abstract: DNA is a unique, highly programmable and addressable biomolecule. Due to its reliable and predictable base recognition behavior, uniform structural properties, and extraordinary stability, DNA molecules are desirable substrates for biological computation and nanotechnology. The field of DNA computation has gained considerable attention due to the possibility of exploiting the massive parallelism that is inherent in natural systems to solve computational problems. This dissertation focuses on building novel types of computational DNA systems based on both DNA reaction networks and DNA nanotechnology. A series of related research projects are presented here. First, a novel, three-input majority logic gate based on DNA strand displacement reactions was constructed. Here, the three inputs in the majority gate have equal priority, and the output will be true if any two of the inputs are true. We subsequently designed and realized a complex, 5-input majority logic gate. By controlling two of the five inputs, the complex gate is capable of realizing every combination of OR and AND gates of the other 3 inputs. Next, we constructed a half adder, which is a basic arithmetic unit, from DNA strand operated XOR and AND gates. The aim of these two projects was to develop novel types of DNA logic gates to enrich the DNA computation toolbox, and to examine plausible ways to implement large scale DNA logic circuits. The third project utilized a two dimensional DNA origami frame shaped structure with a hollow interior where DNA hybridization seeds were selectively positioned to control the assembly of small DNA tile building blocks. The small DNA tiles were directed to fill the hollow interior of the DNA origami frame, guided through sticky end interactions at prescribed positions. This research shed light on the fundamental behavior of DNA based self-assembling systems, and provided the information necessary to build programmed nanodisplays based on the self-assembly of DNA. / Dissertation/Thesis / Ph.D. Chemistry 2014

abstract: Colloidal quantum dots (QDs) or semiconductor nanocrystals are often used to describe 2 to 20 nm solution processed nanoparticles of various semiconductor materials that display quantum confinement effects. Compared to traditional fluorescent organic dyes, QDs provide many advantages. For biological applications it is necessary to develop reliable methods to functionalize QDs with hydrophilic biomolecules so that they may maintain their stability and functionality in physiological conditions. DNA, a molecule that encodes genetic information, is arguably the smartest molecule that nature has ever produced and one of the most explored bio-macromolecules. DNA directed self-assembly can potentially organize QDs that are functionalized with DNA with nanometer precision, and the resulting arrangements may facilitate the display of novel optical properties. The goal of this dissertation was to achieve a robust reliable yet simple strategy to link DNA to QDs so that they can be used for DNA directed self assembly by which we can engineer their optical properties. Presented here is a series of studies to achieve this goal. First we demonstrate the aqueous synthesis of colloidal nanocrystal heterostructures consisting of the CdTe core encapsulated by CdS/ZnS or CdSe/ZnS shells using glutathione (GSH), a tripeptide, as the capping ligand. We next employed this shell synthesis strategy to conjugate PS-PO chimeric DNA to QDs at the time of shell synthesis. We synthesized a library of DNA linked QDs emitting from UV to near IR that are very stable in high salt concentrations. These DNA functionalized QDs were further site-specifically organized on DNA origami in desired patterns directed by DNA self-assembly. We further extended our capability to functionalize DNA to real IR emitting CdxPb1-xTe alloyed QDs, and demonstrated their stability by self-assembling them on DNA origami. The photo-physical properties of the QDs were further engineered by attaching a QD and a gold nanoparticle in controlled distances on the same DNA origami, which revealed a much longer range quenching effect than usual Forster Resonance Energy Transfer. We are currently engaged in enhancing photoluminescence intensity of the QDs by bringing them in the plasmonic hot spots generated by cluster of larger plasmonic nanoparticles. / Dissertation/Thesis / Ph.D. Chemistry 2014

