This dissertation focuses on four research topics: self-assembly of colloidal nanoparticles, surface modifications of the properties of ionically self-assembled multilayer films, surface enhanced Raman spectroscopy of functionalized gold nanoparticles, and two photon uncaging in gel. Those techniques are used for development of novel nanofabrication methods for top-down and bottom-up assembly of nanostructures, by modifying the properties of nanopatterned surfaces with photoactive ligands, and other technologies. First I describe the development of an improved method for nanosphere lithography, a variation of the convective self-assembly technique. The method exhibited high reproducibility and yielded high quality monolayer crystals by withdrawing a meniscus of liquid polystyrene spheres solution and subsequent evaporation of the solvent. The monolayer crystal was used as an evaporation mask to create surface arrays of gold nanotriangular particles. Metal nanoparticles, with sharp features or narrow gaps, exhibit strong plasmonic properties. I took advantage of those properties to attempt to create patchy modifications of the surface functionalization of gold nanotriangular particles treated with photosensitive molecules. Two molecules denoted, P3-DTC, and LIP3, were used as functional molecules attached to the gold nanoparticles. After interaction with 356nm UV light, part of those molecules cleaves off the surface of the nanoparticles rendering the surface modified with a new functional group. The modification takes place only at the plasmonic hot spots of those nanoparticles, resulting in a patchy modification of the properties of the nanoparticles. I built polymer Ionically Self-assembled Multilayer (ISAM) films using a Layer-by-Layer deposition technique and treated them to alter their surface adhesion properties. Poly (allylamine hydrochloride) (PAH), and poly (styrene sulfonate) (PSS) are a very well-studied system of polyelectrolytes for LbL deposition. ISAM films built from those polyelectrolytes are rich in amine groups to which nanoparticles, cells, tissue cultures, ligands can be made to adhere. In my work I developed a method for selective modification of the surface adhesiveness, by neutralizing the amine groups trough acetylation with acetic anhydride. With resolution from a few microns to a few hundred nanometers, I selectively passivated some areas of the ISAM film while others I left unaltered. I tested the effect of the acetic anhydride passivation by performing Horse Radish Peroxidase (HRP) test which quantifies the amount of free amines on the surface of the film. I also demonstrated the patchy modification of surface adhesiveness by introducing gold nanospheres which attached only to the amine active areas of the modified ISAM film. Photoactivatable fluorophores, i.e. compounds and other entities that may transform into a fluorescent form on absorption of a photon can be employed in multidimetional volume patterning. I studied the photoactivation of aryl azides in gelatin matrix. Specifically, I used Azidocoumarin 151 as a test molecule to undergo two-photon activation, and then measured the resulting photoluminescence. The activation of the Azidocoumarin 151 can be used to create arbitrary 3D patterns of modified functionality inside the gel. The activated molecules can be used as sites for further modification of the patterning inside the volume of the gel. Possible modifications include attaching biomolecules, nanoparticles, or individual cells. / Ph. D.

No / Peptides that self-assemble into nanostructures are of tremendous interest for biological, medical, photonic and nanotechnological applications. The enormous sequence space that is available from 20 amino acids probably harbours many interesting candidates, but it is currently not possible to predict supramolecular behaviour from sequence alone. Here, we demonstrate computational tools to screen for the aqueous self-assembly propensity in all of the 8,000 possible tripeptides and evaluate these by comparison with known examples. We applied filters to select for candidates that simultaneously optimize the apparently contradicting requirements of aggregation propensity and hydrophilicity, which resulted in a set of design rules for self-assembling sequences. A number of peptides were subsequently synthesized and characterized, including the first reported tripeptides that are able to form a hydrogel at neutral pH. These tools, which enable the peptide sequence space to be searched for supramolecular properties, enable minimalistic peptide nanotechnology to deliver on its promise.

No / Discovery of new catalysts for demanding aqueous reactions is challenging. Here, we describe methodology for selection of catalytic phages by taking advantage of localized assembly of the product of the catalytic reaction that is screened for. A phage display library covering 109 unique dodecapeptide sequences is incubated with nonassembling precursors. Phages which are able to catalyze formation of the self-assembling reaction product (via amide condensation) acquire an aggregate of reaction product, enabling separation by centrifugation. The thus selected phages can be amplified by infection of Escherichia coli. These phages are shown to catalyze amide condensation and hydrolysis. Kinetic analysis shows a minor role for substrate binding. The approach enables discovery and mass-production of biocatalytic phages.

