Dissertations / Theses on the topic 'Electron nuclear double resonance spectroscopy'

The human α-lactalbumin (α-LA) molten globule formed at low pH is a model for the study of protein folding intermediates. The molten globule lacks native-like side-chain interactions, resulting in a fluctuating ensemble of tertiary structures, characterisation of which has been precluded by severe line-broadening in NMR spectra and a lack of long-range NOEs. Paramagnetic relaxation enhancements (PREs) have been measured in a variant of α-LA in which all native cysteines have been mutated to alanine (all-Ala α-LA). Cysteine residues have been mutated into regions of interest and spin labelled with MTSL. These measurements have confirmed that all-Ala α-LA forms a compact molten globule. Transient, long-range interactions that are stabilising the compact fold have also been identified using PREs measured in urea-denatured states. This has identified several interactions formed by hydrophobic residues from both the α- and β-domain, which could be important for initiating and driving folding. The molten globule’s 3D topology has been probed by measuring long-range distances between MTSL pairs using Double Electron-Electron Resonance (DEER). Broad distance distributions have been identified between elements of secondary structure, indicative of a fluctuating but compact fold. By contrast, a narrower distance distribution has been measured within one of the major helices, indicative of native-like secondary structure. The surface accessibility of all-Ala α-LA and that of two other variants ([28-111] α-LA and 4SS α-LA) has been probed using solvent PREs obtained using TEMPOL, a paramagnetic co-solute. This has revealed differences in the solvent-exposure of hydrophobic residues due to the removal of disulphide bonds. This method has also identified buried hydrophobic residues that contribute to forming the molten globule’s stable, native-like core.

Thesis (M.S.)--West Virginia University, 1999.
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Thesis (Ph. D.)--West Virginia University, 1999.
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Thesis (M.S.)--West Virginia University, 2005.
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Osmium-based materials exhibit unconventional magnetism due to the interplay between spin orbit coupling and strong electronic correlations. In this thesis we investigate for the first time the effect of charge doping on the Dirac Mott insulator double perovskites Ba2Na(1-x)CaxOsO6 by using Nuclear Magnetic Resonance technique. We study in details the evolution of the magnetic phase diagram as a function of doping and applied magnetic field. The system rapidly evolves from a canted to a collinear antiferromagnetic ground state with a monotonic increase of the magnetic transition temperature. Furthermore, the system remains insulating in the whole range of doping, despite the injection of extra electrons. This indicates that the Dirac-Mott insulating state of this material is unusually robust. In particular, the results show an unexpected thermally activated charge dynamics which suggests the presence of polarons dominating the high temperature excitations of this Dirac-Mott insulator.

ATP-dependent chromatin remodellers represent a class of proteins that restructure chromatin through the action of a conserved helicase-like ATPase domain. Remodellers typically have several accessory binding domains alongside the ATPase. These confer target specificity and most commonly recognise histone post-translational modifications. SMARCAD1 is a ubiquitous chromatin remodeller involved with DNA replication and re- pair. It binds directly to PCNA at the site of DNA replication and recruits co-repressor KAP1 in order to silence newly produced chromatin. In contrast to most other chromatin remodellers, SMARCAD1 does not contain several different types of accessory domains. Only two CUE do- mains have been identified in addition to the SMARCAD1 core ATPase domain. CUE domains are a type of helical ubiquitin-binding domain. This thesis presents the findings of an investigation into the structure and function of the SMARCAD1 double CUE domain. The solution NMR structure is presented with results from NMR binding experiments mapped onto the structure. Each CUE domain was found to be an independent helix bundle connected by a dynamic flexible linker. The N-terminal CUE domain, CUE-1, binds ubiquitin and has an adjacent SUMO (a ubiquitin-like protein) binding motif on a protruding extended helix. The C-terminal CUE domain, CUE-2, has a very similar structure to several published CUE domains but does not bind ubiquitin due to a charged substitution at a highly conserved CUE consensus position. The SMARCAD1 double CUE domain binds KAP1 from nuclear extract and is likely to mediate the interaction between SMARCAD1 and KAP1. SMARCAD1 double CUE domain is not involved with PCNA binding.

