abstract: Deoxyribonucleic acid (DNA) has emerged as an attractive building material for creating complex architectures at the nanometer scale that simultaneously affords versatility and modularity. Particularly, the programmability of DNA enables the assembly of basic building units into increasingly complex, arbitrary shapes or patterns. With the expanding complexity and functionality of DNA toolboxes, a quantitative understanding of DNA self-assembly in terms of thermodynamics and kinetics, will provide researchers with more subtle design guidelines that facilitate more precise spatial and temporal control. This dissertation focuses on studying the physicochemical properties of DNA tile-based self-assembly process by recapitulating representative scenarios and intermediate states with unique assembly pathways. First, DNA double-helical tiles with increasing flexibility were designed to investigate the dimerization kinetics. The higher dimerization rates of more rigid tiles result from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. Next, the thermodynamics and kinetics of single tile attachment to preformed “multitile” arrays were investigated to test the fundamental assumptions of tile assembly models. The results offer experimental evidences that double crossover tile attachment is determined by the electrostatic environment and the steric hindrance at the binding site. Finally, the assembly of double crossover tiles within a rhombic DNA origami frame was employed as the model system to investigate the competition between unseeded, facet and seeded nucleation. The results revealed that preference of nucleation types can be tuned by controlling the rate-limiting nucleation step. The works presented in this dissertation will be helpful for refining the DNA tile assembly model for future designs and simulations. Moreover, The works presented here could also be helpful in understanding how individual molecules interact and more complex cooperative bindings in chemistry and biology. The future direction will focus on the characterization of tile assembly at single molecule level and the development of error-free tile assembly systems. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

abstract: As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA nanotechnology which is the main topic of this dissertation. The ability of rationally designed DNA strands to self-assemble into arbitrary nanostructures without external direction is the basis of this field. A series of novel design principles for DNA nanotechnology are presented here, from topological DNA nanostructures to complex and curved DNA nanostructures, from pure DNA nanostructures to hybrid RNA/DNA nanostructures. As one of the most important and pioneering fields in controlling the assembly of materials (both DNA and other materials) at the nanoscale, DNA nanotechnology is developing at a dramatic speed and as more and more construction approaches are invented, exciting advances will emerge in ways that we may or may not predict. / Dissertation/Thesis / Ph.D. Chemistry 2012

This dissertation presents new insight into the ability of small molecule passivated NCs to achieve intimate approach distances, despite being well passivated, while developing guiding principles in the area of ligand mediated microstructure control and the resulting macroscopic optical and electronic properties that close packing of high quality NCs enables. NC ligand coverage will be characterized quantitatively through thermogravimetric analysis (TGA), and qualitatively by photoluminescence and electroluminescence, in the case of functional devices; illustrating the importance of practitioner dependent control of ligand coverage through variations in the dispersion precipitation purification procedure. A unique examination of the relative contribution of energy and charge transfer in NC LEDs will demonstrate the ability to achieve charge transfer, at a level competitive with energy transfer, to well passivated NCs at various wt% loading in a polymer matrix. The observation of potential dependent recombination zones within an active layer further suggest novel, NC surface passivation mediated control of blend microstructure during solution processing towards the development of a bi-continuous network. Next, NC self-assembly and resulting microstructure dependent optical and electronic properties will be examined through electroluminescence and high-resolution transmission electron microscopy (TEM) micrographs of functional NC/polymer bulk heterojunction LEDs. The joint characterization of NC optical properties, and self-assembly microstructure provide a deeper understanding of the significant and inseparable effects of minimal changes in NC surface passivation on structure and function, and emphasize the potential to rely on strongly passivating ligands to control physical properties and processing parameters concurrently towards higher efficiency devices via low cost processing. Finally, micro-contact printing of blazed transmission gratings, using stable dispersions of core and core/shell NCs will be shown to produce close packed assemblies of NCs forming near-wavelength luminescent superstructures separated in space. We show the dominant contribution of a two-monolayer thick sharp interface CdS shell to the diffraction efficiency, and necessarily the refractive index, of the NCs, independent of core size. Utilization of these gratings as in-coupling elements at various positions within a device architecture are also examined. These new observations were achieved by unprecedented control of NC architecture during dispersion processing, while maintaining high luminescence, made possible by optimized NC surface passivation. These studies enable the formation of new LED architectures, and new optoelectronic devices based on angle resolved, monochromatic fluorescence from diffraction gratings prepared from simple solution processing approaches. Further, the novel observation of angle amplified interfering fluorescence from these features is argued to be a result of long range radiative coupling and superradiance enabled by the monodispersity and high-quality NC surface passivation described herein.