Under specific conditions short peptides modified with an N-terminal fluorenyl-9-methoxycarbonyl (Fmoc) group can self-assemble into hydrogel scaffolds similar in properties to the natural extracellular matrix. Fmoc-diphenylalanine (Fmoc-FF) for instance, has been shown to form hydrogels at physiological pH that have the ability to support 2D and 3D cell culture. The aim of this investigation is to provide further understanding of the self-assembly mechanism of such systems in order to progress towards the establishment of design rules for the preparation of scaffolds with tuneable properties.First, Fmoc-dipeptides composed of a combination of hydrophobic aromatic residues phenylalanine (F) and glycine (G) were studied with a particular emphasis on the effect of pH variations. The systems were investigated in order to assess what influence the position of such residues in the peptide sequence had on the physical properties of the molecules, and what impact the chemical structure had on the self-assembly behaviour and the gelation properties of the materials. Subsequently, phenylalanine was replaced by leucine (L), a non-aromatic amino acid that had the same relative hydrophobicity in order to determine whether the self-assembly of such molecules is driven by aromatic interactions or hydrophobic effects.Using potentiometry, the behaviour of the systems in solution has been investigated, revealing that they were all characterised by pKa shifts of up to six units above the theoretical values. Fmoc-FF exhibited two transitions whereas the other Fmoc-dipeptides only displayed one. These transitions were found to coincide with the formation of distinct self-assembled structures with differing molecular conformations and properties that were characterised using transmission electron microscopy, infrared and fluorescence spectroscopy, X-ray scattering and shear rheometry.π-stacking of the aromatic moieties was thought to be the driving force of the self-assembly mechanism, generating dimers that corresponded to the building blocks of the supramolecular structures formed. On the other hand, the peptide components were stabilised via hydrogen bonding and could form antiparallel β-sheets depending on the amino acid sequence and the associated influence on the rigidity of the molecules. Below their (first) apparent pKa transition, Fmoc-FF, Fmoc-LL, Fmoc-FG, Fmoc-LG and Fmoc-GG formed hydrogels, with the mechanical properties and stability varying depending on the amino acid sequence. Fmoc-FF and Fmoc-LL exhibited the lowest storage modulus values (G′ ~ 0.5–5 Pa) of the studied systems while Fmoc-LG displayed the highest (G′ ~ 1000–2100 Pa). Fmoc-FG and Fmoc-LG had the peculiarity of being obtained upon heating and where found to be particularly stable, as opposed to Fmoc-GG gels which showed a tendency to crystallise. On the microscopic scale, these gels were all associated with the presence of entangled fibrillar networks of different size and morphology, which in some cases could self-assemble further through a lamellar organisation. Again, Fmoc-FG and Fmoc-LG distinguished from the other systems as they were the only Fmoc-dipeptides to show a supramolecular chirality in the form of twisted ribbons under specific pH conditions. In contrast, Fmoc-GF and Fmoc-GL did not form hydrogels below their apparent pKa due to the formation of sheet-like and spherical structures respectively.

L'auto-assemblage est une technique de structuration qui permet de contrôler la forme et la construction de systèmes organisés à différentes échelles de longueur. Dans cette thèse, nous nous sommes intéressés à l'auto-organisation de films de savon formés dans des milieux confinés et structurés. Les supports de séchage sont constitués d'un réseau de plots cylindriques en PDMS dont les positions peuvent varier et ainsi permettre le contrôle de la structure finale. Nous avons étendu une étude préexistante en réseaux carrés à des réseaux rectangulaires pour créer une anisotropie de manière à orienter les films dans des directions préférentielles. Nous avons pu montrer que les films de savon s'alignaient toujours dans la direction pour laquelle la distance entre les plots était la plus courte, et ce pour seulement 5 à 10% de différence de distance entre les axes. En outre, l'augmentation de l'épaisseur des plots permet de rendre plus brusque la transition (2%) entre désordre et alignement des films. Ces résultats ont été complétés par des simulations numériques permettant de modéliser l'ensemble des séchages. Nous avons enfin pu effectuer des expériences de séchage complémentaires dans des réseaux en losanges et dans des réseaux quasicristallins. La forme des plots a également été modifiée de façon à créer un contraste visuel du dépôt de séchage. / Self-assembly is a structuration technique which allows to control the shape and to build organized systems at different length scales. In this Thesis, we have studied the self-assembly of soap films formed in confined and structured media. Surfaces are composed of a grid of cylindrical pillars in PDMS which positions can vary allowing to control the final structure. We have expanded a previous study performed with square grids, using rectangular grids to create an anisotropy in order to guide the orientation of films. We showed that films always aligned in the shortest direction, even with only 5 to 10% difference between axes. Furthermore, the increase of pillar thickness allows to sharpen this transition (2%) between disorder and films alignment. These results have been completed by numerical simulations allowing to model all the grids. Finally, we made additional drying experiments in diamond and quasicrystalline grids. The shape of the pillars has also been changed in order to create a visual contrast of the drying deposit.