In this thesis the synthesis and full characterization of a new bulky diphosphine, tetrakis-(2,6-diisopropylphenyl)diphosphine, are described. This compound displays facile oxidation and a thorough investigation of its redox properties has been studied by combining solution electrochemical techniques such as cyclic voltammetry (CV) and rotating disk electrode (RDE) voltammetry, with spectroscopic methods such as electron paramagnetic resonance (EPR) and Simultaneous Electrochemical Electron Paramagnetic Resonance (SEEPR) spectroscopy over a wide temperature range. Density functional theory (DFT) calculations were carried out to aid in structural characterization of the radical cation that is produced and to provide computed hyperfine splitting (HFS) constants for comparison with experimental results. For comparison to this species with bulky aromatic substituents, similar studies were conducted that have identified the previously unreported radical cation of tetrakis-tert-butyldiphosphine with a bulky aliphatic substituent that provides even higher steric pressure than the 2,6-diisopropylphenyl group. DFT calculations are reported, as is full characterization with fluid and frozen-solution EPR spectroscopy. Further CV and EPR (SEEPR) studies are reported that led to the identification of radical cations of tris(2,6-diisopropylphenyl)arsine and bis(2,4,6-triisopropylphenyl)(2,6-diisopropylphenyl)phosphine. DFT calculations are reported, as is full characterization with fluid and frozen-solution EPR spectroscopy.
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Conventional computing faces a huge technical challenge as traditional transistors will soon reach their size limitations. This will halt progress in reaching faster processing speeds and to overcome this problem, require an entirely new approach. Quantum computing (QC) is a natural solution offering a route to miniaturisation by, for example, storing information in electron or nuclear spin states, whilst harnessing the power of quantum physics to perform certain calculations exponentially faster than its classical counterpart. However, QCs face many difficulties, such as, protecting the quantum-bit (qubit) from the environment and its irreversible loss through the process of decoherence. Hybrid systems provide a route to harnessing the benefits of multiple degrees of freedom through the coherent transfer of quantum information between them. In this thesis I show coherent qubit transfer between electron and nuclear spin states in a ¹⁵N@C₆₀ molecular system (comprising a nitrogen atom encapsulated in a carbon cage) and a solid state system, using phosphorous donors in silicon (Si:P). The propagation uses a series of resonant mi- crowave and radiofrequency pulses and is shown with a two-way fidelity of around 90% for an arbitrary qubit state. The transfer allows quantum information to be held in the nuclear spin for up to 3 orders of magnitude longer than in the electron spin, producing a ¹⁵N@C₆₀ and Si:P ‘quantum memory’ of up to 130 ms and 1.75 s, respectively. I show electron and nuclear spin relaxation (T₁), in both systems, is dominated by a two-phonon process resonant with an excited state, with a constant electron/nuclear T₁ ratio. The thesis further investigates the decoherence and relaxation properties of metal atoms encapsulated in a carbon cage, termed metallofullerenes, discovering that exceptionally long electron spin decoherence times are possible, such that these can be considered a viable QC candidate.

The study of quadrupolar nuclei using NMR spectroscopy in the solid state significantly increased in popularity from the end of the 20th century, with the introduction of specific methods to acquire spectra free from the effects of the quadrupolar interaction, that results in broadened lineshapes that cannot be completely removed by spinning the sample at the magic angle (MAS), unlike most of the other interactions present in the solid state. The first technique which allows, without any specific hardware, the removal of this broadening has been the Multiple-Quantum MQMAS experiment. The method quickly gained a popularity within the NMR community, with numerous successful applications published. However, the multiple-quantum filtration step in this experiment relies on severely limits sensitivity, restricting application to the most sensitive nuclei. Extending the applicability of MQMAS to less receptive nuclei requires the use of signal improvement techniques. There are multiple examples of such approaches in the literature, but most of these require additional optimisation that may be time-consuming, or simply impossible, on less receptive nuclei. This work introduces a novel signal improvement technique for MQMAS, called FAM-N. Its optimisation is solely based on density matrix simulations using SIMPSON, implying no additional experimental optimisation is required, while improving the signal in MQMAS spectra by equivalent or higher amounts than other common methods. In order to prove the applicability of this method on virtually any system, FAM-N has been investigated by simulation, and tested experimentally using a number of model samples, as well as samples known to be challenging to study by NMR. This work also explores other aspects of NMR spectroscopy on quadrupolar nuclei. Adiabatic inversion of the satellite populations can be performed to improve the central transition signal in static or MAS spectra. A range of methods has been tested and compared, with particular attention given to hyperbolic secant-shaped pulses, for which its performance have been described. Finally, cross-polarisation from a spin I = 1/2 nucleus to a quadrupolar nucleus has been investigated. After reviewing the theory for the static case, simulations have been performed under MAS in order to identify the conditions for efficient magnetisation transfer, with applications in spectral editing or for the combination with MQMAS.

Spin dynamics simulations are used to gain insight into important magnetic resonance experiments in the fields of chemistry, biochemistry, and physics. Presented in this thesis are investigations into how to accelerate these simulations by making them more efficient. Chapter 1 gives a brief introduction to the methods of spin dynamics simulation used in the rest of the thesis. The `exponential scaling problem' that formally limits the size of spin system that can be simulated is described. Chapter 2 provides a summary of methods that have been developed to overcome the exponential scaling problem in liquid state magnetic resonance. The possibility of utilizing the multiple processors prevalent in modern computers to accelerate spin dynamics simulations provides the impetus for the investigation found in Chapter 3. A number of different methods of parallelization leading to acceleration of spin dynamics simulations are derived and discussed. It is often the case that the parameters defining a spin system are time-dependent. This complicates the simulation of the spin dynamics of the system. Chapter 4 presents a method of simplifying such simulations by mapping the spin dynamics into a larger state space. This method is applied to simulations incorporating mechanical spinning of the sample with powder averaging. In Chapter 5, implementations of several magnetic resonance experiments are detailed. In so doing, use of techniques developed in Chapters 2 and 3 are exemplified. Further, specific details of these experiments are utilized to increase the efficiency of their simulation.

