Access Type

Open Access Dissertation

Date of Award

January 2017

Degree Type


Degree Name




First Advisor

Mary T. Rodgers


Experiments examining the structures and stabilities of protonated and sodium cationized nucleobases, and deprotonated DNA and RNA mononucleotides are presented and discussed in this dissertation. These studies were carried out using the infrared multiple photon dissociation (IRMPD) action spectroscopy technique that utilizes a Fourier transform ion cyclotron mass spectrometer (FT-ICR MS) coupled to a free electron laser (FEL) located at the Radboud University Nijmegen. Ionic species of these biologically important complexes were generated using an electrospray ionization source and then mass isolated to have their infrared (IR) spectra measured by the experimental apparatus. Detailed analysis of the IR spectra measured by this technique, the IRMPD action spectra, are accomplished by high level theoretical calculations, which enable the structures accessed in the experiments to be determined and visualized.

In the first part of this thesis, the structures of protonated and sodium cationized complexes of uracil (Ura), one of the four nucleobases of RNA, and its thioketo modified forms, 2-thiouracil (S2Ura), 5-methyl-2-thiouracil (m5S2Ura), 6-methyl-2-thiouracil (m6S2Ura), 4-thiouracil (S4Ura), and 2,4-dithiouracil (S2,4Ura), were examined via IRMPD action spectroscopy and density functional theory calculations. The IRMPD action spectra for these complexes were measured over the range of ~1000–1900 cm-1, and they exhibit distinct features that allow rapid differentiation of these complexes. The stable structures probed in these studies reveal that the binding of proton and sodium cation stabilize alternative tautomers of uracil and these thiouracils. And in doing so, the base pairing pattern of the nucleobase is changed dramatically.

Gas phase structures of each of the four deprotonated DNA and RNA mononucleotides are examined in the second part of this thesis using IRMPD action spectra measured between 600–1800 cm-1 and several different theoretical models. Structures obtained from these experiments are highly parallel to DNA and RNA nucleotides observed in dehydrated environments in which the ribose moiety adopts a C3'-endo conformation and the nucleobase is in an anti conformation, except in the case of [pdGuo H]¯ and [pGuo H]¯, where the nucleobase is in a syn conformation. These experiments were the first step in a broader program to understand other factors that influence the structures and stabilities of DNA and RNA nucleotides under common physiological conditions. A short list of common factors includes protonation, metal cationization, chemical modification, and solvation.