School of Chemistry - Theses
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Investigation of optically transparent non-wetting coatings
Surfaces that exhibit extreme non-wettability are the result of the combination of surface chemistry and a high degree of roughness. Typically, such materials are visibly opaque, predominantly due to the enhanced light-scattering from the rough interfaces. In the present study, particle-based coatings with carefully controlled surface and bulk roughness parameters are investigated in multiple length scales to identify conditions under which extreme surface-phobicity and visible transparency can coexist. Visibly transparent micron-thick fumed silica nanoparticle (7–40nm) seeded sol-gel coatings were fabricated. Nano-scale surface and bulk features with varying degrees of water-repellency (hydrophobicity) were correlated with visible optical transparency. Furthermore, alternative tuneable hollow silica spheres in the sub- micron scale range were utilised to create a finely detailed range of roughness, which simultaneously changes both the refractive index through lowering relative optical permittivity and film density, and the surface wettability. Surface morphology and roughness of individual samples were examined in detail using atomic force microscopy, non-contact optical profilometry, scanning electron microscopy and synchrotron-based small-angle X-ray scattering (SAXS) in transmission mode. The latter was employed to investigate the nano-scaled common length scale (repeating) features in the coating. Coatings consisted of hierarchically ordered structures similar to fractals, with nano-scale (12–30nm) features superimposed on top of larger (200–400nm) sub-micron features displaying coexistence of optical transparency and water repellency. Extended surface studies were achieved by sputtering a thin (8–15nm) layer of sputter-coated Cr metal, which enhanced the surface X-ray scattering. Coatings fabricated using colloidal fractals with enrichment of both nano (20–30nm) and sub-micron (50–270nm) length scale on its surface structure displayed an enhancement to the roughness-induced water-repellency behaviour. Analysis of the bulk features alone was performed through the cross-sectional imaging under dual- beam FIB/SEM. Visible optical transparency in the film required nanoparticle cluster size to be between 130–180nm in length, to minimise the scattering of visible light. Alternatively, through the manipulation of the size of hollow core and silica shell thickness, the optical transparency at specific wavelengths of visible light correlated to the size of hollow silica spheres is enhanced without the loss of roughness. Hollow silica spheres within the sub-micron length scale (300–700nm) provide an alternative system for fabricating roughness-induced optically transparent non-wettable coating.
Supramolecular Assemblies of Cyclotricatechylene
This thesis presents the results of synthetic and structural investigations of novel cyclotricatechylene-based supramolecular assemblies. Cyclotricatechylene is a bowl-shaped tris-catechol that has been shown to associate with other chemical species through hydrogen bonding and metal coordination. The research focuses on the synthesis and characterisation of novel crystalline supramolecular assemblies of cyclotricatechylene. The compounds described in the four experimental chapters include assemblies of cyclotricatechylene and its related anions with s, p, d and f-block elements of the periodic table. The compounds have been characterised X-ray crystallography. Synthetic and structural investigations of compounds formed from the combination of cyclotricatechylene with s-block metal cations reveal a diverse array of network materials, with cyclotricatechylene in various protonation states. The s-block cations are commonly found to associate with the oxygen atoms of the ligand, however Rb+ and Cs+ also exhibit an affinity for the inner and outer aromatic surfaces of the ligand. Two compounds containing cyclotricatechylene ‘clams’, H[Cs(ctcH5)(ctcH5)] and [Cs(ctcH6)2]+ are reported, in which cyclotricatechylene is found in different protonation states. In these compounds, the large group 1 metal cation Cs+ associates with the electron-rich aromatic surfaces of the cyclotricatechylene bowls, an interaction present in many structures described in this thesis. Metal-cyclotricatechylene polymeric structures are reported, in which s-block metal cations are chelated by catechol(ate) oxygen atoms. These structures include 2D sheets containing Ca2+, Sr2+ and Ba2+ cations, [Cs2Li4(ctcH3)4]6- metallocycles that hydrogen bond to each other to form a 3D network that has the topology of diamond, undulating ‘honeycomb’ networks with Cs+ or Rb+, and a 3D network with the topology of the (10,3)-a net, containing Cs+ in cyclotricatechylene bowls and Sr2+ chelated by catecholate units. Four high-symmetry cubic structures formed from the specific combination of cyclotricatechylene with Cs+ or Rb+, K+, acetone, water and an oxyanion contain metallocubes of formula [K4(ctcH6)4(H2O)8]4+. The assemblies are arranged in a symmetrical manner, which reflects high level of complementarity in these crystalline supramolecular assemblies. The combination of cyclotricatechylene with vanadyl or uranyl units leads to the formation several large, anionic coordination ‘cage’ assemblies with fully deprotonated cyclotricatechylene. An aesthetically pleasing example is an assembly with trigonal prismatic geometry, of formula [(VO)9Cs6(ctc)6]18-, in which vanadyl oxo groups are directed both into and out of the cage. Systems containing the uranyl cation (UO22+) were found to exhibit considerable structural diversity that can be attributed to the formation small clusters of uranyl cations with oxo, hydroxo, peroxo and aqua ligands. The co-precipitation of uranyl-based side products provides significant challenges with respect to the characteristion of these materials. A robust tetrahedral assembly of cyclotricatechylene with silicon, [(PhSi)6(ctc)4]6-, was found to be identical in topology to, but much easier to characterise than, its d-block metal analogues. Unlike geometrically similar metal-based cages, all bonds within the anionic assembly are covalent. The cage has been shown to persist in the gas phase and also when crystals of the compound are boiled in water. The crystalline material can also uptake Cs+ cation guests, which occupy the bowls of the tetrahedra.