O objetivo deste trabalho foi implementar a técnica de dupla ressonância denominada Desacoplamento Heteronuclear em Banda Larga. Tal técnica consiste em eliminar a interação dipolar magnética nuclear existente entre núcleos atômicos raros que desejamos observar (13C, por exemplo) e núcleos atômicos abundantes que existem em sua vizinhança (1H, por exemplo). Para implementar algumas das técnicas de Desacoplamento Heteronuclear em Banda Larga (DBL), foi desenvolvido o instrumental eletrônico necessário, que consistiu em projeto e construção de moduladores de pulsos de radiofreqüência com controle de fase, em programação de seqüências especiais de pulsos para DBL e em sistemas de controle digital. As técnicas de DBL implementadas foram: \"Noise Modulation\", \"Squarewave modulation\", \"MLEV-64\" e \"WALTZ-16\". Avaliamos o desempenho destas técnicas através de resultados experimentais obtidos utilizando o composto ADAMANTANO (Cl10H16). Todos os equipamentos desenvolvidos foram incorporados ao espectrômetro de alta resolução por ressonância magnética nuclear existente no Laboratório de Espectroscopia de Alta Resolução (LEAR), do Departamento de Física e Informática, Instituto de Física de São Carlos, USP, e estão sendo utilizados rotineiramente nos experimentos de espectroscopia de alta resolução
The goal of this work was to improve the double resonance technique called Broadband Heteronuclear Decoupling. This technique consists on eliminate the dipolar heteronuclear interaction that exists between rare nucleous (13C, for example) and abundant nucleous that exists around (1H, for example). To improve some techniques of Broadband Heteronuclear Decoupling (BBDec), an electronic apparatus was made, which consisted of design and implementation of radiofrequency pulse modulators with phase control, special BBDec pulse sequences programming and digital control systems. The implemented Broadband Heteronuclear Decoupling techniques were: Noise Modulation, Square-wave Modulation, MLEV-64 sequence and WALTZ-16 sequence. We evaluated the performance of these techniques utilizing the experimental results obtained with the sample ADAMANTANO (Cl10H16). All developed apparatus was incorporated with the high resolution NMR spectrometer that exists at the High Resolution Spectroscopy Laboratory (LEAR), of the Instituto de Física de Sao Carlos, USP, and are being used at all high resolution NMR experiments

The Escherichia coli infecting T7 bacteriophage shares a common dsDNA packaging mechanism with other bacteriophages of the Caudovirales order, Herpesviruses and Adenoviruses. The packaging machinery comprises the portal protein and the terminase complex. The portal protein is a channel located at a unique portal vertex that provides a conduit for DNA translocation, while the terminase complex recognizes a long concatemer of DNA, performs the nuclease catalytic activity and hydrolyses ATP. Available structural information about portal proteins describes them as oligomeric rings with an axial channel. High quality samples suitable for structural characterization of the portal protein of T7 bacteriophage were obtained and characterized. Both X-ray crystallography and cryo-electron microscopy (cryo-EM) data were collected, and an initial model built on the 5.8Å cryo-EM map was used to phase the crystallographic data, which allowed the building of a model of a tridecameric particle at 2.8Å resolution. The T7 portal particle is 170Å tall and 110Å wide toroidal protein with a central channel that ranges from 23Å to 95Å in diameter. Four domains have been identified in the structure: the wing, the stem, the clip and the crown. The a10-tunnel loop valve is proposed to play an important functional role. During packaging, it may adapt while DNA is translocated and rotated, and once the genome has been packed the side chain of tunnel loop residue Arg368 may be able to seal the channel and stabilize the DNA inside the capsid before tail assembly. Interestingly, these mechanisms would not only imply the flexibility of a loop region, but also the kink of the longer helix of the portal structure, a10.

[1] Four specimens of zoned tourmaline from granitic pegmatites are characterised in detail, each having unusual compositional and/or morphologic features: (1) a crystal from Black Rapids Glacier, Alaska, showing a central pink zone of elbaite mantled by a thin rim of green liddicoatite; (2) a large (~25 cm) slab of Madagascar liddicoatite cut along (001) showing complex patterns of oscillatory zoning; and (3) a wheatsheaf and (4) a mushroom elbaite from Mogok, Myanmar, both showing extensive bifurcation of fibrous crystals originating from a central core crystal, and showing pronounced discontinuous colour zoning. Crystal chemistry and crystal structure of these samples are characterised by SREF, EMPA, and 11B and 27Al MAS NMR and Mössbauer spectroscopies. For each sample, compositional change, as a function of crystal growth, is characterised by EMPA traverses, and the total chemical variation is reduced to a series of linear substitution mechanisms. Of particular interest are substitutions accommodating the variation in [4]B: (1) TB + YAl ↔ TSi + Y(Fe, Mn)2+, where transition metals are present, and (2) TB2 + YAl ↔ TSi2 + YLi, where transition metals are absent. Integration of all data sets delineates constraints on melt evolution and crystal growth mechanisms. [2] Uncertainty has surrounded the occurrence of [4]Al and [4]B at the T-site in tourmaline, because B is difficult to quantify by EMPA and Al is typically assigned to the octahedral Y- and Z-sites. Although both [4]Al and [4]B have been shown to occur in natural tourmalines, it is not currently known how common these substituents are. Using 11B and 27Al MAS NMR spectroscopy, the presence of [4]B and [4]Al is determined in fifty inclusion-free tourmalines of low transition-metal content with compositions corresponding to five different species. Chemical shifts of [4]B and [3]B in 11B spectra, and [4]Al and [6]Al in 27Al spectra, are well-resolved, allowing detection of very small (< ~0.1 apfu) amounts of T-site constituents. Results show that contents of 0.0 < [4]B, [4]Al < 0.5 apfu are common in tourmalines containing low amounts of paramagnetic species, and that all combinations of Si, Al and B occur in natural tourmalines.

