Preferred Phosphodiester Conformations in to Estimate Lone-Pair Interactions in a Phosphodiester Nucleic Acids. A Virtual Bond Torsion Potential

The preferred orientations around the internucleotide P-0(3’)(0’) and P-O(5)(w) bonds of the phosphodiester which link the successive nucleotide residues are crucial in discerning the helical as well as nonhelical bend conformations of nucleic acids and polynucleotides. Experimental investigations other than the single-crystal x-ray diffraction methods are unable to provide directly information about P-0 bond conformations, except possibly for the stacked conformation, although the results of these studies have also conclusively substantiated the predominance of the preferred nucleotide conformations in diand oligonucleotides. Calculations using semiempirical potential fun~ t ions l -~ and semiempirical quantum mechanical method^^,^ on model sugar-phosphate-sugar backbone segments have aided in delineating the stereochemically possible and the preferred conformations around the P-0 bonds in di-, oligo-, and polynucleotides. However, some of these remained less satisfactory to the extent that a low-energy minimum occurred corresponding to the fully extended phosphodiester conformation (w’,w) ( 180°,1800) ( t t ) , which was argued6 to be a considerably high energy conformation owing to the repulsive interactions between the lone-pair orbitals associated with the backbone ester oxygen O(5’) and O(3’) atoms. Also, no such conformation has been experimentally observed. Recent quantum chemical calculat i o n ~ ~ ~ have shown that the fully extended phosphodiester conformation ( t t ) is indeed energetically unfavorable, in agreement with the earlier