Rapid separation of biologically important low molecular weight compounds by microchip electrophoresis and ultra-fast performance liquid chromatography

The research work in this thesis reports rapid separation of biologically important low molecular weight compounds by microchip electrophoresis and ultrahigh liquid chromatography. Chapter 1 introduces the theory and principles behind capillary electrophoresis separation. An overview of the history, different modes and detection techniques coupled to CE is provided. The advantages of microchip electrophoresis are highlighted. Some aspects of metal complex analysis by capillary electrophoresis are described. Finally, the theory and different modes of the liquid chromatography technology are presented. Chapter 2 outlines the development of a method for the capillary electrophoresis of (R, S) Naproxen. Variable parameters of the separation were optimized (i.e. buffer concentration and pH, concentration of chiral selector additives, applied voltage and injection condition).The method was validated in terms of linearity, precision, and LOD. The optimized method was then transferred to a microchip electrophoresis system. Two different types of injection i.e. gated and pinched, were investigated. This microchip method represents the fastest reported chiral separation of Naproxen to date. Chapter 3 reports ultra-fast separation of aromatic amino acid by capillary electrophoresis using the short-end technique. Variable parameters of the separation were optimized and validated. The optimized method was then transferred to a microchip electrophoresis system where the separation time was further reduced. Chapter 4 outlines the use of microchip electrophoresis as an efficient tool for analysis of aluminium complexes. A 2.5 cm channel with linear imaging UV detection was used to separate and detect aluminium-dopamine complex and free dopamine. For the first time, a baseline, separation of aluminium dopamine was achieved on a 15 seconds timescale. Chapter 5 investigates a rapid, ultra-sensitive and highly efficient method for quantification of histamine in human psoriatic plaques using microdialysis and ultrahigh performance liquid chromatography with fluorescence detection. The method utilized a sub-two-micron packed C18 stationary phase. A fluorescent reagent, 4-(1-pyrene) butyric acid N-hydroxysuccinimide ester was conjugated to the primary and secondary amino moieties of histamine. The dipyrene-labeled histamine in human urine was also investigated by ultrahigh pressure liquid chromatography using a C18 column with 1.8 μm particle diameter. These methods represent one of the fastest reported separations to date of histamine using fluorescence detection.

Synthesis and reactivity of pyridine substituted α-diazocarbonyl compounds and exploration of rhodium carboxylates as asymmetric catalysts

The primary objective of this thesis was the preparation of a series of pyridine-containing α-diazocarbonyl compounds and subsequent investigation of the reactivity of these compounds on exposure to transition metal catalysts. In particular, the reactivity of the pyridyl α-diazocarbonyls was compared to that of the analogous phenyl α-diazocarbonyl compounds to ascertain the impact of replacement of the phenyl ring with pyridine. The first chapter initially provides a brief introduction into α-diazocarbonyl chemistry, comprising a compendium of well-established and recently developed methods in the preparation of these compounds, as well as an outline of the reactivity of these versatile substrates. The substantive element of this introductory chapter comprises a detailed review focused on transition metal-catalysed transformations of heterocyclic α-diazocarbonyl compounds, highlighting the extraordinary diversity of reaction products which can be accessed. This review is undertaken to set the work of this thesis in context. The results of this research are discussed in the second and third chapters together with the associated experimental details, including spectroscopic and analytical data obtained in the synthesis of all compounds during this research. The second chapter describes the preparation of a range of novel pyridine-containing α-diazocarbonyl compounds via a number of synthetic strategies including both acylation and diazo transfer methodologies. In contrast to the phenyl analogues, the generation of the pyridine α-diazocarbonyl substrates was complicated by a number of factors including the inherent basicity of the pyridine ring, tautomerism and existence of rotamers. Rhodium- and copper-mediated transformations of the pyridine-containing α-diazocarbonyl compounds is discussed in detail displaying very different reactivity patterns to those seen with the phenyl analogues; oxidation to 2,3- diketones, 1,2-hydride shift to form enones and oxonium and sulfonium ylide formation/rearrangement are prominent in the pyridyl series, with no evidence of aromatic addition to the pyridine ring. The third chapter focuses on exploration of novel chiral rhodium(II) catalysts, developed in the Maguire team, in both intermolecular cyclopropanations and intramolecular C–H insertion reactions. In this chapter, the studies are focused on standard α-diazocarbonyl compounds without heteroaryl substituents. The most notable outcome was the achievement of high enantiopurities for intramolecular C–H insertions, which were competitive with, and even surpassed, established catalyst systems in some cases. This work has provided insight into solvent and temperature effects on yields as well as enantio- and diastereoselectivity, thereby providing guidance for future development and design of chiral rhodium carboxylate catalysts. While this is a preliminary study, the significance of the results lie in the fact that these are the first reactions to give substantial asymmetric induction with these novel rhodium carboxylates. While the majority of the α-diazocarbonyl compounds explored in this work were α-diazoketones, a number of α-diazoesters are also described. Details of chiral stationary phase HPLC analysis, single crystal analysis and 2D NMR experiments are included in the Appendix (Appendix III-V).