Ce travail de thèse s’articule autour de la synthèse et de la caractérisation d’hydroxydes doubles lamellaires (HDLs) par une approche combinant spectroscopie vibrationnelle, RMN du solide et diffraction des rayons X. Les objectifs portent sur la description de la distribution cationique dans les feuillets ainsi que sur l’étude des propriétés structurales et dynamiques des espèces interfoliaires. Les investigations sont principalement menées pour des HDLs de type MgII/AlIII (ratio compris entre 2 et 4) avec une complexification progressive des espèces intercalées : de l’anion carbonate pour lequel les matériaux possèdent une affinité préférentielle, à d’autres anions inorganiques comme les halogénures, le perchlorate et le nitrate, pour finir sur des hybrides organo-minéraux formés par intercalation d’anions organiques/biomolécules (acides aminés et cyclodextrines). Les recherches effectuées ont permis de mettre en évidence un ordre cationique local au sein des feuillets, conservé après échange anionique. Par ailleurs, il a été possible de rationaliser les comportements propres à chaque espèce anionique dans l’espace interfoliaire, qui dépendent fortement de la densité de charge des feuillets, ainsi que du taux d’hydratation des composés. En particulier, la coexistence des anions carbonate et hydrogénocarbonate dans l’espace interfoliaire et leur dynamique d’échange avec le dioxyde de carbone atmosphérique sont révélées. D’autre part, une nouvelle sonde de dynamique interfoliaire par RMN 27Al est proposée. Enfin, l’étude pas à pas des HDLs intercalant tout d’abord l’oxalate puis des acides aminés a permis le transfert des connaissances obtenues pour les HDLs inorganiques aux hybrides organo-minéraux. Le manuscrit se termine sur une application des hybrides contenant des cyclodextrines pour le traitement d’eaux polluées par des composés organiques polycycliques
This thesis work is based on the synthesis and the characterization of layered double hydroxides (LDHs) by an approach combining vibrational spectroscopy, solid-state NMR and X-ray diffraction. The objectives include a description of the cations distribution in the layers, as well as a study of the structural and dynamic properties of the interlayer species. Investigations are mainly carried out for MgII/AlIII LDHs (ratio between 2 and 4) with an increased complexity of the intercalated species: from carbonate for which the materials have a preferential affinity, to other inorganic anions such as halides, perchlorate and nitrate, to finish with organo-mineral hybrids obtained by intercalation of organic anions/biomolecules (amino acids and cyclodextrins).The research carried out highlighted a local cationic order in the layers, preserved after anionic exchange. Furthermore, it has been possible to rationalize the behaviour of each anion in the interlayer space, which strongly depends on the layers charge density, as well as on the hydration state of the compounds. In particular, the coexistence between carbonate and hydrogenocarbonate anions in the interlayer space and their dynamic exchange with atmospheric carbon dioxide are revealed. On the other hand, a new interlayer dynamics probe by 27Al NMR is proposed. Finally, the step-by-step study of LDHs, first intercalating oxalate and then amino acids, allowed the transfer of the knowledge obtained for inorganic LDHs to organo-mineral hybrids. The manuscript ends with an application of cyclodextrins-containing hybrids for the treatment of water polluted with polycyclic organic compounds

This thesis describes the synthesis and characterisation of titania photocatalysts for incorporation into a polyethylene film. Monodisperse, anatase-phase titania nanoparticles are prepared and the synthesis conditions necessary for attraction to a laponite clay support are determined. Methods of preventing agglomeration of the laponite system such as the use of a polyethylene oxide surfactant or chemical modification of the laponite plate edges with a dimethyloctyl methoxysilane are also explored. Finally, photocatalytic studies on the laponite-supported titania nanoparticles are performed, and the compatibility and photoactivity of these materials in the polyethylene film are examined.

This thesis describes the synthesis and characterisation of titania photocatalysts for incorporation into a polyethylene film. Monodisperse, anatase-phase titania nanoparticles are prepared and the synthesis conditions necessary for attraction to a laponite clay support are determined. Methods of preventing agglomeration of the laponite system such as the use of a polyethylene oxide surfactant or chemical modification of the laponite plate edges with a dimethyloctyl methoxysilane are also explored. Finally, photocatalytic studies on the laponite-supported titania nanoparticles are performed, and the compatibility and photoactivity of these materials in the polyethylene film are examined.

