Thesis (Ph. D.)--Dept. of Chemistry and Dept. of Physics. University of Missouri--Kansas City, 2006. / "A dissertation in chemistry and physics." Advisor: James R. Durig. Typescript. Vita. Description based on contents viewed Jan. 29, 2007; title from "catalog record" of the print edition. Includes bibliographical references (leaves 447-460). Online version of the print edition.

Thesis (Ph. D.)--University of Idaho, 2005. / Also available online in PDF format Abstract. "October 2005." Includes bibliographical references.

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Vibrational imaging approaches including Raman microscopy and IR-absorption micro-spectroscopy can provide rich chemical information about biological samples. This dissertation contributes to improve the capabilities of vibrational microscopy in three aspects each with corresponding biological applications. First, along the line of combining electronic resonant effect with stimulated Raman scattering (SRS), we studied the spectroscopic characteristics for on-resonant SRS case and demonstrated the utility of electronic pre-resonant SRS on super-multiplexed imaging for live cells and tissue sections. Second, we provided a new light-matter interaction as a hybrid technique of Raman and fluorescence, called stimulated Raman excited fluorescence (SREF), bringing the long-sought-after goal of detecting single-molecule Raman scattering without plasmonic enhancement into view. Coupling SREF with vibrational sensing, local electric field and hydrogen-bonding environment can thus be visualized in situ. Third, we brought small vibrational probes into mid-infrared imaging for the goal of rich-information-content, high-throughput metabolic imaging. Chapter 1 introduces some basis of Raman scattering, and provides an overview of state-of-art SRS microscopy. Chapter 2 explores on the rigorous electronic resonant region with SRS (er-SRS) through suppression of electronic background and subsequent retrieval of vibrational peaks. In agreement with theoretical prediction, changing of vibrational band shapes from normal Lorentzian, through dispersive shapes, to inverted Lorentzian is observed when approaching electronic resonance. As large as 10-23 cm2 of resonance Raman cross section is estimated in er-SRS. In Chapter 3, a new light-matter interaction called stimulated Raman excited fluorescence (SREF) is studied. Through stimulated Raman pumping to an intermediate vibrational eigenstate followed by an upconversion to an electronic fluorescent state, SREF encodes vibrational resonance into the excitation spectrum of fluorescence emission. By leveraging superb sensitivity of SREF, we achieved all-far-field single-molecule Raman spectroscopy and imaging without plasmonic enhancement. Chapter 4 details the development of SREF into a novel water-sensing tool, by coupling with vibrational solvatochromism of environment-sensitive Raman mode. This new technique allows direct visualization on spatially-resolved distribution of water states inside single mammalian cells. Interesting intracellular heterogeneity of water states between nucleus and cytoplasm has been revealed. Chapter 5 demonstrates the utility of epr-SRS in super-multiplexed imaging with either commercial fluorophores in lives cells or our MARS probes on tissue sections. Multiplex protein-based tissue imaging is completed with newly-designed functional MARS dye with up to 12 channels simultaneously. Chapter 6 focus on metabolic imaging by mid-infrared (MIR) microscopy with vibrational probes. Raman scattering microscopy has made a major advance in metabolic imaging utilizing vibrational probes, yet is limited to relatively low throughput. As an alternative solution, MIR microscopy provides significantly higher cross section and exhibits as a rich-information-content, high-throughput technique with recent rapid technical advances. We introduced three types of small vibrational probes as azide, 13C and carbon-deuterium for studying dynamic metabolic activities of protein, lipids and carbohydrates in cells, small organisms and mice for the first time. Two MIR microscopy platforms as Fourier transform infrared (FTIR) absorption microscopy and discrete frequency mid-infrared (DFIR) microscopy were utilized to validate the generality of our vibrational probes and applicability for single-cell metabolic profiling and metabolism study on large-scale tissues.

Ab initio Hartree-Fock and density functional theory calculations were carried out to investigate the structure and vibrational spectrum of 1,3-dithiole-2-thione. All the calculations predicted a planar structure with C2v symmetry. Harmonic force field and vibrational mode calculations provided convincing theoretical evidence for reassignments of some fundamental vibrational modes. The reassignments are in line with the observed polarization data of Dyer et al. This study shows that the density functional theory is a powerful tool for understanding the vibrational spectra of organic molecules.