No / We demonstrate the self-assembly of bola-amphiphile-type conjugates of dipeptides and perylene bisimide (PBI) in water and other polar solvents. Depending on the nature of the peptide used (glycine-tyrosine, GY, or glycine-aspartic acid, GD), the balance between H-bonding and aromatic stacking can be tailored. In aqueous buffer, PBI-[GY]2 forms chiral nanofibers, resulting in the formation of a hydrogel, while for PBI-[GD]2 achiral spherical aggregates are formed, demonstrating that the peptide sequence has a profound effect on the structure formed. In water and a range of other polar solvents, self-assembly of these two PBI-peptides conjugates results in different nanostructures with highly tunable fluorescence performance depending on the peptide sequence employed, e.g., fluorescent emission and quantum yield. Organogels are formed for the PBI-[GD]2 derivative in DMF and DMSO while PBI-[GY]2 gels in DMF. To the best of our knowledge, this is the first successful strategy for using short peptides, specifically, their sequence/structure relationships, to manipulate the PBI nanostructure and consequent optical properties. The combination of controlled self-assembly, varied optical properties, and formation of aqueous and organic gel-phase materials may facilitate the design of devices for various applications related to light harvesting and sensing.

Yes / Phenylacetyl-peptide amphiphiles were designed, which upon cleavage by a disease-associated enzyme reconfigure from micellar aggregates to fibres. Upon this morphological change, a doxorubicin payload could be retained in the fibres formed, which makes them valuable carriers for localised formation of nanofibre depots for slow release of hydrophobic anticancer drugs.

Miniaturization of electronic circuits and systems continue to pose great difficulties in meeting the demand and anticipated growth for information services and their associated electronics. Of the several information processing techniques under consideration for devices of the future, optical systems are considered to offer significant advantages in terms of speed and bandwidth. Unfortunately, at the dimensions of contemporary electronics, optical waveguides will fail to assist significantly due to the fact that standard optical waveguides will have dimensions below the diffraction limit and hence optical waveguiding at such scales will be impractical. In order to circumvent this, recent work in the area of using nano-sized protrusions to guide light below the diffraction limit has been receiving a decent amount of attention. Such systems have typically involved using electron beam lithography to create these perturbations on metallic surfaces called plasmonic waveguides. While these waveguides are fairly efficient, in the amounts required to make real circuits this method would be impractically slow and prohibitively expensive. However, such waveguides could be made much more cheaply if means could be found to arrange colloidal nanoparticles on suitable substrates. In this project, nanoscale self-assembly has been investigated with the aim of achieving such ends. Colloidal nanoparticles have been synthesized and self-assembled onto substrates such that they show near field interactions necessary for plasmonic waveguiding without any aggregation. Absorption peak shifts, which were obtained during the experimental phase of this project confirmed that such nanoparticle assemblies can be achieved and that they do demonstrate some plasmonic waveguiding action. With this first step, it is hoped that films like these may find use for quick and cheap plasmonic waveguiding sometime in the near future. / Master of Science

