CONFORMATIONAL ANALYSIS OF SACCHARIDES WITH MONTE CARLO / STOCHASTIC DYNAMICS SIMULATIONS

Mixed-mode Monte Carlo/stochastic dynamics (MC/SD) simulations, as implemented in MACROMODEL, provide an effective and affordable way of modeling mono-and disaccharides, fully accounting for extra-annular bond flexibility. The simulation parameters were refined using methyl mannoside 1 as a model. Calculations on Man-(α-1,3)-Man-OMe 2 and 3, performed with the AMBER* force field and the GB/SA solvation model, allowed comparison with experimental data, and gave ensemble average interproton distances which were compatible with the reported relative NOE values.