Nanoscale, conductive wires fabricated from organic molecules have attracted considerable attention in recent years due to their anticipated applications in the next generation of optical and electronic devices. Such highly ordered 1D nanostructures could be made from a number of routes. One route of particular interest is to self-assemble the wires from biomolecules due to the wide range of assembly methods that can be adapted from nature. For example, biomolecules with aromatic motifs can be self-assembled so that good π-π stacking is achieved in the resultant nanostructure. An additional advantage of using biomolecules is that it enables the interface of the electronic materials with biological systems, which is important for many applications, including nerve cell communication and artificial photosynthesis. In this study, nanowires were prepared by the molecular self-assembly of oligopeptides that were coupled to aromatic components. In order to achieve charge transport though the nanowires, it was imperative that the aromatic components were arranged so that there was π-π stacking with very few structural defects. Therefore, enzymes were used to control the formation of the hydogelators which subsequently self-assembled to produce nanowire networks. Two main systems were studied in this thesis.In the first system, hydrogelators were produced from aromatic peptide amphiphiles via the enzymatic hydrolysis of the methyl ester of fluorenylmethoxycarbonyl (Fmoc)-di/tripeptides. These hydrogelators formed nanostructures due to π-π stacking between the Fmoc groups and H-bonding between the peptides. The nanostructures in turn produced macroscale gel networks. The nanostructures were analyzed by wide angle X-ray diffraction and fluorescence spectroscopy. A combination of Fourier transform infra-red (FTIR), Transmission Electron Microscopy (TEM), Cryo-TEM, and Atomic Force Microscopy (AFM) was used to characterize the networks. The charge transport properties of the dried networks were studied using impedance spectroscopy. Fmoc-L₃ was found to assemble into nanotubes whose walls consisted of 3 self-assembled layers and possessed inner and outer diameters of ~ 9 nm and ~ 18 nm, respectively. The Fmoc-L₃ networks were structurally stabile and were electronically conductive under a vacuum. The sheet resistance of the peptide networks increased with relative humidity due to the increasing ionic conductivity. The resistance of the networks was 0.1 MΩ/sq in air and 500 MΩ/sq in vacuum (pressure: 1.03 mbar) at room temperature. The networks had a band gap of between 1 to 4 eV as measured by UV-Vis spectroscopy and the temperature-impedance studies. Possible routes for aligning the Fmoc-L3 networks were studied in an attempt to improve their conductivity in one direction. In particular, the peptides were assembled under an electric field (0 to 3.75 kV/cm). Random networks were produced at low field strengths, whereas a degree of alignment was obtained at a field strength of 3.75 kV/cm. The conductivity of the aligned networks in the direction of alignment was a factor of three times higher than that of the random networks.The second system studied was Fmoc-dipeptide-OMe hydrogels produced by the enzymatic condensation of an Fmoc-amino acid and an amino acid ester. Preliminary results found that Fmoc-SF-OMe assembled into nanosheets, nanoribbons and spherulites, depending on the temperature at which self-assembly occurred. The Fmoc-XY-OMe films possessed an extremely high resistance (1012 Ω).

This dissertation contains six chapters detailing recent advances that have been made in the synthesis and characterization of metal-semiconductor hybrid nanocrystals (HNCs), and the applications of these materials. Primarily focused on the synthesis of well-defined II-VI semiconductor nanorod (NR) and tetrapod (TP) based constructs of interest for photocatalytic and solar energy applications, the research described herein discusses progress towards the realization of key design rules for the synthesis of functional semiconductor nanocrystals (NCs). As such, a blend of novel synthesis, advanced characterization, and direct application of heterostructured nanoparticles are presented. Additionally, for chapters two through six, a corresponding appendix is included containing supporting data pertinent to the experiments described in the chapter. The first chapter is a review summarizing the design, synthesis, properties, and applications of multicomponent nanomaterials composed of disparate semiconductor and metal domains. By coupling two compositionally distinct materials onto a single nanocrystal, synergistic properties can arise that are not present in the isolated components, ranging from self-assembly to photocatalysis. While much progress was made in the late 1990s and early 2000s on the preparation of a variety of semiconductor/metal hybrids towards goals of photocatalysis, comprehensive understanding of nanoscale reactivity and energetics required the development of synthetic methods to prepare well-defined multidimensional constructs. For semiconductor nanomaterials, this was first realized in the ability to tune nanomaterial dimensions from 0-D quantum dot (QD) structures to cylindrical (NR) and branched (TP) structures by exploitation of advanced colloidal synthesis techniques and understandings of NC facet reactivities. Another key advance in this field was the preparation of "seeded" NR and TP constructs, for which an initial semiconductor QD (often CdSe) is used to "seed" the growth of a second semiconductor material (for example, CdS). These advances led to exquisite levels of control of semiconductor nanomaterial composition, shape, and size. Concurrently, many developments were made in the functionalization of these NCs with metallic nanoparticles, allowing for precise tuning of metal nanoparticle deposition position on the surface of preformed semiconductor NCs. To date, photoinduced and thermally induced methods are most widely used for this, providing access to metal-semiconductor hybrid structures functionalized with Au, Pt, Ag2S, Pd, Au/Pt, Ni, and Co nanoparticles (to name a few). With colloidal nanomaterial preparation becoming analogous to traditional molecular systems in terms of selectivity, property modulation, and compositional control, the field of nanomaterial total synthesis has thus emerged in the past decade. With a large toolbox of reactions which afford selectivity at the nanoscale developed, to date it is possible to design a wider array of materials than ever before. Only recently (the past ~ 5 years), however, has the transition from design of model systems for fundamental characterization to realization of functional materials with optimized properties begun to be demonstrated. The emphasis of chapter 1 is thus on the key advances in the preparation of metal-semiconductor hybrid nanoparticles made to date, with seminal synthetic, characterization, and application milestones being highlighted. The second chapter is focused on the synthesis and characterization of well-defined CdSe-seeded-CdS (CdSe@CdS) NR systems synthesized by overcoating of wurtzite (W) CdSe quantum dots with W-CdS shells. 