Vibrational analysis of nucleic acids. IV. Normal modes of the DNA phosphodiester structure modeled by diethyl phosphate
1996
Guan, Y. | Thomas, G.J. Jr
Raman and ir spectra are reported for diethyl phosphate [(CH3CH2O)2PO2(-)] and diethyl phosphate isotopomers incorporating carbon-13 at methylene group sites [(CH3(13)CH2O)2PO2(-)] and deuterium substituents on methyl and methylene carbons [(CH3CD2O)2PO2(-), (CD3CH2O)2PO2(-), (CD3CD2O)2PO2(-)]. The vibrational spectra are analyzed to develop a consistent set of assignments for the C-C-O-P(O2(-))-O-C-C network, which serves as a model for the nucleic acid phosphodiester backbone. The present study resolves previously conflicting vibrational assignments for the phosphodiester skeleton and provides a firm empirical basis for interpreting conformationally sensitive modes of DNA and RNA. Ab initio vibrational analyses have also been conducted on the above isotopomers of diethyl phosphate in the trans-gauche-gauche-trans conformation, optimized using the 3-21+G* basis set at the restricted Hartree-Fock level. The ab initio calculations are in good agreement with the empirical results, thus strengthening the proposed assignment scheme for Raman and infrared spectra. The present study provides a basis for improvement of empirical force fields utilized in previous normal coordinate analyses of the nucleic acid phosphodiester group.
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