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.
CONFORMATIONAL ANALYSIS OF SACCHARIDES WITH MONTE CARLO / STOCHASTIC DYNAMICS SIMULATIONS / A. BERNARDI, L. RAIMONDI, D. ZANFERRARI. - In: JOURNAL OF MOLECULAR STRUCTURE. THEOCHEM. - ISSN 0166-1280. - 395-396:1-3(1997), pp. 361-373.
CONFORMATIONAL ANALYSIS OF SACCHARIDES WITH MONTE CARLO / STOCHASTIC DYNAMICS SIMULATIONS
A. BERNARDIPrimo
;L. RAIMONDISecondo
;
1997
Abstract
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.
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