1-dimensional NRs have been interesting constructs for applications such as solar concentrators, optical gains, and photocatalysis. In each of these cases, a critical step is the localization of photoexcited excitons from the light-harvesting CdS NR "antenna" into the CdSe QD seed, from which emission is primarily observed. However, effects of seed size and NR length on this process remained unexplored prior to this work. Previous work had demonstrated that, for core@shell CdSe@CdS systems, small CdSe seed sizes (< 2.8 nm in diameter) resulted in quasi-type II alignment between semiconductor components (with photoexcited electrons delocalized across the structure and holes localized in the CdSe seed), and large seed sizes (> 2.8 nm) resulted in type I alignment (with photoexcited electrons and holes localized in the CdSe seed). Through synthetic control over CdSe@CdS NR systems, materials with small and large CdSe seeds were prepared, and for each seed size, multiple NR lengths were prepared. Through transient absorption studies, it was found that band alignment did not affect the efficiency of charge localization in the CdSe core, whereas NR length had a profound effect. This work indicated that longer NRs resulted in poor exciton localization efficiencies owing to ultrafast trapping of photoexcited excitons generated in the CdS NR. Thus, with increasing rod length, poorer efficiencies were observed. This work served to highlight the ideal size range for CdSe@CdS NR constructs targeted towards photocatalysis, with ~ 40 nm NRs exhibiting the best rod-to-seed localization efficiencies. Additionally, it served to expand the understanding of exciton trapping in colloidal NC systems, allowing development of a predictive model to help guide the preparation of other nanorod based photocatalytic systems. The third chapter describes the synthesis of Au-tipped CdSe NRs and studies of the effects of selective metal nanoparticle deposition on the band edge energetics of these model photocatalytic systems. Previous studies had demonstrated ultrafast localization of photoexcited electrons in Au nanoparticles (AuNP) (and PtNP) deposited at the termini of CdSe and CdSe@CdS NR constructs. Also, for similar systems, the hydrogen evolution reaction (HER) had been studied, for which it was found that noble metal nanoparticle tips were necessary to extract photoexcited electrons from the NR constructs and drive catalytic reactions. However, in these studies, energetic trap states, generally ascribed to surface defects on the NC surface, are often cited as contributing to loss of catalytic efficiency. In this study, we found that the literature trend of assuming the band-edge energetics of the parent semiconductor NC applies to the final metal-functionalized catalyst did not present a complete picture of these systems. Through a combination of ultraviolet photoelectron spectroscopy and waveguide based spectroelectrochemistry on films of 40 nm long CdSe NRs before and after AuNP functionalization, we found that metal deposition resulted in the formation of mid-gap energy states, which were assigned as metal-semiconductor interface states. Previously these states had only been seen in single particle STS studies, and their identification in this study from complementary characterization techniques highlighted a need to further understand the nature of the interface between metal/semiconductor components for the design of photoelectrochemical systems with appropriate band alignments for efficient photocatalysis. The fourth chapter transitions from NR constructs to highly absorbing CdSe@CdS TP materials, for which a single zincblende (ZB) CdSe NC is used to seed the growth of four identical CdS arms. These arms act as highly efficient light absorbers, resulting in absorption cross sections an order of magnitude greater than for comparable NR systems. In the past, many studies have been published on the striking properties of TP nanocrystals, such as dual wavelength fluorescence, multiple exciton generation, and inherent self-assembly owing to their unique geometry. Nonetheless, these materials have not been exploited for photocatalysis, primarily owing to challenges in preparing TP from ultrasmall ZB-CdSe seed size (owing to phase instability of the zincblende crystal structure), thus preventing access to quasi-type II structures necessary for efficient photocatalysis. In this study, we successfully break through the type I/quasi-type II barrier for TP NCs, reclaiming lost ground in this field and demonstrating for the first time quasi-type II behavior in CdSe@CdS TPs through transient absorption measurements. This was enabled by new synthetic protocols for the synthesis and stabilization of ultrasmall (1.8 – 2.8 nm) ZB-CdSe seeds, as well as for the synthesis of CdSe@CdS TPs with arm lengths of 40 nm. Easily scalable, TPs were prepared on gram scales, and the quasi-type II systems showed dramatically enhanced rates of selective photodeposition of AuNP tips under ultraviolet and solar irradiation. These are promising materials for photocatalytic and solar energy applications. The fifth chapter continues with the study of CdSe@CdS TPs, and elaborates on a new method for the selective functionalization of the highly symmetrical TP construct. Previous studies had demonstrated that access to single noble metal NP tips was vital for efficient photocatalytic HER from NR constructs. However, TP materials have been notoriously difficult to selectively functionalize, owing to their symmetric nature. Using a novel photoinduced electrochemical Ostwald ripening process, we found that initially randomly deposited AuNPs could be ripened to a single, large (~ 7 nm) AuNP tip at the end of one arm of a type I CdSe@CdS TP with 40 nm arms. To demonstrate the selectivity of this tipping process, dipolar cobalt was selectively overcoated onto the AuNP tips of these TPs, resulting in dipolar Au@Co-CdSe@CdS TP nanocrystals. These particles were observed to spontaneous self-assemble into 1-D mesoscopic chains, owing to pairing of N-S dipoles of the ferromagnetic CoNPs, resulting in the first example of “colloidal polymers” (CPs) bearing bulky, tetrapod ("giant t-butyl") pendant groups. The sixth chapter elaborates further on the preparation of colloidal polymers, further extending the analogy between molecular and colloidal levels of synthetic control. One challenge in the field of colloidal science is the realization of new modes of self-assemble for compositionally distinct nanoparticles. In this work, it was found that Au@Co nanoparticle dipole strength could be systematically varied by tuning of AuNP size on CdSe@CdS nanorods/tetrapods. In the first example of a colloidal analogue to reactivity ratios observed for traditional chain growth polymerization systems, highly disparate AuNP tip sizes (and thus final Au@Co NP dipole strength) were found to result in segmented colloidal copolymers upon dipolar self-assembly, whereas similar AuNP tip sizes ultimately led to random dipolar assemblies. Clearly visualized through incorporation of NR and TP sidechains into these colloidal polymers, this study presented a compelling case for continued exploration of colloidal analogues to traditional molecular levels of synthetic control.

