Dissertation (PhD)--Stellenbosch University, 2004 / ENGLISH ABSTRACT: Over the past decade peptide bola-amphiphiles have been the subject of much attention because of their role as potential models of functionalised membranes and as new generation surfactants. In the quest for new surfactants a peptidomimetic-based approach was used to design a library of novel 'hybrid' bola-amphiphilic peptide surfactants derived from sapecin B and a model symmetrical oligo-glycine bola-amphiphile. The library was divided into different series, each one purpose-built; first, to investigate hierarchal supramolecular architecture and, second, to investigate potential antimicrobial activity. The bola-amphiphiles were synthesised using Fmoc-polyamide based solid phase peptide synthesis and purified via high performance liquid chromatography. The peptide hybrids were characterised using electro spray mass spectrometry, nuclear magnetic resonance, different modes of electron microscopy, Fourier-transform infrared spectroscopy and, in some cases, further studies were done using circular dichroism and bioactivity tests. The model bola-amphiphile suberamide(GGh was synthesised using peptide fragment condensation based on solid phase peptide synthesis. The synthesis is bi-directional (N~C and C~N) and versatile, making it possible to synthesis new dicarboxylic oligopeptide bola-amphiphiles and other analogous compounds. The product, suberarnide(GG)2, was purified using its inherent ability to self-assemble in an acidic solution. Novel asymmetrical bola-amphiphiles composed of dipeptide head groups linked via an aliphatic (I)-amino acid, serving as a hydrocarbon spacer, were also synthesized. Two small libraries of bola-amphiphiles were established - the first involved variation in to-amino acid length and the other variation in the C-terminal amino acid. The bolaamphiphiles were self-assembled in either 0.1% trif1uoroacetic acid or 0.1% triethylamine. Electron microscopy revealed the formation of a variety of higher order supramolecular architectures based on ~-sheet self-assembly. FT-IR spectrometry indicated that interlayer and intralayer hydrogen bond networks, together with strong selfassociation, promoted by the hydrophobic effect and, in certain instances, electrostatic interactions, are responsible for the variety of supramolecular architectures. Variations in the higher order structures can be attributed to amino acid composition, specifically length of m-amino acid, nature of the C-terminal amino acid and the optimised solvent conditions used for the self-assembly process. A third library of novel 'hybrid' bola-amphiphilic peptide surfactants, in which a cationic tripeptide motif from antimicrobial peptides was combined in a hybrid molecule containing a oi-amino acid residue, was established. These bola-amphiphiles displayed potent antimicrobial activity against both Gram-positive and Gram-negative bacteria; the analogues were as active or more active than the leader peptides yet, remarkably, displayed little or no appreciable haemolytic activity. These organopeptide bolaamphiphiles thus demonstrated selective toxicity towards bacteria. The hydrophobicity imparted by the co-amino acid has contrasting effects on haemolysis and antimicrobial activity of the peptide analogues. The other unique feature of these peptides and their analogues is the fact they self-assembled into complex supramolecular architectures, composed primarily of ~-sheets. Their self-assembly is primarily governed by hydrophobic interactions together with inter and intralayer hydrogen bonding. Electron microscopy clearly revealed higher order structures for both peptides and analogues. The generation of higher order supramolecular architecture is dependent on optimisation of ~- sheet self-assembly whereas antimicrobial activity is dependent on the balance between net positive charge and optimum hydrophobicity of the peptide hybrids. This study has demonstrated that it is possible to design hybrid peptide surfactants capable of producing higher order supramolecular architecture and improving the antimicrobial activity whilst reducing the haemolytic effect. The study and design of these versatile 'purpose-built' bio-inspired surfactants heralds a novel approach, one that shows tremendous potential. / AFRIKAANSE OPSOMMING: Die afgelope dekade het bola-amfifiliese peptiede baie aandag geniet weens hulle rolle as potensiële modelle van gefunksionaliseerde membrane en as 'n nuwe generasie surfaktante. In die soeke na nuwe surfaktante is 'n peptiedornimetiese benadering gevolg om 'n biblioteek van nuwe "hibried" bola-amfifiliese peptiedsurfaktante van sapesien B en 'n simmetriese oligoglisien bola-amfifil af te lei. Die biblioteek is in verskillende reekse onderverdeel. Elke reeks is doelmatig vervaardig om ondersoek in te stel na twee aspekte, nl. die rangorde van die supramolekulêre strukture en die potensiële antirnikrobiese aktiwiteit. Fmoc-poliamied gebaseerde soliedefase-peptied-sin-tese is aangewend vir die sintese van die bola-amfifile en hulle is met behulp van hoë doeltreffendheid vloeistofchromatografie gesuiwer. Die peptiedhibriede is gekarakteriseer met behulp van elekrosproei massaspektrometrie, kern-magnetiese resonansie, verskillende modusse elektronrnikroskopie, Fourier-transform infrarooispektrometrie en, in sommige gevalle is verdere studies met sirkulêre dichroïsme en bioaktiwiteitstoetsing uitgevoer. Die bola-amfifilsuberamiedtflfij--model is met behulp van peptiedfragment-konden-sasie gesintetiseer gegrond op soliedefase-peptiedsintese. Dit sintese vind in twee rigtings plaas (N~C en C~N) en is veelsydig aangesien dit die sintese van sowel nuwe dikar-boksielbola- amfifile as ander analoë verbindings moontlik maak. Die produk, suber-arnied(GG)2, is gesuiwer met behulp van die verbinding se inherente vermoë tot self-montering in suur oplossings. Nuwe assimetriese bola-amfifile, saamgestel uit dipeptiedkopgroepe, gekoppel via 'n alifatiese ro-aminosuur, wat as koolwaterstofspasieerder dien, is ook gesintetiseer. Twee klein bola-amfifilbiblioteke is saamgestel - die een het variasies in die ro-aminosuur se lengte omvat en die ander een variasies in die C-terrninale aminosuur. Selfmontering van die bola-amfifile het plaasgevind in of 0,1 % trifluorasynsuur Of 0,1 % trietielamien. Elektronrnikroskopie het die bestaan van 'n verskeidenheid hoërorde supramolekulêre strukture, gegrond op p-plaatselfmontering, aangetoon. Uit FT-IR-spektrometrie blyk dit dat inter - en intralaag waterstofbinbdingsnetwerke en sterk selfassosiasie, 19. word bevorder deur die hidrofobiese effek en, in sekere gevalle, elektrostatiese interaksies, is verantwoordelik vir die verskeidenheid supramolekulêre strukture. Variasies in die hoërorde strukture kan toegeskryf word aan aminosuursamestelling, in besonder die lengte van die ro-aminosuur, die aard van die C-terminale aminosuur en die geoptimiseerde oplosmiddelkondisies wat gebruik is vir die selfmonteringsproses. 'n Derde biblioteek nuwe "hibried" bola-amfifiliese peptiedsurfaktante, waarin 'n kationiese tripeptiedmotief uit antimikrobiale peptiede gekombineer is met 'n m-aminosuurresidu, is geskep. Sommige van hierdie bola-amfifile het 'n kragtige antimikrobiese aktiwiteit teenoor sowel Gram-positiewe as Gram-negatiewe bakterieë gertoon. Die analoë strukture was aktief, of selfs meer aktief as die voorste peptiede maar het, verbasend genoeg, nie 'n beduidende hemolitiese aktiwiteit vertoon nie. Hierdie organopeptied bola-amfifil het dus 'n selektiewe toksisiteit teenoor bakterieë vertoon. Die hidrofo-bisiteit, as gevolg van die ui-aminosuur, het 'n resiproke effek op hemolise en die antimikrobiese aktiwiteit van die peptiedanaloë. Die ander uitstaande kenmerk van die peptiede en hulle analoë is die vermoë om te selfmonteer en komplekse supramolekulêre strukture, bestaande hoofsaaklik uit ~-plate, te vorm. Hierdie selfmontering word in hoofsaak beheer deur hidrofobiese interaksies asook inter - en intralaagwaterstofbinding. Elektronmikroskopie het duidelik hoërorde strukture getoon by sowel dié peptiede as hulle analoë. Die ontwikkeling van hoërorde supramolekulêre struktuurvorms is afhanklik van die optimalisering van die ~-plaatselfmontering. Daarteenoor is die antimikro-biese aktiwiteit afhanklik van die balans tussen die netto positiewe lading en die opti-male hidrofobisiteit van die peptiedhibriede. Hierdie studie het getoon dat dit moontlik is om hibriedsurfaktante te ontwerp wat hoërorde supramolekulêre strukture te produseer en om die antimikrobiese aktiwiteit te verbeter terwyl die hemolitiese effek verminder word. Die studie en ontwerp van hier-die veeldoelige, "doelmatig-gesintetiseerde" biogeïnspireerde surfakante stel 'n unieke benadering daar, wat oor groot potensiaal beskik.

