Agreement between Single Crystal X-Ray and Molecular Mechanical Sugar Ring Conformations

Abstract

We have calculated the deoxyribose sugar energy for a wide range of puckering parameters, (q, W), using different force fields. The intra-ring bond lengths, bond angles, and dihedral angles are calculated for every energy minimized structure and compared with 224 sugar ring structures available from DNA single crystal x-ray data. A modified Weiner's force field yields an excellent agreement with x-ray data.

The calculated energy surface shows a variable amplitude repuckering path, with an average distortion of 0.42 Å. Most of the experimental values of (q, W) fall within 1.0 Kcal/mol from the calculated minimum.