Microporous catalysts belong to a class of materials that exhibit pore networks in the molecular dimension, that is, channel diameters less than 2 nm. The industrially most important microporous catalysts are zeolites, which are crystalline aluminosilicates and consist of interlinked alumina (AlO4) and silica (SiO4) tetrahedra forming pores and cavities of molecular dimensions. Zeolites can act as very strong solid acids and function as heterogeneous catalysts in various industrial processes used to obtain polyethylene terephthalate (PET) or polyvinyl chloride (PVC). They are crucial for products with a significant market demand such as plastics used in bottles, packaging materials and household consumable goods as well as for coatings of pharmaceutical pills and detergents. Recently, zeolites have been found to have increased applications in aqueous and biphasic reactions that use reactants derived from biomass to arrive at petrochemical products. Thus, surface acidity in zeolites is crucial to understand to tune parameters such as activity and selectivity of zeolite catalysts to optimize product distributions. The objective of this dissertation was to validate the use of non-invasive nuclear magnetic resonance (NMR) techniques to characterise surface acidity in zeolites by benchmarking the NMR results to various more established zeolite characterisation techniques, such as Fourier transform infrared (FTIR) spectroscopy and temperature-programmed desorption (TPD). Furthermore, the use of the tapered element oscillating microbalance (TEOM) to characterise internal and external acidity in zeolites was explored. IR and TPD techniques were used to assess important acidity parameters such as type, number, location and strength of acid sites of ZSM-5 zeolites with varying silica-alumina ratio (SAR = SiO2/Al2O3). The use of NMR relaxation time analysis of pyridine adsorbed in ZSM-5 was then explored as a model system to study surface acidity in microporous materials. Correlation with pyridine TPD results suggested that NMR relaxation time analysis probes the effective strength of pyridine adsorption sites, which varies with SAR. NMR relaxation time analysis was then further shown to be applicable to characterise non-acidic surface properties such as the hydrophilic and hydrophobic surface character. Lastly, the NMR techniques developed at high magnetic field strength (300 MHz) were transferred to a portable, low-cost benchtop low-field (43 MHz) magnet and shown to be applicable for base probe molecules other than pyridine, that is, ammonia (NH3) as well as zeolite framework types other than ZSM-5, that is, chabazite (CHA).

Standard catalyst characterisation techniques such as gas adsorption porosimetry and mercury porosimetry only account for some of the physical heterogeneity of the catalyst surface. They completely ignore the chemical heterogeneity present and in most cases consider pores present in the medium to be independent of each other. Thus, most results of characterisation (pore space descriptors such as BET surface area, BJH pore size distribution, mercury porosimetry surface area, etc.) are not accurate. This has been a major issue that remains to be resolved during the characterisation of fresh and coked catalysts. In this thesis, the use of a multi-component adsorption system is recommended as a step-change solution to this limitation. Two approaches are adopted. Firstly, integrated nitrogen-waternitrogen gas adsorption experiments are performed on fresh and coked catalysts. This established the significance of pore coupling by showing the presence of advanced adsorption. The method also helped to determine the location of coke deposits within catalysts and indicated that water vapour adsorption was a good probe to understand the sites responsible for coking. Secondly, coadsorption of immiscible liquids – cyclohexane and water – was performed on fresh and coked catalysts following which the displacement of cyclohexane by water was studied using NMR relaxometry and diffusometry. This novel approach takes the wettability of the surface into consideration, unlike the former methods. It is therefore a method that accounts for the chemical heterogeneity of the surface. It also helped determine the location of coke within catalysts. The different approaches are presented in the context of combustion of heavy oil in bitumen reservoirs, and the use of supercritical conditions that help to dissolve coke precursors in the isomerisation of 1-hexene. Thus, the solutions provided in this thesis are directions in which catalyst characterisation, especially distinguishing fresh and coked catalysts, and other porous materials, must be carried out.

