Physics & Astronomy ETDs

Publication Date

7-14-1970

Abstract

Extended Huckel, semi-empirical, molecular orbital analyses were performed for deoxycytidine-31 -monophosphate and cytidine-3'-monoohosphate corresponding to single nucleotides of double helical DNA and RNA to determine whether the experimentally derived models correspond to theoretically stable configurations. The A, B, and C models of DNA, and linearly interpolated intermediate con­figurations were investigated. For RNA, the experimental A configuration, a pseudo RNA nucleotide formed from the B configuration of DNA, and intermediate conformations were used.

From the B model of DNA the base was displaced and angles adjusted until close coordinate fits were obtained at the A and C configurations. Intermediate points were selected by linearly interpolating all displacements and angles. Extrapolated coordinates were also calculated beyond the A and C models.

Molecular orbitals were calculated using the normal form of the extended Huckel method. Total energy, molecular orbital energies, wave functions, bond and atomic overlaps, and charge distributions were calculated for each config­uration. Minima in the total energy were obtained for ONA at the Band C configurations but not at the A. A minimum for RNA was obtained at the A configuration as expected. No minimum was obtained at a configuration corresponding to the B form in RNA confirming the experimental absence of this structure.

The lack of a DNA A minimum was traced to carbon C3, of the sugar ring which has an endo pucker in the A form. When the C3, endo pucker was replaced with a carbon C2, endo pucker for all configurations, a minimum was obtained at A. The change in pucker lowered the energy at A by approximately 0.45 ev.

An energy barrier of approximately 0.25 ev was found between the B and C forms. The C form is 0.06 ev higher in energy. The barrier between the B and A forms when a minimum was obtained for the C2, endo pucker, was 0.34 ev in going from A to B and 0.5 ev in the revere direction. The cause of the energy barriers in the A to B and C to B transitions was traced to changed in bond strengths and orbital occupations at the atoms in the vicinity of the glycosidic bond between the base and the sugar.

Analysis of the absence of a B minimum for RNA supports the hypothesis that this form is not stable because of close oxygen contacts between the sugar and phosphate.

Degree Name

Physics

Level of Degree

Doctoral

Department Name

Physics & Astronomy

First Committee Member (Chair)

Charles Leroy Beckel

Second Committee Member

John Lee Howarth

Third Committee Member

Illegible

Fourth Committee Member

Donald Reed McLaughlin

Language

English

Document Type

Dissertation

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