Taming hazardous chemistry in flow: The continuous processing of diazo and diazonium compounds

The synthetic utilities of the diazo and diazonium groups are matched only by their reputation for explosive decomposition. Continuous processing technology offers new opportunities to make and use these versatile intermediates at a range of scales with improved safety over traditional batch processes. In this minireview, the state of the art in the continuous flow processing of reactive diazo and diazonium species is discussed.

Quantum chemical study of the effect of precursor stereochemistry on dissociative chemisorption and surface redox reactions during the atomic layer deposition of the transition metal copper

Using quantum chemical calculations, we investigate surface reactions of copper precursors and diethylzinc as the reducing agent for effective Atomic Layer Deposition (ALD) of Cu. The adsorption of various commonly used Cu(II) precursors is explored. The precursors vary in the electronegativity and conjugation of the ligands and flexibility of the whole molecule. Our study shows that the overall stereochemistry of the precursor governs the adsorption onto its surface. Formation of different Cu(II)/Cu(I)/Cu(0) intermediate complexes from the respective Cu(II) compounds on the surface is also explored. The surface model is a (111) facet of a Cu55 cluster. Cu(I) compounds are found to cover the surface after the precursor pulse, irrespective of the precursor chosen. We provide new information about the surface chemistry of Cu(II) versus Cu(I) compounds. A pair of CuEt intermediates or the dimer Cu2Et2 reacts in order to deposit a new Cu atom and release gaseous butane. In this reaction, two electrons from the Et anions are donated to copper for reduction to metallic form. This indicates that a ligand exchange between the Cu and Zn is important for the success of this transmetalation reaction. The effect of the ligands in the precursor on the electron density before and after adsorption onto the surface has also been computed through population analysis. In the Cu(I) intermediate, charge is delocalized between the Cu precursor and the bare copper surface, indicating metallic bonding as the precursor densifies to the surface.

Isolation and characterisation of antifungal compounds from lactic acid bacteria and their application in wheat and gluten-free bread

As part of the “free-from” trend, biopreservation for bread products has increasingly become important to prevent spoilage since artificial preservatives are more and more rejected by consumers. A literature review conducted as part of this thesis revealed that the evaluation of more suitable antifungal strains of lactic acid bacteria (LAB) is important. Moreover, increasing the knowledge about the origin of the antifungal effect is fundamental for further enhancement of biopreservation. This thesis addresses the investigation of Lactobacillus amylovorus DSM19280, Lb. brevis R2: and Lb. reuteri R29 for biopreservation using in vitro trials and in situ sourdough fermentations of quinoa, rice and wheat flours as biopreservatives in breads. Their contribution to quality and shelf life extension on bread was compared and related to their metabolic activity and substrate features. Moreover, the quantity of antifungal carboxylic acids produced during sourdough fermentation was analysed. Overall a specific profile of antifungal compounds was found in the sourdough samples which were strain and substrate dependently different. The best preservative effect in quinoa sourdough and wheat sourdough bread was achieved when Lb. amylovorus DSM19280 fermented sourdough was used. However, the concentration of the antifungal compounds found in these biopreservatives were much lower when compared with Lb. reuteri R29 as the highest producer. Nevertheless, the artificial application of the highest concentration of these antifungal compounds in chemically acidified wheat sourdough bread succeeded in a longer shelf life than achieved only by acidifying the dough. This evidences their partial contribution to the antifungal activity and their synergy. Additionally, a HRGC/MS method for the identification and quantification of the antifungal active compounds cyclo(Leu-Pro), cyclo(Pro-Pro), cyclo(Met-Pro) and cyclo(Phe-Pro) was successfully developed by using stable isotope dilutions assays with the deuterated counterparts. It was observed that the concentrations of cyclo(Leu-Pro), cyclo(Pro-Pro), and cyclo(Phe-Pro) increased only moderately in MRS-broth and wort fermentation by the activity of the selected microorganism, whereas the concentration of cyclo(Met-Pro) stayed unchanged.

Novel DNA sensor for guanine content.