Development and application of theoretical models for molecular magnetism
My thesis consists of two projects. In the first, I have worked on the development of scalar relativistic and spin-orbit coupling methods within the ab-initio framework of the package CERES, developed in our group. In the other project, I have explored for the possibility of attaining toroidal moments in magnetic rings with weak or zero spin-orbit coupling. I managed to theoretically identify entirely new families of molecules that have a degenerate ground state where it is possible to prepare a purely toroidal quantum state. In Project 1, I have implemented the Douglas Kroll Hess method of 2nd order in the quantum chemistry code CERES to incorporate the scalar relativistic effects. I have also explored approximations to the Breit-Pauli Hamiltonian and found that the bare one-electron operator is often sufficient to obtain reasonably good crystal field energy levels within the lowest spin-orbit multiplet. I also present a comparison between different mean-field approximations for incorporating the two-electron terms. In Project 2, I have theoretically investigated new spin-frustrated molecular triangles that show the first known example of a toroidal quartet, composed of two degenerate toroidal doublets, solely as a consequence of spin-frustration, and despite having no spin-orbit coupling. Finally, I have generalized these findings to extended odd-membered ring and managed to identify infinite families of molecular rings that show a ground multiplet composed of one or more toroidal doublets.
Porous coordination polymers for the capture of simple gases and environmentally harmful emissions
The thesis describes a synthetic and structural investigation of coordination polymers in addition to an analysis of their adsorption properties. In chapter 2 the synthesis and structure of Li+ based network materials are described. An open-type network of composition Li(paa)DMF (Hpaa = (2E)-3-(pyridine-4-yl)prop-2-enoic acid) was successfully synthesised. Exposure to the atmosphere, however, resulted in the material redissolving into mother liquor. Crystals of a dense Li(paa) network subsequently separated from the solution. Open-type frameworks have yet to be generated using the longer peb- (Hpeb = 4-[(E)-2-(pyridin-4-yl)ethenyl]benzoic acid) ligand. The coordination environment of Li+ ions in [Li2(peb)(H2O)7](peb)H2O is dominated by water molecules whilst the presence of a coordinated DMSO molecule in Li(peb)DMSO prevents the formation of channels. In chapter 3 the synthesis and structures of five framework materials analogous to Zn(hba) (H2hba = 4-hydroxybenzoic acid) are reported. The single crystal X-ray diffraction data of the structures are of poor quality, with broad streaky diffraction spots and low resolution, however X-ray powder diffraction unambiguously confirms that all frameworks adopt the same topology to that of Zn(hba). The tetrafluoro hba2- ligand did not form Zn(hba)-type frameworks. Instead two dense frameworks, Zn2(tetrafluoro hba)(OAc)2 and Zn(tetrafluoro hba)(MeOH)MeOH, were formed. Zn2(tetrafluoro hba)(OAc)2 is formed when Zn(OAc)2 is combined with tetrafluoro hba2- while Zn(tetrafluoro hba)(MeOH)MeOH is formed when Zn(SiF6) is used instead of Zn(OAc)2. Attempts to synthesise Zn(hba) family like frameworks with ligands related to cma2- (H2cma = (2E)-3-(4-Hydroxyphenyl)prop-2-enoate) have proven unsuccessful to date with the ligands HhpOa- and HhpHNa- (H2hpOa = 4-hydroxyphenoxyacetic acid and H2hpHNa = N-(4-Hydroxyphenyl)glycine) chelating to metal centres. The HhpOa- ligand formed a relatively simple mononuclear complex with Cu2+. The complexes participate in extensive hydrogen bonding resulting in a 3D hydrogen bonded network. The combination of HhpHNa- ligands with Zn2+, results in binuclear Zn2+ clusters, bridged by HhpHNa- ligands to form chains. These chains are linked through phenol-phenol and phenol-carboxylate hydrogen bonds to give a 3D hydrogen bonded network. In chapter 4 and 5 the sorption properties of the Zn(hba) family of networks are reported. The networks are robust and exhibit the capability of adsorbing a variety of small molecules including the gases N2, CH4, CO2, H2 and the anaesthetics, isoflurane, sevoflurane, xenon and nitrous oxide. The smaller non-intersecting channels in the Zn(hba) family of networks lead to lower overall gas uptake capacity, although the adsorption of gases at 100 kPa is comparable to MOF materials that do not possess open metal sites. Collaboration with Prof Cameron Kepert and Dr Peter Southon from the University of Sydney showed that Zn(hba) is capable of capturing significant quantities of sevoflurane and isoflurane well below the concentration of the anaesthetics exhaled by patients. Thermogravimetric analysis revealed that Zn(hba) is capable of retaining approximately 83% of captured isoflurane below 60 degrees Celsius. A prototype anaesthetic capture device was shown to capture 74% of the anaesthetic passed through an anaesthesia machine. The sevoflurane that was captured by the host in theatre was then transported to the candidate’s laboratory and separated from the host network by application of gentle heating under vacuum. The sevoflurane vapour was then condensed by cooling. The isolated sevoflurane was then characterised by NMR.
