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The overall focus of this thesis is investigations into the preferential locations of biomolecules, including membrane proteins, in orientated self-assembled lipid nanostructured materials known as QII phases. The three QII phases, known as the QII G, QII D and QII P , consist of 3 dimensional periodic self-assembled surfaces over which a lipid bilayer is draped. The lipid bilayer in each QII phase consists of regions of flat or high curvature into which it has been hypothesised that guest biomolecules will preferentially partition. Research efforts focus on orientated QII phase domains as more information can be extracted from characteristic Small Angle Scattering (SAS) experiments than from polydomain samples. Different lipid mesophases including the QII phases, were prepared as orientated lipid films and an automated method of 2D Small Angle X-ray Scattering (SAXS) analysis for orientated samples was created. The addition of biomolecules to a QII phase was achieved by co-dissolving with the lipids in an organic solvent before formation of the orientated QII phase, or by addition to an already formed QII phase. Both methods are presented here and the incorporation of various biomolecules into a QII D phase bilayer was monitored in two separate fashions, via SAXS and Raman Spectroscopy. Finally, the addition of biomolecules to orientated QII phases was undertaken and any preferential partitioning into flat or highly curved regions of the bilayer was investigated. It was found via Grazing Incidence Small Angle Neutron Scattering (GISANS) that monopalmitin and cholesterol in a monoolein QII D phase, preferentially partition into the flatter regions of the bilayer. At several instances during my research, variable humidity control was required. Lipid films require particular humidity to maintain specific phase behaviour and for the neutron experiments, the host lipid was contrast matched to a D2O environment. To meet this requirement, two separate humidity control systems were designed and created: the first a low cost, portable, and chamber independent system, the second a fully automated system calibrated to a chamber at Diamond Light Source. A separate study into the relaxed curvature of four lipids, monoolein, monolinolein, phytantriol, and phytantetrol using inverse micelles is also detailed. The relaxed curvature was obtained by calculating the parameters of the neutral surface, or the surface whose area does not change due to bending within a lipid monolayer.

The Flexibility Window (FW) is a universal, geometric feature that can explain thefeasibility of all existing zeolites. Using template-based geometric simulations, it hasbeen shown that all known, IZA framework types can be made geometrically idealover a range of densities, yet less than 10% of hypothetical structures have thisproperty. This is an important distinction that can help narrow the search for newframeworks. The geometric method employed is highly efficient for routine screeningover large databases, where more exhaustive techniques involving energy minimisation and atomic potentials are too demanding. A FW search should, therefore, be the first point of call when evaluating the feasibility of a hypothetical structure. In this study, 255 existing and 5,824 hypothetical zeolite structures have beenevaluated and characterised using the FW criterion. High-similarity groups of existing and hypothetical frameworks have been identified based on (i) common FW descriptors (shape, length and area), and (ii) structural characteristics (d6r/d8r connectivity). As a result, 26 target, ABC-6 hypothetical frameworks have been selected that are of practical interest. Remarkably, five of these predicted structures, 194_3_1140 (SWY), 194_4_47060 (ANO), 164_2_612 (PTT), 166_4_600690 (AVE) and 229_3_4866 (PWN), have been approved as real materials during the course of this work (2018-2021).The FW is, however, more than just a yes/no parameter of feasibility. It providesvaluable insight into fundamental relationships between framework geometry, flexibility and physical properties. Using geometric simulations, it is possible to predict behaviour of known and hypothetical frameworks at the atomic level under non-ambient conditions. Within the FW, frameworks can respond to external stimuli, such as temperature, pressure and guest materials, by "ideal" deformations i.e. those that leave the tetrahedra undistorted. Furthermore, it is the orientation and connectivity of closed polyhedral building units, d6r, d8r and can, that determines the specific flexibility of each topology. This is confirmed experimentally for K-L zeolites which have been studied under high-pressures using synchrotron, ToF neutron diffraction. As a result, a new method of combining geometric modelling with Rietveld refinement has been developed to determine the crystal structures of zeolites at high-pressures. Furthermore, it is possible to predict framework compositions based on the observed trend in FW areas and ∠T-O-T distributions. Now, more than ever, there is a great demand for new zeolite materials with unique topologies that offer potential solutions to tackle many of the 21st century global sustainability challenges. Here, we have developed a robust protocol that should be used to narrow the search so that efforts are focussed on targeting only the most promising framework types. It is hoped that the strategies presented here will assist in the discovery of many new zeolites in the near future.

