Vibrational Analysis of Nucleic Acids. 2. Ab Initio Calculation of the Molecular Force Field and Normal Modes of Dimethyl Phosphate

Author

Yifu Guan
Godwin Sik Cheung Choy
Rainer Glaser, Missouri University of Science and TechnologyFollow
George J. Thomas

Abstract

The gauche-gauche (g,g) conformation of the dimethyl phosphate anion serves as a simple model for the phosphodiester group of nucleic acids. Detailed knowledge of the normal modes of vibration of dimethyl phosphate and other phosphodiester analogues is expected to provide a foundation for understanding the conformation-sensitive bands in vibrational spectra of DNA and RNA. In the previous paper of this series (Guan, Y.; et al. Biophys. J. 1994, 66, 225-235), infrared and Raman spectra of the g,g conformer of dimethyl phosphate [(CH₃O)₂PO₂^-], including deuterium [(CD₃O)₂PO₂^-] and carbon-13 [(¹³CH₃O)₂PO₂^-] isotopomers, were reported and assigned in conjunction with a complete normal coordinate analysis. The normal mode calculations were accomplished by use of a generalized valence force field. Here, we demonstrate that an ab initio molecular force field for the g,g conformer of dimethyl phosphate, computed using the 3-21+G* basis set, is consistent with the empirically based valence force field reported previously. We have obtained the force field scaling factors which produce satisfactory agreement between the calculated and experimental vibrational frequencies of each of the three dimethyl phosphate isotopomers in the g,g conformation. Ab initio normal mode assignments, in terms of the potential energy distribution, are in general accord with those obtained from the normal coordinate analysis. Agreement between the ab initio and normal coordinate results supports the reliability of the empirically derived force field for extension to other phosphodiester conformations of dimethyl phosphate, as well as to more complex diester derivatives of the nucleic acid orthophosphate group.

Recommended Citation

Y. Guan et al., "Vibrational Analysis of Nucleic Acids. 2. Ab Initio Calculation of the Molecular Force Field and Normal Modes of Dimethyl Phosphate," Journal of Physical Chemistry, vol. 99, no. 31, pp. 12054 - 12062, American Chemical Society (ACS), Aug 1995.

The definitive version is available at https://doi.org/10.1021/j100031a039

Department(s)

Chemistry

International Standard Serial Number (ISSN)

0022-3654

Document Type

Article - Journal

Document Version

Citation

File Type

text

Language(s)

English

Rights

© 1995 American Chemical Society (ACS), All rights reserved.

Publication Date

01 Aug 1995