Dynamic combinatorial chemistry (DCC) is a powerful method for synthesising complex molecules and identifying unexpected receptors. Chapter 1 gives an overview of the concept of DCC and its applications, and discusses its evolution to date. Chapter 2 describes the discovery of a new generation of donor-acceptor [2]catenanes in aqueous dynamic combinatorial systems. The assembly of these [2]catenanes is promoted by a high salt concentration (1 M NaNO3), which raises the ionic strength and encourages hydrophobic association. More importantly, a mechanism that explains and predicts the structures formed is proposed, giving a fundamental insight into the role played by hydrophobic effect and donor-acceptor interactions in this process. Building on these results, Chapter 3 describes the assembly in high salt aqueous libraries of a larger structure: a [3]catenane. Remarkably, the [3]catenane exhibits strong binding interactions with a biologically relevant target - spermine - in water under near-physiological conditions. Its synthesis is improved if the salt is replaced by a sub-mM concentration of spermine, acting as a template. Chapter 4 explores in further detail how subtle variations in the building block design influence the selective formation of either [2] or [3]catenanes. This last section underlines both the advantages and the limitations of the method developed in Chapter 3. After a short conclusion (Chapter 5), Chapter 6 gives experimental details.

Over the past few decades, supramolecular self-assembly has become an alternative synthetic tool for constructing targeted discrete molecular architectures. Among various interactions, metal-ligand coordination has attracted great attention owing to high bond enthalpy (15−50 Kcal/mol) and predictable directionality. The basic principle of metal-ligand directed self-assembly relies on the proper designing of information encoded rigid complementary building units (a transition metal based acceptor and a multidentate organic donor) that self-recognize themselves in a chemically reasonable way (depends on their bite angle and symmetry) during self-assembly process. As far as acceptor units are concerned, Pd(II) and Pt(II) metal-based cis-blocked 90° acceptors have so far been used greatly for the construction of a library of 2D/3D discrete supramolecular architectures due to their rigid square planar geometry and kinetic lability. However, in some cases the efforts to design finite supramolecular architectures using a cis-blocked 90° acceptor in combination with a bulky donor ligand were unsuccessful, which may be due to the steric demands of donor ligand. Moreover, the resulted assemblies from such cis-blocked 90° building unit are mostly non-fluorescent in nature and limit the possibility of using them as chemosensors for various practical applications. Unlike that of rigid square-planar Pt(II) and Pd(II)-metal based building blocks, the use of other transition metal-based building units for the construction of discrete nanoscopic molecular architectures are known to lesser extent, mainly because of their versatile coordination geometries. However, some of the half-sandwiched piano-stool complexes of late transition metals like Ru, Os, Ir and Rh are known to maintain the stable octahedral geometry under various reaction conditions. Moreover, the self-assembly using redox active transition metal-based building units may lead to redox active assemblies. On the other hand, symmetrical rigid donors have been widely used as the favorite choices for the purpose of constructing desired product mainly due to their predictable directionality. Flexible linkers are not predictable in their directionality during self-assembly process and thus results mostly in undesired polymeric products. Furthermore, metal-ligand directed self-assembly provides opportunity to introduce multifunctionality in a single step within/onto the final supramolecular architectures. Among various functional groups, the incorporation of unsaturated ethynyl functionality is expected to enrich the final assemblies to be π-electron-rich and the attachment of ethynyl functionality with heavy transition metal ions are known to be luminescent in nature due to the facile metal to ligand charge transfer (MLCT). Hence, the final supramolecular complexes can be used as potential fluorescence sensors for electron-deficient nitroaromatics, which are the chemical signature of most of the commercially available explosives. The main thrust of the present investigation is focused on the judicious design and syntheses of multifaceted 2D/3D supramolecular architectures of finite shapes, sizes and functionality using Pt(II)/Ru(II) based “shape-selective” organometallic building blocks and investigation of their application as chemosensors. CHAPTER 1 of the thesis presents a general review on the core concepts of self-assembly and supramolecular chemistry. In particular, it underlines the importance of