Despite the successes of global vaccination programs, infectious diseases continue to claim or devastate millions of lives each year. Reductions in this number will require dramatic improvements in vaccines via strategies including the development of efficacious adjuvants which augment vaccine-induced immune responses and elimination of the refrigerated cold chain through vaccine thermostabilisation. Recent investigations have revealed Staphylococcus aureus binder of immunoglobulin (Sbi) harbours potential as a novel adjuvant as (1) Sbi III-IV has the unique ability to encourage the consumptive cleavage of the central complement component C3 to C3b, iC3b and the natural molecular adjuvant C3d, and (2) C3d-opsonised antigens promote C3d-complement receptor 2 (CR2) and antigen-B cell receptor (BCR) coligation on B cells and generate enhanced immune responses. In addition, ensilication, a method that encases proteins in a resistant silica cage, has been shown to physically prevent the thermal denaturation of a number of model proteins and has potential for vaccine thermostabilisation. The research presented in this thesis reveals Sbi III-IV-mediated C3 consumption involves the formation of dimeric tripartite complexes with C3b and Factor H-related proteins and induces opsonisation of tuberculosis antigen Ag85b and anthrax protective antigen with C3 activation products. Opsonised Ag85b is shown to elicit a rapid and heightened humoural immune response in a C3 and CR2 dependent manner in vivo, establishing the application of Sbi III-IV in enhancing the immunogenicity of antigens key to the development of novel vaccine candidates. Subsequent analyses uncover the thermal lability of the Sbi III-IV adjuvant, antigen Ag85b and a newly-developed Sbi III-IV-Ag85b conjugate and provide evidence of the utility of ensilication in improving the thermal stability of these vaccine-relevant constructs, thus demonstrating its use in a vaccine setting for the first time. Finally, C3d is shown to form disulphide-linked dimers that crosslink CR2, a new discovery with further potential implications for vaccine design. In the future, Sbi III-IV and dimeric C3d could serve as robust adjuvants that potentiate immune responses induced by multiple vaccines and ensilicationmediated thermostabilisation could eliminate the need for the cold chain and thereby improve the global distribution of safe and effective vaccines.

Mesoporous materials have been widely applied in the field of separation and catalysts. Surfactant templating is one of the widely used methods for the preparation of mesoporous materials. Many methods based on surfactant templating, such as spin coating, dip coating and co-precipitation, have been developed to prepare mesoporous materials. Free-standing film synthesis method using the surfactant templating method, which has been extensively studied by our group, enables the investigation of the change in the surface structure while the film is growing using surface sensitive techniques. Previously used silica precursors (tetramethyl orthosilicate and tetraethyl orthosilicate), produce organic species that disrupt the organisation of the micelles. Sodium silicate solution, used in this work produces water instead so is a potential precursor that could give better control of the pore size and the strength of the film. The growth of the film was followed using cutting-edge techniques: in situ X-Ray Reflectivity (XRR) and in situ Grazing Incidence Small Angle X-Ray Scattering (GISAXS), which suggest a possible growth mechanism. Functionalisation of mesoporous materials is required to improve their catalytic properties. Novel surfactants (POM-2Cn, n is the carbon number of the hydrocarbon chain length, n= 12, 14, 16 and 18) were designed and were prepared through grafting double hydrocarbon chains onto a Dawson structured polyoxometalates ([P2W17O61] 10-), to use these species as both templates and a source of polyoxometalate to functionalize the mesoporous materials prepared. The self-assembly of the prepared surfactants and their mixture with commercial nonionic surfactants (C12EO6 and C12EO8) in water have been studied using Small Angle Neutron Scattering (SANS) and Small Angle X-Ray Scattering(SAXS). The pure POM-2Cn molecules form less elongated micelles in water with increasing hydrophobic tail length, suggested by the SANS analysis. The