Molecular Modelling of Six-Ring Agarose Chains: Effects of Explicit and Implicit Solvent

A study on the molecular dynamics of agarose-type oligosaccharide chains in water is presented. In the field of molecular modelling one is able to use either explicit water molecules or a representative bulk dielectric constant: the two methods are compared here. The starting conformation was taken from X-ray fibre diffraction data for agarose double helices, which are neutral molecules. The resulting trajectories were analysed for the behaviour of dihedral linkages, and these were compared to systematic searches performed on isolated agarobiose and neo-agarobiose units. The results showed that when explicit water molecules are used the oligosaccharide chains are stiffer and have a reduced mobility.Electronic Supplementary Material available.