The bifunctional complex [Ru(TAP)(2)POQ-Nmet](2+), 1, formed with a [Ru(TAP)(2)Phen](2+) metallic unit linked to a quinoline moiety, and [Ru(TAP)(2)Phen](2+), 2, as reference, have been tested as photoprobes of DNA. Interestingly, 1 exhibits an emission enhancement of a factor of 16-17 upon binding to calf thymus DNA. Moreover, this emission is modulated by the nucleic base content of the polynucleotide. It varies by almost an order of magnitude from a polynucleotide containing 100% of G-C to a guanine-free nucleic acid where the excited-state lifetime reaches about 2 micros. The origins of these interesting properties are analyzed by comparing 1 with reference 2 in the presence of different polynucleotides.

Probing polarization and dielectric function of molecules with higher order harmonics in scattering-near-field scanning optical microscopy

The idealized system of an atomically flat metallic surface [highly oriented pyrolytic graphite (HOPG)] and an organic monolayer (porphyrin) was used to determine whether the dielectric function and associated properties of thin films can be accessed with scanning-near-field scanning optical microscopy (s-NSOM). Here, we demonstrate the use of harmonics up to fourth order and the polarization dependence of incident light to probe dielectric properties on idealized samples of monolayers of organic molecules on atomically smooth substrates. An analytical treatment of light/sample interaction using the s-NSOM tip was developed in order to quantify the dielectric properties. The theoretical analysis and numerical modeling, as well as experimental data, demonstrate that higher order harmonic scattering can be used to extract the dielectric properties of materials with tens of nanometer spatial resolution. To date, the third harmonic provides the best lateral resolution (∼50 nm) and dielectric constant contrast for a porphyrin film on HOPG. © 2009 American Institute of Physics.

Three-dimensional dispersive metallic photonic crystals with a bandgap and a high cutoff frequency.

The goal of this work is to analyze three-dimensional dispersive metallic photonic crystals (PCs) and to find a structure that can provide a bandgap and a high cutoff frequency. The determination of the band structure of a PC with dispersive materials is an expensive nonlinear eigenvalue problem; in this work we propose a rational-polynomial method to convert such a nonlinear eigenvalue problem into a linear eigenvalue problem. The spectral element method is extended to rapidly calculate the band structure of three-dimensional PCs consisting of realistic dispersive materials modeled by Drude and Drude-Lorentz models. Exponential convergence is observed in the numerical experiments. Numerical results show that, at the low frequency limit, metallic materials are similar to a perfect electric conductor, where the simulation results tend to be the same as perfect electric conductor PCs. Band structures of the scaffold structure and semi-woodpile structure metallic PCs are investigated. It is found that band structures of semi-woodpile PCs have a very high cutoff frequency as well as a bandgap between the lowest two bands and the higher bands.

Outcomes of metallic stents for malignant ureteral obstruction.

PURPOSE: Malignant ureteral obstruction often necessitates chronic urinary diversion and is associated with high rates of failure with traditional ureteral stents. We evaluated the outcomes of a metallic stent placed for malignant ureteral obstruction and determined the impact of risk factors previously associated with increased failure rates of traditional stents. MATERIALS AND METHODS: Patients undergoing placement of the metallic Resonance® stent for malignant ureteral obstruction at an academic referral center were identified retrospectively. Stent failure was defined as unplanned stent exchange or nephrostomy tube placement for signs or symptoms of recurrent ureteral obstruction (recurrent hydroureteronephrosis or increasing creatinine). Predictors of time to stent failure were assessed using Cox regression. RESULTS: A total of 37 stents were placed in 25 patients with malignant ureteral obstruction. Of these stents 12 (35%) were identified to fail. Progressive hydroureteronephrosis and increasing creatinine were the most common signs of stent failure. Three failed stents had migrated distally and no stents required removal for recurrent infection. Patients with evidence of prostate cancer invading the bladder at stent placement were found to have a significantly increased risk of failure (HR 6.50, 95% CI 1.45-29.20, p = 0.015). Notably symptomatic subcapsular hematomas were identified in 3 patients after metallic stent placement. CONCLUSIONS: Failure rates with a metallic stent are similar to those historically observed with traditional polyurethane based stents in malignant ureteral obstruction. The invasion of prostate cancer in the bladder significantly increases the risk of failure. Patients should be counseled and observed for subcapsular hematoma formation with this device.

Comprehensive search for new phases and compounds in binary alloy systems based on platinum-group metals, using a computational first-principles approach

We report a comprehensive study of the binary systems of the platinum-group metals with the transition metals, using high-throughput first-principles calculations. These computations predict stability of new compounds in 28 binary systems where no compounds have been reported in the literature experimentally and a few dozen of as-yet unreported compounds in additional systems. Our calculations also identify stable structures at compound compositions that have been previously reported without detailed structural data and indicate that some experimentally reported compounds may actually be unstable at low temperatures. With these results, we construct enhanced structure maps for the binary alloys of platinum-group metals. These maps are much more complete, systematic, and predictive than those based on empirical results alone.

