Conformational Flexibility of Sucrose

Abstract

In analyzing the conformational properties of carbohydrates, it has often been the practice to consider individual monomer rings to be rigid units, with the only molecular flexibility lying in torsional rotations about the linkage bonds. However, conformational energy maps prepared using this assumption can be quite misleading in deciding which conformations are energetically allowed, and almost useless in understanding the likely motions of disaccharides, such as might be computed in molecular dynamics simulations. Molecular flexibility can be incorporated into conformational energy maps by preparing relaxed or adiabatic energy maps. However, a number of operational difficulties complicate the calculation of relaxed energy maps. This paper discusses some of these practical problems which arise in the preparation of relaxed conformational energy maps for complex dimers like disaccharides, and how these problems complicate the physical interpretation of such maps. The importance of molecular flexibility is illustrated through the application of flexible conformational energy mapping and molecular dynamics simulations to sucrose.