title: Conformational analysis and molecular dynamics simulation of alpha-(1-->2) and alpha-(1-->3) linked rhamnose oligosaccharides: reconciliation with optical rotation and NMR experiments.
abstract: Molecular mechanics and dynamics calculations were carried out on the disaccharides alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->OMe) (1) and alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->OMe) (2), and the trisaccharide alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1--> 3)-alpha-L-Rhap-(1-->OMe) (3). The semiflexible conformational behavior of these molecules was characterized by the occupation of a combination of different glycosidic linkage and side-chain conformational positions whose relative occupations were sensitive to dielectric screening. Molecular dynamics simulations of the trisaccharide 3 showed little difference between the linkage conformations in the trisaccharide and the component disaccharides 1 and 2 Experimental optical rotation data of 1 and 2 were obtained as a function of temperature in varying solvents. The molecular models were combined with the semiempirical theory of Stevens and Sathyanarayana to yield calculated optical rotations. Interpretation of the data of both 1 and 2 implied that a combination of conformations, both in glycosidic and side-chain positions, could explain the experimental data. Solvents effects were important in influencing the conformational mix and averaged optical rotation. Three-bond heteronuclear coupling constants 3JC H were obtained for the glycosidic linkages of 1 and 2 in D2O and DMSO. Analysis of the coupling constants with a Karplus curve showed that small reductions in the glycosidic torsion angles of the conformations of the models used here of ca. 10 degrees-15 degrees in phi and 5 degrees-10 degrees in psi were required to give better agreement with experiment; a combination of conformations for both 1 and 2 was consistent with the data. There was a negligible influence on the coupling constants of 1 on changing the solvent from D2O to DMSO.
authors.affiliation: Physical and Theoretical Chemistry Laboratory Oxford University, UK.
authors.forename: B J
authors.initials: BJ
authors.lastname: Hardy
authors.forename: S
authors.initials: S
authors.lastname: Bystricky
authors.forename: P
authors.initials: P
authors.lastname: Kovac
authors.forename: G
authors.initials: G
authors.lastname: Widmalm
mesh_terms: D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008969:Molecular Sequence Data; D009844:Oligosaccharides / Q000737:chemistry*; D009904:Optical Rotation; D012210:Rhamnose / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009844:Oligosaccharides; D012210:Rhamnose