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Conformational studies on polynucleotide chains. V. A comparison between the quantum‐mechanical and the consistent force field approach

Consistent force field (CFF) calculations were performed for the sugar–phosphate–sugar fragment, taken as a model of the polynucleotide backbone. The potential‐energy‐function is the sum of four contributions, accounting for bond and angle deformation, torsional motions, and nonbonded interactions. Both deoxyribose and ribose systems, with either C(2′)‐endo or C(3′)‐endo puckering in the starting geometry of ribose rings, were considered. A fair number of minima of the conformational‐energy hypersurface were found. Although the numerical method employed in the CFF context cannot solve the problem of finding the global minimum in a definite way, one of the final conformations has a total energy much more attractive than the others, and may be regarded as the most stable conformation attainable with our potential‐energy function. The energy‐minimization affects the puckering of the first ribose ring differently from that of the second: in general, for the C(2′)‐endo system the second ring retains its starting conformation (Ψ′ = 152°), while in the first the Ψ′ is modified by up to 70°; the opposite occurs for the C(3′)‐endo system. This is explained by the different positions of the two rings relative to the phosphate group.