Molecular dynamics simulation of the α-D-Manp-(1→3)-β-D-Glcp-OMe disaccharide in water and water DMSO solution

Molecular dynamics simulation studies of solvation structure, conformational behavior, and dynamics of alpha-D-Manp-(1 --> 3)-beta-D-Glcp-OMe in water and in the binary 1:3 molar mixture of dimethylsulfoxide and water are reported. Several combinations of different force fields are evaluated for both the disaccharide and the solvent components. The disaccharide molecule is found to be fairly rigid, showing no high-amplitude rotation around the glycosidic linkage, which is consistent with previous experimental findings. Also, the preferred conformation of the disaccharide in the water simulation is in agreement with experiment. The predominant conformation of alpha-D-Manp-(1 --> 3)-beta-D-Glcp-OMe in the water-dimethylsulfoxide solution was found to be dependent on the potential models for the solvent components, thus stressing the importance to carefully evaluate the potentials used against available experimental data. In general, the different hydroxyl groups of the disaccharide prefer different solvent components as hydrogen bond accepters.