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Anthropogenic activities have caused environmental damage for thousands of years, which has been exacerbated since the industrial revolution. Mining is one such activity that has caused damage to the environment, primarily through the creation of acid-mine drainage (AMD) waters. These are created when pyrite in rocks is exposed to oxygen and water, through mining, causing the formation of sulphuric acid. As the waters become more acidic, metals disassociate from the rocks leading to acidic and metal polluted waters. One such AMD system is Parys Mountain, Wales, where our lab has isolated an acidophilic microalga, Chlamydomonas acidophila - strain PM01. It exhibits higher tolerance levels of copper than other strains of the same species. Whilst tolerance ranges and physiological responses of eukaryotic extremophiles have been well studied, many of their mechanisms of adaptation have yet to be elucidated. PM01 provides a fantastic model to begin to understand some of these tolerance mechanisms. In order to tolerate the harsh conditions of AMD it is likely that C. acidophila has evolved differential responses to both pH differences and metal toxicity to non-adapted organisms, such as Chlamydomonas reinhardtii which is mesophilic in both its pH tolerance and its ability to survive metal toxicity. Firstly, in this thesis the physiological and biochemical responses of PM01 compared to the model organism Chlamydomonas reinhardtii (strain 11/32c) as well as other strains of C. acidophila (strains CCAP 11/136 and CCAP 11/137) were analysed in response to copper. Here it was found that PM01 is capable of growing at much higher copper concentrations than the other strains tested. Also, PM01 shuts down photosystem II after being exposed to copper for 3 hours, without the photosynthetic machinery appearing stressed. Additionally, a 2-stage non-photochemical quenching (NPQ) process was observed, where PM01 has different types of NPQ, depending on the actinic light intensity. The antioxidant capability of PM01 and C. reinhardtii was also measured. PM01 exhibited higher catalase activity, whilst the two isoforms of iron superoxide dismutase show different isoelectric points (pI). It was found that PM01 exhibits high levels of lipid oxidation in both short- and long-term copper stress, whereas C. reinhardtii only exhibited high lipid oxidation under a short-term copper stress. Finally, low lipid oxidation levels were shown in the other C. acidophila species, CCAP strains 11/136 and 11/137. Secondly, fast, high-throughput fingerprinting techniques were used to examine the metabolic and proteomic changes of PM01 and C. reinhardtii in response to copper stress. FT-IR spectroscopy revealed an increase in protein content upon copper exposure in PM01, but a decrease in lipids and carbohydrates. Whilst a similar response was seen in C. reinhardtii it was not to the same extent as PM01. MALDI-TOF mass spectroscopy provided a rapid overview of the proteome. Here protein peaks with a high m/z arising in the long-term copper-stress treated for both PM01 and C. reinhardtii. These protein peaks also suggested that a protein can 'switch' between a single charge and double charge and could play an important role in either metal binding or reactive oxygen species quenching. An in-depth metabolomic analysis using LC-MS techniques reveal greater insights into PM01's adaption to copper through the identification of several key metabolic changes between PM01 and C. reinhardtii. Thiol groups in metabolites such as cysteine and glutathione play a central role in copper adaptation. Additionally, amino acids such as proline, a known osmolyte, was found at elevated levels in PM01. Finally, I conducted a transcriptomic experiment was conducted to observe the global response of PM01 and C. reinhardtii to a long- and short-term copper stress. A whole host of transcripts were differentially expressed under copper stress, however, we managed to find 3 main processes that were altered. Transcripts related to the antioxidant response and lipid breakdown were found to be more highly expressed in C. reinhardtii under a copper stress. Intracellular transport systems and reorganisation was found to be more highly expressed in PM01 under a short- and long-term copper stress. Finally, transcripts related to photosynthesis were found to be reduced in PM01 under both a short- and long-term copper stress. I also found a series of transcripts that were much more highly expressed in the PM01 cells exposed to a short-term copper stress with a wide array of biological functions. These provide an exciting source of potential biological pathways to a copper adaptation. We also investigated individual transcripts of interest, with the putative copper exporter CTP3, being a standout candidate to copper tolerance it was constitutively expressed in PM01 at higher levels than all other C. reinhardtii treatments. This study provides an exciting insight into the copper tolerance mechanisms of PM01, an extremophile microalga that exhibits high copper tolerance levels. In this I have generated large data sets that provide a lot of further avenues for further investigation.

The thesis presents a stylistic and technological study on Western Asian ceramics dating from 1000-1500 CE. The production and consumption of ceramics is used as a proxy to explore how social practices at the local level were formulated within the broader framework of Islam. The Islamic world has been studied as a relatively cohesive whole, due to the perceived connectivity of religion. This top-down approach favors elites (economic or political), larger cities, and precious materials (silk, porcelain, metals, etc.). This bias is mirrored in archaeological research which tends to focus on large palaces/castles/mosques, capital and large cities, and prestige goods. This dissertation focuses on the full repertoire of ceramic assemblages, not just glazed wares, to emphasize the potters' choices in creating the ceramics, as well as the consumers' choices in acquiring and using the ceramics. Both choices (production and consumption) are influenced by a myriad of factors, including vessels' function, environment, and socio-cultural contexts. For this dissertation, I have three main questions: (1) What is the range of ceramic technology and style across Western Asia in the Middle Islamic period? How can the study of ceramic technology elucidate the ceramic traditions existing at these sites/regions? What is the structure of ceramic craft organization in these areas? (2) How can the ceramic traditions in combination with social dimensions of ceramic production be used to connect sites, regions, and interregional areas? How does the consumption of ceramics indicate links between these areas? (3) What can the study of ceramic traditions in the Middle Islamic period tell us about the connections between rural areas and larger urban areas? This dissertation focuses on 12 ceramic assemblages from various sites across Western Asia, all dating from 1000 - 1500 CE. These ceramics are recovered from both survey and excavation of sites of different natures, including eight rural sites (Erbil Plain Archaeological Survey (seven sites), Firuzabad), three intermediate types of sites (Nippur, Hasanlu, Chal Tarkhan), and a capital city (Rayy). The majority of the assemblages are from rural sites, but a few are from non-rural sites to lend a comparative edge and help define what is and is not rural. The ceramics are analyzed using a combination of macroscopic observation, thin-section petrography, portable X-Ray fluorescence (pXRF), and Fourier Transform Infrared Spectroscopy (FT-IR). These analyses are specifically selected to establish the potential provenience of the ceramics, reconstruct technical choices and social practices, and characterize production and consumption traditions. This area has been discussed as a homogenous whole (from 600 CE to present) under the assumption that the spread of Islam brought all areas under the larger cultural mainframe. However, this dissertation shows that there is heterogeneity in both ceramic consumption and production. The established overarching links do not seem to be influenced by the spread of Islam as the ceramic traditions identified (forms, fabrics, functions) also are present before the rise of Islam in these areas. This bottom-up approach marks significant contributions to Islamic Archaeology by shedding light on the diversity of dynamics that existed in local areas and among local populations and how these local dynamics play in the interconnected societies of Western Asia during the Middle Islamic period.