Ultrasonic emulsification in biopolymer complex emulsion systems
An emulsion is a colloidal mixture of two immiscible liquids, in which one is dispersed into another with the help of shear forces and the presence of surface-active compounds. The range of applications for emulsions is enormous, with emulsions found in industries such as food, cosmetics, medicine and petrochemicals. Understanding how to control the physical properties of emulsions has been a long-standing research challenge. In particular, the ability to achieve long-term stability of emulsions is of great significance in many practical applications. The physical stability of emulsions can be improved with a reduction in the droplet size of the dispersed phase, which is determined by the extent and intensity of the emulsification process and the associated balance between droplet breakup and coalescence. High-intensity low-frequency ultrasound (US) is a promising high-shear emulsification method that leverages the physical effects created by acoustic cavitation. Biopolymers are naturally occurring polymers that have many applications in food and personal care products. In particular, biopolymer emulsions are found in many daily products. The ability to tailor the physical properties of such emulsions, including texture, stability and flow behaviour, is a focus of much research and development. Emulsions are commonly fluid suspension, however they can also undergo a solution-gel transition, greatly altering the macroscopic texture into a semi-solid material. Emulsion gel formation has been reported in the literature, however, little is understood about the role of the emulsification process, in particular, associated turbulent flow, on the mechanisms on emulsion gel transition. In this thesis, ultrasonic emulsification involving complex biopolymer systems has been studied. The thesis presents new fundamental understandings of this process, in particular the effect of the turbulent environment on biopolymer emulsion gel formation. This understanding has been used to develop a novel type of emulsion gel, for which the formation mechanism has been investigated and described. A novel demulsification technology has been also developed for enhanced oil separation from biomass systems. The basic concepts underlying emulsions, emulsification and biopolymers are introduced first introduced in Chapter 1 along with fundamentals of US and sonochemistry. In Chapter 2, a detailed review of the literature is presented describing the current understanding of emulsification in turbulent flows, the mechanism and control of ultrasonic emulsification, the mechanism of colloidal sol-gel transition in biopolymer emulsion systems, and flow-induced phase inversion. Additional attention is given to literature on casein micelles and dairy emulsion, as this was the system explored in most detail experimentally in the thesis. Knowledge gaps in the literature are identified and the research aims and thesis scopes placed into this context. The experimental details, including materials, methodologies and analytical techniques are presented in Chapter 3. The experimental research results are presented and discussed in Chapter 4 to 6. In Chapter 4, three essential experimental parameters in the ultrasonic emulsification process, namely sonication time, acoustic amplitude and processing volume, are individually investigated, theoretically and experimentally, and correlated to the emulsion droplet sizes produced. The results show that with a decrease in droplet size, two kinetic regions can be separately correlated prior to reaching a steady-state droplet size: a fast size reduction region and a steady-state transition region. In the fast size reduction region, the power input and sonication time can be correlated to the volume-mean diameter by a power-law relationship, with separate power-law indices of -1.4 and -1.1, respectively. A proportional relationship is found between droplet size and processing volume. The effectiveness and energy efficiency of droplet size reduction has been compared between US and high-pressure homogenisation (HPH) based on both the effective power delivered to the emulsion and the total electric power consumed. Sonication could produce emulsions across a broad range of sizes, while high-pressure homogenisation is able to produce emulsions at the smaller end of the range. For ultrasonication, the energy efficiency is higher at increased power inputs due to more effective droplet breakage at high US intensities. For HPH the consumed energy efficiency is improved by operating at higher pressures for fewer passes. At the laboratory scale, the US system requires less electrical power than HPH to produce an emulsion of comparable droplet size. The energy efficiency of HPH is greatly improved at large scale, which may also be true for larger-scale ultrasonic reactors. In Chapter 5, shear-induced emulsion gel formation has been demonstrated for the first time in a micellar casein emulsion system subjected to micro-turbulent environments created by ultrasonication and high-pressure homogenisation. Importantly, the emulsion and gel-like properties are stabilised solely by the casein micelles in combination with the droplet packing structure, circumventing the usual requirement for chemical surfactants and stabilisers. The mechanism of shear-induced emulsion gel formation has been investigated experimentally in relation to the roles of casein micelles, oil fraction and shear environments, and discussed in relation to existing theories. Based on this, the mechanism of gel formation has been proposed as a novel colloidal packing phenomenon, triggered by the formation of droplet breakup under micro-turbulent environments, which results in fractal packing of droplets and casein micelles over three orders of magnitude from 10-1 to 101 micron. In Chapter 6, the proposed mechanism underlying the shear-induced formation of casein micelle emulsion gels has been extended to other systems by providing a more general explanation on a fundamental level. The effect of micellar casein concentration on the sol-gel transition is investigated to reveal a shear- and concentration-dependency and non-monotonic rheological behaviour. A successful imaging protocol is developed to examine the in-situ interfacial rearrangement of micellar casein. The method involved substituting food oils with a volatile solvent, so that both the oil phase and water can be removed and the micellar bridging network inspected in detail by scanning electron microscopy. A large degree of interfacial deformation of micellar casein has been observed, from spheres to discs, which were further inter-connected to form cellular protein 3D networks. The combination of emulsion microstructure and the rheological profiles could be simply explained by the established sol-gel transition models in colloidal suspension systems. Rather, these experimental results are explained using a combination of two theories: random Apollonian packing and droplet size distribution scaling under turbulent flows. The existence of a sol-gel transition could be related to power-law correlations in the number size distribution of the droplets within a certain size range. The results confirm that the casein micelles and emulsion droplets could be unified as ‘spheres’ participating collectively in random close packing. The mechanism of sol-gel transition under turbulent flows has been proposed more generally as a result of turbulence-driven dynamic changes in the number size distribution of ‘spheres’. The formation of shear-induced emulsion gels has been then further extended with key criteria proposed, based on the new multi-theory mechanism framework. The understandings gained in this thesis are summarised and concluded in Chapter 7. Future research directions are also discussed based on these new findings. Highlights of two commercialisable extensions of the work of the thesis are also provided as supplementary material in Appendices A and B.