The rational design, synthesis, and characterization of several systems that undergo self-assembly are described. Systems were chosen based on their ability to self-assemble in a highly ordered and predictable fashion that imparts order on the structure such that it is able to perform a given device function. Herein we describe self-assembled multilayered thin films on gold that can behave as molecular wires with tunable length, photocurrent generating films, and surfaces with photoswitchable wettability, and self-assembling peptide nanotubes that can potentially function as long range energy and electron transfer conduits. A non-covalent, modular approach to multilayered thin film fabrication was used to generate three thin film systems that function as molecular scale wires, photocurrent generating devices, and photoswitchable thin films, respectively. These films were based on 4-[(10-mercaptodecyl)oxy]pyridine-2,6-dicarboxylic acid self-assembled monolayers on gold. These monolayers are able to chelate metal (II) ions, and thus multilayers were assembled based on metal-ligand coordination chemistry. The three systems described were characterized by contact angle measurements, electrochemical methods, and grazing angle IR spectroscopy. All three systems emphasize the versatility of a modular approach to thin film construction, and provide proof-of-concept for future studies. A cyclic octapeptide architecture was employed as a scaffold for the predictable self-assembly of photoactive groups within a nanotubular structure. The degree of cyclic peptide aggregation in stacking nanotube systems and non-stacking monomer systems, was studied via fluorescence emission spectroscopy. Based on the spectral results, it was determined that peptide nanotubes can be constructed such that photoactive side chains can be assembled in stacks. Future experiments for the determination of long range energy and/or charge transfer in these systems are also discussed.