Effects of Gallium-Desferrioxamine Compounds on Bacteria

Over 70% of nosocomial infections in the United States are resistant to one or more traditional antibiotics, necessitating research for alternative treatment options. This study aims to chelate gallium (Ga) onto a bacterial siderophore, desferrioxamine (DFO), to retard bacterial growth. By exploiting natural bacterial pathways, metal-siderophore treatments are hypothesized to circumvent traditional resistance mechanisms. Additionally, the GaDFO complex will be tested against several bacterial species to determine the specificity of DFO uptake. This research aims to prove the feasibility of siderophore piracy as an alternative to antibiotics. In showing the feasibility of siderophore piracy mechanisms, this research will enable the development of future avenues for protecting against resistant nosocomial infections.

Phenolic compounds, antioxidant and antibacterial activities of three Ericaceae from Algeria

Herbs of the Ericaceae family are commonly found in Algeria and used in traditional medicine as anti- septic, diuretic, astringent, depurative, and to treat scalds and wounds. The methanolic extracts of three species, Arbutus unedo L. (A. unedo, leaves), Erica arborea L. (E. arborea, flowered aerial parts), and Erica multiflora L. (E. multiflora, flowered aerial parts), were compared regarding their content in pheno- lic compounds, their antioxidant, and antibacterial activities. A. unedo harbors the highest content in total phenolics and flavonoids, followed by E. arborea E. multiflora. The contents in total phenolics and flavonoids showed a correlation with the measured antioxidant (hydrogen-donating) activities; this was particularly the case for flavonoids content. The A. unedo extract showed antibacterial activity against all the tested strains (Staphylococcus aureus ATCC 6538, S. aureus C100459, Escherichia coli ATCC 25922, and Pseudomonas aeruginosa ATCC 9027); however, the E. arborea and E. multiflora extracts showed antibacterial activity only against Gram positive bacteria. Some polyphenols were identified in the three herbs by thin-layer chromatography and high-performance liquid chromatography coupled with diode array and mass spectrometry detection; from these, caffeic acid, p-coumaric acid, naringin, quercetin and kaempferol are reported for the first time in E. multiflora.

Photophysics of bifunctional Ru(II) complexes bearing an aminoquinoline organic unit. Potential new photoprobes and photoreagents of DNA

[Ru(BPY)2POQ-Nmet]2+ and [Ru(TAP)2POQ-Nmet]2+ (1 and 3) are bifunctional complexes composed of a metallic unit linked by a flexible chain to an organic unit. They have been prepared as photoprobes or photoreagents of DNA. In this work, the spectroscopic properties of these bifunctional complexes in the absence of DNA are compared with those of the monofunctional analogues [Ru(BPY)2Phen]2+, [Ru-(BPY)2acPhen]2+, [Ru(TAP)2Phen]2+, and [Ru(TAP)2acPhen]2+ (2 and 4). The electrospray mass spectrometry and absorption data show that the quinoline moiety exists in the protonated and nonprotonated form. Although the bifunctional complex containing 2,2′-bipyridine (BPY) ligands exhibits photophysical properties similar to those of the monofunctional compounds, the bifunctional complex with 1,4,5,8-tetraazaphenanthrene (TAP) ligands behaves quite differently. It has weaker relative emission quantum yields and shorter luminescence lifetimes than the monofunctional TAP analogue when the quinoline unit is nonprotonated. This indicates an efficient intramolecular quenching of the 3MLCT (metal to ligand charge transfer) excited state of the TAP metallic moiety. When the organic unit is protonated, there is no internal quenching. In organic solvent, the nonquenched excited metallic unit (bearing a protonated quinoline) and the quenched one (bearing a nonprotonated organic unit) are in slow equilibrium as compared to the lifetime of the two emitters. In aqueous solution this equilibrium is faster and is catalysed by the presence of phosphate buffer. Flash photolysis experiments suggest that the intramolecular quenching process originates from a photoinduced electron transfer from the nonprotonated quinoline to the excited Ru(TAP)2 2+ moiety.

A multi-scale numerical modelling of crack propagation in a 2D metallic plate

A new multi-scale model of brittle fracture growth in an Ag plate with macroscopic dimensions is proposed in which the crack propagation is identified with the stochastic drift-diffusion motion of the crack-tip atom through the material. The model couples molecular dynamics simulations, based on many-body interatomic potentials, with the continuum-based theories of fracture mechanics. The Ito stochastic differential equation is used to advance the tip position on a macroscopic scale before each nano-scale simulation is performed. Well-known crack characteristics, such as the roughening transitions of the crack surfaces, as well as the macroscopic crack trajectories are obtained.