Molecular recognition, particularly as it applies to strong binding interactions between complementary ligand/receptor molecules in solution, is important in such varied areas as molecular biology, pharmacology, synthetic chemistry, and chemical detection. Strong binding is the additive result of a number of specific, weak, non-covalent interactions occurring between complementary molecules. This dissertation reports on the energetics of forming complexes between small molecules and model DNA constructs. Ligands included cationic and metallated cationic porphyrins and polyheterocyclic ruthenium compounds. DNA receptors included double stranded B-DNAs (hairpin and short linear sequences) as well G-quadruplex DNAs. Thermodynamic data were collected using isothermal titration calorimetry, circular dichroism spectropolarimetry, ultraviolet-visible spectroscopy, and mass spectrometry. The measured thermodynamic parameters included the changes in free energy, enthalpy and entropy for ligand/receptor complex formation as well as the stoichiometry of the stable complexes. The first section of this dissertation reports that the binding of cationic porphyrins to model G-quadruplex DNA may proceed through two pathways, end stacking and intercalation. Modulating the number of pyridinium groups on a pyridinium substituted porphyrin yielded differing binding thermodynamics leading to the understanding that a balance of surface area, charge, and geometry affect the ability of a porphyrin to bind to G-quadruplex DNA. Further investigations into the binding of metallated porphyrins developed the understanding that the geometry of the central metal ion affected not only the thermodynamics but could also inhibit the intercalative mode. It was previously shown that the high affinity binding for binuclear polyheterocyclic ruthenium compounds proceeds through an intercalative mode. To further understand the binding process and the structureunction relationship of the ligand components, the binding of smaller mononuclear complexes that were representative of portions of the binuclear complex was examined in this dissertation. While limiting the intercalative ability lowered the binding affinity, the mononuclear complex with the full intercalating bridge was able bind to DNA with a higher affinity than the binuclear complex. These studies have been successful in part in determining the contributions of numerous weak interactions including: charge (Coulombic interactions), H-bonding, hydrophobic interactions, and solvent structure (solvation changes), to the overall energetics of this molecular recognition process. The first section of this dissertation reports that the binding of cationic porphyrins to model G-quadruplex DNA may proceed through two pathways, end stacking and intercalation. Modulating the number of pyridinium groups on a pyridinium substituted porphyrin yielded differing binding thermodynamics leading to the understanding that a balance of surface area, charge, and geometry affect the ability of a porphyrin to bind to G-quadruplex DNA. Further investigations into the binding of metallated porphyrins developed the understanding that the geometry of the central metal ion affected not only the thermodynamics but could also inhibit the intercalative mode. It was previously shown that the high affinity binding for binuclear polyheterocyclic ruthenium compounds proceeds through intercalation. To further understand the binding process and the structureunction relationship of the ligand components, the binding of smaller mononuclear complexes that were representative of portions of the binuclear complex was examined in this dissertation. While limiting the intercalative ability lowered the binding affinity, the mononuclear complex with the full intercalating bridge was able bind to DNA with a higher affinity than the binuclear complex. These studies have been successful in part in determining the contributions of numerous weak interactions including: charge (Coulombic interactions), H-bonding, hydrophobic interactions, and solvent structure (solvation changes), to the overall energetics of this molecular recognition process.

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This project focused on the development and validation of an ultra-performance liquid chromatography tandem mass spectrometer (UPLC-MS/MS) method for the determination of Patulin in apple-based products. Patulin is one of the many mycotoxins that are secondary metabolites from about 60 filamentous fungi. The mold often appears as black or blue on fruit, vegetables or crops. To determine the concentration of Patulin in consumer products is important since it may affect consumer health. The symptoms are often flu-like and can lead to kidney-failure and neurotic damage. The Swedish Food Agency is tasked to analyze consumer products to determine if they are safe to ingest. The European Commission has set maximum residue limits for several toxins that can potentially appear in groceries on the market. Using an UPLC-MS/MS allows for the accurate qualification and quantification of Patulin in apple juice and purees. The method was validated by analyzing several lots of apple juices and a proficiency test from Fapas®. The recovery rate ranged between 70.5-103.8% and were accepted because they met the recovery criteria in Regulation (EC) No. 401/2006 for Patulin.

Research was conducted on thirteen 100% cotton denim samples using an acid wash, established by Murray, to extract oligosaccharides from the cellulosic material. The oligosaccharide ion groups (+, +, and +) for molecules with degrees of polymerization between two and seven (DP2-DP7) were analyzed using liquid chromatography coupled to mass spectrometry with an electrospray ionization interface (LC-ESI-MS). The results were compared using the least-squares means in a Multivariate ANOVA (MANOVA) test followed by Univariate ANOVA and Tukey HSD tests and demonstrated that the method could correctly determine that two samples were statistically different 85.9% of the time when analyzing the amount (ng) of each of the oligosaccharide ion groups separately, and 82.0% when analyzing the total moles of monosaccharide units released. A dye extraction was performed on the denim materials and the extract analyzed using gas chromatography coupled with mass spectrometry (GC-MS). Indigo dye was present in all of the denim samples except one. When these results were combined with the two oligosaccharide statistical analyses, the discriminating power was increased to 88.5% and 85.9%, respectively. Additional cellulosic materials were also investigated including four white 100% cotton t-shirts as well as five raw cotton samples grown in Tajikistan, Uzbekistan, Egypt, Iran, and Benin West Africa. The analytical methodology gave results for the white cotton t-shirts and raw cotton samples that were inconsistent with those obtained from the denim samples.

The work in this thesis has demonstrated the chiral recognition through the adaptation of chromatographically derived chiral recognition systems by electrospray ionization mass spectrometry (ESI-MS). Mass-labeled, pseudoenantiomeric chiral selectors (where each pseudoenantiomer had the opposite stereochemistry, but was slightly different in mass due to labeling of one enantiomer) were prepared as soluble analogues of Pirkle type chiral stationary phases. When mixed with a chiral analyte, solutions containing these pseudoenantiomeric selectors afforded selector-analyte complexes in the ESI-MS, and the relative peak intensities of the complexes could be related back to the enantiomeric composition of the analyte. In each case of this study, the complex intensity fraction for either of the selector-analyte complexes in the ESI-MS varies linearly with the enantiomeric composition of the analyte. This linear relationship provides a measure of the extent of enantioselectivity and allows quantitative analysis of the enantiomeric composition of analyte.

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No / Lipidomics aim to generate qualitative and quantitative information on different classes of lipids and their species, and when applied in conjunction with proteomic and genomic assays, facilitate the comprehensive study of lipid metabolism in cellular, organ or body systems. Advances in mass spectrometry have underpinned the expansion of lipidomic methodologies. Prostanoids are potent autacoids present in a plethora of cellular systems, known best for their intimate role in inflammation. Electrospray ionisation (ESI) allows the efficient ionisation of prostanoids in aqueous systems. ESI can be readily coupled to liquid chromatography (LC) followed by tandem mass spectrometry (MS/MS)-based detection, thus allowing the development of a potent and selective LC/ESI-MS/MS quantitative assays. The protocol we describe in this chapter outlines the steps we follow to a) extract prostanoids from solid or liquid samples, b) semi-purify the metabolites using solid phase extraction c) set-up the HPLC separation using reverse phase chromatography and d) set up the MS/MS assay using a triple quadrupole mass spectrometer. The experimental details and notes presented here are based on the detailed protocols followed in our group