Antisense-Oligonucleotides (ASOs) are a next generation of therapeutic pharmaceutical, synthesised to be complementary to short lengths of mRNAs that are implicated in diseases such as Huntingtons and Spinal Muscular Atrophy. ASOs reduce or alter the expression of target mRNA. The secondary structure of ASOs is intrinsically linked to their binding affinity and efficacy. Secondary structure unfolding and folding can occur as a result of pharmaceutical (temperature and concentration changes) and environmental stresses (buffer and pH changes). Structural characterisation of ASOs using crystallography and Nuclear Magnetic Resonance (NMR) can be both expensive and challenging. Vibrational spectroscopies (Raman Spectroscopy, Fourier-Transform Infrared Spectroscopy, Raman Optical Activity and Circular Dichroism) have the potential to be quick methods for relating small changes in oligonucleotide secondary structure to stability or efficacy, prior to experiments with Small Angle X-Ray Scattering (SAXS)/NMR for more detailed structural analysis. Vibrational spectroscopies were used on increasingly complex single-stranded RNA (ss-RNA) structures. Raman is used to look at distinct spectral features of Nucleotides; examples include the sugar pucker of the Ribose ring and Imidazole ring peaks in Purines. A collaboration to generate Density Functional Theory (DFT) data has been used to improve on assignments of RNA nucleotides. Raman peaks are then identified for mono-, di- and tri- phosphate RNA nucleotides as well as Poly-RNA samples (Polyuridylic acid) and the hybridisation of a short 12-mer oligo. This library is used to assign the identity of an additional nucleotide within an N+1-mer of an AstraZeneca/Ionis Pharmaceuticals ASO: AZD9150. Combining Raman Optical Activity with Raman spectroscopy has previously been used to characterise secondary and tertiary RNA structural motifs, including a U-C mismatch and a hairpin (Hobro, 2007). In two AstraZeneca/Ionis Pharmaceuticals ASOs (AZD4785 and AZD Compound A), nucleotide and phosphate backbone modifications (such as Locked Nucleic Acids) affect spectroscopic assignments by inducing new secondary structure conformations. Raman has been used to look at experimental conditions related to pharmaceutical stresses (Hobro, 2008); concentration, buffer exchange and pH changes were observed to cause structural changes in AZD4785. SAXS is used to look at a fibril like hybridisation of ASOs at a high concentration; following this, NMR NOESY data is used to demonstrate how heat can prevent this conformation, potentially increasing drug efficacy. Raman, ROA and SAXS were used to observe the structure of ss-RNA within the Cowpea Mosaic Virus and detect changes following modification of the RNA to encode for GFP. Transmission Electron Microscopy and SAXS were used to compare viral capsids of a CPMV virus and a Virus Like Particle. The potential of plant viruses to be used to produce unmodified RNA on a large scale, as well as act as a delivery system for ASOs, is discussed.

An exceptionally important stress response of Pseudomonas putida strains to toxic chemicals is the induction of efflux pumps that extrude solvents, as well as other toxicants, into the surrounding medium. However, the bacterial tolerance mechanisms are still not fully understood, thus in this thesis metabolomic approaches were used to detect and identify metabolites involved in P. putida DOT-T1E tolerance to abiotic stresses, in particular focussing on the role of efflux pumps. To elucidate any metabolome alterations several strains of P. putida, including the wild type DOT-T1E, and the efflux pump knockouts DOT-T1E-PS28 and DOT-T1E-18, were challenged with different levels of propranolol. Fourier-transform infrared (FT-IR) spectroscopy, which provided a rapid, high-throughput metabolic fingerprint of P. putida strains, was used to investigate any phenotypic changes resulting from exposure to propranolol. FT-IR data illustrated phenotypic changes associated with the presence of propranolol within the cell that could be assigned to the bacterial protein components. To complement this phenotypic fingerprinting approach metabolic profiling on the same samples was performed using gas chromatography mass spectrometry (GC-MS) to identify metabolites of interest during growth of bacteria following this toxic perturbation with propranolol. GC-MS revealed significant changes in ornithine levels which can be directly linked to bacterial tolerance mechanisms, and alterations in the levels of several other metabolites which were also modified in response to propranolol exposure. Moreover, the effect of the organic solvent toluene was also investigated using the same approach. Examination of FT-IR data indicated that protein and fatty acids were the most affected components of P. putida strains due to the presence of toluene within the cell. Moreover, application of GC-MS allowed for the identification and quantification of several metabolites which were differentially produced or consumed in the presence of toluene. To investigate the role of efflux pumps in P. putida DOT-T1E, several analytical techniques were employed including Raman spectroscopy, gas and liquid chromatography to identify and quantify the level of propranolol or toluene in P. putida cells. These analyses showed that propranolol and toluene accumulated in the mutant P. putida DOT-T1E-18 (lacking the TtgABC pump) at higher levels in comparison with the levels found in the wild-type DOT-T1E and the mutant DOT-T1E-PS28 (lacking the TtgGHI pump), indicating the key role of efflux pumps in solvent tolerance. Furthermore, the effect of Mg2+ and Ca2+ on the stabilisation of the toluene tolerance of P. putida DOT-T1E strains was examined in order to elucidate whether divalent cations interact with efflux pumps or other resistant mechanisms to improve solvent tolerance. FT-IR analysis suggested that the influence of divalent cations on the stabilisation of the toluene tolerance could be due to the contribution of metal ions towards other tolerance mechanisms such as lipopolysaccharide (LPS) instead of enhancing the activity of efflux pumps. In conclusion, this thesis presents evidence that phenotypic fingerprinting and metabolic profiling approaches in combination with chemometric methods can generate valuable information on phenotypic responses occurring within microbial cultures subjected to abiotic stress.

Small quantities of amorphous content can have a profound influence on the properties of a material, however their instability means that quantifying amorphous content over time is important for proving the stability of a drug. Quantifying amorphous content in α-lactose monohydrate by solid state 13C CP MAS NMR, has been carried out by use of proton saturation recovery relaxation and differentiating between spectra by partial least squares (PLS), however these techniques have not proved sensitive on their own, this work investigates their sensitivity in combination. Crystalline α-lactose monohydrate and a rapidly quenched melt were combined to create a set of calibration mixes, whose spectra were recorded using proton saturation recovery relaxations ranging from 2 to 60 seconds. This technique showed a limit of detection of 0.17% (LOD = intercept + 3xSy/x), with a relaxation delay of 15 s and was able to recognise amorphous materials generated by spray and freeze drying. The atmospheric effects on the proton saturation recovery relaxation times of different amorphous lactose preparations were investigated. This found that an oxygen atmosphere reduced the relaxation times, of amorphous lactose that was prepared from a rapidly quenched melt. The loss of moisture from spray dried and freeze dried samples to less than 1% removed the significance of this effect. Lactose is an important excipient in pharmaceuticals and a key ingredient of confectionary, very little research has been carried out in to the quantification of the isomers of different preparations of amorphous lactose. This work quantifies the isomer content by Gas Chromatography with Flame Ionisation Detection (GC-FID) using a DB-17 15m 0.53mm 1.00 μm column and derivatisation with N- (trimethylsilyl)imidazole.