The Queensland University of Technology (QUT) allows the presentation of a thesis for the Degree of Doctor of Philosophy in the format of published or submitted papers, where such papers have been published, accepted or submitted during the period of candidature. This thesis is composed of Seven published/submitted papers and one poster presentation, of which five have been published and the other two are under review. This project is financially supported by the QUTPRA Grant. The twenty-first century started with the resurrection of lignocellulosic biomass as a potential substitute for petrochemicals. Petrochemicals, which enjoyed the sustainable economic growth during the past century, have begun to reach or have reached their peak. The world energy situation is complicated by political uncertainty and by the environmental impact associated with petrochemical import and usage. In particular, greenhouse gasses and toxic emissions produced by petrochemicals have been implicated as a significant cause of climate changes. Lignocellulosic biomass (e.g. sugarcane biomass and bagasse), which potentially enjoys a more abundant, widely distributed, and cost-effective resource base, can play an indispensible role in the paradigm transition from fossil-based to carbohydrate-based economy. Poly(3-hydroxybutyrate), PHB has attracted much commercial interest as a plastic and biodegradable material because some its physical properties are similar to those of polypropylene (PP), even though the two polymers have quite different chemical structures. PHB exhibits a high degree of crystallinity, has a high melting point of approximately 180°C, and most importantly, unlike PP, PHB is rapidly biodegradable. Two major factors which currently inhibit the widespread use of PHB are its high cost and poor mechanical properties. The production costs of PHB are significantly higher than for plastics produced from petrochemical resources (e.g. PP costs $US1 kg-1, whereas PHB costs $US8 kg-1), and its stiff and brittle nature makes processing difficult and impedes its ability to handle high impact. Lignin, together with cellulose and hemicellulose, are the three main components of every lignocellulosic biomass. It is a natural polymer occurring in the plant cell wall. Lignin, after cellulose, is the most abundant polymer in nature. It is extracted mainly as a by-product in the pulp and paper industry. Although, traditionally lignin is burnt in industry for energy, it has a lot of value-add properties. Lignin, which to date has not been exploited, is an amorphous polymer with hydrophobic behaviour. These make it a good candidate for blending with PHB and technically, blending can be a viable solution for price and reduction and enhance production properties. Theoretically, lignin and PHB affect the physiochemical properties of each other when they become miscible in a composite. A comprehensive study on structural, thermal, rheological and environmental properties of lignin/PHB blends together with neat lignin and PHB is the targeted scope of this thesis. An introduction to this research, including a description of the research problem, a literature review and an account of the research progress linking the research papers is presented in Chapter 1. In this research, lignin was obtained from bagasse through extraction with sodium hydroxide. A novel two-step pH precipitation procedure was used to recover soda lignin with the purity of 96.3 wt% from the black liquor (i.e. the spent sodium hydroxide solution). The precipitation process is presented in Chapter 2. A sequential solvent extraction process was used to fractionate the soda lignin into three fractions. These fractions, together with the soda lignin, were characterised to determine elemental composition, purity, carbohydrate content, molecular weight, and functional group content. The thermal properties of the lignins were also determined. The results are presented and discussed in Chapter 2. On the basis of the type and quantity of functional groups, attempts were made to identify potential applications for each of the individual lignins. As an addendum to the general section on the development of composite materials of lignin, which includes Chapters 1 and 2, studies on the kinetics of bagasse thermal degradation are presented in Appendix 1. The work showed that distinct stages of mass losses depend on residual sucrose. As the development of value-added products from lignin will improve the economics of cellulosic ethanol, a review on lignin applications, which included lignin/PHB composites, is presented in Appendix 2. Chapters 3, 4 and 5 are dedicated to investigations of the properties of soda lignin/PHB composites. Chapter 3 reports on the thermal stability and miscibility of the blends. Although the addition of soda lignin shifts the onset of PHB decomposition to lower temperatures, the lignin/PHB blends are thermally more stable over a wider temperature range. The results from the thermal study also indicated that blends containing up to 40 wt% soda lignin were miscible. The Tg data for these blends fitted nicely to the Gordon-Taylor and Kwei models. Fourier transform infrared spectroscopy (FT-IR) evaluation showed that the miscibility of the blends was because of specific hydrogen bonding (and similar interactions) between reactive phenolic hydroxyl groups of lignin and the carbonyl group of PHB. The thermophysical and rheological properties of soda lignin/PHB blends are presented in Chapter 4. In this chapter, the kinetics of thermal degradation of the blends is studied using thermogravimetric analysis (TGA). This preliminary investigation is limited to the processing temperature of blend manufacturing. Of significance in the study, is the drop in the apparent energy of activation, Ea from 112 kJmol-1 for pure PHB to half that value for blends. This means that the addition of lignin to PHB reduces the thermal stability of PHB, and that the comparative reduced weight loss observed in the TGA data is associated with the slower rate of lignin degradation in the composite. The Tg of PHB, as well as its melting temperature, melting enthalpy, crystallinity and melting point decrease with increase in lignin content. Results from the rheological investigation showed that at low lignin content (.30 wt%), lignin acts as a plasticiser for PHB, while at high lignin content it acts as a filler. Chapter 5 is dedicated to the environmental study of soda lignin/PHB blends. The biodegradability of lignin/PHB blends is compared to that of PHB using the standard soil burial test. To obtain acceptable biodegradation data, samples were buried for 12 months under controlled conditions. Gravimetric analysis, TGA, optical microscopy, scanning electron microscopy (SEM), differential scanning calorimetry (DSC), FT-IR, and X-ray photoelectron spectroscopy (XPS) were used in the study. The results clearly demonstrated that lignin retards the biodegradation of PHB, and that the miscible blends were more resistant to degradation compared to the immiscible blends. To obtain an understanding between the structure of lignin and the properties of the blends, a methanol-soluble lignin, which contains 3× less phenolic hydroxyl group that its parent soda lignin used in preparing blends for the work reported in Chapters 3 and 4, was blended with PHB and the properties of the blends investigated. The results are reported in Chapter 6. At up to 40 wt% methanolsoluble lignin, the experimental data fitted the Gordon-Taylor and Kwei models, similar to the results obtained soda lignin-based blends. However, the values obtained for the interactive parameters for the methanol-soluble lignin blends were slightly lower than the blends obtained with soda lignin indicating weaker association between methanol-soluble lignin and PHB. FT-IR data confirmed that hydrogen bonding is the main interactive force between the reactive functional groups of lignin and the carbonyl group of PHB. In summary, the structural differences existing between the two lignins did not manifest itself in the properties of their blends.

