The structures of protonated and alkali metal cationized nucleobase self-assemblies and base pairs by infrared multiphoton dissociation spectroscopy and computational methods

Cheng, Ruodi (2019) The structures of protonated and alkali metal cationized nucleobase self-assemblies and base pairs by infrared multiphoton dissociation spectroscopy and computational methods. Doctoral (PhD) thesis, Memorial University of Newfoundland.

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Abstract

Nucleobases are the bricks of nucleic acids such as deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) molecules. In the current research, ionic nucleobase self-assemblies and base pairs were studied using gas-phase ion techniques in either a Fourier transform ion cyclotron resonance (FTICR) or ‘paul-type’ quadrupole ion-trap (QIT) mass spectrometers. Sustained off-resonance irradiation collision-induced dissociation (SORI-CID) and infrared multiphoton dissociation (IRMPD) were used to fragment the target ions. IRMPD spectroscopy was employed to collect spectra by using tunable IR lasers, either an optical parametric oscillator or amplifier (OPO/A) or a free-electron laser (FEL). Density functional theory (DFT) was mainly used to study the structural information, calculate thermodynamic results, and perform IR frequency calculations for isomers. Besides, computed IR intensities were compared to experimental IRMPD spectra to explore their consistency. The study of uracil with Ca²⁺ clusters was presented in Chapter 3. There were agreements between the global minima IR spectra and the experimental results. Uracil tetramer, pentamer and hexamer with Ca²⁺ are composed of both tautomerized and canonical uracils, which were not proposed by previous work. Further research on discovering the structures of 1-methylcytosine dimers with alkali metal cations has revealed two possible structures; a new one which is in planar geometry containing the interbase hydrogen bonding as well as being bound by the metal cation (Chapter 4). There was a conclusion that, as alkali metal cations’ radii increased, the ion-dipole interaction weakened. In Chapter 5 the research dug into the effects of alkali metal cations and proton on guanine:cytosine (G:C) base pair. The heavier metal cations were found less likely to interrupt the hydrogen bonds between Watson-Crick G:C base pairs. Moreover, an unexpected great abundance of protonated cytosine for the dissociation of protonated G:C molecule, termed an anomaly by previous works, was explained because of the high proton transfer barrier but not the proposed thermochemistries. Guanine-involved base pair mismatches with protons were discussed in Chapters 6. For (9eG:1mT)H⁺ and (9eG:9eG)H⁺, the lowest energy structures were sufficient to explain their IRMPD spectra while the global minimum of (9eG:9eG)H⁺ presented only one classical hydrogen bond. For (9eG:9mA)H⁺ the lowest energy structures’ weighted-average spectrum was substantially consistent with its IRMPD spectrum.

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