Modelling of beta-D-glucopyranose ring distortion in different force fields: a metadynamics study

作者：Spiwok Vojtech^*; Kralova Blanka; Tvaroska Igor

来源：Carbohydrate Research, 2010, 345(4): 530-537.

DOI：10.1016/j.carres.2009.12.011

• Force field
• Pyranose ring distortion
• Metadynamics
• Free energy
• Molecular dynamics simulation

Modelling of carbohydrate conformations is a challenging task for force field developers. Three carbohydrate force fields, namely GLYCAM06, GROMOS 45a4 and OPLS were evaluated. Free energies of different ring conformations of beta-D-glucopyranose were calculated using metadynamics in vacuum as well as in explicitly modelled water. All three force fields model the (4)C(1) conformation as the most stable by at least 6 kJ/mol, as compared to other conformations. Interconversion from the (4)C(1) to any other conformation is associated with a barrier of no lower than 26 kJ/mol. The free energy surface calculated in the GLYCAM06 force field is in remarkably good agreement with the recent Car-Parrinello metadynamics study. The effect of a water environment is relatively low and analogous in all tested force fields. Namely, the presence of water stabilizes the upper-left ((3,O)B) Versus bottom-right (B(3,O)) area of Stoddard's plot, relative to the situation in vacuum. Comparison of free and potential surfaces is also provided for vacuum calculations.

• 出版日期2010-2-26