micelles formed by POM-2Cn were used to template titanium dioxide. The prepared materials, denoted as POM-TiO2, have been proven to bear POM units well-dispersed in the porous TiO2 materials using Energy Dispersive X-Ray Analysis (EDX). The POM-TiO2 materials showed enhanced photodegradation properties for rhodamine B compared to the unfunctionalised TiO2 materials. This is attributed to the charge transfer from TiO2 conduction band to POM that prevent the recombination of the photo-excited holes and electrons during the photodegradation process. The insertion of the nonionic surfactant into the POM-2Cn system induces a micellar growth. The comparison of SANS studies of the two binary surfactant systems (POM-2Cn/C12EO6 and POM-Cn/C12EO8) have shown that the micellar growth caused by nonionic surfactant with a smaller polyethylene oxide group is more pronounced than that caused by that with a larger hydrophilic headgroup. The POM-2Cn/C12EO8 mixtures form Liquid Crystal P hases (LCP) when the total concentration is increased to 133 mM. The type of LCP formed depends on the mixing mole ratio of the POM-2Cn and C12EO8. The POM-2Cn rich mixtures form a cubic phase, while the C12EO8 rich mixtures form a lamellar phase. The lamellar phase formed by the mixture was then used to template long-range ordered silica. Porous silica was obtained after the organic part of the template was removed, with a relatively small surface area (ca. 313 m2/g) and small pore size (1 nm - 4 nm). This work includes several individual systematic investigations, the understanding of the growth of the silica film using sodium silicate solution, the basic understanding of surfactant behaviour of the POM-2Cn surfactants and their mixtures with C12EOm (m = 6 and 8). Their applications in fabricating hybrid porous materials with enhanced properties were also studied. It is hoped that these results could give a good understanding of the surfactant behaviour of both traditional and novel surfactants and would contribute to the future study of the functionalisation of inorganic materials using a surfactant templating method.

The majority of vaccines consist of proteins derived from pathogens that, upon vaccination, provide humans with long-term immunity against infectious disease. Vaccine proteins are susceptible to environmental changes. Fluctuations in temperature are the foremost cause of protein degradation and will result in vaccines being ineffective. In short, many vaccines lack thermal stability. Vaccine manufacturer's therefore store and transport vaccines under continuous refrigeration (2-8 °C), known as the "cold-chain". This increases the longevity of vaccines but is also a very costly procedure. Studies have shown several operational problems within cold-chain and this is reflected in the high prevalence of vaccine-preventable diseases, especially in developing countries. This project investigated the application of a previously developed method, ensilication, to stabilise vaccine proteins with use of silica to prevent thermal denaturation. This could provide an alternative to freeze-drying (lyophilisation) as some vaccines use excipients to improve efficacy which makes them unsuitable for lyophilisation. The 'sol-gel' method on which ensilication is based uses an inorganic compound, tetra-ethyl ortho-silicate (TEOS), to produce a polymer particle which can link around and interact with biomolecules present in buffered aqueous solution. This protects against temporal fluctuations in dry powdered form. After storage, the ensilicated protein can be released using a chemical method that removes the silica shell. Recombinant tetanus toxin c fragment (TTCF) was the model protein (antigen) utilised here to establish the feasibility of vaccine ensilication. Structural and physical analysis of ensilicated TTCF, pre- (native) and post-ensilication (released), showed the retention of protein structure and functional properties. Additionally, in vivo animal experiments confirmed retention of released TTCF immunogenicity in mice. This included ensilicated TTCF that was subjected to extreme heat, displaying the thermal resilience of ensilicated material. Finally, synchrotron small angle x-ray scattering (SAXS) experiments elucidated the mechanism of stabilisation. Overall, this study shows a promising application of ensilication for the development of thermostable vaccines.

