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Title: A Vibrational Analysis of the Exocyclic Amino Group of Adenine
Authors: Lappi, Simon Edward
Advisors: Paul L Wollenzien, Committee Member
Stefan Franzen, Committee Chair
Halbert H. Carmichael, Committee Member
Christopher B. Gorman, Committee Member
Keywords: vibrational analysis
density functional theory
Issue Date: 4-Jan-2003
Degree: PhD
Discipline: Chemistry
Abstract: The vibrational analysis of the exocyclic amino group of adenine using both experimental and computational methods is presented. The Fourier Transform infrared (FT-IR) spectra, of adenine, 2'-Deoxyadenosine and five isotopomers of them are reported. FT-IR attenuated total internal reflection (ATR) spectra of H216O, H218O and D216O in the liquid state were obtained. Molecular modeling of water was conducted and a 9-water PBC model was found to give an exceptionally good fit to the experimental line shapes and isotopic frequency shifts. Both harmonic and anharmonic approximations to the vibrational frequencies are used to analyze the matrix isolation adenine spectra. DFT calculations were made using the B3‑LYP/6‑31G* and GGA/DNP computational methods. The NH2 puckering mode is an out-of plane mode that is poorly modeled by both computational methods. Harmonic shift analysis is presented as a method for estimating mode anharmonicity and for determining mode-mode coupling in DFT calculation. The DFT analysis of the adenine spectra in a hydrogen-bonding environment is reported. The theoretical vibrational spectra of 26 model systems in which water has been hydrogen bonded to adenine is compared with the experimental frequencies of the solid state infrared spectra of polycrystalline adenine and the experimental frequencies observed in matrix isolation spectra of adenine. Density functional theory calculations of the vibrational spectra and potential energy surfaces of guanine and cytosine and adenine and thymine base pairs are reported and compared to the experimental FT-IR spectra of double-stranded dodecamer DNA (dsDNA) of adenine-thymine d(AT) composition and its isotopic 15N(10)-d(AT) dodecamer. The experimental isotopic shift was modeled using the adenine-thymine nucleotide DFT calculation. The isotopic shift pattern was found to be similar but the magnitude of the shift is too small.
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