A number of compounds were synthesized with the ultimate goal being the synthesis of C₂ symmetric molecules which displayed thermotropic liquid crystalline behaviour. The compounds prepared were 4-alkoxy benzophenones, 3,4-bis-alkoxy benzophenones, 4- alkoxy dibenzylidene acetones, 3,4-bis-alkoxy dibenzylidene acetones and 4-alkoxy- 1, 9-diphenyl-nona-l,3,6,8-tetraen-5-ones. The length of the linear alkoxy side chain was varied from C₆H₁₃ to C₁₂H₂₅. All compounds were characterized by FTIR, ¹H, and ¹³C NMR spectroscopy. Mesophase behaviour of the synthesized compounds was investigated using differential scanning calorimetry and polarizing optical microscopy. It was determined that both the alkoxy side chain length, as well as the number of alkoxy side chains have an effect on the ability of this class of C₂ symmetric compounds to selfassemble into liquid crystalline phases. In addition, the overall core size and extent of conjugation also affected mesophase formation. The mono-alkoxy benzophenones and dibenzylidene acetones were non-mesogenic, while all four of the mono-alkoxy 1,9- diphenyl-nona-l,3,6,8-tetraen-5-ones (alkoxy side chain of lengths C₆H₁₃, C₈H₁₇, C₁₀H₂₁ and C₁₂H₂₅)self-assembled into nematic liquid crystalline phases. Increasing the number of alkoxy side chains from one to two per aromatic moiety helped induce liquid crystalline formation: the corresponding bis-C₆H₁₃ benzophenone and bis-C ₆H₁₃, bis C₈H₁₇, and bis-C₁₀H₂₁ dibenzylidene acetones were mesogenic, displaying smectic A (benzophenone) and nematic (dibenzylidene acetone) mesophases respectively. / Forestry, Faculty of / Graduate

Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / This dissertation describes the application of fluorescence microscopy techniques to investigations of mass transport phenomena in self-assembled nanomaterials. The microscopic morphologies of the materials and the mass-transport dynamics of probe molecules dispersed within them were assessed with high temporal and spatial resolution by single molecule imaging and spectroscopic methods. Three distinct sets of experiments were performed in completing the work for this dissertation. In the first study, single molecule imaging was employed to explore the interactions and field-induced migration of double-stranded DNA (ds-DNA) molecules with nanostructured Pluronic F127 gels. While DNA interactions with nanostructured gels have been explored in the past, none had apparently looked at these interactions in gels comprising hexagonally ordered arrays of cylindrical micelles. Therefore, these studies focused on materials DNA dispersed in flow aligned hexagonal F127. DNA molecules were found to be strongly confined in the hexagonal mesophase structures from their elongation, alignment, and exclusively occurred electrophoretic migration in the direction parallel to the cylinder long axis. These observations will lead to a better understanding of macromolecular interactions with nanostructured gels like those now being investigated for use in drug delivery and chemical separations. In the second study, imaging-fluorescence correlation spectroscopy (imaging-FCS) was used to study the rate and mechanism of sulforhodamine B (SRB) dye within novel bolaamphiphile-based self-assembled nanotubes. These nanotubes were only recently developed and their mass transport properties remain largely unexplored. The nanotubes employed here are unique because they incorporate amine groups and glucose groups on their inner and outer surfaces, respectively. Wide-field fluorescence video microscopy was first applied to locate and image dye-doped nanotubes dispersed on a glass surface. Imaging-FCS was employed as it allows for the dynamics to be recorded simultaneously from a large sample region, thus the SRB mass transport within nanotubes can be spatially resolved. The coulombic interactions between cationic ammonium ions on the inner nanotube surface and the anionic SRB molecules was shown to play a critical role in governing dye dynamics under varied pH and ionic strength conditions. Mass transport of SRB within the nanotubes is concluded to occur by a desorption-mediated Fickian diffusion mechanism. In the third set of experiments, solvatochromic dye molecules were employed in novel imaging-FCS studies of the role played by partitioning in governing mass transport phenomena within the same organic nanotubes used above. Two forms of the solvatochromic dye Nile Red (NR) were employed: the commercial hydrophobic form of NR, and a more polar derivative 2-hydroxybenzophenoxazinone (named NR-OH). The partitioning of dye molecules within the nanotubes was investigated assessing the diffusion rate for each dye. The preliminary results suggested NR and NR-OH preferentially partitioned into the tube walls and the ethanol phase filling the tubes, respectively. The diffusion coefficient data indicated NR-OH diffused faster than NR, consistent with the presence of NR-OH in a relatively less viscous environment (e.g., the ethanol phase filling the tubes). The results of these studies afford information essential to the use of organic nanotubes in controlled drug release and possibly in catalysis applications.