Protein based biopharmaceuticals are becoming increasingly popular therapeutic agents. Recent changes to the legislation governing stem cell technologies will allow many further developments in this field. Characterisation of these therapeutic proteins poses numerous analytical challenges. In this work we address several of the key characterisation problems; detecting glycosylation, monitoring conformational changes, and identifying contamination, using vibrational spectroscopy. Raman and infrared spectroscopies are ideal techniques for the in situ monitoring of bioprocesses as they are non-destructive, inexpensive, rapid and quantitative. We unequivocally demonstrate that Raman spectroscopy is capable of detecting glycosylation in three independent systems; ribonuclease (a model system), transferrin (a recombinant biopharmaceutical product), and GFP (a synthetically glycosylated system). Raman data, coupled with multivariate analysis, have allowed the discrimination of a glycoprotein and the equivalent protein, deglycosylated forms of the glycoprotein, and also different glycoforms of a glycoprotein. Further to this, through the use of PLSR, we have achieved quantification of glycosylation in a mixture of protein and glycoprotein. We have shown that the vibrational modes which are discriminatory in the monitoring of glycosylation are relatively consistent over the three systems investigated and that these bands always include vibrations assigned to structural changes in the protein, and sugar vibrations that are arising from the glycan component. The sensitivity of Raman bands arising from vibrations of the protein backbone to changes in conformation is evident throughout the work presented in this thesis. We used these vibrations, specifically in the amide I region, to monitor chemically induced protein unfolding. By comparing these results to fluorescence spectroscopy and other regions of the Raman spectrum we have shown that this new method provides improved sensitivity to small structural changes. Finally, FT-IR spectroscopy, in tandem with supervised machine learning methods, has been applied to the detection of protein based contaminants in biopharmaceutical products. We present a high throughput vibrational spectroscopic method which, when combined with appropriate chemometric modelling, is able to reliably classify pure proteins and proteins ‘spiked’ with a protein contaminant, in some cases at contaminant concentrations as low as 0.25%.

Prostate cancer is the second most common cause of cancer fatalities in males in the UK (2006) [1]. Therefore any advances in the diagnosis or screening for this form of cancer will yield significant benefits in the treatment of this disease. FT-IR has already been successfully used to assess and grade prostate biopsies by Gazi et al 2006 [2]. The collection of prostate biopsy is however a highly invasive procedure and as current screening methods are highly sensitive, but not very specific, large numbers of patients are referred for biopsy procedures that later come back as negative for prostate cancer [3]. Harvey et al used Raman spectroscopy to classify live cells of a number of prostate cell lines as a first step towards a possible urine screening protocol for prostate cancer [3]. Due to the complementary nature of Raman and FT-IR spectroscopy a similar live cell study should be possible using FT-IR and the combination of this technique with a high-throughput microfluidic device could lead to a useful screening tool for prostate cancer.The aim of the project was therefore to develop a microfluidic system which would enable higher through-put FT-IR analysis of live single cells in an aqueous carrier solution such as PBS or urine than has been previously possible. The design of the microfluidic device must also account for the fact that the materials used to produce the analysis chamber must be highly transparent to mid-IR radiation. The microfluidic device and peripheral systems must be easily transportable as it will be necessary to perform experiments in multiple locations. A design and manufacturing protocol for such a device has been developed.The development of a spectral contribution removal algorithm for the aqueous carrier fluid will also be necessary in order to allow the accurate interpretation of the IR data obtained. A least squares fitting based spectral subtraction algorithm was developed and validated for this purpose.Although it did not prove possible during the project to investigate the possible application of this device to a prostate cancer screening protocol other applications in cell line classification and drug cell interaction studies were performed and yielded encouraging results.

Milk is an important nutritious component of our diet consumed by most humans on a daily basis. Microbiological spoilage affects its safe use and consumption, its organoleptic properties and is a major part of its quality control process. European Union legislation and the Hazard Analysis and the Critical Control Point (HACCP) system in the dairy industry are therefore in place to maintain both the safety and the quality of milk production in the dairy industry. A main limitation of currently used methods of milk spoilage detection in the dairy industry is the time-consuming and sometimes laborious turnover of results. Attenuated total reflectance (ATR) and high throughput (HT) Fourier transform infrared (FTIR) spectroscopy metabolic fingerprinting techniques were investigated for their speed and accuracy in the enumeration of viable bacteria in fresh pasteurized cows' milk. Data analysis was performed using principal component-discriminant function analysis (PC-DFA) and partial least squares (PLS) multivariate statistical techniques. Accurate viable microbial loads were rapidly obtained after minimal sample preparation, especially when FTIR was combined with PLS, making it a promising technique for routine use by the dairy industry. FTIR and Raman spectroscopies in combination with multivariate techniques were also explored as rapid detection and enumeration techniques of S. aureus, a common milk pathogen, and Lactococcus lactis subsp cremoris, a common lactic acid bacterium (LAB) and potential antagonist of S. aureus, in ultra-heat treatment milk. In addition, the potential growth interaction between the two organisms was investigated. FTIR spectroscopy in combination with PLS and kernel PLS (KPLS) appeared to have the greatest potential with good discrimination and enumeration attributes for the two bacterial species even when in co-culture without previous separation. Furthermore, it was shown that the metabolic effect of L. cremoris predominates when in co-culture with S. aureus in milk but with minimal converse growth interaction between the two microorganisms and therefore potential implications in the manufacture of dairy products using LAB. The widespread and high consumption of milk make it a target for potential financial gain through adulteration with cheaper products reducing quality, breaking labeling and patent laws and potentially leading to dire health consequences. The time consuming and laborious nature of currently used analytical techniques in milk authentication enabled the study of FTIR spectroscopy and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF-MS) as rapid analytical techniques in quantification of milk adulteration, using binary and tertiary fresh whole cows', goats' and sheep's milk mixture samples. Chemometric data analysis was performed using PLS and KPLS multivariate analyses. Overall, results indicated that both techniques have excellent enumeration and detection attributes for use in milk adulteration with good prospects for potential use in the dairy industry.

Metabolomics approaches have recently been used to understand the complex molecular interactions of biological systems. One popular area in which these methods are being developed is to understand the biochemical changes during abiotic and biotic stresses; for example, how a cell may respond to a drug. Since metabolites are the end products of gene expression, these can be used to indicate the result of the activities and interaction of the cell or organism with its environment. The investigation of the level and compositional changes of metabolites against metabolic stresses such as chemotherapeutic treatment (drug exposure) are required to understand more fully abiotic perturbation to biological systems. The aim of this project was to understand the metabolic effect that the anti-viral drugs indinavir and lopinavir (currently used by HIV patients) have on HPV-related cervical cancer cell lines by measuring changes in metabolism using a wide range of analytical techniques; including Fourier transform infrared (FT-IR) and Raman spectroscopies, and gas and liquid chromatography-mass spectrometry (GC and LC-MS). The analyses and interpretation of the large volumes of complex multidimensional data generated by metabolomics approaches were performed with a combination of multivariate data analysis techniques such as principal components analysis (PCA) and canonical variates analysis (CVA), as well as univariate approaches such as N-Way analysis of variance (ANOVA). By combining biochemical imaging, metabolite fingerprinting and footprinting, and metabolite profiling, with multi- and uni-variate analyses, the actions and effects of the anti-viral drugs were investigated. FT-IR spectroscopy was initially used to generate global biochemical finger- and foot-prints, and Raman spectroscopy was employed to investigate intracellular distribution of metabolites, and other cellular species, as well as the localisation of drug molecules within cells. FT-IR spectroscopy ascertained that the intra- and extra-cellular metabolomes were being directly influenced in a fashion that correlated with increasing anti-viral dosing; these effects were phenotypic rather than measurements of the drug level. Raman imaging spectroscopy indicated that the indinavir but not lopinavir was being compartmentalised within the cell nucleus, but only in HPV early protein 6 (E6) expressing cells. This observation was further confirmed by fractionation of cell samples into nuclear and cytoplasmic fractions and assessing the indinavir concentrations via LC-MS. Finally, LC-MS and GC-MS metabolite profiling were employed to investigate changes in the intracellular metabolome in response to the anti-viral compounds across a range of physiologically relevant concentrations and in the presence and absence of the E6 oncoprotein. General effects of both anti-viral compounds included the regulation of metabolites such as glutathione, octenedionoic and octadecenoic acids, which may be involved in stress related responses, reduced levels of sugars and sugar-phosphates indicating a potential arrest of glycolysis, and reduced levels of malic acid indicating potential decreased flux into the TCA cycle; all indicating that central metabolism was being reduced. Finally, LC-MS based quantification indicated that in the presence of E6, lopinavir was actively removed from the cell, whereas the indinavir intracellular concentration increased concomitantly with the level of dosing. These investigations have revealed that metabolomics approaches are an apt tool for the study of anti-viral effects within cell cultures, but improvements need to be made with respect to the major limitation of metabolite identification.