The HIV-1 transactivator of transcription (Tat) is a protein essential for both viral gene expression and virus replication. Tat is an RNA-binding protein that, in cooperation with host cell factors cyclin T1 and cyclin-dependent kinase 9, regulates transcription at the level of elongation. Tat also interacts with numerous other intracellular and extracellular proteins, and is implicated in a number of pathogenic processes. The Tat protein is encoded by two exons and is 101 residues in length. The first exon encodes a 72-residue molecule that activates transcription with the same proficiency as the full-length protein. The physico-chemical properties of Tat make it a particularly challenging target for structural studies: Tat contains seven cysteine residues, six of which are essential for transactivation, and is highly susceptible to oxidative cross-linking and aggregation. In addition, a basic segment (residues 48-57) gives the protein a high net positive charge of +12 at pH 7, endowing it with a high affinity for anionic polymers and surfaces. In order to study the structure of Tat, both alone and in complex with partner molecules, we have developed a system for the bacterial expression and purification of polyhistidine-tagged and isotopically enriched (in 15N and 15N /13C) recombinant HIV-1 Tat1-72 (BH10 isolate) that yields large amounts of protein. These preparations have facilitated the assignment of 95% of the non-proline backbone resonances using heteronuclear 3-dimensional nuclear magnetic resonance (NMR) spectroscopy. Analysis by mass spectrometry and NMR demonstrate that the cysteine-rich Tat protein is unambiguously reduced and monomeric in aqueous solution at pH 4. NMR chemical shifts and coupling constants suggest that it exists in a disordered conformation. Line broadening and multiple peaks in the cysteine-rich and core regions suggest that transient folding occurs in two of the five sequence domains. NMR relaxation parameters were measured and analysed by spectral density and model-free approaches both confirming the lack of structure throughout the length of the molecule. The absence of a fixed conformation and the observation of fast dynamics are consistent with the ability of the Tat protein to interact with a wide variety of proteins and nucleic acid lending further support to the concept that Tat exists as an intrinsically disordered protein. / October 2007

The HIV-1 transactivator of transcription (Tat) is a protein essential for both viral gene expression and virus replication. Tat is an RNA-binding protein that, in cooperation with host cell factors cyclin T1 and cyclin-dependent kinase 9, regulates transcription at the level of elongation. Tat also interacts with numerous other intracellular and extracellular proteins, and is implicated in a number of pathogenic processes. The Tat protein is encoded by two exons and is 101 residues in length. The first exon encodes a 72-residue molecule that activates transcription with the same proficiency as the full-length protein. The physico-chemical properties of Tat make it a particularly challenging target for structural studies: Tat contains seven cysteine residues, six of which are essential for transactivation, and is highly susceptible to oxidative cross-linking and aggregation. In addition, a basic segment (residues 48-57) gives the protein a high net positive charge of +12 at pH 7, endowing it with a high affinity for anionic polymers and surfaces. In order to study the structure of Tat, both alone and in complex with partner molecules, we have developed a system for the bacterial expression and purification of polyhistidine-tagged and isotopically enriched (in 15N and 15N /13C) recombinant HIV-1 Tat1-72 (BH10 isolate) that yields large amounts of protein. These preparations have facilitated the assignment of 95% of the non-proline backbone resonances using heteronuclear 3-dimensional nuclear magnetic resonance (NMR) spectroscopy. Analysis by mass spectrometry and NMR demonstrate that the cysteine-rich Tat protein is unambiguously reduced and monomeric in aqueous solution at pH 4. NMR chemical shifts and coupling constants suggest that it exists in a disordered conformation. Line broadening and multiple peaks in the cysteine-rich and core regions suggest that transient folding occurs in two of the five sequence domains. NMR relaxation parameters were measured and analysed by spectral density and model-free approaches both confirming the lack of structure throughout the length of the molecule. The absence of a fixed conformation and the observation of fast dynamics are consistent with the ability of the Tat protein to interact with a wide variety of proteins and nucleic acid lending further support to the concept that Tat exists as an intrinsically disordered protein.

No description available.

