CONFORMATIONAL-ANALYSIS OF SACCHARIDES WITH MONTE-CARLO STOCHASTIC DYNAMICS SIMULATIONS

Mixed-mode Monte Carlo/stochastic dynamics (MC/SD) simulations, as imp lemented in MACROMODEL, provide an effective and affordable way of mod eling mono- and disaccharides, fully accounting for extra-annular bond flexibility. The simulation parameters were refined using methyl mann oside 1 as a model. Calculations on Man-(alpha-1,3)-Man-OMe 2 and 3, p erformed with the AMBER force field and the GB/SA solvation model, al lowed comparison with experimental data, and gave ensemble average int erproton distances which were compatible with the reported relative NO E values. (C) 1997 Elsevier Science B.V.