In this thesis, I present numerical simulations that explore the applications of self-propelled particles to the field of self-assembly and to the design of `smart' micromachines. Self-propelled particles, as conceived of here, are colloidal particles that take some energy from their surroundings and turn it into directed motion. These non-equilibrium particles can move persistently for long times in the same direction, a fact that makes the behavior of dense and semi-dilute systems of these particles very different from that of their passive counterparts. The first section of this thesis deals with the interactions between passive components and baths of hard, isotropic self-propelled particles. First, I present simulations showing how the depletion attraction can be made into a short ranged repulsive, or long ranged attractive interaction for passive components with different geometries in a bath of self-propelled particles, and show how the form of these interactions is consistent with how active particles move near fixed walls. In the next chapter, a rigid filament acts as a flexible wall that engages in a feedback loop with an active bath to undergo repeated folding and unfolding events, behavior which would not occur for a filament in a passive environment. The subsequent chapters deal with self-propelled particles that have long ranged and anisotropic interactions. When the orientations of active particles are coupled, they can undergo remarkable collective motion. While the first chapter in this section begins with a discussion of how active disks interacting via an isotropic potential consisting of a long ranged repulsion and short ranged attraction self-assemble into living clusters of controllable size, I show how replacing the disks with anisotropic dumbbells causes these clusters to rotate coherently. In the last chapter, I show that weakly screened active dipoles form lines and clusters that move coherently. These particles can become anchored to the surface of a passive charged colloid in various ways that lead to two different kinds of active motion: rotations of a corona of dipoles around the colloid, and active translation of the colloid, pushed by a tail of dipoles. Finally, a mixture of many charged colloids and dipoles can reproduce the swarming behavior of the pure dipoles at a larger length scale with coherent motion of the colloids. These are all examples of how activity is a useful tool for controlling motion at the micro-scale.

