This thesis discusses the formation of metal-organic and organic structures grown on surfaces using bottom-up self-assembly techniques. Three systems are investigated primarily using scanning probe microscopy techniques. The growth of metal-organic frameworks (MOFs) on functionalised surfaces is investigated using high resolution atomic force microscopy (AFM). The earliest stages of MOF crystal nucleation are imaged using a layer-by-layer (LBL) growth technique and the ability to track the growth of individual nanocrystallites throughout the LBL process is demonstrated. This LBL method has been suggested as a route to fabricating epitaxially grown, oriented thin-films of MOFs. However, results from these studies indicate that, rather than a uniform crystalline layer, the morphology is that of a preferentially oriented but laterally polycrystalline film and the growth rates of the individual nanocrystallites exceed those expected for a LBL growth mode. This has significant implications for the fabrication of novel devices that incorporate MOFs due to the presence of domain boundaries and defects. Self-assembled monolayers of light-harvesting porphyrin nanorings are investigated with scanning tunnelling microscopy (STM) and AFM. The nanorings are found to form large supramolecular networks in ambient conditions on graphite and boron nitride surfaces. The size and order of these networks is found to be dependent on the number of porphyrin macrocycles that make up each ring. In addition, simulations of isolated nanorings are also performed using Monte Carlo methods to model the distortion previously been observed for isolated nanorings on gold surfaces. These are discussed in the context of spectroscopic measurements which suggest that both size dependent and thermally induced distortion affects the lifetime and delocalisation of excited states in these molecules. Graphene is grown on hexagonal boron nitride surfaces using high-temperature molecular beam epitaxy. Large domains of monolayer graphene are successfully grown and are investigated using AFM and Raman spectroscopy. These domains are found to exhibit hexagonal moiré patterns on the graphene surface which is suggestive of orientational alignment with the underlying boron nitride substrate. Regions with high period and distorted moiré patterns are also observed which suggest that the graphene is under tensile strain which is attributed to the high growth temperatures used. The strain is found to significantly affect the Raman spectrum of graphene and a relationship between the strain and the shifting of Raman spectral peaks is determined. Successful attempts are also made to modify the strain in the graphene monolayer using an AFM tip which is observed to relax when defects are introduced in a controlled manner to the graphene monolayer. These results represent new approaches to the introduction and control of strain in graphene which may be useful for the fabrication of high-performance graphene devices.

The primary focus of this work is the investigation into the nature and origin of the electron density between the ortho-hydrogens in the higher energy, planar transition state of biphenyl. This interaction has been the subject of debate within the scientific community for almost three decades with no clear consensus being made. Since the distance between these hydrogens is smaller than their summed van der Waals radii (2.4 Å), classically one can assume that they partake in a steric clash, however the Quantum Theory of Atoms in Molecules (QTAIM) depicts a bond path for this H,H contact. This presence of a bond path caused the rift in the scientific community. To investigate the problem, we made use of cross-section decomposition analysis whereby the electron density at any given coordinate is decomposed into the components that contribute to its presence. In this dissertation, three methods using this analysis were made, namely (i) MO-ED, (ii) FALDI-ED, and (iii) NBO-ED. These represent the decomposition products that the density is decomposed into; the MO-ED method decomposed the density between the ortho-hydrogens into its molecular orbital (MO) contributions, the FALDI-ED method decomposed the density into fragment and diatomic contributions, and the NBO-ED method decomposed the density into its natural bond orbital (NBO) contributions. With all three methods, when decomposing the density along eigenvector-2 from the bond critical point (BCP) between the ortho-hydrogens in the planar conformer, it was found that the total electron density is concentrating, shown by the directional second partial derivative. This means that the electron density is purposefully accumulated in the H,H contact rather than dissipated as one would expect from a classical steric clash. Furthermore, this density decomposition analysis revealed that this density is due to a large molecular-wide delocalisation, rather than a classical 2-centred approach, with the largest contributions (in both conformers) being from the two covalent ortho C-H bonds. This delocalisation forms a density channel between two hydrogens, of an overwhelmingly concentrating/bonding nature, forming a weak covalent bond. Due to these findings, it is clear that the classical idea of a steric clash cannot be the case for this system, and that QTAIM correctly predicts the bond path between these ortho-hydrogens. / Dissertation (MSc (Chemistry))--University of Pretoria, 2021. / Chemistry / MSc (Chemistry) / Unrestricted

1) species show a preference for the MJ = ±1 sub-levels. For these bands the electronic alignment is very similar to that observed in the dissociation of OCS, indicating a similar mechanism, at least in the exit channel, is responsible for the polarisation in both systems.