metal-ligand directional bonding approach for designing a vast plethora of discrete 2D/3D supramolecular architectures with tremendous variation in topology. CHAPTER 2 describes the design and syntheses of a series of 2D metallamacrocycles using carbazole-functionalized shape-selective 90° building units. A new Pt2II organometallic 90° acceptor 3,6-bis[trans-Pt(PEt3)2(NO3)(ethynyl)]carbazole (M1) containing ethynyl functionality is synthesized via Sonagashira coupling reaction and characterized. The combination of M1 with three different flexible ditopic donors (L1−L3) afforded [2 + 2] self-assembled molecular squares (1−3), respectively [where L1 = 1,3-bis(4-pyridyl)isophthalamide; L2 = 1,3-bis(3-pyridyl)isophthalamide; L3 = 1,2-bis(4-pyridyl)ethane] (Scheme 1). Scheme 1: Schematic presentation of the formation of a series of [2 + 2] self-assembled molecular squares. An equimolar (1:1) combination of same acceptor M1 with rigid linear ditopic donors (L4-L5) yielded [4 + 4] self-assembled octanuclear molecular squares 4 and 5, respectively [L4 = 4,4’-bipyridine; L5 = trans-1,2-bis(4-pyridyl)ethylene]. Conversely, a similar reaction of M1 with an amide-based unsymmetrical linear flexible ditopic donor L6 resulted in the formation a [2 + 2] self-sorted molecular rhomboid (6a) as a single product [L6 = N-(4-pyridyl)isonicotinamide]. Despite the possibility of several linkage isomeric macrocycles (rhomboids, triangles and squares) due to different connectivity of the ambidentate linker, the formation of a single and symmetrical molecular rhomboid 6a as an exclusive product is an interesting observation. This chapter also presents the synthesis and characterization of a complementary 90° dipyridyl donor 3,6-bis(4-pyridylethynyl)carbazole (L7). Stoichiometric combination of L7 with several PdII/PtII-based 90° acceptors (M2−M4) yielded [2 + 2] self-assembled molecular “bowl” shaped macrocycles (7−9) respectively, in good yields [M2 = cis-(dppf)Pd(CF3SO3)2; M3 = cis-(dppf)Pt(CF3SO3)2; M4 = cis-(tmen)Pd(NO3)2]. All these newly synthesized macrocycles were characterized by various spectroscopic techniques and molecular structures of some of them were confirmed by single crystal X-ray diffraction analysis. In addition to their syntheses and characterization, fluorescence chemosensing ability for various analytes was investigated. Macrocycle 1 is a system composed of amide-based receptor units and carbazole-based fluorophore moieties. The fluorescence study of 1 elicited a dramatic enhancement in the fluorescence intensity upon gradual addition of P2O74- anion in DMF/H2O solvent mixture, whereas similar titration under identical condition with other anions like F-, ClO4-, and H2PO4- did not show such change. Hence, molecular square 1 can be used as selective fluorescence sensor for pyrophosphate (P2O74-) anion. Due to their extended π-conjugation, macrocycles 3-4 were used as fluorescence sensors for electron-deficient nitroaromatics, which are the chemical signatures of many commercially available explosives. The fluorescence study showed a marked quenching of initial fluorescence intensity of the macrocycles(3-4) upon gradual addition of picric acid (PA) and they exhibited large fluorescence quenching responses with high selectivity for nitroaromatics among various other electron deficient aromatic compounds tested. As macrocycle 7 has large concave aromatic surface, it was utilized as a suitable host for large convex guest such as fullerene C60. The fluorescence quenching titration study suggested that macrocycle 7 forms a stable ~1:1 host-guest complex with C60 and the calculated association constant (KSV) is 1.0 × 105 M-1. CHAPTER 3 presents two-component coordination-driven self-assembly of a series of [2 + 2] molecular rectangles and a [2 + 4] self-assembled molecular tetragonal prism. An equimolar combination of pre-designed linear PtII2-acceptors M5−M6 separately with three different “clip” donors (L2, L8−L9) led to the formation of [2 + 2] self-assembled tetranuclear cationic molecular rectangles (10−15), respectively [M5 = 1,4-bis[trans-Pt(PEt3)2(NO3)(ethynyl)] benzene; M6 = 4,4’-bis[trans-Pt(PEt3)2(CF3SO3)(ethynyl)]biphenyl; L8 = 1,3-bis(3-pyridyl)ethynylbenzene; L9 = 1,8-bis(4-pyridyl)ethynylanthracene]. Rectangles 10-15 showed strong fluorescence in solution owing to their extended π-conjugation. Amide-functionalized rectangle 10 was used as a macrocyclic receptor for dicarboxylic acids. Solution state fluorescence study showed that rectangle 10 selectively binds (KSV = 1.4 × 104 M-1) with maleic acid by subsequent enhancement in emission intensity and addition of other analogous aliphatic dicarboxylic acids such as fumaric, succinic, adipic, mesaconic and itaconic acids causes no change in the emission spectra; thereby demonstrated its potential use as macrocyclic receptor in sensor applications. Since rectangle 15 is enriched with π-conjugation, it was examined as a fluorescence sensor for