Excipients are used in pharmaceutical formulations as fillers and drug carriers. Their successful function is inextricably linked to their physicochemical properties and, in turn, these properties are directly related to their structure. This thesis is concerned with the structural and spectroscopic characterisation of a selection of excipients by powder and single crystal X-ray diffraction, Raman and IR spectroscopy and MASNMR and an investigation of their stability as a function of temperature, humidity and particle size. As well as being a well-known excipient used in the pharmaceutical industry, lactose is also a common food additive. The diverse usage of lactose has led to a wealth of contradictory information relating to both structure and properties of this material. The first part of experimental work in this thesis identifies the four real lactose polymorphs; the naturally occurring a-lactose monohydrate; the anhydrous stable form of a-lactose; the hygroscopic unstable form of a-lactose; and the anomeric equivalent, p-lactose using powder X-ray diffraction. The work shows that anhydrous lactose formed by solvent dehydration often termed aM is simply the anhydrous stable form of a-lactose formed via a different route. Simple methods for discerning between the polymorphs using standard laboratory equipment are suggested. IlC MASNMR data were collected on all four forms of lactose for the first time and illustrate key differences between the four structures. Single crystal data were successfully collected on the a-lactose monohydrate and refinement carried at low temperature to determine the hydrogen bonded arrangement for the first time. Rietveld refmement of the hygroscopic unstable form of a-lactose using in-situ temperature resolved X-ray diffraction has shown that the hygroscopic form can be produced as a single phase. Refinement of Plactose using the Rietveld method has shown that powder diffraction data were comparable with single crystal data, with respect to structure refinement but attempts at both crystallisation and refinement of the stable anhydrous a-lactose polymorph were unsuccessful due to the complexity of the structure. Powder X-ray diffraction analysis was shown to be an effective tool in the quantification of mixed phase lactose samples with respect to both mixed phase stable anhydrous a-lactose and a-lactose monohydrate; and mixed p-Iactose and a-lactose monohydrate samples. The accuracy of the technique was determined to be at least 5%. Quantification was carried out using relative intensities of a well resolved unique reflection for each phase within the system. Dehydration techniques applied to lactose were applied to other hydrated pharmaceutical sugars; trehalose dihydrate and raffmose pentabydrate. Solid state techniques; powder X-ray diffraction, Raman and IR spectroscopy; showed that discrimination of other sugar hydrates became more complex with increasing levels of hydration.

Tire particles (TP) are the largest source of microplastics in nature. However, theadsorption behavior of TP needs to be better understood. TP used in this study weregenerated from cryo-milling and aged with 30% nitric acid. Single and competitiveadsorption isotherm experiments were conducted to investigate the potential of TP ascarriers of heavy metals. Langmuir and Freundlich models were used to analyzeadsorption data. Competitive adsorption demonstrated a reduction in the adsorptioncapacity of TP. The preference for lead to copper by TP was explained by the physicaland chemical properties of the metals. The adsorption capacity was maximum at the pHrange of 6-12 for lead, and for copper, it was pH 10. pH, zeta potential, FT-IR, and XPSresults indicated that electrostatic attraction and surface complexation were involved inthe heavy metal adsorption on TP.

Cosmic Microwave Background (CMB) experiments like Advanced ACTPol (AdvACT) and Simons Observatory (SO) seek to uncover the physics of the early Universe, just ~10^-32 seconds after its formation, and its evolution since. With just 6 parameters, the Lambda-CDM model of cosmology describes our Universe exceptionally well, but leaves some questions unanswered. The CMB can answer questions left unanswered by Lambda-CDM, including whether the early Universe underwent a period of inflation, if there are particles beyond the Standard Model, the sum of the neutrino masses, and the nature of dark matter and dark energy. However, reaching the level of precision necessary to measure the signals in the CMB that can answer these questions is extremely difficult and requires unprecedented sensitivity, which presents a number of instrumental challenges. Additionally, measurements can be contaminated by polarized foregrounds such as dust and synchrotron emission. To recover the CMB signal, we must characterize and remove these polarized foregrounds with high precision, which requires multiple frequency bands and highly stringent instrument calibration. Previous experiments have never needed to calibrate to such extreme levels, but future experiments seeking to improve CMB measurements will require sub-percent level uncertainties in detector bandpass characterization. This will necessitate new calibration techniques. In this thesis, I present my work towards achieving this unprecedented level of precision in detector bandpass calibration for AdvACT, SO, and future experiments such as CMB-S4, through analyzing current measurements and using novel techniques to improve Fourier transform spectrometer (FTS) bandpass calibration, including characterizing the FTS transfer function, design improvements, and improved coupling optics. I will discuss the viability of these methods for future CMB experiments. This work will improve the frequency calibration needed to remove polarized foregrounds from CMB maps, which will enable CMB measurements that will advance our understanding of the fundamental physics of the Universe.

Melanin is a ubiquitous pigment found in animals, plants, and microorganisms, which is widely known for its UV light absorption capacity, high antioxidant activity, and other unique properties. The most common commercial sources are synthetic melanin: polydopamine (PDA) and poly(L-3,4-dihydroxyphenylalanine) (PDOPA), and natural melanin: sepia melanin. Here, we extract melanin from black knot fungus (Apiosporina morbosa), a pathogenic fungus that grows on several fruit trees, using acid/base extraction method and elucidate the chemical structure of the extracted melanin by Fourier transform infrared spectroscopy (FT-IR) and solid-state nuclear magnetic resonance (ssNMR) spectroscopy. The extraction yield is around 10% and the characterization results prove that its chemical structure is similar to synthetic melanin, PDA and PDOPA, which illustrates that the extracted melanin is eumelanin. Scanning electron microscopy (SEM) images show irregular morphology of melanin. Also, the extracted melanin shows a broadband UV light absorption similar to melanin extracted from other sources. Because of the low cost of black knot fungus and it being an invasive species, it can serve as a cheaper alternative source of melanin, which could be applied as UV light absorbers and antioxidant reagents in the future.

Cellulose Acetate (CA) based biomaterials are being used as substrates for bone ingrowth applications due to their nontoxic and nonirritant nature coupled with optimum morphology and stiffness. Electrospinning with additives and/or post-treatment has emerged as a viable protocol to further improve mechanical properties of CA and expand its utility. Herein, we highlight the role of potassium chloride (KCl) in association with airdrying to enhance the elastic modulus and tensile strengths of CA fibers. Salt aggregation in between fibers is observed through Scanning Electron Microscopy (SEM), however, Fourier-transform infrared (FTIR) analysis signifies the interactions between K+ ions and acetyl groups. The increase in KCl concentration (2 to 4 to 6%) boosts the elastic modulus to 176 MPa (52 times than pure CA) and tensile strength to 1.2 MPa (9 times than pure CA). The presence of K+ ions, indeed, offers osteoconduction to fibers and thus the outcome has potential in bone tissue engineering applications.