One-dimensional (1D) nanomaterial self-assembly offers an excellent approach to the fabrication of highly complex nanodevices. Despite considerable effort and research, precisely controlling the orientation and positioning of nanowires (NWs) on a large-scale area and assembling into a functional device is still a state of the art problem. This thesis focuses on the dimensionally controlled copper nanowires (Cu NWs) synthesis, and magnetic field assisted self-assembly of cupronickel nanowires (Cu/Ni NWs) into interconnect structures on a carbon doped silicon dioxide (CDO) wafer. CDO is a low dielectric constant (k) material used for copper interconnects in multilayered complex integrated circuits (ICs). Here, a strong affinity of copper (Cu) and nickel (Ni) to thiol (-SH) functional groups were exploited to strongly adhere the nanowires (Cu/Ni NWs) onto the CDO substrate. Thiol (-SH) functionalization of the CDO surface was achieved via a series of reactions involving (1) esterification of the surface exposed ≡Si-OH functional group to its triflate (≡Si-O-Tf), (2) reduction of triflate to ≡Si-H using DIBAL-H, and (3) hydrosilylation of ≡Si-H using 2-propene thiol (≡Si-(CH2)3-SH) in a photochemical reaction. The thiol functionalization of CDO surface enhances the interaction of Cu/Ni NWs with strong chemical bonds. The same reaction scheme was also used in the functionalization of the hydrophilic (Si-OH) surface to the hydrophobic long alkyl chain derivatized (≡Si-CH2-(CH2)16-CH3) surface. This long alkyl chain modified surface acts as an excellent moisture resistant film, which helps to maintain the low-k value of CDO. The dimensionally controlled Cu NWs were synthesized by a wet chemical approach. Optimization of the reducing agent, hydrazine (N2H4), controlled the surface morphology of nanowires (NWs). Interestingly, the high concentration of reducing agent produced particle decorated and/or with a rough NW surface, and conversely decreasing its concentration resulted in a comparatively thin, particle-free and smooth surface. The reaction temperature affected the aspect ratio (Length/Diameter) of the NWs. As the reaction temperature increased from 60 to 90 °C, the aspect ratio decreased from 140 to 21. Controlling the orientation of Cu NWs in a magnetic field was accomplished by coating them with a thin layer (~20 nm) of ferromagnetic nickel (Ni). This Ni-coated NWs showed an excellent degree of alignment (half-width ≈10 degrees) in the direction of an applied magnetic field over a large surface area at field strength as low as 2500 Gauss. Also, the Ni coating helped in protecting the copper core from oxidation resulting in better electrical wire-to-wire contacts. A nanowire-based interconnect channel was fabricated by combining magnetic field assisted alignment and deposition of aligned NWs on a thiol-modified and photolithography patterned CDO substrate. The NWs, deposited in the trenches, strongly bonded to the thiol-derivatized CDO substrate while an acetone wash removed loosely bound NWs on the photoresist surface. In electrical characterization, the directionally well-aligned Cu/Ni NWs channel displayed surprisingly two-fold higher conductivity than randomly arranged NWs channel.

The road map of the semiconductor industry has followed Moores Law over the past few decades. According to Moores Law the number of transistors in an integrated circuit (IC) will double for a minimum component cost every two years. The features made in an IC are produced by photolithography. Industry is now producing devices at the 65 nm node, however, for every deceasing node size, both the materials and processes used are not only difficult but also expensive to develop. Ultimately, the feature size obtainable via photolithography is dependent on the wavelength used in the process. The limitations of photolithography will eventually make Moores Law unsustainable. Therefore, new methodologies of creating features in the semiconductor substrate are desired. Here we present a new way to make patterns in silicon (Si) and silicon dioxide (SiO2), molecular lithography. Individual molecules and polymers, in a monolayer, serves directly as the etch mask; eliminating the photolighographic size limitation of light at a specific wavelength. The Ohnishi- and Ring parameter suggests that cyclic carbon rich molecules have a high resistance towards the plasma process, used to create the features in the substrate. Therefore highly aromatic molecules were investigated as candidates for molecular lithography. A monolayer of poly cyclic hydrocarbons, fullerene containing polymer, and fullerene molecules were created using the versatile photochemistry of benzophenone as the linker between the substrate and the material. First, a chlorosilane benzophenone derivative was attached to the Si/SiO2 surface. A thin film of the desired material is then created on top of the silane benzophenone layer. Irradiation at ~350 nm excites the benzophenone and reacts with neighboring alkyl chains. After covalent attachment the non-bonded molecules are extracted from the surface using a Soxhlet apparatus. Self-assembly, molecular weight, and wetting properties of the material dictates the features shape and size. These features are then serving as an etchmask in a fluorine plasma. The organic etch resist is then removed either in an oxygen plasma or in a piranha solution. AFM analysis revealed that 3 to 4 nm wide defined structures were obtained using C96 as the etch mask. This is about ten times smaller then industry standards. Also a depth profile of 50 nm, which is the minimum feature depth used in industry, was created using a fullerene containing polymer as the etch mask. Directionality and control over the shape and sizes of the features are naturally critical for implementing this technology in device fabrication. Therefore, alignment of the materials used has also been examined. Monolayers of highly stable molecules has successfully been used as etch masks. Further research and development could implement molecular lithography in device fabrication. Self-assembly among other forces would dictate which materials could be used successfully as a molecular resist.