electron-deficient nitroaromatics such as picric acid, which is often considered as a secondary chemical explosive. The fluorescence study of 15 showed a significant quenching of initial emission intensity upon titrating with picric acid (PA) and it exhibited the largest fluorescence quenching response with high selectivity for picric acid. Scheme 2: Schematic representation of formation of [2 + 4] self-assembled of molecular tetragonal prism. This chapter also describes two-component coordination [2 + 4] self-assembly of a pyrene-based PtII8 tetragonal prism (16) as shown in Scheme 2, using a newly designed tetratopic organometallic acceptor (M7; 1,3,6,8-tetrakis[trans-Pt(PEt3)2(NO3)(ethynyl)]pyrene) in combination with an amide-based “clip” donor (L2) and propensity of this prism (16) as a selective fluorescence sensor for nitroaromatic explosives has been examined both in solution as well as in thin-film. CHAPTER 4 reports the synthesis and structural characterization of a series of Ru(II)-based bi-and tetra-nuclear metallamacrocycles and hexanuclear trigonal prismatic cages. In principle, the self-assembly of a “clip” acceptor with an asymmetrical ditopic donor is expected to give two different linkage isomeric (head-to-tail and head-to-head) molecular rectangles because of different bond connectivity of the donor. However, the equimolar combination of half-sandwiched p-cymene binuclear Ru(II)-based “clip” acceptors (M8−M9) and an amide-based ambidentate donor (L6) resulted in the self-sorting of single linkage (head-to-tail) isomeric rectangles 17−18 as only products, respectively [M8 = [Ru2(μ-η4-C2O4)(MeOH)2(η 6-p-cymene)2](CF3SO3)2; M9 = [Ru2(μ- η4-C6H2O4)(MeOH)2(η 6-p-cymene)2](CF3SO3)2]. Molecular structures of these head-to-tail linkage isomeric rectangles were unambiguously proved by single crystal X-ray diffraction analysis. Likewise, the self-assembly of oxalato-bridged Ru(II) acceptor M8 with a rigid dipyridyl “clip” donor L8 yielded a tetranuclear cationic pincer complex 19, while a similar reaction of M8 with an anthracene-functionalized “clip” donor L9 having shorter distance (between their reactive sites) compared to L8 led to the formation of [1 + 1] self-assembled macrocycle 20. This chapter also represents the design and synthesis of two hexanuclear trigonal prismatic cages (21−22) from the self-assembly of a π-electron rich tripyridyl donor (L10; 1,3,5-tris(4-pyridylethynyl)benzene) in combination with binuclear acceptors M8 and M9, respectively (Scheme 3). Formation of these prismatic cages was initially characterized using various spectroscopic techniques and the molecular structure of oxalato-bridged prism 21 was confirmed by single crystal X-ray diffraction analysis. In addition to the structural characterization, the pincer complex 19 and trigonal prismatic cages 21−22 were used as fluorescence sensors for nitroaromatic explosives owing to their large internal porosity and their π-electron rich nature. Scheme 3: Schematic representation of the formation of [3 + 2] self-assembled trigonal prismatic cage. CHAPTER 5 covers the syntheses of a few discrete metallamacrocycles using flexible imidazole/carboxylate based donors instead of much widely employed polypyridyl donors. The metal-ligand directed self-assembly of oxalato-bridged acceptor M8 and an imidazole-based tetratopic donor (L11; 1,2,4,5-tetrakis(imidazol-1-yl)benzene) in methanol afforded [2 + 1] self-assembled tetranuclear macrocycle 23. Conversely, the similar combination of L11 with 2,5-dihydroxy-1,4-benzoquinonato-bridged binuclear complex (M9) in 1:2 molar ratio in methanol resulted in an octanuclear cage 24. Both the complexes (23−24) were isolated as their triflate salts in high yields and were characterized by various spectroscopic methods including single crystal X-ray diffraction analysis. Scheme 4: Schematic representation of formation of an octanuclear incomplete Ru(II) open prism via ruthenium-oxygen coordination driven self-assembly. This chapter also explains the self-sorting of an unusual octanuclear incomplete prism [Ru8(η6-p-cymene)8(tma)2(μ-η4-C2O4)2(OMe)4](CF3SO3)2 (25) via ruthenium-oxygen coordination driven self-assembly of building block M8 and sodium benzene-1,3,5-tricarboxylate (L12) (Scheme 4). Electronic absorption study indicated that prism 25 exhibited a remarkable shape-selective binding affinity for 1,3,5-trihydroxybenzene (phluoroglucinol) via multiple hydrogen bonding interactions and such shape-selective binding was confirmed by single crystal X-ray diffraction analysis. (For figures pl see the abstract file)

