Physics & Astronomy ETDs

Publication Date

4-29-1974

Abstract

The gradient of the energy in extended Hückel theory (EHT) was used in a variable metric algorithm to predict the energy along the pseudorotational path for several five membered ring molecules. The molecules studied were cyclopentane, tetrahydrofuran (THF), cyclopentanol, 4-tetrahydrofuranol, and cis- and trans-3,4-tetrahydrofurandiols. Comparisons of predictions for these molecules to experimental results were made to determine the capabilities of EHT prior to an intended study of sugar rings. A background chapter discusses the recent literature on nucleic acid constituents with emphasis on the geometries of five membered sugar rings. In crystals, these geometries are found to lie mostly in narrow ranges of pseudorotation angle. All bond lengths were constrained. The resulting four degrees of freedom for ring deformations are discussed in relation to the conversion to a two dimensional representation commonly used in the literature. Questions arose concerning the uniqueness of this representation and the interpretation of experimental and theoretical results. Free pseudorotation with a constant pucker amplitude was predicted for cyclopentane using two models. Most details of these results were published. (J. Chem. Phys. 59(4), 1905-13 (1973)). Analysis of the molecular orbitals and energy changes with puckering showed the principal factor in the barrier to planarity to be an increase in antibonding overlaps due to bond eclipsing. Analysis of the cyclopentane geometries along the pseudorotation path indicated that the energy due to each type of term used in force field theories may be independent of the pseudorotation angle when averaged around the ring. Excessively large oxygen valence angles were predicted for THF and cyclopentanol using EHT. Parameter variation for the oxygen did not sufficiently improve the predictions for THF, so oxygen valence angles were constrained. Predictions for both molecules were then found to be in limited agreement with experimental results. The C-O-H angles were not constrained in calculations for the hydroxyl substituted tetrahydrofurans. The resulting angle of about 146° prevented intramolecular hydrogen bonding, which is not commonly observed in crystals of nucleic acid constituents. It was found that the curves of pucker amplitude and energy along the pseudorotation path predicted for these molecules could be approximated by combining appropriate curves for THF and cyclopentanol. Analysis for these molecules was facilitated by this discovery. However, ring geometries for these molecules corresponding to those most frequently found in the sugar crystal studies were found to be near maxima in energy along the pseudorotation path. Because of this and the limited agreement of predictions with experimental results for THF and cyclopentanol, it was concluded that the EHT representation of oxygen was too poor to extend the study to sugar rings. Predicted barriers to pseudorotation varied from 0.021 to 0.070 eV. The pucker amplitude varied along the pseudorotation path, as did exocyclic bond orientations. A low barrier to pseudorotation was found to depend on a delicate balance of endocyclic, exocyclic, and dihedral angles along the path. These findings together with the proven poor predictions for oxygen valence angles may indicate why high barriers to pseudorotation have been predicted in other studies of five membered rings.

Degree Name

Physics

Level of Degree

Doctoral

Department Name

Physics & Astronomy

First Committee Member (Chair)

Charles Leroy Beckel

Second Committee Member

Donald Reed McLaughlin

Third Committee Member

Sandra Z. Engelke

Fourth Committee Member

Colston Chandler

Language

English

Document Type

Dissertation

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