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Initial Excited-state Structural Dynamics of Deuterated and Methylated Uracil Derivatives by Resonance Raman Spectroscopy Open Access


Other title
Type of item
Degree grantor
University of Alberta
Author or creator
Teimoory, Faranak
Supervisor and department
Loppnow, Glen R
Examining committee member and department
Kim, Judy E
Lundgren, Rylan
Brown, Alexander
Serpe, Michael J
Department of Chemistry

Date accepted
Graduation date
Doctor of Philosophy
Degree level
Nucleic acids are biological macromolecules constructed of purine (guanine and adenine) and pyrimidine (cytosine, thymine and uracil) nucleobases. The interaction of ultraviolet (UV) light with pyrimidine nucleobases leads to various photoproducts, such as cyclobutane pyrimidine dimers (CPDs), pyrimidine (6-4) pyrimidinone photoproducts, the dewar photoproduct and photohydrates. The excited-state structural dynamics are the first step of the photochemistry of the pyrimidine nucleobases after UV absorption. The similar structures of uracil and thymine only differ in the C5 substituent (the H atom on C5 in uracil is replaced by a CH3 group in thymine). However, thymine and uracil exhibit different major photoproducts; thymine primarily forms the CPDs, while uracil mainly forms the photohydrates. We have shown that the C5 and C6 substituents determine the excited-state structural dynamics and may play a role in the different photochemistry observed. Here, deuterated and methylated C5 and C6 uracil derivatives are examined and compared for tuning the initial excited-state structural dynamics by absorption and resonance Raman spectroscopy. In this thesis, the initial excited-state structural dynamics of 5-deuterouracil, 6-deuterouracil, 5,6-dideuterouracil and 6-methyluracil are studied. The resonance Raman spectrum is obtained quantitatively at four different UV wavelengths for each of these uracil analogs. The intensity of each resonance Raman peak is directly proportional to the slope of the excited-state potential energy surface along that normal mode at the ground-state geometry (i.e. the Franck-Condon region). Simulation of the absorption spectrum and these resonance Raman excitation profiles with a self-consistent, time-dependent formalism yields this slope for each normal mode. The slope and mode assignments of each normal mode determined from DFT calculations at the B3LYP level, are used to calculate the excited-state reorganization energy of each internal coordinate, as a reporter of the initial excited-state structural dynamics. The results suggest that both substituents at the C5 and C6 positions of the pyrimidine ring determine the initial excited-state structural dynamics. Substitution of deuterium for hydrogen and substitution of CH3 for hydrogen on C5 or C6 doubles or quadruples the excited-state reorganization energy along the C5C6 stretch coordinate, respectively. However, when one site is occupied by a heavier substituent than H, the presence of a heavier mass at the second carbon does not increase this reorganization energy any further. The reorganization energies along the C5X and C6X in-plane bending coordinates are reduced by the substitution of hydrogen by deuterium or methyl on C5 and C6, except when the CH3 group is substituted on C5. In this case, an unexpectedly high reorganization energy is observed along these in-plane bending coordinates. Therefore, the high reorganization energy along all these internal coordinates (C5C6 stretch and C5X + C6X in-plane bends) when a CH3 group is on C5 confirms the highest initial excited-state structural dynamics in thymine, as observed previously. Interestingly, among all the deuterated uracil derivatives, 5-d-U has the highest reorganization energies along these internal coordinates, which highlights the significance of the C5 position further in determining the initial excited-state structural dynamics of these uracil analogs.
This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for the purpose of private, scholarly or scientific research. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
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