In recent years a great deal of research has focussed on understanding and exploiting self assembling peptides as they form fibrillar hydrogels for use in a variety of different applications, such as tissue engineering and drug delivery. A particular class of such peptide systems are ionic-complementary peptides, composed of alternating hydrophobic and hydrophilic amino acids. Their simple structure is generally seen to assemble into β sheet rich fibrils, and easy modification of the primary structure is possible to allow the inclusion of recognition motifs tailored for a specific use. This can be done simply via physical mixing. To maximise the potential of such systems it is important to understand the interactions that govern the self-assembly behaviour. Here a variety of different peptides have been studied to elucidate control of peptide conformation and fibril morphology. The ability to easily tune the mechanical strength of the hydrogel has been explored by mixing peptide systems. The peptide FEFEFKFK (FEKII) was seen to assemble into β sheet rich fibrils of ~3 nm in diameter. Control of pH and hence the charge state of the E and K side chains altered sample properties. Gelation at pH 2.8 occurred at a concentration between 20 30 mg ml 1. At pH 4, 5 and 10 where the peptide has a lower net charge gelation was lowered to ~10 mg ml 1. Mechanical properties varied with G' values of 20-1200 Pa as pH was altered. Stronger gels were formed with lower net peptide charge. Hierarchical fibre assembly was observed for positively charged peptides, with fibres forming from lateral association of fibrils. Negatively charged peptides at pH 10 showed no such hierarchical assembly, and lower fibril persistence length. This was related to the change in charge along the fibril structure. At pH 7, where the peptide has no net charge, precipitation occurred. This showed a net charge was required on the peptide to disperse fibrils and prevent aggregation. The work showed the importance of ionic-interactions in determining both network morphology and bulk properties, and also elucidated control of such behaviour. AEAEAKAK (AEKII) was shown to assemble into α helix fibres. Alanine (A) is less hydrophobic than F, and is a known helix former. The role of F and A in assembly was assessed by the design of peptides FEAEFKAK (FAIEKII) and FEFEAKAK (FAIIEKII). Mixing A with F disrupted the peptides' ability to form a β sheet network by lowering the driving force for assembly given by the F residues. Trace amounts of β sheet were observed at low concentration, but at a critical concentration β sheet content increased and gelation occurred. This was found to be pH dependent. FAIEKII formed β-sheet fibrils at a lower concentration than FAIIEKII. While FAIEKII was able to assemble into different fibril structures, FAIIEKII showed no specific aggregation. This not only highlighted the importance of Hydrophobicity as a key driving force to assembly but also how the grouping of these amino acids in the primary sequence can determine the overall assembly characteristics of the peptide. The peptides FEFEFKFKGGFEFEFKFK (FEKII18-1) and FEFEFKFKGGFKFKFEFE (FEKII18-2) were designed to co-assemble with FEKII. Individually both peptides were seen to assemble into β sheet fibrils. FEKII18-1 formed fibrils of 2.3 3.1 nm in size, a result of folding along the chain caused by intra molecular attractive ionic interactions. FEKII18-2 formed larger fibrils of 4.4 5.2 nm from a straightened peptide chain given by the change in charge distribution. When co assembled with FEKII mechanical properties were enhanced, with G' increasing from 40 Pa at 20 mg ml 1 to 2400 Pa, depending on the concentration of FEKII18-1/FEKII18-2 added to the system. This was a result of these peptides providing fibril connections acting as cross links. This work has detailed control over the assembly process via peptide conformation and fibril interactions and the effect this has on overall macroscopic sample properties. This is vital in determining the viability of such systems in various biomedical applications.

Transition metals complexes have been involved in various catalytic, biomedical and industrial applications, but only lately they have been associated with nanomaterials to produce innovative and well-defined new hybrid systems. The introduction of transition metals into nanomaterials is important to bear the advantages of metals to nanoscale and also to raise the stability of nanomaterials. In this dissertation, we study two approaches of associating transition metals into nanomaterials. The first approach is via spontaneous self-organization based assembly of small molecule amphiphiles and bulky hydrophilic polymers to produce organic-inorganic hybrid materials that have nanoscale features and can be precisely controlled depending on the experimental conditions used. These hybrid materials can successfully act as templates to design new porous material with interesting architecture. The second approach studied is via electroless reduction of transition metals on the surface of nanocarbons (nanotubes and nanodiamonds) without using any reducing agents or catalysts. The synthesis of these systems is highly efficient and facile resulting in stable and mechanically robust new materials with promising applications in catalysis.