Properties of structural alloys containing chromium, for example 316L austenitic stainless steel, can be tremendously improved by surface engineering through infusion of interstitial solute, including carbon or nitrogen. However, to make the surface transparent to carbon or nitrogen, it must be “activated”. A potent method that has recently been discovered for such “surface activation” is exposing the alloy to the gaseous products of a pyrolyzed solid reagent. For this purpose, pyrolysis of nitrogen-halide salts with 316L samples has been demonstrated to be highly effective, but the micromechanisms of activation have been elusive.In this thesis project, pyrolysis FT-IR has been used to examine the products of pyrolyzing various solid reagents in an effort to model surface reactions. This work has demonstrated that ammonia and hydrogen chloride evolving from NH4Cl are responsible for reducing the surface oxide and forming chlorides and nitrides in the 316L surface. A new approach has been used to characterize the activated surface: ToF-SIMS paired with isotope-rich solid reagents. This enables observation of transport phenomena and determine surface reaction products. Considerable progress has been made on hybrid-processing (activation separated from infusion) of parts in an industrial capacity. A model has been developed to explain the micromechanisms of activation for low-temperature carburization.Understanding the chemical reactions and microstructural changes occurring during this process is vital for developing more rapid and effective low-temperature surface hardening technologies. One main conclusion of this work is that activation is not simply the reduction of protective surface oxides, but actually the formation of a 3 to 7 micrometer thick layer of chlorides and nitrides in the substrate surface. Also, activation appears to be aided by condensation of pyrolysis products on the fresh surface protecting the newly oxide-free surface from passivation. Likewise, utilizing 15N and 2H rich reagents to activate samples for subsequent analysis with ToF-SIMS has proven to be an effective means of surface analysis with easy means of identifying and tracing formed compounds and transport within the activated layer. Activation with nitrogen-halide pyrolysis has produced samples which remain active and carburize effectively even after 62 days in air. Also, fractal-like structures at the interface between the activated layer and matrix material have been discovered, suggesting a self-accelerating reaction at the reaction front. Lastly, this work has determined that the metal surface affects the nitrogen-halide pyrolysis process, leading to increased measurement of ammonia in the pyrolysis product gases and decreased occurrence of acid gas component (e.g. HCl) and recombination product (NH4Cl) in the vapor phase. Overall, the pyrolysis products responsible for activation are ammonia and an acid-gas which react with the metal sample surfaces.

The research described herein examines the effect of hydrolytic decomposition on the work function of polyurethane rain erosion coatings (REC). Two groups of panels, one group coated with REC containing carbon black and one group coated in REC without carbon black, were exposed to high temperature and humidity conditions in a steam autoclave for various periods of time. The work function of each unique exposure time was measured with a scanning Kelvin probe (SKP) and compared to unexposed coated panels to determine the magnitude of change in the REC coating. For both sample groups, results from the SKP analysis showed that as the coated panels were exposed for longer periods of time, the work function increased compared to an identical panel that was not exposed. The extent of the polymer coating degradation was determined by Raman spectroscopy and thermomechanical analysis (TMA). Raman analysis indicated a decrease in ester bonds, while with TMA a decrease in polymer strength was observed with increasing exposure time. These results demonstrate that there is decomposition of the REC occurring from the exposure and it is due to hydrolysis of the ester bonds. The change in REC structure/composition was able to be detected by the Kelvin probe in a non-destructive manner, making it a valuable tool in assessing the decomposition of polyurethane rain erosion coatings.

Improve the enantioselectivity to obtain chiral product has been the major concern in pharmaceutical and biochemical engineering. In most cases, separation of racemic product is extremely time consuming and requires special equipment, thus it usually becomes a less efficient and economic option than chiral synthesis even though such synthesis often involves modified noble metal catalyst. In this work, chiral modification of platinum has been studied to gain better understanding of adsorption mechanism of surface modifiers on Pt surface as well as it affects the conversion and enantioselectivity of our model reaction—hydrogenation of activated keto-esters.Majority of this work has been focused on exploring the factors that may play an important role in the adsorption of chiral modifier onto a variety of Pt surfaces including polycrystalline Pt and Pt nanoparticles supported on oxide. Several in-situ FT-IR (Fourier Transform- Infrared) spectroscopy setup has been designed and built based on a Bruker Tensor IR spectrometer. In-situ IR spectroscopy has been proved itself to be overwhelmingly powerful and efficient to study the adsorption geometry of modifiers at solid/liquid interfaces. Pt surface is probed with advanced IR characterization methods such as RAIRS (Reflection-Absorption Infrared Spectroscopy) and Multi-bounce ATR-IR (Attenuated Total Reflection) methods due to their ability to distinguish adsorbed species from dissolved molecules in solution phase. A series of modifiers are involved in this project, not only limited to the well-studied classic cinchona-alkaloid such as cinchonidine and cinchonine, but also naphthyl-based chiral compounds including (R)- or (S)-(−)-1-(1-naphthyl) ethylamine (NEA), naphthylmethyl amine, and dimethyl naphthyl ethylamine. The adsorption strength of the different modifier molecules was found to be quite different among those compounds, which is illustrated by the fact that quinoline can displace s-NEA from Pt but not vice versa, for instance, and by the observation that when Pt is exposed to a solution containing both quinoline and s-NEA only the quinoline’s signature peaks can be detected by ATR-IR spectroscopy. The ordering of the modifiers studied in terms of adsorption strength was found to correlate with their ability to chirally modify the Pt catalyst during the hydrogenation of unsaturated aldehydes. In addition, adsorption geometry of s-NEA/r-NEA shows that these modifiers adsorb on Pt surfaces through the nitrogen atom of the primary amine moiety not aromatic ring as commonly believed in the past. Future follow-up work of this project might include: optimizing the IR instrumentation to minimize the interference from polar solvent and efficiently run and monitor hydrogenation reactions using in-situ IR spectroscopy.

Abstract: Northern Alberta houses massive tailings ponds, that store aqueous waste as a result of the processes employed to recover bitumen from the oil sand deposits. The aqueous waste, or tailings pond water (TPW), houses numerous toxic chemicals including naphthenic acids (NAs) - a complex group of naturally occurring hydrophobic organic acids that can have adverse and even irreversible effects on their surrounding environment. The Lowary group has shown that methyl mannose polysaccharides (MMPs) have a high binding affinity for NAs, while the Serpe group has demonstrated that poly(N-isopropylacrylamide) (pNIPAM)-based micro-particles have a high binding affinity for organic molecules in general. Our research group has been developing a unique class of microgels for the removal of NAs from TPW by utilizing pNIPAM-based porous micro-particles and incorporating unmethylated and methylated derivatives of long-chained saccharide(s)-amines. Several pNIPAM-based microgels coupled or polymerized with a series of carbohydrates have been developed and their effectiveness to treat TPW was monitored using Microtox bioassay toxicity tests and Fourier-transform infrared spectroscopy (FT-IR). According to the Microtox data the carbohydrate-modified microgels have only a marginal effect treating medium fine tailings (MFT) and the top recyclable tailings water layer. However, FT-IR analysis shows that few carbohydrate-modified poly(N-isopropylacrylamide)-co-acrylic acid (pNIPAM-co-AAc) microgels lower NAs concentration in MFT: pNIPAM-co-50 % AAc-di-mann-octylamine shows the best performance by decreasing the NAs concentration within a similar range as the standard sorbent: powdered activated carbon (PAC). Overall, PAC shows the best performance treating MFT according to both Microtox bioassay and FT-IR analysis.