Exponential iterative coupling for low dispersity conjugated polymers
Organic conjugated polymers form an interesting class of materials in organic electronics, which is expected to find many applications in the near future. Though polymerisation reactions can allow the rapid synthesis of systems with large conjugation lengths, conjugated polymers are most often obtained from step-growth polymerisation reactions. Therefore, they are prone to having broad molecular weight distributions, which can reduce synthetic reproducibility and hinder structure-property correlations. This thesis investigates exponential iterative coupling (IC) for producing discrete large conjugated molecules, whereby chain lengths double in each cyclic sequence of reactions while maintaining full control of molecular structure. I discuss the theoretical properties of general IC processes and show the contributions of each individual activation and coupling step towards the overall yield. This leads to the definition of the cycle yield to characterise IC processes. Having laid down the basic mathematical framework, a hybrid approach is also considered, where an initial disperse macromolecule sample is used in an exponential iterative process. I find exponential IC furnishes a mechanism capable of strongly decreasing the dispersity of a polymer sample, and may be a general basis for new syntheses aiming towards low dispersity polymer samples. Experimental investigation begins with the synthesis of functionally desymmetrised fluorene and thiophene monomers containing N-methyliminodiacetic acid (MIDA) boronate and trimethylsilyl functionalities as precursors to functional groups active in Suzuki-Miyaura coupling. Efficient and orthogonal activation of these groups is shown. Next, a prolonged selective coupling optimisation study is performed, eventually finding a set of conditions capable of yielding the doubly-protected bisfluorene in 60% cycle yield. The process is iterated, leading to the synthesis of up to a doubly-protected octafluorene. However, cycle yields quickly decline. This is attributed to a conflict between the hydrolytic instability of MIDA boronates and the necessity of trace amounts of water for an effective Suzuki-Miyaura coupling reaction. Seeking to generate a more robust exponential IC scheme, I then investigate 1,8-diaminonaphthalene (DAN) boronamides. The synthesis of a new doubly-protected fluorene monomer is performed in large scale, and another set of effective activation reactions is developed. With the new functional groups, the selective Suzuki-Miyaura coupling reaction is found to be far more reliable, and the synthesis of the doubly-protected bisfluorene is performed in an almost 10 g scale with a high cycle yield of 81%. Having observed deficiencies in both MIDA boronates and DAN boronamides as protected boronic acids, I analyse their shortcomings and propose a set of guidelines for new potential boronic acid protecting groups, providing structures for promising tridentate ligands; diphenolypyridine (DPPY), dianilinepyridine (DAPY), di(o-hydroxybenzyl)methylamine (DOMA) and di(o-aminobenzyl)methylamine (DAMA). Syntheses of DAPY and DOMA are shown. Synthesis of DPPY is optimised in large scale and the ligand coordinated to boronic acids. The resulting DPPY boronates are found to be exceptionally stable under a wide variety of conditions. However, retrieval of the boronic acid is found to be difficult, with deborylation being preferable to furnishing the free boronic acid. Nevertheless, the other proposed ligands may lead to new effective protecting groups.
New methods for the synthesis of biologically active cyclic peptides
A number of cyclic peptides have emerged as valuable pharmaceutical templates due to their resistance to chemical or enzymatic hydrolysis and high selectivity. In 2001, the celogentin family of bicyclic peptides was isolated from the seeds of Celosia argentea. The celogentins have been shown to be t potent anti-mitotic agents that inhibit tubulin polymerization, with celogentin C exhibiting four-fold higher activity than the clinically used anti-cancer drug vinblastine.1,2 The celogentins have two unusual side-chain to side-chain cross-links; one between the Beta-position of Leu2 and the indole C-6 of Trp5 and the other between the indole C-2 of Trp5 and the imidazole of the histidine side chain. These unusual cross-links make the chemical synthesis of the celogentins very tedious, lengthy, and low yielding. We have developed a new protocol for the formation of the C–C and C–N cross-links on solid phase to generate celogentin precursors. We have also designed and synthesized simplified celogentin mimetics, including analogues with improved biological activity. The cyclic peptide can form by a different method such as head to tail cyclization, side-chain to side -chain, side-chain to head/tail cyclization. The easy way to synthesize cyclic peptide is head to tail cyclization. Chemical synthesis of head-to-tail cyclic peptides challenging using standard peptide coupling methods forms a dimer of peptide and reaction rate of cyclization is slow. Efforts to overcome the intrinsic limitations of peptide head-to-tail cyclization include metal ion templating, the use of ‘capture’ auxiliaries and ring expansion/contraction approaches. Over recent decades, the preparation of proteins and long peptides has been achieved using either recombinant methods or total chemical synthesis employing native chemical ligation (NCL). These methods each have limitations; recombinant expression techniques cannot be used for unnatural amino acids and modified amino acids, while native chemical ligation requires cysteine at the ligation site. Their several methods have been developed ( including desulfurization of cysteine to alanine) to overcome the limitations of NCL. Nevertheless, all NCL-type methods rely on thioester (or selenoester) exchange as a crucial step. To overcome this significant limitation of NCL methods, We have now developed a novel chemoselective peptide ligation strategy that further exploits the reactivity of peptides containing backbone thioamides. The key accomplishments are reported herein with the goal mentioned above. Firstly, toward of total synthesis of celogentin C two unusual cross-link between Leu–Trp and Trp–His reaction protocol established individually. Secondly, simplified celogentin mimetic developed and which has shown more activity than Vinblastin. Higher yield simplified celogentin analogue can be used for further investigation. Moreover, a new head to tail cyclization method was developed by thioamide Ag(I) promoted chemistry. Further chemoselective peptide ligation strategy was stabilized with the unique reactivity of thioamides. Overall this project established a new head-to-tail cyclization method and a strong foundation for the pharmacological investigation of celogentin C as well as the development of new simplified celogentin mimetic based therapeutics.