Monolayer organic thin films and heterostructures are of great interest for their optical and electronic properties and as systems which allow the interplay between the structural and functional properties of organic molecules to be investigated. In the first experimental section of this thesis, sub-monolayer coverages of perylene tetracarboxylic diimide (PTCDI) were grown on hBN substrates and found to form needle-like monolayer islands at room temperature, while higher growth temperatures gave larger monolayer islands. The molecular packing of monolayer PTCDI was confirmed, using AFM, to correspond to the canted phase. The 0-0 fluorescence peak of this structure was found to occur at 2.208 ± 0.002 eV. The fluorescence of multi-layer PTCDI samples was mapped, with additional peaks measured at 2.135 ± 0.002 eV (580.7 ± 0.5 nm) and 2.118 ± 0.002 eV (585.4 ± 0.5 nm). Relating the morphology and fluorescence of such films using AFM and fluorescence microscopy is a promising way to investigate structural effects on the optical properties of multi-layer organic systems. Using solution deposition techniques, the PTCDI-melamine supramolecular network and the canted phase of PTCDI were deposited on hBN. The molecular packing of both structures was confirmed using AFM and the 0-0 fluorescence peaks were measured to be 2.245 ± 0.002 eV and 2.214 ± 0.002 eV for the PTCDI-melamine network and PTCDI respectively. The fluorescence of sublimed PTCDI, solution deposited PTCDI, PTCDI-melamine and measurements of Me-PTCDI doped helium nano droplets (HND) were compared. A 0.031 ± 0.002 eV red shift was measured from PTCDI-melamine to PTCDI while a 0.346 ± 0.002 eV red shift was measured from doped HND to PTCDI on hBN. A second perylene derivative, perylene tetracarboxylic dianhidride (PTCDA), was also deposited on hBN. Comparing the fluorescence of PTCDA monolayers on various dielectric substrates suggested a large shift due to the coupling of transition dipole moments and image dipoles beneath the dielectric surface. The shift between PTCDI and PTCDI-melamine was attributed to the coupling of transition dipole moments, for which the exciton bandstructure of both phases has been calculated with and without screening. The growth of sublimed C60 was also investigated, with monolayer islands observed for growth at room temperature and faceted bi-layer islands observed at 212 °C. The growth of PTCDI/C60 ¬heterostructures was also investigated, with C60 found to form monolayer islands on monolayer PTCDI at room temperature. At higher growth temperatures, C60 was found to form multilayers, with a reduced island density at PTCDI island edges, suggesting upward and downward hopping from the PTCDI surface to the second C60 layer and hBN respectively. C60 was found to quench the fluorescence of PTCDI and led to a 0.032 ± 0.02 eV blue shift. Finally, the growth of cyanuric acid-melamine (CA.M) on CVD graphene and CA.M/PTCDI heterostructures on hBN was investigated. Cyanuric acid-melamine was found to form monolayers with a honeycomb packing structure on CVD graphene. On monolayers of CA.M, PTCDI was found to form needle-like monolayer islands, the row direction of PTCDI is thought to have an on-axis registry with the substrate. Finally, the fluorescence of CA.M/PTCDI heterostructures on hBN was measured, with a 0.045 ± 0.002 eV blue shift from PTCDI on hBN.

