Photodissociation methods have been explored for structural analysis of peptides and oligosaccharides. Ultraviolet photodissociation (UVPD) was applied to carboxylated derivatized peptides and reducing end derivatized oligosaccharides which offer selective dissociation and specific fragmentation pathways in comparison to CID. Upon UVPD of the modified peptides at carboxylate comprised of reduced y ions and increased immonium ions. The derivatized oligosaccharides via reductive amination and hydrazide conjugation can undergo highly efficient 355 nm UVPD and offer different fragmentation pathways. Both derivatization methods upon UVPD yielded [superscript 0,2] A-type ions, however reductive amination and hydrazide conjugation produced dominant [superscript 0,1] A and [superscript 2,4] A-type ions, respectively. Ultraviolet photodissociation at 193 nm (ArF laser, 6.4 eV / photon) has been applied to sialylated oligosaccharides and glycans which were analyzed in negative mode due to their acidic condition. Primarily, UVPD provides a greater array of fragment ions including cross-ring cleavages and dual cleavage internal ions in comparison to CID. In addition, the UVPD generates unique fragment ions which arise from site-specific cleavage of the trial substituent of the sialic acid residue. UVPD of doubly deprotonated sialylated oligosaccharides produced mostly singly deprotonated fragment ions, whereas the product ions in the CID spectra were overwhelmingly doubly charged ions, an outcome attributed to the more extensive cleavages of sialic acid residue upon UVPD. Although electron transfer dissociation (ETD) has shown superior capabilities for the characterization of post-translational modifications of peptides due to its non-eragodic property, ETD has intrinsic drawback arising from its significant dependence on the charge state of the selected precursor ion. Precursor ions in low charge states tend to undergo charge reduction, often preferentially relative to production of the informative cand z-type ions. In order to increase charge states of peptides and ETD efficiencies, peptides were derivatized at their carboxylate groups via attachment of amine with fixed charge or hydrophobic group. The carboxylate-derivatized peptides exhibited higher ETD efficiencies relative to underivatized peptides along with greater numbers of diagnostic fragment ions. The carboxylate derivatization strategy in combination with ETD for proteomics applications by the proteolytic digestion, the derivatization, and LC-MS purification was demonstrated with Cytochrome C.

Many anticancer and antibacterial therapies are based on the interaction of small molecule drugs with DNA. Increasing interest in the development of DNA-interactive agents has fostered the need for sensitive and versatile analytical techniques that are capable of characterizing the DNA/ligand interactions and are compatible with librarybased screening methods. Electrospray ionization mass spectrometry (ESI-MS) has emerged as a useful technique for the analysis of non-covalent complexes formed between DNA and small molecules due to its low sample consumption and fast analysis time. The work presented in this dissertation is aimed at exploring, optimizing, and validating ESI-MS methods for characterizing DNA-ligand interactions. ESI-MS is first used to assess the binding of threading bis-intercalators to duplexes containing different sequences to determine high affinity binding sites of the ligands. Preliminary DNAse footprinting experiments identified possible specific binding sites of the ligands and ESI-MS experiments revealed that the ligands bound to DNA duplexes containing the respective specific binding sequences. The metal-mediated binding of benzoxazole ligands with different side chains to duplex DNA is also examined. Cu²⁺ and Ni⁺ were found to promote the most dramatic increase in ligand binding, and ligands exhibiting the most dramatic metal-mediated or metal-enhanced binding were also determined to be the most cytotoxic. The quadruplex DNA binding selectivity of perylene diimides is evaluated by screening the binding of the ligands to quadruplex, duplex and single strand DNA by ESI-MS. Three ligands, one containing basic side chains, one containing anionic sidechains, and one benzannulated compound were determined to be the most-quadruplex selective. The ESI-MS results correlated well with spectroscopic experiments. The relative gas-phase stabilities of different quadruplex DNA structures were investigated using molecular dynamics simulations and ESI-MS. The stabilities from the E[subscript 1/2] values generally paralleled the RMSD and relative free energies of the quadruplexes based on MD energy analysis. Finally an ESI-MS technique employing the KMnO₄ reaction with DNA to determine conformational changes to the duplex structure upon ligand binding is detailed. Thymines in most intercalator/duplex complexes are more susceptible to oxidation by KMnO₄ than those in duplex DNA. CAD and IRMPD experiments are used to identify the site of oxidation. / text

The interaction between metal nanoparticles and small molecules has been investigated by FTIR and UV-visible absorption spectroscopy. Electrospray deposition into an argon matrix was chosen as the initial method. An electrospray metal source was tested in development stage. Both the formation of a stable corona discharge as well as a stable Taylor cone were successfully completed. Problems arose when the entire system was tested. It was determined that the vacuum was insufficient for the length of the flight path. Focus then shifted to nanoparticles in more conventional environments. Sol-gel encapsulated nanoparticles were generated, in the form of both monoliths as well as thin film coatings on silicon wafers. The gels were exposed to 1atm of carbon monoxide in a gas cell. The method encountered problems due to spectral interference from the matrix. The next attempt consisted of solution stabilized nanoparticles. The solution was exposed to various amounts of both ammonium sulphate and diethylamine. There was again the problem of solvent interference, even when attempting to observe the system using Raman spectroscopy. Finally, surface stabilized nanoparticles were generated, using 3-mercaptopropyltrimethoxysilane to adhere the particles to glass slides. While the coating was successfully applied to the glass slides, as confirmed with Raman spectroscopy, it was not possible to get the nanoparticles to adhere. Future outlook for this project is briefly reviewed. / Thesis (Master, Chemistry) -- Queen's University, 2009-06-26 10:30:58.295

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 5 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 6 uppsatser.

Thesis (Ph.D.)--University of Wollongong, 2005. / Typescript. EMBARGOED-this thesis is subject to a six months embargo (07/09/06) and may only be viewed and copied with the permission of the author. For further information please Contact the Archivist. Includes bibliographical references: leaf 159-194.

Thesis (Ph.D.)--University of Melbourne, School of Chemistry, 2007. / Typescript. Includes bibliographical references (leaves 151-169).

Dissertation (Ph.D.)--Auburn University, 2005. / Abstract. Vita. Includes bibliographic references (p.113-125).

Thesis (M.S.)--Michigan State University. Dept. of Biochemistry and Molecular Biology, 2008. / Title from PDF t.p. (viewed on July 29, 2009) Includes bibliographical references (p. 78-81). Also issued in print.

Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: Jennifer S. Brodbelt. Vita. Includes bibliographical references. Also available from UMI.