Search

This thesis is concerned with the study of polyphenyl compounds and their derivatives, and throughout the work is the overarching theme of analysis and understanding of complex mixtures. The analysis of complex mixtures is not only an academic pursuit but something of value to industry. Individual components of complex systems may have advantageous or detrimental effects to the overall performance of materials. Without suitable analysis the development of optimal products is not possible. This work begins to address the identification and understanding of aromatic or aromatic derived mixtures which are used in, or of interest to industrial applications. Chapter one focuses on the homocoupling of methyl benzoate, which yields six isomeric products. The desired 4,4''-biphenyl dicarboxylate product is of interest as a specialist monomer. The aim of synthesis via a double C-H activation was challenging and ultimately no improvement on the literature precedents was made. Chapter two addresses the challenges in studying purely aromatic compounds of closely related structures. The pyrolysis of benzene is an industrial process which produces a complex mixture with little control over selectivity. The aim of this chapter was to understand the possible products of pyrolysis. This was achieved by the synthesis of seven aromatic hydrocarbons of the skeleton C24. Using HPLC a method for the rapid analysis of 14 closely related compounds was developed using commercially available stationary phases. A comparison of alkyl and aromatic phases was made. Lastly a series of NMR techniques were used to provide spectral data on linear quaterphenyl isomers, allowing each isomer to be identified from a proton spectrum. Chapter three is concerned with the synthesis of the partially and fully hydrogenated terphenyls. The focus is the synthesis of para substituted three-ring structures, from fully aromatic p-terphenyl to fully saturated p-tercyclohexyl and the intermediary partially reduced compounds. These compounds are successfully synthesised. The methods used are extended to some equivalent isomers of ortho and meta substitution. These compounds can be used to identify regio- and stereoisomers and closely related compounds from the complex mixtures in which they are found.

Recent advances in genomic sequencing technology have facilitated relatively inexpensive, high-fidelity sequencing of microbial genomes. Increased genome sequencing capacity has been accompanied by developments in bioinformatics, which enable rapid homology searching to predict gene products, such as enzymes involved in the production of small-molecules. The recent surge in genomic information revealed that only a small percentage of genes involved in small-molecule biosynthesis had previously been characterized. In fact, it appears that we have only scratched the surface in understanding the full biosynthetic potential of microorganisms. The current void in small-molecule discovery is in part because of the particular challenges associated with identifying new compounds and in part because of the nature of microbial small-molecule production. Perhaps the largest obstacle in the path to characterizing new small-molecules is the absence of a templated structure. For instance, in genomics, the number of building blocks is extremely limited, just four different bases, which fit together predictably through phosphodiester bonds. Moving up in complexity to proteomics, the number of building blocks increases to roughly twenty amino acids, however still assembled in a predictable manner, through peptide bonds. Additionally, protein primary sequence can be derived directly from the corresponding genetic sequence, which coupled with homology searching enables quick judgments as to whether or not a detailed characterization is warranted. The situation in metabolomics is starkly more complicated as the number of building blocks increases to over one-hundred chemical entities that can be assembled in virtually any imaginable way that obeys the laws of chemistry. Moreover, small-molecule structural insights simply cannot be attained from the genetic sequence alone, meaning every compound must be individually characterized. In addition to the challenges of small-molecule characterization, the very nature of microbial biosynthesis has significantly hindered more thorough annotation of the metabolome. Expression of genes encoding biosynthetic enzymes is tightly regulated and responsive to various natural environments. Simple laboratory culturing conditions usually fail to reproduce the necessary cues to promote small-molecule production. While media screening methods or so called fermentation optimization is an option to overcome this barrier, the power of genetic engineering offers a far more straightforward solution and has the added benefit of precision. The production of small-molecules can be turned on or eliminated in a controlled manner by creating over-expression or knock-out mutant microbial strains. Comparison of mutant and wild-type strains using differential analysis by 2D-NMR spectroscopy (DANS) and LC-MS-based comparative metabolomics enables a systems biology prospective of metabolic changes resulting from genetic engineering. Described herein is the utilization of DANS and LC-MS-based comparative metabolomics to discover novel metabolites from orphan microbial biosynthetic gene clusters. Applied to the has gene cluster in Aspergillus fumigatus DANS revealed the biosynthesis of a novel iron(III)-complex, which was shown to increase A. fumigatus’ virulence. Results from the has study led to an investigation of diketopiperazine formation in the notorious gliotoxin biosynthetic pathway. Gliotoxin biosynthesis was shown to be dependent on a cluster-encoded cyclization domain, which ultimately functioned to cyclize a modified dipeptide into the diketopiperazine core of the gliotoxin structure. In another A. fumigatus gene cluster, called fsq, DANS and LC-MS-based comparative metabolomics revealed the elusive fungal isoquinoline formation pathway, which despite having been described in plants more than twenty years ago, remained unknown in fungi until now. The fungal isoquinoline pathway was shown to be conserved through the characterization of another isoquinoline producing gene cluster in the plant pathogenic fungus A. flavus. Lastly, the identification and characterization of an additional set of fsq-dependent metabolites, called the fumizinones, is described. The fumizinones derive from an alternative biosynthetic mechanism, resulting in pyrazinone formation, rather than isoquinoline formation, as observed for the main products of the fsq pathway.

