Computerized models of carbohydrates

Abstract

Some history of computerized modeling is furnished to set the stage for modern work, including the development of the justification for using flexible monosaccharide residues. Modeling studies of mono-and disaccharides, primarily by the author and colleagues, have been reviewed and additional analyses were furnished that relate the conformations found in crystal structures to the adiabatic energies through a Boltzmann-like distribution. Those decreases in the numbers of observed crystal structures with increasing energy, discussed earlier by Dunitz and coworkers, suggest that the consequences of crystal packing forces are equivalent to the distribution of structures that would be found at about 500 K for non-crystalline molecules. A closing study of a large oligosaccharide, a cycloamylose with 26 glucose residues (CA26), revealed the extent to which energy minimization studies could retain molecular features found in crystal structures of a large carbohydrate. As also done for the disaccharides, both empirical force fields (molecular mechanics) and density functional theory (quantum mechanics) were employed. Some intrinsic features of the CA26 were reproduced, but the detailed results from the different modeling methods diverged. Results from the CA26 calculations based on normal termination criteria changed significantly when tighter criteria were employed; it was not practical to tighten the criteria for the quantum calculations.