Stepwise covalent synthesis of large molecules is often time consuming and laborious and thus generally ends in a low yield of the target product. It is also difficult to achieve a large desired product where the controlling force is a non-directional weak interaction. Instead, by utilizing stronger metal-ligand directional coordination bonding approach, one can easily prepare the desired large molecules using appropriate molecular units. Further attractive feature of this approach is the incorporation of functional groups into final structures to make the assemblies functional. It is found that symmetrical polypyridyl and rigid linkers have been used widely in the construction of finite supramolecules of Pd (II) and Pt(II). Flexible linkers are rarely used since they are less predictable in self-assembly and have a tendency to form undesired polymer. However, flexible linkers may generate pseudo rigid assemblies that can distort their shapes to obtain a more thermodynamically stable conformation for host-guest interactions. Similarly, use of non-symmetric or ambidentate linkers is not explored much. These linkers may generate a mixture of several linkage isomeric products and thus difficult to monitor the reaction. Moreover, isolation of these products in pure form is also a challenging task. On the other hand, recent research revealed that porous polyacetylene organic compounds are suitable sensors for the detection of electron deficient nitroaromatics, which are the chemical signatures of many commercial explosives. Possibility of discrete supramolecules as sensors for these explosives is very less studied. The main thrusts of the present investigation are to incorporate flexible and nonsymmetrical linkers in the construction of finite discrete assemblies of Pd/Pt; and to design appropriate π-electron rich supramolecules as sensors for the detection of electron deficient nitroaromatics. Chapter 1 of this thesis gives a brief introduction to the supramolecular chemistry. It also gives a brief introduction to the design principle of metal-ligand coordination driven selfassembly approach towards the generation of large architectures. Chapter 2 reports the synthesis of a series of two-dimensional supramolecular architectures via coordination driven self-assembly of Pt/Pd containing ditopic acceptors and non-symmetrical donor ligands. The use of non-symmetrical donor ligands in coordination driven self-assembly is a challenging task because they may generate a mixture of isomers due to different connectivity of the non-symmetric (ambidentate) linkers. But in all the cases exclusive formation of a single linkage isomer was established. Na-nicotinate was treated with [cis-(dppf)Pd(OTf)2] to yield [(dppf)3Pd3(L3)](CF3SO3)3(H2O)2(MeOH)7(Et2O) as the single linkage isomeric triangle. An analogous treatment using Na-isonicotinate instead of Na-nicotinate yielded a mixture of single isomeric square and triangle with the later one as the major product in solution. Further extension of this study using cis-(tmen)Pd(NO3)2 instead of [cis-(dppf)Pd(OTf)2] also showed the formation of a mixture of square and triangle [tmen = N,N,N’,N’- tetramethylethane-1,2-diamine]. Surprisingly, in both the cases square was the product which was crystallized exclusively in solid state though triangle was the major component in solution. The square-triangle equilibria in both the cases were studied by diffusion ordered NMR spectroscopy (DOSY) and variable temperature multinuclear NMR. Moreover, this chapter reports the incorporation of amide functionality into a Pt(II) nanoscopic molecular rectangle via self-assembly of an organometallic “clip” and a non-symmetric amide ligand. Chapter 3 presents synthesis of several metallamacrocycles via coordination driven selfassembly using Pd/Pt-P bonding interaction as driving force instead of much widely used Pd/Pt-N bonding interaction. It is also established that Pd/Pt-P bonding interaction is indeed better than the widely used Pd/Pt-N interaction. Several macrocycles were also synthesized by the combination of several Pd containing 90° angular subunits and a bisimidazole ditopic flexible donor. In this case also the bonding interaction between the imidazole and Pd(II) was found to be stronger than the interaction between pyridyl donor and Pd(II). Chapter 4 describes synthesis of several new Pt2 and Pt3 shape selective organometallic linkers incorporating ethynyl functionality. The Pt2 molecular clip was assembled with several linear dipyridyl linkers to prepare a series of molecular rectangles. In one case N, N’-bis(4-pyridylidene)ethylenediamine was used as donor to create a N4 pocket in the macrocycle. This rectangle was fluorescent in nature and showed efficient fluorescence quenching in solution upon binding of hard transition metal ions (Fe3+, Cu2+ and Ni2+) into the N4 pocket. The non-responsive nature of the fluorescence quenching upon addition of soft metal ions (Zn2+ and Cd2+) containing d10 configuration makes it an interesting example of sensor for transition metal ions. The Pt3 linkers were used in combination with organic clip-type linkers to prepare a series of molecular prisms by [2 + 3] self-assembly (Scheme 1). Incorporation of ethynyl functionality helped to make the resulting supramolecules π-electron rich and luminescent in nature. Possibility of these supramolecules as sensors for the detection of electron deficient nitroaromatics (TNT and picric acid), which are the chemical signatures of explosives has been explored. A complementary approach was also used to prepare trigonal prism using organic tritopic donor and the Pt2 molecular clip. Chapter 5 presents the design and self-assembly of two new flexible supramolecular nanoballs. These assemblies incorporate two flexible tritopic amide/ester based building blocks and were prepared in excellent yields (96-97%) via coordination driven selfassembly. The first one was resulted from the reaction of four equivalents of a new tritopic ester ligand N, N', N''-tris(4-pyridylmethyl) trimesic ester with three equivalents of C4 symmetric Pd(NO3)2. The second analogous structure was obtained by the selfassembly of the flexible N, N', N''-tris(3-pyridylmethyl)trimesic amide and Pd(NO3)2. The assemblies were characterized with multinuclear NMR spectroscopy, electrospray ionization mass spectroscopy, elemental analysis and TGA. The ester based ball showed the inclusion of NEt4 + in solution. This chapter also describes the exclusive formation of a Pt(II) trigonalbipyramidal (TBP) cage upon the treatment of a Pt(II) 90° acceptor with a new tripodal flexible ligand containing ester functionality. The formation of Pt(II) TBP cage in this case is due to the flexibility of the donor arms of the ligand due to the presence of flexible ester functional group. In continuation of this work, a rigid tripodal ligand 1,1,1-tris(4-pyridyl)COOR with an ester cap [where R = Ph-CH(C2H5)] was assembled with cis-(PEt3)2Pt(OTf)2 to yield a somewhat unusual double-square cage by [4 + 6] self-assembly.