Site-specific protein labelling presents an important tool for protein structural biology by spectroscopic techniques. This thesis focuses on the development of new spectroscopic labels and labelling strategies to improve the sensitivity, accuracy and scope of NMR and EPR spectroscopy experiments of proteins. Double electron–electron resonance (DEER) spectroscopy measures the distance between two paramagnetic metal centres introduced by site-specific attachment of suitable tag molecules. Good DEER tags possess rigid tethers to position their paramagnetic centres at a well-defined location relative to the protein and deliver narrow DEER distance distributions with high sensitivity, which can provide accurate information about protein flexibility. This thesis introduces new, cyclen-based Gd 3+ tags and small, Gd 3+ chelating tags designed to deliver narrow DEER distance distributions. Chapter 2 describes the development of two cyclen-based double-arm Gd 3+ tags designed for binding to the target protein at two and three points to obtain the narrowest Gd 3+ –Gd 3+ DEER distance distributions ever recorded with proteins. It also describes DEER distance measurements with the iminodiacetic acid tag attached to cysteine (Cys), where tags attached to two neighbouring Cys residues combine to chelate a single Gd 3+ ion. These results have been published in a journal article (Welegedara et al., Chem. Eur. J. 2017, 23, 11694−11702). Chapter 3 discusses two single-armed Gd 3+ tags, a cyclen-based Gd 3+ tag and a PyMTA tag that forms a heptadentate Gd 3+ binding motif. Both tags deliver the shortest possible tethers to cysteine residues and are shown to produce narrow DEER distance distributions in proteins. For applications in NMR spectroscopy, proteins can be labelled site-specifically with NMR probes such as trimethylsilyl (TMS) probes, which deliver readily detectable 1D 1 H-NMR signals. Introduction of paramagnetic tags and NMR probes by attachment to Cys residues requires mutations of native Cys residues to achieve site-selectivity, which is not possible with structurally and functionally important Cys residues. Chapter 4 demonstrates a solution to this limitation by introducing a selenocysteine (Sec) residue, which can be selectively reacted with probe molecules at slightly acidic pH without iiiaffecting naturally occuring Cys residues. To achieve this, a Sec residue was introduced as a photocaged unnatural amino acid (UAA), PSc, to bypass the otherwise unavoidable challenges associated with the natural Sec incorporation mechanism. UV illumination of PSc yielded Sec with no evidence for the formation of undesired dehydroalanine byproducts. Selective tagging of Sec residues with TMS tags was shown to deliver a useful tool for studies of ligand binding to proteins. These results have also been published in a journal article (Welegedara et al., Bioconjugate Chem. 2018, 19, 2257−2264). Site-selective incorporation of isotope-labelled PSc, photolysis and anaerobic deselenization opens an indirect route to labelling a single specific alanine residue in a protein with stable isotopes. Such samples would have important applications in heteronuclear NMR, as they allow the selective detection of the labelled alanine residue with maximal spectral resolution. As shown in Chapter 5, deselenization of selenoproteins into alanine is possible but requires extremely anaerobic conditions to eliminate serine as the main unwanted byproduct. A range of UAAs has been developed to serve as spectroscopic probes or facilitate the introduction of spectroscopic probes via biorthogonal reactions. The increasing demand for proteins with different UAAs and the significant cost of some of these UAAs has led to increasing popularity of cell-free protein synthesis (CFPS) systems, which use amino acids more sparingly than in vivo expression systems. Mutants of pyrrolysyl-tRNA synthetase (PylRS)/tRNA CUA pairs have been developed into a particularly versatile tool for the incorporation of many structurally different UAAs, but most produce disappointedly poor protein yields in vivo. Chapter 6 describes attempts to develop an in- house CFPS system with a PylRS/tRNA CUA pair. In addition, the polyspecific G2 synthetase has been reported to facilitate the incorporation of sterically demanding UAAs and Chapter 7 of this thesis describes attempts to develop a CFPS system with the G2 synthetase.

