Vibrational analysis of nucleic acids .5. Force field and conformation-dependent modes of the phosphodiester backbone modeled by diethyl phosphate

A generalized valence force fields is derived for the diethyl phosphate anion [(CH3CH2O)(2)PO2-] and its deuterium [(CH3CD2O)(2)PO2-, (CD3CH2O)(2)PO2- and (CD3CD2O)(2)PO2-] and carbon-13 [((CH3CH2O)-C-13)(2)PO2-] derivatives in the stable trans-gauche-gauche-trans conformation. Normal coordinate analysis of the trans-gauche-gauche-trans conformer, which serves as a structural analog of the nucleic acid phosphodiester group, is based on comprehensive infrared and Raman spectroscopic data and vibrational assignments obtained for the diethyl phosphate anion. The generalized valence force field is in good agreement with the scaled ab initio force field of diethyl phosphate and represents significant improvement over earlier modeling of the phosphodiester moiety and dimethyl phosphate. The conformational dependence of skeletal C-C-O-P(O-2(-))-O-C-C stretching virbations is also explored. Starting with the trans-gauche-trans conformation, the frequency dependence of skeletal stretching modes has been obtained by stepwise rotation of the torsion angles of the P-O and C-O bonds corresponding to nucleic acid torsions alpha(P-05'),beta(05'-C5'),epsilon(C3'-O3'), and zeta(O3'-P). Both symmetric and antisymmetric phosphoester stretching modes are highly sensitive to P-O and C-O torsions, whereas symmetric and antisymmetric phosphodioxy (PO2-) stretching modes are less sensitive. The present results provide an improved structural basis for understanding previously developed empirical correlations between vibrational marker bands and nucleic acid backbone conformation.