Structural fluctuation of methyl N,N′-diacetyl-β- d-chitobioside in vacuo and in aqueous solution: Molecular dynamics simulations and proton NMR spectroscopy

Abstract

Molecular dynamics (MD) simulations of methyl N,N′-diacetyl-β- d-chitobioside (GIcNAcβ-(1 → 4)GIcNAcβ-OMe) have been performed both in vacuo and in aqueous solution with the explicit inclusion of the solvent water molecules. The β-(1 → 4) glycosidic linkage fluctuates considerably, over a range of ± 10°, in each of the MD simulations in vacuo and in aqueous solution. The intra- and inter-residue hydrogen bonds in vacuo are replaced by intermolecular hydrogen bonds with the solvent water molecules in aqueous solution. Multiple conformations ( gg and gt) exist for the exocyclic hydroxymethyl groups. The results of the MD simulations are compared with those of 1H- 1H nuclear Overhauser effect measurements.