Aromatic peptide amphiphiles that self-assemble in response to a trigger, such as pH or enzymes, have the ability to support the culture of somatic cell types, in both two-dimensional (2D) and three-dimensional (3D) culture. Although a fully defined synthetic substrata is required for the successful clinical applications of Embryonic Stem (ES) cells hydrogels of SA aromatic peptide amphiphiles have not been investigated for this purpose. The aim of this investigation is to produce alkaline phosphatase (AP) triggered hydrogels as a substratum for ES cell culture. This SA trigger was chosen as it utilizes inherent biological processes, through the enhanced AP activity of ES cells, with SA occurring in otherwise constant conditions. We also sought to overcome the current inability to consistently control ES cell behaviour in vitro through two different routes that have previously been demonstrated to effect stem cell culture. Firstly, control of the hydrogels mechanical properties and secondly through the incorporation of biological function, principally through the addition of glycosaminoglycans (GAGs). Firstly AP triggered hydrogels of 9-fluorenylmethoxycarbonyl-Tyrosine-OH (Fmoc-Y-OH) were studied and compared with those formed by pH trigger. An unexpected relationship between AP concentration and molecular order was detected. It was observed that the hydrogels stiffness was controlled through the AP concentration; ideal for ES cell culture as Engler et al. (2006) has previously demonstrated the effect material stiffness had on the differentiation pathways chosen by mesenchymal stem cells. Differences between the SA trigger were detected with the hydrogels formed by pH trigger exhibiting significantly lower mechanical properties. This was attributed to the SA process and the disorder that arises from forming all of the hydrogelators instantaneously. The SA process of AP triggered Fmoc-Y-OH showed a 4 stage process. The first stage, dephosphorylation, occurred in a time and AP concentration dependent manner. The second stage transpired due to the spontaneous SA of Fmoc-Y-OH providing a temporary change in fluorenyl environment. The final stages, formation of chiral one dimensional (1D) fibres through proposed -β interactions and gelation through the entanglement of fibres are closely linked. Secondly we investigated AP triggered Fmoc-Phenylalanine-Tyrosine-OH (Fmoc-FY-OH) hydrogels in two distinct physiological environments. When formed in buffer (0.15M, pH 7) an optimum AP concentration was observed in terms of molecular interactions, -β interactions, which translated to the hydrogels mechanical properties. In these conditions helical fibres were imaged by AFM. The second medium for SA was KnockOUT™ DMEM, developed for ES cell culture. Although similarities in the molecular interactions were detected it appears the SA environment effects the structures formed with non-helical fibres imaged. GAGs were successfully incorporated into the hydrogels at biologically relevant levels at the extremes of sulphation. The sulphation patterns of the GAGs secreted by ES cells changes during differentiation and may provide a way to guide cell behaviour through growth factor binding. However the GAGs were not entrapped in the fibre network and leached out into solution limiting their ability to guide ES cell behaviour. Unfortunately both of the hydrogels produced in this study were deemed unsuitable as ES cell substrata due to their instability (Fmoc-Y-OH) or low biocompatibility (Fmoc-FY-OH). However we have demonstrated that it was possible for endogenous AP to trigger SA, indicating that in the future ES cells may be able to form their own substrata preventing the need for exogenous AP.