The advancement of both electronics and instrumentation technology has fostered the development of multi-physics platforms that can probe the earth’s subsurface. Remote, non-destructive testing techniques have led to the increased deployment of electromagnetic waves in sensor technology. Electromagnetic wave techniques are reliable and have the capacity to sense materials and associated properties with minimal perturbation. However, meticulous data analyses and mathematical derivations reveal inconsistencies in some formulations. Thus, revisiting the fundamental physics that underlies both electrical impedance experimental setups and electromagnetic properties are paramount. This study aims to unravel inherent limitations in the understanding of the relationships between electromagnetic and non-electromagnetic properties that are relevant to the characterization of fluids in porous media. These correlations pervade porosity, permeability, specific surface, pore size distribution, tortuosity, fluid discrimination, diffusion coefficient, degree of saturation, viscosity, temperature, phase transformation, miscibility, salinity, and the presence of impurities. The focus is on the assessment of liquids, soils, rocks, and colloids using broad spectral frequency complex permittivity, conductivity, magnetic permeability, and nuclear magnetic resonance relaxometry. Broadband electrical properties measurement for saturated porous media can provide multiple physical phenomena: Ohmic conduction, electrode polarizations, Maxwell-Wagner spatial polarizations, rotational, and segmental polarizations. Liquids dominate the electromagnetic signatures in porous media as dry minerals are inherently non-polar and non-conductive. Results reveal that voltage drops due to the discontinuity of charge-carrier at the electrode-electrolyte interface named electrode polarization inherently affect the low-frequency electrical measurements both in two- and four-probe configurations. Rotational polarizations that occur in MHz-GHz ranges are defined by the electrical dipole moment and effective molecular volume. Both viscosity and effective molecular volume govern the NMR transverse relaxation time. An engineered soil suspension with ferromagnetic inclusions exhibits excellent characteristics for drilling fluid application. Overall, the study highlights the complementary nature of conductivity, permittivity, and NMR relaxation for the advanced characterization of fluid saturated geomaterials.

No description available.

Carbohydrates are essential biomolecules that decorate cell membranes and proteins in organisms. They are important both as structural elements and as identification markers. Many biological and pathogenic processes rely on the identification of carbohydrates by proteins, thereby making them attractive as molecular blueprints for drugs. This thesis describes how NMR spectroscopy can be utilized to study carbohydrates in solution at a molecular level. This versatile technique facilitates for investigations of (i) shapes, (ii) motions and (iii) interactions. A conformational study of an E. coli O-antigen was performed by calculating atomic distances from NMR NOESY experiments. The acquired data was utilized to validate MD simulations of the LPS embedded in a membrane. The agreement between experimental and calculated data was good and deviations were proven to arise from spin-diffusion. In another study presented herein, both the conformation and the dynamic behavior of amide side-chains linked to derivatives of D-Fucp3N, a sugar found in the O-antigen of bacteria, were investigated. J-couplings facilitated a conformational analysis and 13C saturation transfer NMR experiments were utilized to measure rate constants of amide cis-trans isomerizations. 13C NMR relaxation and 1H PFG diffusion measurements were carried out to explore and describe the molecular motion of mannofullerenes. The dominating motions of the mannofullerene spectral density were found to be related to pulsating motions of the linkers rather than global rotational diffusion. The promising inhibition of Ebola viruses identified for a larger mannofullerene can thus be explained by an efficient rebinding mechanism that arises from the observed flexibility in the linker. Molecular interactions between sugars and caffeine in water were studied by monitoring chemical shift displacements in titrations. The magnitude of the chemical shift displacements indicate that the binding occurs by a face to face stacking of the aromatic plane of caffeine to the ring plane of the sugar, and that the interaction is at least partly driven by solvation effects. Also, the binding of a Shigella flexneri serotype Y octasaccharide to a bacteriophage Sf6 tail spike protein was investigated. This interaction was studied by 1H STD NMR and trNOESY experiments. A quantitative analysis of the STD data was performed employing a newly developed method, CORCEMA-ST-CSD, that is able to simulate STD data more accurately since the line broadening of protein resonances are accounted for in the calculations. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript.</p>

NMR relaxation and Raman lineshape analysis are well known methods for the study of molecular reorientational dynamics in liquids. The combination of these two methods provides another approach to tackle the characterization of molecular dynamics in liquids. Investigations presented here include (1) NMR relaxation study of polycyclic compounds in solution, (2) the study of nitromethane reorientational dynamics using the NMR and Raman methods, and (3) Raman lineshape analysis of reorientation hexafluorobenzene/benzene mixtures.

No description available.