This dissertation describes the development and application of methods and instrumentation for qualitative and quantitative sample analyses by infrared and Raman spectroscopies. An introduction to the concepts and methods utilized is provided in Chapter 1. A comparative evaluation of solid-core silver halide fiber optics and hollow silica waveguides was performed on the basis of the transmission of mid-infrared radiation using a fiber optic coupling accessory and an infrared microscope is presented in Chapter 2. Increased transmission was reproducibly observed between two identical hollow waveguides due to minimization of insertion and scattering losses resulting from the hollow core. Chapter 3 presents an evaluation of a mid-infrared, attenuated total (internal) reflection (ATR) probe accessory utilizing hollow waveguides based on transmission and signal-to-noise. Quantitative analyses of aqueous succinylcholine chloride and ethanol solutions were also performed. An in situ Raman study of nitrogen incorporation in thin films of zinc oxide using a temperature-controlled reaction cell is discussed in Chapter 4. Monitoring nitrogen incorporation in thin films of zinc oxide at elevated temperatures in the presence of nitrogen-containing precursor reagents proved inconclusive using the proposed method. Chapter 5 presents an evaluation of dispersive and Fourier transform (FT-) Raman spectroscopies for on-line process control in the bottling industry. FT-Raman was determined to be more applicable for on-line determinations of poly(ethylene terephthalate) bottle thickness due to the availabilities of such benefits as increased laser power and fluorescence rejection. Preliminary data from the development of an inverted ATR imaging microscope are discussed in Chapter 6. The inverted optical design of the microscope permits simultaneous viewing of the sample with white light and the collection of infrared spectral images. Summaries of the presented research are provided in Chapter 7.

This dissertation explores various effects of deuterium oxide (D2O also known as heavy water) in nature. Water is everywhere and interacts with just about everything. As such, it would be quite a daunting task to characterize every effect that water exhibits on everything in the universe. This research is a small piece of the puzzle, and provides some fundamental understanding of how water interacts with other molecules. This is done from two viewpoints: (1) the effects of heavy water on living cells and (2) the effects of heavy water on molecules. Varying concentrations of deuterium oxide were used as the growing solvent for four different organisms: S. cerevisiae, E. coli, A. thaliana, and N. tabacum. In each case growth rates and morphology was assessed and compared to the wild type. Organisms were surveyed for potential phenotypes exhibited in the presence of extremely low and high concentrations of D2O. In every organism, growth is increasingly inhibited in higher concentrations of D2O compared to lower concentrations of D2O. In the case of tobacco, a root hair phenotype was exhibited in the presence of deuterium depleted water (atoms). Roots also grew faster in 1% D2O and DDW, compared to natural water. For Arabidopsis, root germination is statistically indistinguishable between DI water and 33% D2O. Growth of the plant in 10% D2O is identical to that of natural water, and potentially healthier. Meanwhile, plants grown in 60% D2O exhibit slower growth and leaf discoloration. Tests on E. coli reveal inconsistent growth rates, but exhibit increased growth in DDW when adapted to D2O. Cellular and colonial morphology is also very distinguished from the wt. Cells appear to remain joined after cellular fission, while colonies exhibit brainy structures. Yeast morphology is quite different. Yeast cells remain joined after mitosis in 99% D2O, causing large cellular aggregates, while colonies become slightly asymmetric. Adaptation of yeast to D2O was not possible. Molecular effects were examined using a variety of tools including: dynamic light spectroscopy, Fourier transform-infrared spectroscopy, cavity ring-down spectroscopy, and optical tweezers. Heat induced protein aggregation was possible in H2O, but prevented in the presence of D2O and analyzed via DLS. Deuterium exchange and replacement was observed and quantified using both FT-IR and CRDS. With FT-IR it was possible to identify differences between solvents, while the time-scale of hydrogen-deuterium exchange was quantified for bulk water with CRDS. Using optical tweezers, DNA was overstretched in both H2O and D2O. The average force for DNA overstretching was found to be ~2.5pN higher in D2O compared to H2O. Deuterium oxide has a stabilizing force on biomolecules, which prevents protein denaturing and can affect the timing for cellular processes. It is because of this molecular property that D2O is observed to affect organisms grown with D2O instead of H2O. Despite this, there seems to be an optimal concentration of deuterium which is above the natural concentration of 155.6ppm. In the presence of deuterium depleted water, cells exhibit signs of stress, further demonstrating that deuterium isnt merely tolerated in solution, but actually required as hypothesized by Gilbert N. Lewis in 1934.

With the increase in anthropogenic pollutants such as: atmospheric CO2 [carbon dioxide], fossil fuel combustion and fertilizer run off, the fate of the environment is of great importance. Through industrialization, the greenhouse gas, CO2, is a major contributor to global warming; while nitrogen based fertilizer, causes the production of toxins due to harmful algal blooms. Both chemical impacts dissolve into marine ecosystems effecting the chemical composition of organisms such as microalgae. Microalgae remediate these changes by sequestering carbon and nitrogen; thus there is a need to understand how these impacts affect the ecosystem by detecting the change and relating it to its chemical source. It was demonstrated that microalgae respond sensitively to changes in their environment, the present dissertation expands the utilization of phytoplankton as an in-situ biological probe. The goal of this dissertation is to develop analytical methodologies for investigations of chemical impacts on marine ecosystems via microalgae for examining the relationship between ambient chemical changes and microalgae remediation processes. Thus, experiments performed simulated the chemical shifts of selected chemical parameters. Impacts are measured by means of microscopic imaging and FT-IR spectroscopy for determining physical and chemical responses of microalgae. In order to quantitate these processes, novel chemometric algorithms were developed for determining ambient conditions based on imaging and spectroscopic data. The first step to understanding these effects was developing an innovative image analysis technique to measure cell size and shape as a function of species and ambient conditions. This technique discriminated microalgae cells based on their physical parameters. For chemical analyses, FT-IR spectroscopy was used for detecting species chemically induced shifts in microalgae’s chemical composition. Within mixture species spectrum new chemical information was found and the suppression of chemical features was also revealed. Results demonstrated chemical change is present in the biomass and are nutrient source and concentration dependent. These novel analytical methodologies developed have demonstrated the ability to detect chemical changes under varying environmental conditions.

The goal of the research performed for this thesis was to further develop and evaluate vibrational spectroscopic techniques, specifically infrared and Raman spectroscopies, in challenging sampling situations. Some experiments focused on analyzing samples with techniques that had limited to no previous research while others focused on modifying current techniques providing alternate and possibly improved methods of detection and analysis. Chapter 1 provides background into the fundamentals of infrared and Raman spectroscopy and briefly covers sampling techniques available. Chapter 2 demonstrates that a commercial Raman microscope can be externally modified to sample using attenuated total internal reflectance (ATR). This modification allowed the collection of nanometer thin films without spectral contamination from sub-layers and demonstrated improved collection parameters. Chapter 3 evaluated a constructed dispersive Raman spectrometer operating with near–infrared (NIR) wavelengths to determine polyethylene terephthalate film thickness for process monitoring purposes. Chapter 4 demonstrated the potential capabilities of NIR-diffuse reflectance spectroscopy for the detection of high energy materials to provide alternative methods of detection and increase safety in the battlefield. Chapter 5 was an investigation of a planar array spectrograph employed as a real-time detector for liquid chromatography separations.