Clostridium autoethanogenum is an important organism for biofuel production. Other 'omics' approaches have been used to understand the mode of operation of the organism but metabolomics gives information on the cellular activities in the cell. Metabolomics combined with other 'omics' data can provide a deeper understanding for pathway interpretation. This project sets out to develop an analytical method that is suitable for analysis of highly charged polar compounds found in C. autoethanogenum metabolic pathways. Also investigate suitable isotope labelled internal standards to improve matrix effects to the metabolites as a result of the biological matrix. A high-throughput hydrophilic interaction liquid chromatography isotope dilution mass spectrometry (HILIC-IDMS) was developed and validated using high resolution hybrid orbital trap MS for both targeted and untargeted metabolomics analysis of intracellular metabolic pathways of Clostridium autoethanogenum. Extraction of intracellular metabolites from C. autoethanogenum was achieved using a specifically developed sample preparation protocol using freeze thaw cycles (freeze in liquid nitrogen and thaw on ice repeated 3x). A total of 133 metabolites were monitored and validated. Limits of detection (LODs) ranged from 0.001 µM to 5 µM reported for compounds such as NADPH and NADH. Limits of quantification (LOQs) for all metabolites ranged from 0.001 µM to 10 µM for metabolites such as glucose-6-phosphate and glyceraldehyde-3 phosphate. Precision and accuracy were evaluated for all metabolites and found to be within the acceptable limits of ±15 % with few exceptions for some nucleotides and organic acids. Stable isotopically labelled internal standards were generated from C. pasteurianum cells that provided coverage for about 100 metabolites. This enabled absolute intracellular concentrations to be obtained in combination with the estimated cell volume of C. autoethanogenum that was obtained from microscopy and flow cytometry measurements. The developed HILIC-IDMS method was applied to various solvent production optimisation experiments conducted using C. autoethanogenum and the main findings are reported below. In chapter 4, the HILIC-IDMS method was applied to C. autoethanogenum in an experiment where the pH of the media was reduced to improve ethanol and solvent production. The metabolomics studies of this experiment gave intracellular concentrations that differentiated the acidogenic phase from the solventogenic phase. A total of 86 metabolites were quantified in this experiment. Intermediates in the tricarboxylic acid (TCA) cycle were the most affected during the acidogenic/solventogenic transition. Metabolites concentrations were used for metabolic pathways analysis to understand the pathways affected during the pH shift. The pathway analysis also confirmed the TCA cycle was the most affected pathway during the acidogenic/solventogenic transition. In chapter 5, The HILIC-IDMS method was applied to a gas shift experiment to optimise ethanol and solvent production. Gas shift is another approach that can be used to optimise solvent production in similar as the pH shift experiment. The use of gas shift to induce solventogenic phase can be difficult as C. autoethanogenum has little tolerance for high levels of CO hence the increase in gas (CO) flow rate has to be done in a gradual fashion. Equally, TCA intermediates were observed to be the most affected as observed in the pH shift experiment. In chapter 6, the method was applied to a study where pantothenate and phosphate concentrations in the growth media of C. autoethanogenum were reduced to increase ethanol production. Pantothenate is the precursor for coenzyme A (CoA) production and metabolomics study confirmed a decrease in CoA concentration when pantothenate concentration was reduced. Metabolomics also showed decrease in concentration of metabolites directly linked to CoA synthesis such as L- Aspartate. Metabolic pathway analysis also confirmed the pantothenate and CoA biosynthesis and its associated pathways were the most affected pathways during the pantothenate-limiting phase. Both targeted and untargeted metabolomics analysis were performed on these nutrient-limiting experiments and there were clear differences between the two different conditions before and after nutrient limitation. Supervised multivariate data analysis using OPLS-DA was used to compare higher pantothenate and low pantothenate concentration and there were clear separation and clustering between the two conditions. Cross validation obtained for R2Y and Q2 were 0.993 and 0.941 respectively. OPLS-DA plots for phosphate limitation also showed clustering and separation between the high phosphate concentration and reduced phosphate concentration with R2Y and Q2 0.981and 0.837 respectively. In conclusion, a novel high-throughput HILIC-IDMS method was developed and validated for analysis of different classes of polar compounds in bacteria. The method has the potential to be applied in other biological matrices for coverage of diverse range of polar compounds.

This Thesis describes the application of niobium oxide and niobium phosphate as solid acids for conducting continuous flow reactions, such as the Friedel-Crafts Reaction and the Skraup Reaction, and also as supports for photosensitiser immobilisation. Chapter 1 introduces the concepts of green and sustainable chemistry, and give a review of niobium and niobium compounds, especially niobium oxide and niobium phosphate as well as their applications. A summary of flow chemistry is also presented. The continuous flow systems used to conduct the work of this Thesis are described in Chapter 2. Chapter 3 introduces continuous alkylation of aniline with dimethyl carbonate or methanol over niobium solid acids. The synthesis process is automated by a self-optimisation system to search the best conditions for different products, including the NH2 group methylation product monomethyl aniline and dimethyl aniline, and the Friedel-Crafts alkylation product N,N-dimethyl-p-toluidine. Chapter 4 describes the first exploration of the continuous Skraup synthesis of quinolones with heterogeneous catalyst niobium phosphate. A dissymmetrics substituted quinoline compound, 4-(quinolin-6-yl methyl)aniline, was synthesized, and its crystal was grown and the structure was determined by crystallographic analysis for the first time. Chapter 5 discussed the immobilisation of a photosensitiser meso-tetraphenylporphyrin on niobium solid acids, and the activity of these supported photocatalysts in continuous photo-oxidation, including the photo-oxidation of α-terpinene to ascaridole and the semi-synthesis of an antimalarial drug, artemisinin ART. Finally, Chapter 6 summarises the work described in this Thesis and examines the success of the techniques and approaches discussed. A summary of potential routes for further study is also presented.

