A GROMOS Force Field for Furanose-Based Carbohydrates

The
article describes a GROMOS force field parameter set for molecular
dynamics simulations of furanose carbohydrates. The proposed united-atom
force field is designed and validated with respect to the conformational
properties of furanose mono-, di-, oligo-, and polymers in aqueous
solvent. The set accounts for the possibility of arbitrary glycosidic
linkage connectivity between units, O-alkylation, as well as of different
anomery. The compatibility with the already existing, pyranose-dedicated
GROMOS 56A6CARBO/CARBO_R set allows one to use the presently
proposed extension for studying more diverse and biologically relevant
carbohydrates that exploit both pyranose and furanose units. The validation
performed against the quantum-mechanical and experimental data concerning
the structural and conformational features shows that the newly developed
set is capable to reproduce conformational equilibrium within the
furanose ring, relative free energies of anomers, hydroxymethyl rotamers,
and glycosidic linkage conformers. Additionally, the results concerning
the conformation of the furanose ring with relation to the two-state
model as well as other conformational features of furanose-containing
saccharides are discussed.