The application of infrared spectroscopy techniques to problems in the food and beverage industry has yielded many novel methods. With the increase in computational power, multivariate analysis has brought the unique properties of mid-infrared (MIR) systems to the forefront. The distinct, high intensity MIR absorption bands are well-suited to authentication, classification and quantification of components in complex matrices. This technique has been applied to a variety of food systems, with particular success in the analysis of edible oils. Methods for trans-fat determination, monitoring of oxidative indices, and discrimination of adulterated oils represent only a few of the developments in field of oils. The objective of this study was to utilize MIR spectroscopy in the analysis and characterization of products and processes related to edible oils. A temperature-controlled, ZnSe ATR sampling accessory was used with a benchtop FT-IR system to monitor oxidative changes in frying oils under the influence of a patented anti-oxidation device. In addition, reference methods for free fatty acids (FFA), anisidine value (AV), and color were used to monitor oil stability. FT-IR combined with chemometrics showed differences between control and treatment, with discrimination provided by regions associated with fatty acid hydrolysis and oxidation products. As compared to the control treatment, the anti-oxidation technology decreased the rate of FFA and aldehyde formation, as well as showing a marked effect on total color difference (¿E). Overall, our results showed that a patented induction device slows the rate of lipid degradation, resulting 7-20% reduction in formation rate of key quality parameters and significantly longer utilization of frying oil. Omega-3 dietary supplements have been linked with health benefits due to their contents of EPA and DHA. The concentration of these active components in fish is highly variable; species, catch location, environment, season and processing parameters are all factors in determining the ratio of fatty acids found in the oil. Our objective was to characterize the composition of commercial Omega-3 dietary supplements using mid-infrared spectroscopy, gas chromatography, and chemometrics. Twenty-nine fish body oil (FBO), cod liver oil (CLO), and flaxseed supplements were purchased from retailers. Fatty acid composition of oils, determined by GC-FAME, encompassed a wide range of fatty acid profiles and delivery methods. Mid-infrared spectral data was collected on portable infrared systems and the spectra were used to classify supplements using SIMCA, a pattern recognition technique. In addition, PLSR was used to correlate the spectra with GC-FAME results. SIMCA analysis allowed for tight clustering of fish oil supplements into distinct classes, dependent upon the source and processing. Discriminating power showed a strong influence of the 1038 cm-1 band, which is typically associated with C-O stretching vibrations. PLSR generated multivariate models with high correlation (R = 0.99) between the infrared spectrum and fatty acid composition, and SECV of 1.74 and 1.89 for EPA and DHA, respectively. Our results indicate that ATR FT-IR spectroscopy combined with pattern recognition analysis provides for rapid, robust screening and characterization of edible oils.

In this thesis, a digital signal processing (DSP) strategy for the Fourier transform infrared (FT-IR) spectrometer called Super Clip Mathematics is presented. This work is motivated by the issue of collecting a reliable FT-IR background spectrum while collecting data in a dynamic environment. Super Clip Mathematics addresses this problem by extracting data contained within a single interferogram in lieu of collecting a background spectrum. This regime utilizes the pre-established technique of super clip apodization (SCA) and defines a new DSP strategy called complementary super clip apodization (CSCA), where both methods are generally defined by the umbrella term of Super Clip Mathematics. SCA is a DSP strategy that calculates a background spectrum by isolating and Fourier transforming the central burst of an interferogram. A secondary strategy is described herein as CSCA, where all of the interferogram except the center-burst is Fourier transformed for the calculation of an absorbance spectrum. Upon isolation of these regions of the time-domain waveform, each method may subsequently calculate a quantitative absorbance spectrum. Interferogram manipulation in this fashion has been previously discounted by its community because there is a lack of systematic investigation into its potential. The outcomes of this work suggest that the limitation of Super Clip Mathematics is not the signal processing strategy itself, but the way in which it is implemented. An implementation algorithm that systematically optimizes the number of points truncated or included during Super Clip Mathematics analysis is presented. With this protocol, carbon dioxide, nitromethane, ethanol and acetone interferograms are analyzed to calculate quantitative absorbance spectra. This is significant because the latter three substances have spectral widths that are considered too wide by convention, yet their successful analysis in univariate and multivariate studies is shown. For comparison, the linear regression models built with Super Clip Mathematics spectra are compared to those built with spectra calculated by taking the logarithmic ratio of a background and sample spectra; and the results indicate that there is almost no statistical difference between them. The issue of collecting a characteristic background may be circumvented by utilizing data already present in the sample interferogram with Super Clip Mathematics.

Photographs of an ecosystem are an important tool in macro-community ecology. The photograph is a permanent record of species phenotype. In microbiology, biochemical activity provides the most descriptive information of an organism’s phenotype. A method for fingerprinting all biochemical activities occurring within a microbial community is analogous to a photograph. Infrared spectroscopy in the region between wavelengths 2500 to 20,000 nm (mid-IR) is a well established instrumental method for fingerprinting the total biochemical profile of axenic cultures. Spectra are complex and sensitive as demonstrated by the ability to discriminate between strains of bacteria, fungi, and algae. This thesis develops the method to apply mid-IR spectroscopy in order to attain a biochemical fingerprint by attenuated total reflectance. Chapter 2 establishes methods for obtaining mid-IR spectra by prefiltering and concentrating lake water onto a 0.2 µm filter membrane. In order to optimize signal, a combined spectrum from PVDF and nylon membranes is used following a 20-25 µm prefilter. Chapter 3 verifies that the established method is capable of discriminating the biochemical fingerprints of six interdunal lakes from Western Nebraska with differing chemistries and community structures. Mid-IR spectra provide functional data, but do not mirror structure, based on 16S rRNA data, identically. Now, a record of biochemical activity within a microbial community can be captured for future comparison. This technique is culture-independent and provides functional, in situ information. In the future, more information can be deduced by comparing different functional communities to one another, assigning spectral information to particular biochemical activities in a community.

Concord grape juice is an especially valuable fruit juice due to its unique composition, sensory sttributes, and health benefits. Currently, methods of authentication are impractical at production scale. We propose Fourier-Transform Infrared spectroscopy in combination with chemometric analysis as a rapid means of authenticating Concord grape juice. Authentic grape juice samples were used as training sets to create SIMCA and PLS models capable of qualitative and quantiavie analysis respectively. The SIMCA model was effective at discriminating pure 100% juices on the basis of variety and capable of predicting the varieties of unknown samples. The PLS model was capable of predicting the content of Concord grape juice in a grape juice blend with an associated error of 8.4%. These simple models show the feasibility of FT-IR coupled with chemometrics as production scale tools for Concord grape juice authentication.

