The utility of MS, LC and LC-MS analytical methods to study some important biological macromolecules and small molecules

In this dissertation, the research effort is focused on the utility of two important analytical techniques---liquid chromatography (LC) and mass spectrometry (MS)---for the study of both biological macromolecule and pharmaceutically related small molecules. The dissertation contains three separate projects.; The first research project uses electrospray ionization mass spectometry (ESI-MS) to study the relative stabilities of non-covalently bound RNA duplexes in gas phase, which are compared with their stabilities in solution as determined spectrometrically. The relative stabilities of the RNA duplexes in solution are different from those in the gas phase. The differences in the trends are caused by changes in the primary interaction within the RNA duplexes. In the gas phase, hydrogen bonding is the major interaction but in solution stacking is the dominant interaction. The results show that hydrogen bonding, base stacking, the RNA sequence, and media influence the stabilities of RNA duplexes.; The second research project is an investigation of the separation and retention mechanisms of hydrophilic interaction chromatography (HILIC) on a silica column. The separation of various amino acids, pyridine derivatives, and polar pharmaceutically related compounds was achieved. Their retentions were studied as a function of organic solvent, percentage of aqueous mobile phase, and buffer conditions. A retention model with mixed mode interactions involving ion exchange, polar interactions with the stationary phase, and non-polar interactions in the mobile phase was proposed.; The final research project combined LC and MS to elucidate the mechanisms for impurity formation during drug development. In this study impurities, from the final two synthetic steps of an amino acid-drug candidate, were identified and mechanisms for their formation were proposed using LC, MS or LC-MS techniques.