|French, Alfred - Al|
Submitted to: Carbohydrate Research
Publication Type: Peer reviewed journal
Publication Acceptance Date: 8/18/2009
Publication Date: 9/14/2009
Citation: Stortz, C.A., Johnson, G.P., French, A.D., Csonka, G.I. 2009. Comparison of different force fields for the study of disaccharides. Carbohydrate Research. 344:2217-2228. Interpretive Summary: Computerized molecular models are useful for augmenting experimental studies as well as for studying molecules for which experiments would be very difficult. However, molecular models for carbohydrate molecules are less well developed than models for other molecules such as proteins. Even so, the potential user can choose among a variety of programs for modeling carbohydrates, including cotton cellulose. This paper shows that there are similarities in the results from the various programs, but there are also important differences. There is greater similarity among results from several relatively new systems as well as one of the older programs. This work is targeted at bench scientists who might want to use molecular modeling programs for carbohydrates.
Technical Abstract: Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying ß-cellobiose, a-maltose, and a-galabiose [a-D-Galp-(1'4)-a-D-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl and glycosidic linkage orientations were minimized by the different methods, some at two dielectric constants. By comparing these results and available crystal structure data and/or higher level density functional theory results, it was concluded that the newer parametrizations for force fields (GROMOS, GLYCAM06, OPLS-2005 and CSFF) give results that are reasonably similar to each other, whereas the older parameterizations for Amber, CHARMM or OPLS were more divergent. However, MM3, an older force field, gave energy and geometry values comparable to those of the newer parameterizations, but with less sensitivity to dielectric constant values. These systems worked better than MM2 variants, which were still acceptable. PM3CARB-1 also gave adequate results in terms of linkage and exocyclic torsion angles. GROMOS, GLYCAM06 and MM3 appear to be the best choices, closely followed by MM4, CSFF and OPLS-2005. With GLYCAM06 and to a lesser extent, CSFF and OPLS-2005, a number of the conformers that were stable with MM3 changed to other forms.