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Mechanistic aspects of phosphorylation, dephosphorylation, pyrophosphorylation and depyrophosphorylation reactions that mimic phosphorylases, dephosphorylases, pyrophosphorylases and depyrophosphorylases have been studied in the biologically important middle pH region. The different systems monitored are; (a) the reactions between [{CoN4(OH)(OH2)}]2+ and [HPO4]- for 1:1, 2:1 and 3:1 [{CoN4(OH)(OH2)}]2+ to [HPO4]2- ratios. (b) the reactions between [{CoN4PO4] and [O2NC6H4O]- (abbreviated as NP-) for 1:1, 2:1 and 3:1 [{CoN4PO4] to [O2NC6H4O]- ratios. (c) the reactions between [{CoN4(OH)(OH2)}]2+ and [O2NC6H4PO4]2- (abbreviated as NPP2-) for 1:1, 2:1 and 3:1 [{CoN4(OH)(OH2)}]2+ to [O2NC6H4PO4]2- ratios. (d) the reactions between [{CoN4(OH)(OH2)}]2+ and [H2P2O7]2- for 1:1, 2:1 and 3:1 [{CoN4(OH)(OH2)}]2+ to [H2P2O7]2- ratios. (e) the reactions between [{CoN4P2O7}]- and [O2NC6H4O]- for 1:1, 2:1 and 3:1 [{CoN4P2O7}]- to [O2NC6H4O]- ratios. Significant phosphorylation was noted for systems containing 1:1 molar ratio [{CoN4PO4] and [O2NC6H4O]-. Enhanced phosphorylation was depicted for system containing 1:1 molar ratio of [{CoN4(OH)}2PO4]+ and [O2NC6H4O]-. Pyrophosphorylation was noted for reactions of 1:1 molar ratio of [{CoN4P2O7}]- and [O2NC6H4O]-. The rate of pyrophosphorylation was substantially reduced for systems that were 2:1 in molar ratio of [{CoN4P2O7}]- and [O2NC6H4O]-. No appreciable pyrophosphorylation was noted for systems, which has a 3:1 molar ratio of [{CoN4P2O7}]- and [O2NC6H4O]-. Specific mechanistic features and the possible roles metal ions play in phosphorylase, dephosphorylase and pyrophosphorylase are highlighted from results of UV-Visible spectroscopy, 31P {1H} NMR spectroscopy and Surface Enhanced Raman Scattering (SERS) studies / Chemistry / D.Phil. (Chemistry)

The problem of a vibrating-rotating polyatomic molecule is treated, with emphasis given to the case of molecules with C_3v symmetry. It is shown that several of the gross features of the rotational spectra of polyatomic molecules in excited vibrational states can be predicted by group theoretical considerations. Expressions for the rotational transition frequencies of molecules of C_3v symmetry in the ground vibrational state, singly excited degenerate vibrational states, and doubly excited degenerate vibrational states are given. The derivation of these expressions by fourth order perturbation theory as given by Amat, Nielsen, and Tarrago is discussed. The ground and V_10=1 rotational spectra of propyne have been investigated in the 17 to 70 GHz, and 17 to 53 GHz regions, respectively, and compared with predictions based on higher frequency measurements. The V_9=1 and V_10=2 rotational spectra of propyne have been investigated and assigned for the first time. A perturbation of the V_9=1 rotational spectra for K=-l has been discovered and discussed.

The Raman linewidths of the carbon-halogen stretching mode was measured as a function of temperature in ethyl bromide, isopropyl chloride, isopropyl bromide, t-butyl chloride, t-butyl bromide, chlorobenzene, bromobenzene, iodobenzene and o-dichlorobenzene. The vibrational relaxation times showed a very clear trend. Together with earlier work on methyl iodide, these results provide evidence that the vibrational dephasing efficiencies (T^-1_iso) of the carbon-halogen mode vary in the order of Cl > Br > I. Vibrational dephasing times were calculated from the Fischer-Laubereau Isolated Binary Collision Mode. If further work shows this transferability to extend to other types of skeletal modes in molecular systems, this would have significant ramifications on future vibrational lineshape studies.

Thesis. 1977. Ph.D.--Massachusetts Institute of Technology. Dept. of Physics. / Microfiche copy available in Archives and Science. / Includes bibliographical references. / Ph.D.