Structures in nature exhibit unique and complex architectures whose order propagates from nano- (10-9 m) to macro-scales (mm to m). These structures give rise to a rich diversity of adaptive function that allows for life in all environments on Earth. This complex functionality has driven research into bio-inspired materials where scientists investigate the complex relationship between sequence, structure and function of these materials. A good illustrative example of the effect that hierarchical structure can have is a brick wall. Bricks are laid so that the layer on top is shifted in either direction by half of a brick. This alternating pattern is what gives the wall its strength. If a crack occurs in the mortar, it will only propagate until it hits a boundary (a neighboring brick). Designing nanostructures can have similar effects on materials we use every day. Some of the most prevalent are adhesives that mimic the structures on gecko feet, which allow them to stick to any surface. This work presents bottom-up design strategies for self-assembling protein materials whose hierarchical structure may prove useful in a variety of applications in soft-robotics and energy storage. Proteins are a useful class of molecules, because they contain a level of structural complexity beyond that of synthetic materials. They are an inherently 'green' material feedstock; made in a lab using microbes like E. coli. Additionally, with the ease and availability of genetic engineering techniques we can easily modify the structure. This is especially true for the class of proteins, repeat proteins, which are the focus of this manuscript. Repeat proteins comprise small repeated sequences which are structurally independent from each other and can be strung together to create open, extended architectures. Here we explore the self-assembly emergent properties of the consensus tetratricopeptide repeat (CTPR18) . We show that this protein assembles into highly ordered 1D and 2D arrays that are shape tunable based the molecular environment (solvents, charge, etc). These nanomaterials may prove useful as molecular recognition scaffolds. We further explore the hierarchical self-assembled films of CTPR18. These films form highly oriented lamellar structures that seemingly propagate the entire length of the films. These lamellae directly affect the materials mechanical properties. Accordingly, by changing the film casting conditions, we can impart a structural gradient in the film, which proves useful in tuning the water-induced bending motion of these films. Herein, we show the ability to change the speed and directionality of actuation by simply changing the underlying film morphology. Lastly, we show that these films are electroresponsive as well, owing this function to ion transport through the inherently charged character of CTPR18. These dual responsive materials may prove useful in soft robotics. Additionally we are beginning investigations into the usefulness of CTPR18 films as alternate materials for ion-transport materials like those used in lithium polymer (more commonly LiPo) and sodium-ion batteries. / PHD / Structures in nature exhibit unique and complex architectures whose order propagates from nano- (10⁻⁹ m) to macro-scales (mm to m). These structures give rise to a rich diversity of adaptive function that allows for life in all environments on Earth. This complex functionality has driven research into bio-inspired materials where scientists investigate the complex relationship between sequence, structure and function of these materials. A good illustrative example of the effect that hierarchical structure can have is a brick wall. Bricks are laid so that the layer on top is shifted in either direction by half of a brick. This alternating pattern is what gives the wall its strength. If a crack occurs in the mortar, it will only propagate until it hits a boundary (a neigh-boring brick). Designing nanostructures can have similar effects on materials we use every day. Some of the most prevalent are adhesives that mimic the structures on gecko feet, which allow them to stick to any surface. This work presents bottom-up design strategies for self-assembling protein materials whose hierarchical structure may prove useful in a variety of applications in soft-robotics and energy storage. Proteins are a useful class of molecules, because they contain a level of structural complexity beyond that of synthetic materials. They are an inherently ‘green’ material feedstock; made in a lab using microbes like E. coli. Additionally, with the ease and availability of genetic engineering techniques we can easily modify the structure. This is especially true for the class of proteins, repeat proteins, which are the focus of this manuscript. Repeat proteins comprise small repeated sequences which are structurally independent from each other and can be strung togeth-er to create open, extended architectures. Here we explore the self-assembly emergent properties of the consensus tetratricopeptide repeat (CTPR18) . We show that this protein assembles into highly ordered 1D and 2D arrays that are shape tunable based the molecular environment (sol-vents, charge, etc). These nanomaterials may prove useful as molecular recognition scaffolds. We further explore the hierarchical self-assembled films of CTPR18. These films form highly oriented lamellar structures that seemingly propagate the entire length of the films. These lamellae directly affect the materials mechanical properties. Accordingly, by changing the film casting conditions, we can impart a structural gradient in the film, which proves useful in tuning the water-induced bending motion of these films. Herein, we show the ability to change the speed and directionality of actuation by simply changing the underlying film morphology. Lastly, we show that these films are electroresponsive as well, owing this function to ion transport through the inherently charged character of CTPR18. These dual responsive materials may prove useful in soft robotics. Additionally we are beginning investigations into the usefulness of CTPR18 films as alternate materials for ion-transport materials like those used in lithium polymer (more com-monly LiPo) and sodium-ion batteries.

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.

