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A vibrational analysis of the exocyclic amino group of adenine

by 1962- Lappi, Simon Edward

Abstract (Summary)
LAPPI, SIMON EDWARD. A Vibrational Analysis Of The Exocyclic Amino Group Of Adenine. (Under the direction of Stefan Franzen.) The purpose of this research has been the vibrational analysis of the exocyclic amino group of adenine using both experimental and computational methods. The Fourier Transform infrared (FT-IR) spectra (1500-1750 cm-1), of adenine and its five isotopomers are reported. Both peaks in this region, which showed shifts for all the isotopomers, studied and are explained as resulting from the hydrogen bonding of water to the exocyclic amino group of adenine in the polycrystalline material. The FT-IR spectra of the related compound 2’- Deoxyadenosine and five isotopomers of it are reported for the same infrared range as adenine. For 2’-Deoxyadenosine there are three peaks in this region, two of which showed shifts for all the isotopomers, studied and are explained as resulting from the hydrogen bonding of the exocyclic amino group of the adenine moiety to the nitrogen’s of adjacent 2’- Deoxyadenosine molecules in this polycrystalline material. Mid-infrared attenuated total internal reflection (ATR) spectra of H216O, H218O and D216O in the liquid state were obtained and normal coordinate analysis was performed by density functional theory (DFT). The midinfrared spectra of liquid H218O are presented for the first time. Molecular modeling of water was conducted on seven systems, two with periodic boundary conditions (PBC) consisting of 4 and 9 H2O molecules, and five without PBC consisting of 4, 9, 19, 27 and 32 H2O molecules. The 9-water PBC model was found to give an exceptionally good fit to the experimental line shapes and was also used to calculate the frequency shifts observed in the water isotopomers. The analysis of adenine spectra using both harmonic and anharmonic approximations to the vibrational frequencies are reported for matrix isolation studies. The harmonic approximation procedure consists of the application of a scaled ab initio calculated harmonic force field to predict the frequencies, and infrared intensities, of adenine. Theoretical calculations were made using (DFT) B3-LYP/6-31G* and GGA/DNP computational methods. Good agreement is found except for the in-plane X-H bending or stretching and the out-of-plane X-H bending or wagging modes (X=C,N) which exhibit cubic and quartic anharmonicity respectively. The NH2 puckering mode is an out-of plane mode that is poorly modeled by both DFT methods, which is most probably due to its quarticquadratic anharmonicity. The anharmonicity is documented and mode-mode coupling is estimated using harmonic shift analysis. The method of harmonic shift analysis is presented as a tool for the estimation of mode anharmonicity and for the determination of mode-mode coupling in the DFT calculation of adenine. A density functional theory (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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School:North Carolina State University

School Location:USA - North Carolina

Source Type:Master's Thesis

Keywords:north carolina state university

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