Microalgae are a promising feedstock for the production of sustainable, 3rd generation biofuels; however, current lipid-based processes are too expensive to effectively compete with existing transportation fuels. A potential solution is to convert the entire algae via hydrothermal liquefaction (HTL) instead, therefore allowing the use of faster-growing, and cheaper microalgae. This project sought to address some of the main challenges with this technology, currently restricting its use for large-scale fuel production. Fuels are low value products and unlikely to pay for the entire fuel production process on their own. Consequently, the possibility of producing additional by-products from the conversion of polymer- containing algae, or combining HTL with a more conventional lipid- extraction process, was explored. In addition, the project studied the conversion of microalgae produced during the bioremediation of domestic wastewater, in order to help to offset the overall biomass production costs. The majority of research into algal HTL has been confined to batch systems, which are not fully representative of the continuous flow processes used for large-scale fuel production. Consequently, an inexpensive laboratory-scale system was designed to study the continuous HTL of algae under a range of operating conditions. Using this system, it was found that, compared to a batch reactor, significantly enhanced oil yields could be obtained from the system, as a result of increased heating rates, together with prolonged reaction times. Finally, the poor quality of the bio-oils produced by the HTL of microalgae is a major challenge. Particularly their high nitrogen content restricts their conversion within conventional petrochemical refineries. Therefore, significant upgrading is required before the oil can be fractionated into fuels. In order to achieve this, a range of zeolite-supported nickel phosphide catalysts were synthesised in this project, and tested for the denitrogenation of the model compound quinoline, before they were applied to the upgrading of bio-oil obtained from the continuous liquefaction of the wastewater-derived algae. Although the synthesised catalysts showed only low activity towards the denitrogenation of the bio- oil, they were more active for the hydrogenation of quinoline, compared to two conventional sulphided transition metal catalysts, and following further optimization, could therefore represent a viable class of oil upgrading catalysts.

Stability of biological substances based on proteins, including vaccines, antibodies, and enzymes, is critically linked to its thermal environment. Temperature stress over time results in protein denaturation. Denaturation is a loss of structure and function in proteins. Their storage and distribution therefore relies on a “cold chain” of continuous refrigeration, which is costly and not always effective in medical and biological applications. Due to this issue, access to insulin for treating diabetes is still beyond the reach of millions of people around the world [1]. Diabetes is predicted to be the 7th leading cause of death in the next decade [2].This project therefore sought to develop an innovative protocol of “ensilication” ef- fectively enclosing protein in a deposited silica “cage” to protect the protein from the denaturing process. To evaluate this aim, a release protocol involving treatment with a dilute solution of acidified NaF was designed to release the ensilicated proteins into solution. As test subject, covalently bonded sol-gel silica network was first exam- ined to surround lysozyme, then applied to haemoglobin, a heterotetrameric protein with a complex tertiary and quaternary structure. Remarkably, insulin is profitably ensilicated (80%) here along with a mediator, chitosan. The mechanism for the formation of protein ensilication was investigated using Syn- chrotron SAXS and DLS. The structures of ensilicated protein were confirmed using multiple microscopy and spectrometry methods. In order to test the product’s stabil- ity, the ensilicated protein was subjected to heating at 100 ◦C for hours or long-term ambient temperature storage. Analysis of the proteins released from their ensilica- tion with a wide range of methods including SAXS, ELISA, CD and FT-IR revealed that even after exposure to such extreme temperatures, the protein structure remains consistent with that of the native protein. The results demonstrate that the process produces a storable solid protein-loaded material directly from solution, and may thus be suitable for use with proteins that do not tolerate lyophilisation. Ensilication offers the prospect of a solution to the “cold chain” problem for biological materials, such as insulin.