The study of the DNA has found application beyond our understanding of its cellular function and into a variety of materials assembly and nucleic acid detection systems. The current research investigates double-stranded DNA probes in both a colloidal particle assembly and fluorescent assay format utilizing competitive hybridization events. In both contexts, the affinity of the dsProbes is tuned by the sequence design parameters of duplex length and complementarity. These systems were incubated with nucleic acid targets of interest and, based on the mechanism of competitive hybridization, were responsive to the presence of a high affinity competitive target. In the case of the particle assemblies, incubation with the competitive target resulted in observable disassembly of particle structures. In the case of fluorescently labeled dsProbes, incubation with competitive targets resulted in a quantifiable loss of fluorescence as determined by flow cytometry. Utilizing the fluorescently labeled dsProbe system, the kinetics of competitive hybridization was characterized for nucleic acid targets of varying specificity and strand context. The results indicate promise for the development of the competitive hybridization approach in nucleic acid detection systems providing advantages over current single-stranded probe designs. By utilizing a fluorescently labeled dsProbe approach, it is unnecessary to chemically modify the target of interest to impart a signaling mechanism. Additionally, as the process of competitive hybridization of dsProbes with targets of interest is an affinity driven process, discrimination of targets based on specificity is decoupled from standard measures such as elevated temperature protocols, an important step in translating nucleic acid technologies from the controlled laboratory environment to field applications.

Strain engineering is used as a means of manufacturing micro- and nano- scale particles with the ability to reversibly alter their geometry from three dimensional tubes to two dimensional flat layers. These particles are formed from a bi-layer of two dissimilar materials, one of which is the elastomeric material polydimethylsiloxane (PDMS), deposited under stress on a sacrificial substrate. Upon the release of the bi-layer structure from the substrate, interfacial residual stress is released resulting in the formation of tubes or coils. These particles possess the ability to dramatically alter their geometry and, consequently, change some properties that are reversible and can be triggered by a stimulus. This work focuses on the material selection and manufacturing of the bi-layer structures used to create the responsive particles and methods for characterizing and controlling the responsive nature of the particles. Furthermore, the potential of using these particles for a capture/release application is explored, and a systematic approach to scale up the manufacturing process for such particles is provided. This includes addressing many of the problems associated with fabricating ultra-thin layers, tuning the size of the particles, understanding how the stress accumulated at the interface of a bi-layer structure can be used as a tool for triggering a response as well as developing methods (i.e. experiments and applications) that allow the demonstration of this response.

The fullerene cage provides an ideal, isolated environment for trapping spin active atoms such as nitrogen or phosphorous. Alignment of these endohedral fullerenes in linear arrays would have applications in quantum computing as the interactions between spin-active molecules can be easily controlled. Self-assembled molecular networks such as block copolymers, Langmuir-Blodgett films, and self-assembled monolayers are ideal for this purpose as the spacing and geometry can be easily tuned. This dissertation will discuss using each of these methods to achieve alignment or orientation of fullerenes for application in quantum information processing.

Not available

A variety of “clickable” self-assembling peptide-amphiphile hydrogel systems are reported. Covalently linked hydrogels were prepared using alkyne-azide “click” chemistry and thiolene photochemistry, which were used in combination with short self-assembling peptideamphiphile compounds. For alkyne-azide “click” hydrogels, samples were formed from a mixture of two peptideamphiphiles which were separately disubstituted with alkyne or azide functionalised amino acids. This allowed for production of an extensively triazole-linked hydrogel product when gelation was performed in combination with the appropriate “click” pre-catalyst and reductant. For thiol-ene photochemical hydrogels samples were formed from a mixture of two peptideamphiphiles which were separately disubstituted with cysteine or Alloc-protected lysine. UV exposure was used to catalyse the covalent linking of the asembled hydrogel. Michael addition thiol-ene reactions were also investigated as a potential covalent linking method. A number of model reactions were attempted on specially synthesised amino acids. Results were promising, but a number of difficulties were encountered which made them unsuitable for incorporation in a hydrogel system. The hydrogel samples produced were all found to be viscoelastic hydrogels through analysis by rheological methods. A variation in the stiffness of the samples was observed, with samples having Young’s modulus values in the soft to intermediate range when compared to that of various tissues. SEM analysis indicated the hydrogels exhibited a fibrous nanostructure. The biological activity of the hydrogel samples was investigated by 2D seeding of cells on hydrogel samples. A LIVE/DEAD assay was performed which indicated hydrogel samples were able to support cell attachment and growth in vitro.