Two series monodispersed nanoparticles of hydroxylpropyl cellulose (HPC) and functionalized poly-N-isopropylamide (PNIPAM) particles have been synthesized and used as building blocks for creating three-dimensional networks, with two levels of structural hierarchy. The first level is HPC nanoparticles were made from methacrylated or degradable cross-linker attached HPC. These nanoparticles could be stabilized at room temperature by residual methacrylate or degradable groups are present both within and on the exterior of HPC nanoparticles. Controlled release studies have been performed on the particle and networks .The nearly monodispersed nanoparticles have been synthesized on the basis of a natural polymer of hydropropylcellulose (HPC) with a high molecular weight using the precipitation polymerization method and self-assembly of these particles in water results in bright colors. The HPC nanoparticles can be potential using as crosslinkers to increase the hydrogels mechanical properties, such as high transparency and rapid swelling/de-swelling kinetics. The central idea is to prepare colloidal particles containing C=C bonds and to use them as monomers - vinylparticles, to form stable particle assemblies with various architectures. This is accomplished by mixing an aqueous suspension of hydrogel nanoparticles (PNIPAM-co-allylamine) with the organic solvent (dichloromethane) to grow columnar crystals. The hydrogels with such a unique crystal structure behavior not only like the hydrogel opals, but also have a unique property: anisotropy.

Membrane technology is one of the most promising technologies for addressing the global water crisis as well as in many other applications. One of the drawbacks of current ultra- and nanofiltration membranes is the relatively broad pore size distribution. Block copolymer membranes with ultrahigh permeability and very regular pore sizes have been recently demonstrated with pores being formed by the supramolecular assembly of core/shell micelles. Our study aimed at developing an innovative and economically efficient alternative method to fabricate isoporous membrane by self-assembly of magnetic nanoparticle with a polystyrene shell, mimicking the behavior of block copolymer micelle. Fe3O4 nanoparticles of ~13 nm diameter were prepared by co-precipitation as cores. The initiator for ATRP was covalently bonded onto the surface of magnetic nanoparticles with two strategies. Then the surface initiated ATRP of styrene was carried out to functionalize nanoparticles with polystyrene through a “grafting from” method. Finally, the nanocomposite membrane was cast from 50 wt % Fe3O4@PS brush polymer solution in DMF via non solvent phase inversion. Microscopies reveal an asymmetric membrane with a dense thin layer on top of a porous sponge-like layer. This novel class of asymmetric membrane, based on the pure assembly of functionalized nanoparticles was prepared for the first time. The nanoparticles are well distributed however with no preferential order yet in the as-cast film.I would like to thank my committee chair and advisor, Prof. Suzana Nunes, and other committee members, Prof. Klaus-Viktor Peinemann and Prof. Gary Amy, for their guidance and support throughout the course of this research. My appreciation also goes to my colleagues in our group for useful discussions and suggestions. I also want to extend my gratitude to the staff from the KAUST Core Lab for Advanced Nanofabrication, Imaging and Characterization, especially Dr. Ali Reza Behzad, Dr. Rachid Sougrat, and Dr. Long Chen, for their assistance for various microscopy measurements. Finally, my heartfelt gratitude is extended to my parents and all my friends. I cannot finish this thesis without their encouragement and support.

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