Fourier-Transform infrared (FT-IR) spectroscopy is a simple, fast and highly specific technology that can provide valuable insights into the complex chemical make-up of foods. Infrared provides tools, especially in the fingerprint region of the spectrum, to detect specific compounds in biological systems without the use of time-consuming methods or the use of hazardous organic solvents. Advances in FT-IR instrumentation and pattern recognition techniques have made it possible to extract information related to composition and conformation of food components from the spectra. We have evaluated the capability of infrared spectroscopy in classification and quantification of chemical compounds of interest for the dairy (butter) and tomato industries. Authentication is a critical quality issue for organic products since consumers are willing to pay 10-40% price premiums. There is a need for rapid and reliable analytical tools for determination of authenticity since traditional methods often involve time-consuming and laborious processes. Our objective was to evaluate the application of infrared spectroscopy combined with pattern recognition techniques to discriminate among organically and conventionally-produced butter in relation to quality and authenticity. Spectra from butter purchased from a local market (Columbus, OH) were collected by using Attenuated total reflectance (ATR) spectroscopy and analyzed using soft independent modeling of class analogy (SIMCA), a multivariate classification technique. This simple protocol generated unique mid-infrared signature profiles that permitted the chemically-based classification of butter samples based on manufacturer and production practice (organic vs. conventional). By using the spectral region from 1400-800 cm-1, multivariate (SIMCA) modeling showed well-separated clusters that discriminated among butter samples according to manufacturer, due to -HC=CH- trans bending out of plane vibration modes, (966 cm-1) presumably attributed to conjugated fatty acids. Infrared spectroscopy combined with multivariate analysis provides a simple and efficient tool for monitoring butter authenticity with minimal sample preparation. The objective of the second study was to develop a simple, accurate and cost effective protocol using ATR-IR spectroscopy and multivariate analysis to determine sugars in tomatoes. Tomatoes, the second most produced and consumed vegetable in the United States, are classified for use as fresh or processed tomato products based on their sugar and acid profile. Current methods to analyze sugar content of tomatoes are time and labor intensive making efficient assays for quantification desirable. Samples were obtained from genetically diverse tomato varieties that encompassed hybrids and elite parents used in the processing and fresh market industry. Samples were centrifuged, the supernatant vacuumed dried on a ZnSe crystal and infrared spectra collected. Enzymatic kits for glucose and fructose were used as reference methods. Multivariate models (PLSR) accurately predicted glucose and fructose using the supernatant with R-values > 0.98 and SECV -1 for sugars. Vacuum drying of the sample onto the ATR crystal caused spectral artifacts in some samples. ATR-IR combined with chemometrics could provide the tomato industry with a simple and high throughput method for determination of sugars in tomatoes that could lead to improved varieties with enhanced characteristics for industry and consumer demands.

A series of 1,3-di-substituted-imidazolium lithium phthalocyanines, in which the substituents on the imidazolium nitrogens were combinations of methyl, ethyl, pentyl, hexyl, isopropyl, adamantyl or 2,4,6-trimethylphenyl groups, was synthesized. The cation exchange of a single lithium ion of dilithium phthalocyanine for a 1,3-disubstituted-imidazolium ion was performed by mixing their salts in common organic solvents under ambient conditions. This afforded a number of imidazolium lithium phthalocyanines in moderate yields. They exhibited poor solubility in most solvents. Their composition and purity were initially verified by 1H and 13C-NMR and elemental analysis. The 1H-NMR spectra also indicated that the imidazolium and lithium phthalocyanine ions are present in a 1:1 ratio. Infrared spectra confirmed the C-C and C-N stretching modes that are characteristic of phthalocyanine and imidazolium aromatic structures. UV-Vis spectra for each compound showed essentially no change in absorption from that of dilithium phthalocyanine, which suggests a lack of influence of the imidazolium ions. Thermal properties of the title compounds were determined through melting points and TGA, in which high melting temperatures (330-370°C) were seen for several complexes and lowered thermal stability was seen for all. The crystal structure of the bis(adamantyl)imidazolium derivative was determined through X-ray diffraction. It was found that water molecules are associated to imidazolium and lithium phthalocyanine ions through hydrogen-bonding, which is possibly the basis for crystallization in imidazolium-lithium-phthalocyanines.

Silicon Oxide/Oxynitride (SiO2/SiON) has been the mainstream material used for gate dielectric for MOS transistors for the past 30 years. The aggressive scaling of the feature size of MOS transistor has limited the ability of SiO2/SiON to work effectively as the gate dielectric to modulate the conduction of current of MOS transistors due to excess leakage current dominated by direct quantum tunneling. Due to this constraint, alternative gate dielectric/high-k is being employed to reduce the leakage current in order to maintain the rate of scaling of MOS transistors. However, the cost involved in the implementation of these new gate dielectric materials are high due to the requirements of a change in the process flow for device fabrication. This work presents the results of a novel processing method implementing the use of rapid thermal processing (RTP) on conventional SiO2/SiON gate dielectric to reduce the gate leakage current by three to five orders of magnitude. Electrical properties of the effect were characterized on fabricated MOS capacitors using semiconductor parameter analyzer and LCR meter. Material characterization was performed using FT-IR to understand the mechanism involved in this novel processing method, named PECE (Phonon-Energy-Coupling-Enhancement). By implementing this novel process, the use of SiO2/SiON as gate dielectric can be scaled further in conventional process flow of device fabrication.

The following work describes the instrumentation and application of hyphenated FT-IR techniques specifically involving supercritical fluid extraction (SFE), supercritical fluid chromatography (SFC), and liquid chromatography (LC). Three studies are presented. The first involves the application of SFE/FT-IR towards the extraction of finishes from textile fibers. SFE has previously been applied to less complex finish systems. The proposed method making use of intermediate trapping is viable for more complex systems that show limited solubility in a supercritical fluid. Quantification of the percent finish on yarn was performed and results were favorable when compared with plant data. The range of applications was expanded to on-line SFE/SFC in the extraction and analysis of components from the polymer matrix itself. SFE/SFC/FT-IR was used to identify extractable components from a variety of Nylons. Following identification of one of the primary extractables, caprolactam, SFE/SFC was used to quantitate the amount of residual starting material in a Nylon copolymer. The second study involves the extractables in polystyrene which is a softer polymer with respect to solubility of components in supercritical CO ₂. Dimers and trimers as well as processing agents were identified via FT-IR with relatively mild supercritical extraction conditions. Following these two studies was the expansion of hyphenated FT -IR to mobile phase elimination. A system optimization was carried out using polymer additive standards. The effects of nebulizer flow, sheath flow, and sheath temperature were shown. The data were analyzed at in terms of library matches as well as GramSchmidt reconstruction peak heights. Peak intensities were the primary source for choosing optimum conditions. Under optimized conditions, approximately 200 ng of analyte were analyzed and found to be above the limit of detection. The applicability of the interface was demonstrated by the identification/analysis of triclosan, an antibacterial agent, in Colgate toothpaste. Aside from the identification of the analyte this study was used to show the effect of deposition parameters such as disk rotation rate as well as the effectiveness of FT-IR spectral library searches. The analysis of triglycerides was also carried out to show the effectiveness of using LC/FTIR for viscous liquids which are difficult analytes to deposit onto a solid substrate. Using this FT-IR technique allowed one to look at the degree of saturation/unsaturation in an olive oil sample. The linearity of the method was shown using a set of triglyceride standards. Lastly, the feasibility of using the commercially manufactured mobile phase elimination interface for SFC was demonstrated. Additive standard was deposited using both pure and methanol modified CO₂. No effluent split mechanism was used for decompressed flows up to 150 mL/min. Detection limits are proposed to fall in the low (10 - 25) ng range. The infrared spectra are enhanced over those acquired with a flow cell interface because CO₂ absorbance bands no longer obscure a portion of the analyte absorption spectrum.