The function of biomolecules is very sensitive to structure. Folding in proteins and nucleic acids is a hierarchical process progressing from primary to secondary, then tertiary, and finally, quaternary structures. RNA in its folded form performs a variety of biological activities. Obtaining intramolecular distance measurements makes it possible to generate structural models along the folding pathway that may be related to the overall function of the molecule. Distances can be measured by Site-Directed Spin-Labeling (SDSL), in which nitroxyl spin-label probes are attached and observed by EPR spectroscopy. Spin-labels can provide information concerning structure and conformational changes because they are particularly sensitive to molecular motion and interspin distances. Continuous-wave EPR spectroscopy has been commonly applied to detect and monitor nitroxide spin-label probes within biological systems. A previous published SDSL study from this laboratory investigated a 10-mer RNA duplex model system with spin-label probe succinimdyl-2,2,5,5-tetramethyl-3-pyrroline-1-oxyl-carboxylate; however, an increased spin-labeling efficiency was observed with an isocyanate derivative of tetramethylpiperidyl-N-oxy (TEMPO). In this thesis, a 4-isocyano TEMPO spin-label probe replaced the previously used succinimdyl-2,2,5,5-tetramethyl-3-pyrroline-1-oxyl-carboxylate in 10-mer SDSL studies. The influence of labeling with the 4-iscocyano TEMPO spin-label in a 10-mer RNA model system was investigated with thermal denaturation, Matrix Assisted Laser Desorption Time of Flight Mass Spectrometry (MALDI-TOF-MS), Electron Paramagnetic Resonance (EPR) spectroscopy, and reverse phase high performance liquid chromatography (RP-HPLC). In the 10-mer RNA duplex model system a 4-isocyano TEMPO spin-label is individually attached to one strand and two strands are annealed to measure distances. This methodology is limited to systems in which two oligonucleotides are annealed together. To circumvent this limitation and also to explore single-strand dynamics a new methodology was implemented, double spin-labeling. Double spin-labeled single-stranded RNA was investigated as a single-strand and within a duplex via MALDI-TOF-MS, EPR spectroscopy and RP-HPLC. A double spin-labeling strategy in this work will be applicable to large complex RNAs like Group I intron of Tetrahymena thermophilia.

The structures, vibrational frequencies, and potential energy functions of several molecules in their ground and excited electronic states were determined using various spectroscopic and theoretical methods. High-level ab initio and density functional theory (DFT) calculations were utilized to investigate the previously reported structures and vibrational spectra of 1,3- disilacyclobutane (13DSCB) and its 1,1,3,3-d4 (13DSCB-d4) isotopomer. These calculations confirmed the finding from earlier microwave work that the CSiC angles of the 13DSCB ring are unexpectedly larger than the SiCSi angles. The calculated vibrational spectra using density functional theory agreed well with the experimental data and showed CH2 modes to have unusually low values. The calculations also confirmed that the individual molecules in the vapor phase are puckered whereas in the solid they become planar. The one-dimensional potential energy surfaces (PESs) for the ring inversion vibration of 2-cyclohexen-1-one and its 2,6,6-d3 isotopomer in its ground and singlet S1(π,π*) electronic states were determined using ultraviolet cavity ringdown spectroscopy (CRDS). The CRDS data allowed several of the quantum states of the ring inversion vibration to be determined for both the ground and excited electronic states, and the data were fit very well with PESs with high barriers to inversion. The infrared and Raman spectra and DFT calculations were utilized to complete a vibrational assignment of 2CHO and 2CHO-d3. A remarkable agreement was seen between the experimental and calculated spectra. The fluorescence excitation spectra (FES) and the single-vibronic level fluorescence (SVLF) spectra of jet-cooled 1,4-dihydronaphthalene (14DHN) were acquired to determine its ring-puckering potential energy function for the ground and singlet S1(π,π*) electronic states. Ultraviolet, infrared, and Raman spectra were also recorded to complement the analysis. The potential energy functions showed that the molecule is planar in both the ground and S1(π,π*) states. A complete vibrational assignment was carried out for 14DHN using the infrared and Raman data and aided by DFT calculations. The ab intio calculations carried out on 2-methyl-2-cyclopenten-1-one (2MCP) showed that the molecule can have 3 different conformers. Infrared and Raman spectra of the liquid-phase molecule were recorded and analyzed to complement the theoretical calculations.

Thesis (Ph. D.)--Lehigh University, 2000. / Includes vita. Includes bibliographical references (leaves 207-215).

Thesis (Ph. D.)--University of Texas at Austin, 1999. / Vita. Includes bibliographical references (leaves 156-162). Available also in a digital version from Dissertation Abstracts.

Thesis (Ph. D.)--Open University. BLDSC no. DXN046359.

Thesis (M.S.)--University of Hawaii at Manoa, 2004. / Leaves 86-90 lacking. Includes bibliographical references (leaves 91-93).

Thesis (M.S. in chemical engineering)--Washington State University, December 2009. / Title from PDF title page (viewed on Feb. 12, 2010). "School of Chemical Engineering and Bioengineering." Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Austin, 2002. / Vita. Includes bibliographical references. Available also from UMI Company.

Thesis (Ph. D.)--Ohio State University, 2004. / Title from first page of PDF file. Document formatted into pages; contains xviii, 265 p.; also includes graphics (some col.). Includes abstract and vita. Advisor: Walter R. Lempert, Dept. of Mechanical Engineering. Includes bibliographical references (p. 198-210).

Thesis (Ph. D.)--Oregon State University, 2001. / Typescript (photocopy). Includes bibliographical references (leaves 92-97). Also available on the World Wide Web.