Electronically interesting materials formed from redox-active ligands
The work described in this thesis is targeted towards generating coordination frameworks with redox-active ligands. Redox-active coordination polymers are anticipated to possess interesting and useful electronic properties. Described in chapter two are approaches undertaken towards the generation of coordination polymers with favourable charge-transport. The first approach involves the novel and potentially redox-active ligand 2,3,7-trihydroxyfluorone which was synthesised and structurally characterised. Although the original intent was to generate porous coordination frameworks with this ligand, these efforts were unfortunately unsuccessful. A series of [4+4] Mo and W based metallocycles with the trianion of the 2,3,7-trihydroxyfluorone ligand were synthesised and characterised. The second approach described in chapter two focuses on improving charge transport in coordination polymers through the use of soft donor ligands. The synthesis and structures of several potential thio pro-ligands are reported. In-situ cleavage of the alkyl thiols was not achieved, however several 1D Cu(I) and Ag(I) polymers were structurally characterised with several of the pro-ligands. Whilst the overall focus of the project was coordination frameworks, several systems were explored in which the redox-active ligands were uncoordinated. In the first half of chapter three, charge-transfer complexes of 7,7,8,8-tetracyanoquinodimethane, TCNQ, and its derivatives were examined. Based on structural and spectroscopic characterisation the complexes were found to exist in a mixed-valent state, with the TCNQ/F4TCNQ molecules present in an oxidation state between the dianion and radical monoanion. The second half of the chapter examines an unusual Fe-based coordination polymer with radical TCNQ counter anions. Moessbauer spectroscopy indicates the Fe exists as Fe(III) and the compound exhibits the unusual Goldanskii-Karyagin effect. Magnetic measurements indicate weak antiferromagentic ordering. Chapter 4 is predominately a synthetic and structural study of X4TCNQ2- (X = H or F) based coordination polymers. Products include neutral and anionic metal-X4TCNQ2- coordination polymers. The X4TCNQ2- ligand can act as a tetradentate, tridentate and bidentate bridging ligand allowing for a range of coordination polymers. Co-ligands have been shown to compete for metal coordination sites and may have a significant structure directing influence on the resultant coordination polymer. When nitrile arms are uncoordinated there is a clear tendency for them to participate in hydrogen bonding with solvent molecules or co-ligands. Chapter 5 describes the exploration of the host-guest chemistry of the [MnII(F4TCNQ-II)(py)2] framework. Selective uptake of CO2 occurs, with in-situ powder X-ray diffraction experiments revealing a ’gating’ mechanism. Intercalation of the framework with various electron acceptors is associated with significant changes to the spectroscopic and electrical properties. A correlation is observed between the strength of the electron acceptor and the optical bandgap of the host-guest material. A similar trend is apparent for the electrical conductivity of the framework. Solid-state density functional theory calculations aid in the rationalisation of these experimental observations. Chapter 6 gives a brief overview of the experimental results and provides a discussion of the overarching themes encountered in this thesis.
