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Vibrational analysis of nucleic acids. IV. normal modes of the DNA phosphodiester structure modeled by diethyl phosphate
Author(s) -
Guan Yifu,
Thomas George J.
Publication year - 1996
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(199612)39:6<813::aid-bip7>3.0.co;2-y
Subject(s) - phosphodiester bond , chemistry , isotopomers , raman spectroscopy , nucleic acid , methylene , ab initio , basis set , computational chemistry , ab initio quantum chemistry methods , crystallography , pseudorotation , phosphate , stereochemistry , ring (chemistry) , molecule , density functional theory , rna , organic chemistry , biochemistry , physics , optics , gene
Raman and ir spectra are reported for diethyl phosphate [(CH 3 CH 2 O) 2 PO ‐ 2 ] and diethyl phosphate isotopomers incorporating carbon‐13 at methylene group sites [(CH 13 3 CH 2 O) 2 PO ‐ 2 ] and deuterium substituents on methyl and methylene carbons [(CH 3 CD 2 O) 2 PO ‐ 2 , (CD 3 CH 2 O) 2 PO ‐ 2 (CD 3 CD 2 O) 2 PO ‐ 2 ]. The vibrational spectra are analyzed to develop a consistent set of assignments for the C‐C‐O‐P(O ‐ 2 )‐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. © 1996 John Wiley & Sons, Inc.