Inspired by nature’s use of self-assembled systems to carry out virtually all biological processes, chemists have taken to building simplified synthetic systems that mimic the biotic world. Although transition metal-ligand interactions are rarely used for the purpose of biological self-assembly, they have several advantages over other weak noncovalent interactions, such as pronounced directionality and significant strength. These particular attributes have allowed chemists to construct a comprehensive library of self-assembled polygons and polyhedra, using different transition metal-ligand motifs. Many of these supramolecular assemblies possess cavities of defined shape and size, which are able to accommodate guest molecules. It has further been realised that isolation of guest species from the bulk phase can lead to many interesting functions, such as containment, sensing and catalysis. Herein, a new self-assembly strategy has been used to construct novel cyclometalated Pt cages and assembly of the first known [Ir(ppy)2]-based capsule has also been achieved. Chapter 1 includes an introduction to metallosupramolecular assemblies, followed by a comprehensive review of three-dimensional architectures with accessible cavities, their synthetic strategies and applications. Chapter 2 reports on the construction of novel Pt(II)-based trigonal prisms using an unusual, kinetically controlled protocol. By exploiting asymmetric cyclometalated 2-phenylatopyridine based platinum corner units that possess both labile and non-labile cis-coordination sites, trigonal prismatic stereoisomeric architectures have been selectively prepared by altering the sequence of addition of ditopic 4,4′-bipy (4,4′-bipyridine) and tritopic tpt (2,4,6-tris(4-pyridyl)-1,3,5-triazine) molecular structural components using a template free method. Collision-induced-dissociation mass spectrometry experiments were used to differentiate between the structural isomers due to their significantly different fragmentation profiles. Chapter 3 describes the synthesis and characterisation of the first molecular capsule based on an [Ir(ppy)2]+ 90° metallosupramolecular acceptor unit. Initial work focused on pyridine-based donor ligands from which an Ir2L2 metallamacrocycle was assembled. However, when the highly conjugated tpt “panels” were used, due to postulated constraints in the dihedral angle, self-assembly of the Ir6tpt4 octahedral was unsuccessful. The constraints in the dihedral angle were eliminated by swapping pyridine for nitrile-based ligands and following the development of a method to resolve rac-[(Ir(ppy)2Cl)2] into its enantiopure forms, homochiral Ir6tcb4 (tcb = 1,3,5-tricyanobenzene) octahedral capsules where realised. Photophysical studies on the Ircapsules have shown that the ensemble of cooperative, weakly coordinating ligands can lead to luminescence not present in the comparative mononuclear analogues. X-ray crystallographic analysis revealed that the Ir capsules possess cavities large enough to accommodate 4 triflate counterions. Through a series of titration experiments the ability of the capsules to act as anion sensors was also exposed. Further exploration into the host-guest chemistry of the Ir6tcb4 capsule is reported in Chapter 4. Subsequent experiments have shown that self-assembly is highly dependent on the counterions associated with the system. While a number of different anions (OTf-, BF4 -, ClO4 -, PF6 -) facilitate the formation of the same octahedral scaffold, when triflimide was employed as a bulkier counterion, no capsule was observed. On subsequent addition of smaller counterions, such as triflate, the same Ir6tcb4 cage assembles, demonstrating that the anions also act as templates. Kinetic stability experiments, undertook by monitoring the rate of scrambling of the Δ and Λ-[Ir(ppy)2]+ components within the preformed ensembles, show that the Ir capsules are up to 1.4×104 times more stable than their mononuclear analogues. The counter anions were also observed to play a crucial role in the capsule’s stability with measured scrambling half-lives ranging from 4.7 mins with tetrafluoroborate to as long as 4.5 days with triflate. In contrast, the rate of ligand exchange in simple mononuclear complexes, as ascertained using EXSY NMR experiments, was found to be approximately independent of the associated anion.

The aim of this thesis is to investigate and better understand the mechanisms of protein self-assembly. Specifically, I study three protein systems which form morphologically and structurally distinct brillar protein aggregates. The first of these studies is concerned with the self-assembly of amyloid brils formed from bovine insulin. Amyloid brils are associated with human diseases such as Alzheimers Disease and type-2 diabetes, and are also garnering interest in biomaterial applications. Fragmentation-dominated models for the self-assembly of amyloid brils have had important successes in explaining the kinetics of amyloid bril formation but predict bril length distributions that do not match experimental observations. Here I resolve this inconsistency using a combination of experimental kinetic measurements and computer simulations. I provide evidence for a structural transition demarcated by a critical bril mass concentration, or CFC, above which fragmentation of the brils is suppressed. Our simulations predict the formation of distinct bril length distributions above and below the CFC, which I confirm by electron microscopy. These results point to a new picture of amyloid bril growth in which structural transitions that occur during self-assembly have strong effects on the final population of aggregate species with small, and potentially cytotoxic, oligomers dominating for long periods of time at protein concentrations below the CFC. I further show that the CFC can be modulated by environmental conditions, pointing to possible in vivo strategies for controlling cytotoxicity. I probe the structural nature of the transition by performing small angle neutron scattering. Secondly, I study the formation of amyloid-like brils from the protein ovalbumin. I undertake kinetic experiments of self-assembly and find two key features emerge: the lack of a lag time and the existence of a slow growth regime in the long-time limit. I observe, using TEM, that these brils are worm-like in nature and form closed-loops. I find the growth kinetics are intimately connected to this particular morphology. I present a simple kinetic model which captures the features of the kinetics found in experiments by incorporating end-to-end association of brils. I comment on the ramifications this type of amyloid bril assembly may have on oligomeric toxicity. Thirdly, the DNA-mimic protein ocr is highly charged (-56e at pH 8) and forms non-amyloid brillar assemblies at very high ammonium sulphate concentrations (3.2M). The fact that ocr forms translucent brillar gels at such high salt concentrations is extremely unique. Typically under such high salt conditions, non-specific amorphous aggregates are formed. In order to better understand the mechanism of why ocr forms specific bril aggregates, I used variants of the wile-type protein in which extensive regions of surface have been removed or modified. The structural characteristics of gels formed from the variants were probed using microrheological techniques. I find that non-specific electrostatic charge screening plays an important role in ocr aggregation. However, I also locate a potentially important α-helical region which may play a part in establishing specific interactions so that ocr may form ordered brillar assemblies.