This study was carried out on the synthesis of mordenite zeolite and ZSM-5 zeolite. In Chapter 3 reports the growth of ZnS nanoclusters in the pore channels of mordenite zeolite. ZnS as an important wide-band-gap (3.6 eV) semiconductor nanoclusters and have various technological applications such as photocatalysis, nonlinear optics, sensors, solar cells, injection lasers, flat panel displays, ultraviolet light emitting diodes (LED). Zeolites have several different applications in industries, such as in catalysis, ion exchange adsorption and gas separation. Zeolites are mostly used as a catalyst in the petrochemical industry. ZSM-5 zeolite is widely used a heterogeneous catalyst in the petrochemical industry due to its unique porous structure. Special attention has been made to synthesize nano-ZSM-5 in order to improve its catalytic activity. Catalysis depends on the characteristics length scale of the active sites, while the rate depends on the accessible active sites. In order to improve the performance of ZSM-5 zeolite used as a catalyst in the petrochemical industry, the researchers amid to produce nanocrystalline of the ZSM-5 zeolite. That will help to reduce the path length for the reaction and hence will increase the rate of a reaction. Comparative synthesis nano-particles of ZSM-5 zeolite using two different methods of treatment i.e. pre-treatment and interrupted treatment with ultrasound and without ultrasound was studied, its effect on aging and crystal growth during the hydrothermal treatment. In Chapter 4 the pre-treatment with ultrasound and without ultrasound (static) with an increasing time intervals have been reported. The resulting product the particle size is clearly decreased by using ultrasound pre-treatment. While in Chapter 5 using a different method of treatment called interrupted of the hydrothermal process. As in this method, we stopped the hydrothermal process for 20 minutes and treated the gel with ultrasound for 15 minutes. This treatment was repeated after every 2 hours of hydrothermal treatment. Similarly, the same method was applied to the experiment but without the use of ultrasound called a static method of aging. A 3rd method was also applied to investigate the effect of ultrasound on the particle size distribution of the synthesized crystalline powder. All the results showed that the ultrasound not only effects on the particle size but it also affects the crystallinity too i.e. increased the crystallinity and the reduced in the particle size.

This study focuses on five zeolites: sodalite, zeolite A, linde type N, zeolite Y, and EMC-2, with SOD, LTA, LTN, FAU, and EMT framework topologies respectively. All of these zeolites have β-cages as the framework building units. The aims are to understand the conditions which control the formation of different zeolite phases and some of the physical properties of zeolite frameworks, mainly the framework exibility, and the capacity of β-cage to accommodate guest molecules such as water and methanol. The hydrothermal and microwave syntheses of zeolite with no organic structure directing agents require precise control of synthesis conditions and form the fundamental part of this study. Reaction temperature and synthesis time control the phase purity in zeolite A synthesis. A transformation from zeolite A to sodalite is observed and is related to framework density and reaction temperatures. Microwave syntheses of sodalite show that the batch compositions and methods of preparation also affect the as-synthesised zeolite phases and a new sodalite morphology is found. By using microwaves instead of traditional hydrothermal methods, one of the most complex zeolites, linde type N zeolite, was synthesised. This is the first study to report this new method. The newly defined extrinsic exibility window is studied on more depth in this work. While the intrinsic exibility is defined by the ability of an empty framework to flex with no distortions in the primary tetrahedral building units; the extrinsic exibility window is limited by the host-guest steric interactions between the framework and the extra framework contents. In zeolite Y, the extrinsic exibility window can be limited not only under compression, but also in expansion, as the β-cage in a maximally expanded framework lack the exibility to adapt to bulky contents such as a combination of methanol and water molecules. It is also found that the β-cage in zeolite Y can only accommodate a maximum number of two water molecules and one methanol molecule. The same phenomenon is observed in sodalite under compression. In the sodium form, the framework remains within its intrinsic exibility window when fluorinert is used as pressure transmitting media, as fluorinert does not enter the zeolite pores. However, an extrinsic exibility window is observed in both the sodium and sodium bromide forms with methanol/ethanol/water mixture as pressure transmitting media. An exception is seen in EMC-2. The intrinsic and extrinsic exibility windows are identical to each other. The presence of 18-crown-6 ether molecules in the pores does not affect the exibility window. The crown ether, despite its steric bulk, does not limit the geometric exibility of the framework since the cage of the EMT framework has enough space to accommodate the crown ether molecule and can adapt to the contraction. This shows that the extrinsic exibility window of zeolite frameworks is controlled not only by the extra framework contents, but also by the framework building units.