The conformational analysis of methyl beta-xylobioside: effect of choice of potential functions.
In order to determine the effect of the choice of potential function used in the conformational analysis of a carbohydrate, the NMR spectrum of methyl beta-xylobioside [beta-D-Xyl-(1-->4)-beta-D-Xyl-(1-->O)-Me] was interpreted using calculated J13C-H coupling constants and nuclear Overhauser effects for protons across the anomeric linkage. Conformational flexibility was described by calculating average phi and psi angles, and estimating their standard deviations. ECEPP2, ECEPP83, and HSEA potentials were used in the first series of calculations. The calculated coupling constants and nuclear Overhauser effects were averaged over the Boltzmann distribution of conformations of the disaccharide in which the entire phi, psi space was scanned in ten-degree steps while retaining fixed bond distances and angles in the remainder of the molecule. In the second series of calculations, MM2, MM2CARB, and PCILO parameters were used to calculate conformational energies. Conformational optimization was done. The effect of temperature and solvent on the calculated coupling constants was negligible. Calculated properties from conformations whose energies were based on the ECEPP parameters gave the best agreement with experiment. Exploration of the conformational space in breadth rather than on a detailed level of full optimization appears to be a preferable course of action.
Duben
A J
AJ
Computer Science Department, Southeast Missouri State University, Cape Girardeau 63701-4799.
Hricovini
M
M
Tvaroska
I
I
D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D004187:Disaccharides / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008433:Mathematics; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D015394:Molecular Structure
D004187:Disaccharides; C064985:methyl beta-xylobioside