Development of a molecular description of the Embden-Meyerhof-Parnas sulfoglycolysis pathway
Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is the polar head group of the plant sulfolipid, sulfoquinovoside diacylglycerol (SQDG). SQ is estimated to be synthesized at a scale of some 10 billion tonnes annually and is a major contributor to the biogeochemical sulfur cycle. SQDG is a thylakoid membrane sulfolipid and is involved in membrane structure and function, and modulates the activity of photosynthetic complexes. Two sulfoglycolysis pathways have been discovered in recent years that allow the degradation of SQDG: the sulfoglycolytic Embden-Meyerhof-Parnas (sulfo-EMP) pathway and the sulfoglycolytic Entner-Doudoroff (sulfo-ED) pathway. SQDG hydrolysis to form SQ, enabling entry of SQDG to the sulfur cycle, is catalyzed by glycosidases termed sulfoquinovosidases (SQases). Structural analysis of the first SQase, EcYihQ from Escherichia coli, revealed substrate recognition by a QQRWY motif in the active site. Other putative sulfoquinovosidases contain a KERWY motif; it is not known whether they are genuine sulfoquinovosidases. In Chapter 2 we present the discovery and characterization of a second sulfoquinovosidase that bears a KERWY motif, AtSQase from Agrobacterium tumefaciens. AtSQase catalyzes hydrolysis of the artificial substrate p-nitrophenyl sulfoquinovoside (PNPSQ), which enabled its kinetic and structural characterization. Through the synthesis of a series of analogues of PNPSQ it is shown that EcYihQ and AtSQase are highly specific for both correct substrate stereochemistry and the sulfonate group. The first SQase inhibitor SQ-IFG was designed and synthesized. Structural analysis of both enzymes allowed the identification of catalytic and substrate binding residues. Their roles were supported by mutagenesis and kinetic analysis. Mutual information analysis provided insights into the evolution of these proteins. Chapter 3 covers studies of sulfoquinovose mutarotase activity using a homolog of the putative mutarotase YihR from E. coli, namely the sulfoquinovose mutarotase from Herbaspirillum seropedicae (HsSQM). With the use of 1D and 2D EXSY NMR techniques, unidirectional mutarotation rates in equilibrium mixtures of various hexoses, including SQ were measured. The enzyme exhibited a broad spectrum mutarotase activity but did not tolerate an axial C2 hydroxyl group. Further studies demonstrated that this enzyme is a sulfoquinovose mutarotase with approximately 17 000-fold preference for SQ compared to glucose 6-phosphate. Chapter 4 explored the catalytic activity of E. coli YihS catalyzing isomerization of SQ and 6-deoxy-6-sulfofructose (SF). Both substrates for the enzyme were synthesized, and NMR studies demonstrated the reversible interconversion of SQ to SF with formation of a new product, sulforhamnose (SR, 6-deoxy-6-sulfomannose). HPLC analysis showed that EcYihS catalysed the isomerisation of SQ at a rate approximately 178-fold greater compared to D-mannose (a previously described substrate for this enzyme), in terms of kcat/KM. NMR studies of the rate of YihS catalyzed H/D isotope exchange revealed that EcYihS prefers beta-SQ as the substrate. Chapter 5 of the thesis focused on the EcYihU catalyzed reduction of sulfolactaldehyde (SLA) to dihydroxypropane-1-sulfonate (DHPS). The substrate SLA was synthesized and its stability was defined. By monitoring consumption of cofactor, the rate of EcYihU catalyzed conversion of SLA to DHPS was measured, showing higher activity compared to succinic semialdehyde, a previously described substrate for this enzyme. Reduced forms of the cofactor NADH were synthesized; analysis of their inhibitory potency revealed that tetrahydro-NADH was more potent than hexahydro-NADH. Mechanistic studies using these inhibitors supported a sequential kinetic mechanism for EcYihU. X-ray studies have identified the sulfonate binding residues and revealed domain movements in YihU upon substrate/cofactor binding.
Ultrasound driven synthesis of bio-functional nanostructures
Polyphenolic-, amino acids- and doxorubicin-based nanostructures are of great interest due to their multifarious applications in biomedical field as antibiotics, antioxidants, antimicrobial and anti-cancer agents. Most of the research on the polyphenolic and amino acids based nanostructures adhere to the formation of coordination complexes with metals, self-assembly techniques or chemical functionalization and crosslinking reactions. To improve the efficacy of therapeutic agents, a variety of nanoparticles have been developed for the controlled and targeted delivery of doxorubicin. These include biopolymers-based nano/microcapsules, carbon-based nanoparticles, polymer-drug conjugate, dendrimers, liposomes, micelles, inorganic nanoparticles and nucleic acids nanostructures. The development of simple, one pot and effective synthesis routes to fabricate bio-nanomaterials is in high demand. In particular, the use of polyphenols, doxorubicin and single amino acids as building blocks to fabricate nanostructured materials is still unexplored. In this PhD work, I have used ultrasound-based technologies to synthesize phenolic, amino acid and doxorubicin based micro and nanoparticles for different biomedical applications. Chapter 1 provides an overview on the structural and bio-functional properties of nanoparticles and methods to synthesize nanoparticles for biomedical use, including the ultrasonic techniques have been discussed. Furthermore, fundamentals of ultrasound are also provided. In the literature review (Chapter 2), several studies dealing with the polyphenol, doxorubicin and amino acid molecules have been summarised. In the last section of this chapter, numerous investigations on synthesis of diverse types of nanostructures using ultrasound are reviewed. In Chapter 3 materials and methods, equipment and all other experimental details used are described. Chapter 4 provides a fundamental understanding on the ultrasonic coupling of simple phenolic molecules, where acoustic bubble acts as a catalytic binding site for the generation of bioactive oligomers without the need for utilizing any enzymes, catalysts (organic or inorganic) and other toxic reagents. It has been observed that the extent of oligomerization and nanoparticles formation depends on the ultrasonic frequency, concentration and physiochemical properties of the phenolic building blocks. Chapter 5 demonstrates that cavitation bubbles are simple micro-reactors with reactive surfaces to perform one-pot multiple reactions on complex polyphenolic molecules to convert tannic acid to ellagic acid, namely (i) hydrolysis of an ester linkage, (ii) C–C coupling reactions, (iii) condensation reactions and (iv) crystallization of the product into regularly shaped particles. The size and shape of the crystals can be controlled by ultrasonic frequency, power and time. The synthesized particles exhibit fluorescence properties, anticancer and antioxidant activity and could be further used for drug loading and delivery. In Chapters 6 and 7, the role of the acoustic field in the formation of supramolecular nanoaggregates using tryptophan and phenylalanine as building blocks was investigated. It has been demonstrated that the acoustic bubbles driven at high frequency standing wave, in addition to provide a reactive surface for the dimerization of biomolecules, can also provide an energy source to fuel and refuel the dissipative out of equilibrium assembly of these molecules below the critical aggregation concentration. Furthermore, the unique optical and bio-functional properties of nanoparticles for bioimaging and probing the intracellular trafficking of a drug have also been studied. In Chapter 8 the sound-driven self-assembly of the anticancer drug doxorubicin was investigated to generate nanoparticles solely made of drug molecules. The newly developed nanoparticles were tested on different types of cancer cells and the drug was found to be active in drug resistant cell lines. In addition, the mechanism of action of drug nanoparticles was investigated. Chapter 9 provides a summary of the entire PhD work.
