it still can pattern otherwise irradiation insensitive materials, and enabling direct lithographic patterning of relevant material properties without further processing. In this thesis ion tracks in thin films of polyimide, amorphous SiO2 and crystalline TiO2 were made. Nanopores were used as templates for electrodeposition of nanowires. In lithography patterns are defined by masks. To write a nanopattern onto masks e-beam lithography is used. It is time-consuming since the pattern is written serially, point by point. An alternative approach is to use self-assembled patterns. In these first demonstrations of ion track lithography for micro and nanopatterning, self-assembly masks of silica microspheres and porous alumina membranes (PAM) have been used. For pattern transfer, different heavy ions were used with energies of several MeV at different fluences. The patterns were transferred to SiO2 and TiO2. From an ordered PAM with pores of 70 nm in diameter and 100 nm inter-pore distances, the transferred, ordered patterns had 355 nm deep pores of 77 nm diameter for SiO2 and 70 nm in diameter and 1,100 nm deep for TiO2. The TiO2 substrate was also irradiated through ordered silica microspheres, yielding different patterns depending on the configuration of the silica ball layers. Finally, swift heavy ion irradiation with high fluence (above 1015/cm2) was assisting carbon nanopillars deposition in a PAM used as template.

Discotic liquid crystals (DLCs), which consist of disc-like molecules, are known to be able to form nematic and columnar mesophases through self-assembly. Because of the high electric charge mobility in one-dimension, DLCs are found to have uses in making electronic and photonic devices, such as organic light emitting diode, photovoltaic and molecular wires. In order to achieve better performance of these applications, it is essential to obtain the desired alignment of the DLCs. The purpose of this study is to investigate the stacking of disk-like molecules and to control their alignment. The materials used in the present studies are HDBP-8 and LC10. In this thesis, we will show that the stack of disk-like molecules is strongly influenced by temperature. We will also discuss how the molecules stacking is influenced by surface free energy. The disk-like molecules tend to stack with face-on when the surface free energy of the substrates is high. On a surface with lower surface free energy, molecules tend to stack with edge-up. In the latter part of the research, substrates are specially treated to have different surface free energies, and molecular stack on these substrates is observed.

Design of self-assembling ABC-type collagen triple helical heterotrimers is challenging due to the number of competing species that can be formed in ternary mixture of peptides with a high propensity to fold into triple helices and the fact that well understood rules for pair-wise amino acid stabilization of the canonical collagen triple helix have remained elusive. Given the required one amino acid stagger between adjacent peptide strands in this fold, a ternary mixture of peptides can form as many as 27 triple helices with unique composition or register. Previously we have demonstrated that electrostatic interactions can be used to bias the helix population towards a desired target but the presence of competing states in mixtures has remained an outstanding problem. In this work we use high-resolution structural biology techniques to do a detailed study of stabilizing pair-wise interactions between positively and negatively charged amino acids in triple helices. Two types of contacts with distinct sequence requirements depending on the relative stagger of the interacting chains are observed: axial and lateral. Such register-specific interactions are crucial for the understanding of the registration process of collagens and the overall stability of proteins in this family. Using this knowledge we developed distinct design strategies to improve the specificity of our designed systems towards the desired ABC heterotrimeric target state. We validate our strategies through the synthesis and characterization of the designed sequences and show that they self-assemble into a highly stable ABC triple helices with control over composition in the case of the rational approach and with control over both composition and register in the case of the computational approach.

This thesis is an experimental investigation on the binding of self-assembling peptides to oligodeoxynucleotides (ODNs) and the characterization of the resulting peptide-ODN complexes/aggregates, the first key step in the development of a peptide-based gene delivery system. Effects of pH, charge distribution along the peptide backbone, and oligonucleotide sequences on the peptide-ODN binding were investigated by a series of physicochemical methods. UV-Vis absorption and fluorescence anisotropy experiments demonstrate that aggregates are formed after mixing the peptide and ODN in aqueous solution. The aggregates in solution can be centrifuged out. Based on this property, the fraction of ODNs incorporated in the peptide-ODN aggregates can be obtained by comparing the UV-Vis absorption of the solution before and after centrifugation. Binding isotherms are generated by a binding density function analysis of the UV absorbance results. The binding parameters are extracted from the analysis of the binding isotherms based on the McGhee and von Hippel model. Equilibrium binding parameter studies show that the binding of two self-assembling peptides, EAK16-II and EAK 16-IV, to model single and double-stranded ODNs at pH 4 is stronger than at pH 7, and that no binding occurs at pH 11. These results demonstrate that electrostatic interactions play an important role in the EAK-ODN binding because EAKs are more positively charged at low pH. EAKs bind more strongly to dG16 than to the other ODN sequences dC16 and dGC16. This demonstrates that the hydrogen bond might be involved because they promote the binding of the lysine residues of the peptide to dG16 to a greater extent than to dC16. The charge distribution along the peptides is found to have an effect on the binding. EAK16-IV, whose positively charged residues are clustered at one end of the peptide, binds to the ODNs more strongly than EAK16-II, whose positively charged residues are distributed throughout the peptide chain, at the same pH. The binding process of EAKs to the ODNs was investigated by fluorescence anisotropy and static light scattering experiments. The results show that individual EAK and ODN molecules complex first, followed by the aggregation of these complexes into large aggregates. The nature of the resulting peptide-ODN complexes/aggregates is examined by UV-Vis absorption, fluorescence anisotropy, and PAGE experiments. The results demonstrate that free EAK, free ODNs, and small EAK-ODN complexes, which can not be centrifuged out, exist in the supernatant, and that large aggregates are collected in the pellets after centrifugation of the solution. The size of the resulting EAK-ODN complexes/aggregates measured by AFM and DLS is around a few hundreds of nanometers at low EAK concentrations. The accessibility of the ODNs to the quencher in the solution is reduced by 40 % and 60 % after binding to EAK16-II and EAK16-IV, respectively, as determined by fluorescence quenching experiments on EAK-ODN mixture solutions. An ODN protection from Exonuclease 1 degradation is provided by the EAK16-II or EAK16-IV matrix when they are mixed with the ODNs at pH 4. However, the ODNs are protected to a much lower degree when the EAK-ODN aggregates are prepared at pH 7. The EAK-ODN aggregates prepared at pH 7 are found to dissociate more easily than those prepared at pH 4 when they are incubated with exonuclease I solution at pH 9.5. These results suggest that the ODN protection afforded by the EAK-ODN aggregates is correlated with their structural stability after being incubated with the nuclease solution. The stability of the EAK-ODN aggregates after dilution is determined by UV-Vis absorption. No detectable dissociation of the aggregates is observed over 20 hrs after a 5- and 10-fold dilution of the solution in the same buffer used for their preparation. The EAK-ODN aggregates remain stable after the solutions are centrifuged, and re-dissolved in fresh buffer solutions. The ability of an EAK matix to protect ODNs from nuclease degradation together with its biocompatibility and low-toxicity suggests that EAK self-assembling peptides could be used as carriers for gene delivery.