Nuclear magnetic resonance (NMR) has become an effective borehole measurement option to assess petrophysical and fluid properties of porous and permeable rocks. In the case of fluid typing, two-dimensional (2D) NMR interpretation techniques have advantages over conventional one-dimensional (1D) interpretation as they provide additional discriminatory information about saturating fluids and their properties. However, often there is ambiguity as to whether fluids detected with NMR measurements are mobile or residual. In some instances, rapid vertical variations of rock properties (e.g. across thinly-bedded formations) can make it difficult to separate NMR fluid signatures from those due to pore-size distributions. There are also cases where conventional fluid identification methods based on resistivity and nuclear logs indicate dominant presence of water while NMR measurements indicate presence of water, hydrocarbon, and mud filtrate. In such cases, it is important to ascertain whether existing hydrocarbons are residual or mobile. The radial lengths of investigation of resistivity, nuclear, and NMR measurements are very different, with NMR measurements being the shallowest sensing. Even in the case of several radial zones of NMR response attributed to different acquisition frequencies and DC magnetic field gradients, the measured signal originates from a fairly shallow radial zone compared to that of nuclear and resistivity logs. Depending on drilling mud being used and the radial extent of mud-filtrate invasion, the NMR response of virgin reservoir fluids can be masked by mud filtrate because of fluid displacement and mixing. In order to separate those effects, it is important to reconcile NMR measurements with electrical and nuclear logs for improved assessment of porosity and mobile hydrocarbon saturation. Previously, Voss et al. (2009) and Gandhi et al. (2010) introduced the concept of Common Stratigraphic Framework (CSF) to construct and validate multi-layer static and dynamic petrophysical models based on the numerical simulation of well logs. In this thesis, the concept of CSF is implemented to reconcile 2D NMR interpretations with multi-layer static and dynamic petrophysical models. It is found that quantifying the exact radial zone of response and corresponding fluid saturations can only be accomplished with studies of mud-filtrate invasion that honor available resistivity and nuclear logs. This thesis indicates that the two interpretation methods complement each other and when applied in conjunction, improve and refine the overall petrophysical understanding of permeable rock formations. Examples of successful application include field data acquired in thinly-bedded gas formations invaded with water-base mud, where bed-boundary effects are significant and residual hydrocarbon saturation is relatively high. In such cases, numerical simulation of mud-filtrate invasion and well logs acquired after invasion enables reliable interpretations of petrophysical and fluid properties. The interpretation procedure introduced in this thesis also provides an explicit way to determine the uncertainty of petrophysical and fluid interpretations.