Donor-emitter fluorophore pairs in luminescent solar concentrators: from material synthesis to device fabrication
A luminescent solar concentrator (LSC) is a type of light harvesting device, showing potential as an alternative to the traditional photovoltaics (PV). A typical LSC consists of a planar waveguide system embedded with fluorophores, which absorb light incident on the surface and confines the emission to the edges. As the surface area of the LSC is much bigger than the edge area, the incident light can be concentrated. A PV cell attached to the edge will convert the output light into electricity. Although there are many advantages of LSCs, the unsatisfactory efficiency of LSCs still limits their wide applications. There are four major energy loss pathways of LSCs, which are 1. the photoluminescence quantum efficiency (PLQY) loss, 2. the escape cone loss, 3. the re-absorption effect and 4. the transmittance loss. The donor-emitter fluorophore pair system can potentially improve the performance of LSCs via multiple aspects, in particular, reducing the re-absorption effect. The donor-emitter fluorophore pair is a biomimetic system inspired by the light-harvesting antenna from the natural photosynthesis where a light absorbing donor harvests the incident light and transfers the energy to the acceptor (or emitter), via mainly the Forster resonance energy transfer (FRET) process. By carefully tuning the concentration ratio of the donor and the emitter, one can achieve a fluorophore pair system that is mainly comprised of the donor’s absorption spectrum and the emitter’s emission spectrum. Consequently, the spectral overlap between the absorption and emission spectra of the fluorophore pair can be minimized, leading to a reduction of the re-absorption effect. By using specially engineered donor-emitter pairs one can reduce not only the re-absorption effect but also the escape cone loss and the PLQY loss. To build a highly efficient donor-emitter fluorophore pair system, the concentration of both the donor and the emitter are required to be high enough to fulfill the requirement of the FRET process. However, this may lead to the aggregation caused quenching (ACQ) of the fluorophores, resulting in reduced PLQY. Aggregation induced emission (AIE) is one approach to neutralize the ACQ in the donor-emitter fluorophore pair system. The AIE effect allows the PLQY of fluorophores to remain at a reasonable level in high concentration or in solid state. By replacing the common fluorophores by AIE type of fluorophores in the donor-emitter fluorophore pair system, one can expect a better overall PLQY of the fluorophore pair in the required concentration. The photophysics of an AIE donor-emitter pair was characterized in this thesis and the performance in an LSC evaluated. The other approach to avoid the ACQ effect is to stop the intermolecular interaction of the fluorophores by installing some bulky substituents to keep the fluorophores apart in aggregates. Perylene diimide (PDI) derivatives are a class of molecules that show excellent photophysical properties, but often affected by the ACQ effect. When the bulky substituents are added through the imide position on PDI, the resulting molecule should show a better tolerance to the ACQ effect and leave the photophysical properties untouched. In the thesis, a series of PDI donors with bulky substituents were designed and synthesized and paired with a PDI emitter. The performance of a LSC based on the PDI donor-emitter showed considerable improvement due to the increased PLQY and the reduced re-absorption. Inspired by the success of the PDI donor-emitter pair, a large area LSC device was fabricated based on the same materials. To ensure efficient FRET, the fluorophore concentration of a donor-emitter pair is required to be high. Therefore, a thin layer of the fluorophore coated on a transparent substrate was the chosen device structure for the large-area LSC. Doctor blading thin film deposition was applied to print the dye layer on the surface of the substrate. Two different types of substrate materials and three types of solar cells were investigated to reveal the effects on LSC performance. By optimizing the substrate materials and the attached solar cells, the performance of the resulting large-area LSC was among the best LSCs reported in the literature. The escape cone loss is the last major energy loss pathway in LSCs, which can be also eliminated by using donor-emitter fluorophore pair system. The escape cone loss can be minimized by aligning the transition-dipole of the emitter perpendicular to the surface of the waveguide. However, the absorbance of the LSC with the aligned fluorophore will be reduced, because the transition dipole of the fluorophore is then parallel to the direction of the incident light. One way to avoid the absorption reduction in the emitter-aligned LSC is to introduce a donor fluorophore that is isotropically oriented. The isotropic donors will harvest incident light as normal, but the energy will be transported to the perpendicularly aligned emitter. The emitters then emit light in parallel to the surface of the waveguide, leading to a reduced escape cone loss. A prototype LSC was prepared based on the selectively aligned donor-emitter pair and fully characterized in the thesis.
