Structures of bare and solvated metal ion - uracil complexes through infrared multiple photon dissociation spectroscopy and computational methods

Power, Barry Peter Frederick (2017) Structures of bare and solvated metal ion - uracil complexes through infrared multiple photon dissociation spectroscopy and computational methods. Doctoral (PhD) thesis, Memorial University of Newfoundland.

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Abstract

Metal ions are essential to nucleic acid stability and activity, however at increased levels, unwanted conformational changes are observed in nucleobases as a result of a direct interaction with the ions. These changes can give rise to improper base pairing, and subsequently lead to genetic mutations. Consequently, examination of the structure of metal ion – nucleobase complexes has been of particular interest. These structures are studied using gas phase techniques as a means of replicating the cellular environment, as condensed phase analysis is hindered by bulk solvent effects. In order to observe the impact that solvent molecules have on the isomerization of such complexes, microsolvation is employed in gas phase experiments. Infrared multiple photon dissociation (IRMPD) is a technique commonly used in the determination of these structures. IRMPD spectra of alkaline earth metal complexes with uracil, both monomeric and dimeric at varying degrees of hydration, are compared to those computed using electronic structure calculations to determine the structures of these complexes. The spectra of the structures calculated as lowest in energy offer good agreement with the experimental spectra. In these lowest energy isomers, deprotonation of uracil is found to occur at the N3 position. In the dimeric complexes, the second uracil exists as a keto-enol tautomer, with an intramolecular hydrogen bond formed between uracil moieties. In the case of hydrated complexes, water coordination is always directly to the metal center. Monomeric and dimeric uracil complexes with divalent d-block ions are also examined, both hydrated and ammoniated. For the most part, good agreement is again obtained between the calculated spectra of lowest energy isomers and the experimental spectra. These complexes also generally exhibit uracil deprotonation at the N3 position, with the exception of copper complexes, where a distinct solvent effect is observed. As the degree of hydration increases, the deprotonation site in uracil changes from the N1 to the N3 position. The lowest energy singly hydrated Zn complex experiences proton transfer from the water molecule to the uracil, resulting in a complex of the form [Zn(Ura)(OH)]⁺ where the uracil is a keto-enol tautomer. The ammoniated dimeric complexes adopt a similar structure as that of the alkaline earth hydrated dimers, again with the exception of the copper complex, where Jahn-Teller distortions result in a square planar structure with ammonia coordination to the metal and a tridentate interaction with the neighbouring uracil molecules.

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