Two separate experimental searches for second-order weak nuclear decays to excited final states were conducted. Both experiments were carried out at the Kimballton Underground Research Facility to provide shielding from cosmic rays. The first search is for the two-neutrino double-beta decay of 96Zr to excited final states of the daughter nucleus, 96Mo. As a by product of this experiment, the beta decay of 96Zr was also investigated. Two coaxial high-purity germanium detectors were used in coincidence to detect gamma rays produced by the daughter nucleus as it de-excited to the ground state. After collecting 1.92 years of data with 17.91 g of enriched 96Zr, half-life limits at the level of 10^20 yr were produced. Measurements of this decay are important to test neutrinoless double-beta decay nuclear matrix element calculations, which are necessary to extract the neutrino mass from a measurement of the neutrinoless double-beta decay half-life.

The second experiment is a search for the resonantly-enhanced neutrinoless double-electron capture decay of 156Dy to excited states in 156Gd. Double-electron capture is a possible experimental alternative to neutrinoless-double beta decay, which could distinguish the Dirac or Majorana nature of the neutrino. Two clover high-purity germanium detectors were used in coincidence to investigate the decay. A 213.5 mg enriched 156Dy sample was observed for 0.635 year, producing half-life limits of 10^17 yr. The limits produced by both of these experiments are currently the most stringent limits available for these decays.

Dissertation

Pulse electron paramagnetic resonance (EPR) distance measurements using double electron-electron resonance (DEER) experiments have been established as a powerful tool in structural biology. DEER experiments have the ability to measure the distance between two paramagnetic centres in biological macromolecules in the range of about 2 to 8 nm. The paramagnetic centres are usually introduced into proteins by site-directed spin labelling (SDSL) of cysteine residues. This thesis is based on the use of new lanthanide binding tags (LBTs) for paramagnetic nuclear magnetic resonance (NMR) spectroscopy (reported in papers 2 and 5), DEER distance measurements (reported in papers 1 and 3) and time-resolved luminescence resonance energy transfer (LRET) experiments (reported in paper 4). In particular, use of two complementary techniques, DEER experiments and paramagnetic NMR spectroscopy, was investigated for the study of conformational changes of proteins as a result of protein-ligand interactions. Two proteins were studied, the E. coli aspartate/glutamate binding protein (DEBP) and human calmodulin (CaM). Both proteins have different ligand binding characteristics: DEBP binds to small organic molecules, while CaM binds to specific peptide sequences. DEBP is a periplasmic binding protein responsible for the transport of aspartic acid and glutamic acid across the cell membrane and widely used in the design of biosensors of glutamate. The protein is composed of two domains, which bind one amino acid molecule at the domain interface. As DEBP contains a disulfide bond, an alternative cysteine-independent approach for site-specific protein tagging was used, which involved the use of genetically encoded unnatural amino acids that were site-specifically incorporated into proteins using orthogonal amber-suppressor tRNA/aminoacyl-tRNA synthetase systems. p-azido-L-phenylalanine (AzF) residues were incorporated into DEBP at different positions and paramagnetic lanthanide tags were attached to AzF via Cu(I)-catalyzed click chemistry (papers 1 and 2). Multiple Gd3+-Gd3+ distances measured by DEER experiments were used to define the metal positions, subsequently allowing deltachi-tensor determinations from sparse sets of pseudocontact shifts (PCSs). Both the DEER data and PCSs were in agreement with the closed conformation observed in the crystal structure of the homologue from S. flexneri. On the other hand, the PCSs indicated that the transition to the substrate-free protein involves a movement of the two domains as rigid entities relative to each other. CaM is a two-domain protein that acts as an intermediate messenger protein and intracellular calcium sensor, which responds to changes in Ca2+ concentrations by large conformational changes that enable binding to a range of different proteins involved in signalling pathways. The conformational changes of CaM upon binding of the myristoylated alanine-rich C-kinase substrate (MARCKS) peptide were studied using DEER experiments and paramagnetic NMR. MARCKS was chosen due to its unique binding mode compared to other CaM-target peptide complexes. The DEER results indicated that the binding of MARCKS peptide to CaM does not lock CaM in a single conformation. Deviations between the crystal and solution structure of the complex were also evident in the measured PCS data, highlighting the conformational flexibility of CaM that allows CaM to bind to diverse target proteins.