Organic chromophore aggregates for solid-state photon upconversion
Photon upconversion, a process that creates the excited states at higher energy (shorter wavelength) with excitation at lower energy (longer wavelength), has numerous potentials in photovoltaic, photocatalysis and bioimaging applications. Triplet-triplet annihilation based upconversion (TTA-UC) has attracted significant attentions due to its advantages of harnessing non-coherent and low-power excitation, coupled with intense absorption of the excitation light and high upconversion quantum yield. Two chemical components are required for TTA-UC: the first component, the sensitizer, absorbs a low energy photon and transfers it to the second component, the emitter, through the triplet-triplet energy transfer (TTET). Two or more triplet excited states generated in emitters come together and annihilate to emit one photon of higher energy than that of the initially absorbed photon. To date, the most efficient TTA-UC has been achieved in solution, which allows the rapid diffusion of chromophores, however, the solution-based systems are impractical for real-world applications. Therefore, solid-state upconversion systems are highly desirable for real technical applications. Current endeavours to improve the solid-state upconversion efficiency have been mainly focused on increasing the triplet exciton migration. The efforts to understand the parameters to develop new emitter molecules with efficient TTA and high fluorescence quantum yield in solid-state systems are limited. This work aims to advance our understanding of the effect of molecular geometry on TTA-UC, improve the overall upconversion efficiency in solid-state systems and approach the ultimate goal of developing an efficient solid-state upconversion solar cell device. Firstly, the effect of molecular geometry on the TTA upconversion performance was investigated by employing four new 9,10-diphenylanthracene (DPA) derivatives as the emitters and platinum octaethylporphyrin (PtOEP) as the triplet sensitizer. These new emitter molecules containing multiple DPA subunits linked together via a central benzene core. The upconversion quantum yield values were determined both in solution and solid-state systems. In solution, the meta-substitute dimer exhibited the highest upconversion quantum yield among the new DPA derivatives, but all were inferior to the benchmark DPA-PtOEP couple. The different upconversion quantum yield values between the new DPA derivatives were mainly attributed to the statistical probability for obtaining a high energy singlet excited state from TTA, f, both for inter- and intra- molecular processes. The f value was strongly related to the interactions between the excited state chromophores and also dependent on the magnetic field. Of the dimers, the m-dimer exhibited the largest fint (statistical probability for obtaining a singlet excited state from intramolecular TTA), indicating the highest proportion of upconversion was from intramolecular TTA. The linkage through the meta position resulted in the weakest exchange-coupling between the triplet excited states, leading to a largest magnetic field effect (MEF%). The fall (statistical probability for obtaining a singlet excited state from both inter- and intra- molecular TTA) values of the dimers and trimer were smaller than that of DPA, which were consistent with the upconversion quantum yield results. These results demonstrated that multichromophoric emitters are not necessarily better than single chromophores. In the solid-state, the much lower upconversion quantum yield of new DPA derivatives compared to the DPA reference was attributed to the much smaller fluorescence quantum yield and slower TTET from the sensitizer to the emitter. Further investigation of the effect of arrangement of chromophores in multi-chromophore molecules on TTA-UC was carried out by utilizing tetraphenylethene 9,10-diphenylanthracene (TPE-DPA) derivatives as the emitters. With the TPE chromophore in these multi-chromophore molecules, the new TPE-DPA derivatives exhibited aggregation induced emission (AIE) behaviour as their fluorescence quantum yield increased as increasing the proportion of water in THF solution. Various fluorescence quantum yield values obtained in PMMA, neat films and nanoparticle dispersions indicating that different aggregation states were formed. Upconversion emission was detected from the TPE-DPA/PtOEP nanoparticle dispersions with the gem-DPA/PtOEP showing the highest upconversion emission intensity. A higher upconverted emission intensity was observed in aerated (compared to deaerated) solutions of the derivatives following UV light irradiation, which was attributed to oxidation of the TPE moiety. The effect of oxygen on the photophysics of the TPE-DPA derivatives was further investigated under the UV light irradiation. The TPE moiety in the gem-DPA was found to be more easily oxidized than that in the mono- and cis-DPA. A possible oxidation route was proposed: weak intersystem crossing in TPE-DPA derivatives created a triplet population which can sensitize formation of highly reactive singlet oxygen. This photosensitized singlet oxygen preferred to react with TPE moiety first forming endoperoxide. In the absence of the TPE moiety, the molecules showed enhanced fluorescence in solution. Finally, the solid state upconversion quantum yield of the DPA/PtOEP systems was improved by decreasing the sensitizer’s aggregation and phase separation. Two new DPA derivatives (bDPA-1 and bDPA-2), with bulky isopropyl groups on the phenyl rings, were used as the emitters. Under the sensitization of the PtOEP, TTA-UC performance was comprehensively investigated in various systems: toluene solution, polyurethane thin film and crystals. Only a small difference of upconversion efficiency was observed in toluene solution and polyurethane thin film of b-DPAs compared to the DPA reference. Interestingly, a greater than 10 times improvement in the upconversion quantum yield was obtained in bDPA-2/PtOEP crystals with low excitation intensity threshold compared to that of the DPA/PtOEP crystals. The dispersibility of the sensitizer in emitter crystals was improved in bDPA-2 due to its slower rate of crystal formation. Apart from the excellent TTA-UC performance of the b-DPAs, they also show outstanding stability under UV light irradiation, which is ideal for the real-world long-term application of TTA-UC. Based on the results presented herein, we are moving closer towards the development of highly efficient solid-state upconversion devices for harvesting solar energy.