Physics & Astronomy ETDs

Publication Date

7-6-1973

Abstract

Theoretical calculations were made on conformations of the adenosine mono-, di- and tri-phosphate molecules, AMP, ADP and ATP, respectively. Calculations were done using the semi-empirical quantum mechanical extended Hückel theory. Energy was examined as a function of rotations of whole groups of atoms about P-O bonds in the phosphate groups; about the C5'-05' and C4'-C5' bonds; and about the glycosidic N9-C1' bond. Minimum energies determined preferred conformations. These calculations confirmed the experimentally observed crystal structures of AMP and ATP and predicted a structure for ADP. The calculations on ATP required the addition of supplementary atoms from the crystal for some of the rotations in order to obtain a minimum energy at the experimentally observed configuration. Calculations on a free isolated molecule of AMP were sufficient to show that the observed structure corresponds to a minimum energy, although it was not the lowest minimum energy available to the molecule. Additional calculations were done on AMP and ATP that placed the atoms of these molecules in configurations corresponding to lowest minimum energies. A comparison of the minimized structures of the three molecules AMP, ADP and ATP showed that the minimum energy orientation of a phosphate group with respect to its neighbors was dependent on whether the phosphate had another phosphate group attached to it or whether it was the terminal phosphate. Differences were also observed in the orientation of the adenine in AMP from that resulting for both ADP and ATP. The extended Hückel molecular orbitals (MO's) of the phosphate groups of AMP and ATP were compared with the MO's that result from phosphates where oxygens are placed at the corners of a tetrahedron about the phosphorus atom. Deviations of the AMP and ATP phosphates from tetrahedral symmetry produce mixing of the MO's. Same of the MO's of the isolated AMP phosphate are identified as belonging to particular MO's that result from a calculation that included atoms of the entire molecule. Four appendices include additional information. Appendix I contains a comparison of β parameters within extended Hückel theory when applied to diatomic molecules. The results of using the β parameters of Mulliken-Wolfsberg-Helmholz, Cusachs and Jug are compared with a new proposed β parameter. Appendix II lists atomic coordinates for the AMP and ATP molecules used in the calculations. This appendix also contains the ATP crystal coordinates since these are the result of an unpublished Los Alamos refinement of the ATP crystal data obtained at Cambridge. The computer programs used for the orthogonal transformations of the molecular coordinates for rotations and reorientations are described am listed in Appendix III. Appendix IV contains the computer program used for the extended Hückel calculations along with a detailed description of the program and the time-savings modifications that were done.

Degree Name

Physics

Level of Degree

Doctoral

Department Name

Physics & Astronomy

First Committee Member (Chair)

Charles Leroy Beckel

Second Committee Member

Allen C. Larson

Third Committee Member

Seymour Samuel Alpert

Fourth Committee Member

Ulrich Hollstein

Project Sponsors

A two-year fellowship awarded by Associated Western Universities

Language

English

Document Type

Dissertation

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