This thesis addresses the concept of atomically precise manufacturing and aims to examine some likely aspects of the necessary infrastructure and knowledge that will be required from a theoretical standpoint. By way of introduction, I trace the history of Science Fiction's influence on scientific research and examine some examples that have specifically inspired the thinking behind nanoscience and nanotechnology. More serious speculation, both in favour of and arguing against the possibility of bottom-up manufacturing is also discussed. I look at two schools of thought; directed assembly, typified by the ambition to assemble molecular structures piece by piece and self assembly, where networks of molecules form into arrays on substrates, imparting novel properties. Various methodologies and tools available to the nanotechnologist are examined. Density functional theory, as employed in the AIMpro code, and Molecular Mechanics are discussed, particularly in respect of their strengths and weaknesses for use in simulating the kind of nanoscale processes appropriate to nanomanufacturing. The theoretical basis behind scanning tunneling microscopes is also examined, with particular attention paid to their potential for upscaling in the future. Some components found within scanning tunneling microscopes are simulated using Density Functional Theory. Models of pure tungsten tips are studied at various levels of complexity in order to decide upon a reasonable compromise between accuracy and ease of computation. The nature of the interlayer interaction in few layer graphenes is examined and pristine and defected graphitic surfaces, are studied with a view towards their use as nano-workbenches. Their images as produced in scanning tunneling microscopes are simulated. Density Functional Theory is applied to organic molecules self-assembling on metallic substrates. Specifically, tetracene on a clean copper surface and on an oxygen-terminated copper surface is studied. Finally, I discuss the significance of the results of each section, taken individually and as a whole, and try to put it into perspective regarding the practicality of actually employing this paradigm realistically in the near future.

HTML clipboardIn this thesis, dynamic effects on electron transport in molecular electronic devices are presented. Special attention is paid to the dynamics of atomic motions of bridged molecules, thermal motions of surrounding solvents, and many-body electron correlations in molecular junctions. In the framework of single-body Green’s function, the effect of nuclear motions on electron transport in molecular junctions is introduced on the basis of Born-Oppenheimer approximation. Contributions to electron transport from electron-vibration coupling are investigated from the second derivative of current-voltage characteristics, in which each peak is corresponding to a normal mode of the vibration. The inelastic-tunneling spectrum is thus a useful tool in probing the molecular conformations in molecular junctions. By taking account of the many-body interaction between electrons in the scattering region, both time-independent and time-dependent many-body Green’s function formula based on timedependent density functional theory have been developed, in which the concept of state of the system is used to provide insight into the correlation effect on electron transport in molecular devices. An effective approach that combines molecular dynamics simulations and first principles calculations has also been developed to study the statistical behavior of electron transport in electro-chemically gated molecular junctions. The effect of thermal motions of polar water molecules on electron transport at different temperatures has been found to be closely related to the temperature-dependent dynamical hydrogen bond network. / QC20100630

Because of the generation of polaritons, which are quasiparticles possessing the characteristics of both photonics and electronics, active photonic materials offer a possible solution to transfer electromagnetic energy below the diffraction limit and further increase the density of photonic integrated circuits. A theoretical investigation of these exciting materials is, therefore, very important for practical applications. Four different kinds of polaritons have been studied in this thesis, (1) surface polaritons of negative-index-material cylindric rods, (2) exciton polaritons of semiconductor quantum dots, (3) localized plasmon polaritons of metallic nanoshells, and (4) surface plasmon polaritons of subwavelength hole arrays in thin metal films. All these types of polaritons were found to strongly affect the optical properties of the studied active photonic materials. More specifically, (1) for two-dimensional photonic crystals composed of negative-index-material cylindric rods, the coupling among surface polaritons localized in the rods results in dispersionless anti-crossing bands; (2) for three-dimensional diamond-lattice quantum-dot photonic crystals, the exciton polariton resonances lead to the formation of complete band gaps in the dispersion relationships; (3) for metallic nanoshells, the thickness of the metal shell strongly modifies the localized plasmon polaritons, and therefore influences the degree of localization of the electromagnetic field inside the metallic nanoshells; (4) for subwavelength hole arrays in thin metal films, high-order surface-polariton Bloch waves contribute significantly to the efficient transmission. To numerically simulate these active photonic materials, we introduced three approaches, (1) an extended plane-wave-based transfer-matrix approach for negative- index-material media, (2) a plane-wave method for semiconductor quantum-dot photonic crystals, and (3) an auxiliary-differential-equation finite-difference time- domain approach for semiconductor quantum-dot arrays. A brief perspective is also given at the end of this thesis. / QC 20100825

In this thesis, quantum chemistry, in particular the B3LYP density functional method, is used to investigate a number of methyl transfer enzymes. Quantum chemical methodology is today a very important tool in the elucidation of properties and reaction mechanisms of enzyme active sites. The enzymes considered in this thesis are the S-adenosyl L-methionine-dependent enzymes - glycine N-methyltransferase, guanidinoacetate methyltransferase, phenylethanolamine N-methyltransferase, and histone lysine methyltransferase. In addition, the reaction mechanism of the DNA repairing enzyme O6-methylguanine methyltransferase is studied. Active site models of varying sizes were designed and stationary points along the reaction paths were optimized and characterized. Potential energy surfaces for the reactions were calculated and the feasibility of the suggested reaction mechanisms was able to be judged. By systematically increasing the size of the models, deeper insight into the details of the reactions was obtained, the roles of the various active site residues could be analyzed, and, very importantly, the adopted modeling strategy was evaluated. / QC 20100927