Concrete, due to its low cost, durability and fire resistance, is one of the world’s most widely used construction materials. Concrete is typically reinforced with steel bars and welded wire mesh. Since the cost of steel is increasing and steel corrosion is a significant contributor to structural failure, it is advantageous to find an alternative replacement reinforcement material which can not only replace the steel, but also resist corrosion. Over the past few decades, polymeric fibres have been used as concrete reinforcement. The chemical bond between the polymeric fibre and the cementitious matrix is an important factor in the fibre’s performance as a concrete reinforcement. Despite the great importance of the chemical bonding at the polymeric fibre/concrete interface, the chemical bonding at the interface is not well understood. To investigate the chemical interactions between polymeric materials and concrete, model systems of polymeric powder/white cement and polymeric fibre/white cement were chosen, where white cement was chosen for its suitability for nuclear magnetic resonance (NMR) experiments. The chemical interactions between poly(ethylenevinyl acetate) (EVA), poly(ether imide) (PEI), and poly(vinylidene fluoride) (PVDF) polymeric powders were studied via 13C NMR spectroscopy. It was found that EVA admixture undergoes hydrolysis in a cementitious matrix and follows a pseudo-second order kinetics model up to 32 days of cement hydration. PEI was also found to undergo hydrolysis at the imide functional group in a cementitious matrix. PVDF powder undergoes dehydrofluorination in the cementitious environment, producing a brown coloured polymer which is a result of conjugation of the polymer backbone. The interfacial transition zone between fluoropolymeric powder/white cement and steel and polymeric fibres (high density polyethylene/polypropylene, poly(vinyl alcohol), PEI, PVDF, and Nylon 6.6) was studied at short range using 19F, 27Al, and 43Ca NMR spectroscopy and at long range using the scanning electron microscopy/energy dispersive spectroscopy method. It was concluded that the chemistry of polymeric fibres themselves can alter the surrounding interfacial transition zone such that the calcium silicate hydrate favours a tobermorite or jennite-like structure, which could contribute to a strong or weak interface.

Functionalized nanoparticles provide a wide range of potential applications for Biological Mass Spectrometry (MS). Particularly, we have studied the effects of chromophore activity on the performance of gold nanoparticles (AuNPs) capped with substituted azo (-N=N-) dyes for analyte ion production in Laser Desorption Ionization Mass Spectrometry (LDI-MS) conditions. A series of aromatic thiol compounds were used as Self-Assembled Monolayers (SAM) to functionalize the surface of the AuNPs. Results indicate that AuNPs functionalized with molecules having an active azo chromophore provide enhanced analyte ion yields than the nanoparticles capped with the hydrazino analogs or simple substituted aromatic thiols. We have also conducted experiments using the azo SAM molecules on 2, 5, 20, 30, and 50 nm AuNPs exploring the changes of Relative Ion Yield (RIY) with increased AuNP diameters. Our results indicate that the role of the SAM to drive energy deposition decreases as the size of the AuNP increases. It was determined that 5 nm is the optimum size to exploit the benefits of the SAM on the ionization and selectivity of the AuNPs.

Spin selective MQ-SQ correlation has been demonstrated by either selective pulses in homo-nuclear spin systems in isotropic and weakly orienting chiral media or by nonselective pulses in hetero-nuclear spin systems in strongly aligned media. As a consequence of the spin selective correlation, the coherence transfer pathway from MQ to SQ is spin state selective. This two dimensional approach enables the utilization of the passive couplings (remote couplings) to break a complex one dimensional spectrum into many sub spectra. Each sub spectrum contains fewer transitions and hence fewer couplings (active couplings). The role of the passive couplings is to displace the sub spectra and measurement of the displacements taking into account their relative tilt provides the magnitude of the passive couplings along with relative signs. Further possibility of a spin state selective MQ-SQ resolved experiment to determine very small remote couplings otherwise buried within linewidth in one dimensional spectrum has been demonstrated. The resolution of the multiple quantum spectrum in indirect dimension has also been exploited to separate the sub spectra. The technique renders the analysis of complex spectrum in isotropic system much simpler. The potentialities of the technique have also been demonstrated for discrimination of optical enantiomers and derivation of the residual dipolar couplings from very complicated spectrum. The second order spectrum in strongly aligned media restrict selective excitation, however in hetero-nuclear spin system the nonselective pulses on protons do not interact with the hetero-nuclear spins. Thus the weakly coupled part of a strongly coupled spectrum has been exploited for simplifying the second order spectrum and thereby its analysis. Thus several methodologies derived from spin selective correlation has been demonstrated. Enantiopure spectrum has been recorded from a mixture of R and S enantiomers by a novel pulse scheme called Double Quantum Selective Refocusing Experiment. The dipolar coupled methyl protons in weakly orienting media are utilized. The selective excitation of double quantum coherence reduces the three spin system into a two spin system and remote couplings are refocused which otherwise leads to broadening. The sum of passive couplings being different for the enantiomers resolution in the DQ dimension is enhanced and thereby their discrimination. Finally several decoupling schemes has been compared in the indirect dimension of HSQC experiment to resolve 13C satellite spectra otherwise buried within line width for increased confidence in determining hetero-nuclear framework information.