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Date of Award

Spring 2011

Document Type

Restricted Thesis: Campus only access

Degree Name

Bachelor of Science



First Advisor

Dr. Carol Parish

Second Advisor

Dr. Kelling Donald


The work summarized in the following report includes a number of conclusions. Both damaged and natural DNA base pairs were computationally examined with density functional theory. It was found that these base pairs most closely model thermal experimental results when the ribose ring attached to form the nucleotide is substituted with a methoxymethylene and methoxy linkages at the 4’ and 3’ positions. A close structural inspection of these base pairs revealed that much of the stability of OdG:dA as a DNA mismatch is owed to the N-nucleoside character of the nucleotide, an added pseudo-hydrogen bonding interaction between the C8 carbonyl of OdG(syn) and the C2 hydrogen of dA, and a preferred “pre-orientation” of the nucleotide before forming the base pair.

The same model systems used for damaged base pair analysis were applied to test the strength of halogen bonding in DNA base pairs. Either all or only one of the H-bonding sites between the bases of the pair were substituted with Cl-, Br-, and I-bonds. Structures where only one halogen was substituted for an H-bond were more stable than those where all H-bonds were replaced, with bromine forming the strongest base pairs overall. In certain cases, base pairs with one H-bond replaced were stronger than their normal H-bonding counterparts. Two examples of this are OdG:dA and SdG:dA.

Lastly, on a different note, the singlet-triplet splitting energy and vertical excitations of thiophene-2,5-diyl. The types of theory involved multiconfigurational self-consistent field (MCSCF), multireference configuration interaction with single and double excitations (MR-CISD), and multireference averaged quadratic coupled cluster (MR-AQCC) using the complete active space (CAS) approach. Thiophene-2,5-diyl was found to be similar to the well-known para-benzyne, with a moderate singlet-triplet splitting energy of ~16 kcal/mol and a high density of excited states within ~5-7.5 eV of the ground state.