Molecular dynamics study on the conformational stability of laminaran oligomers in various solvents.
Solution conformations of the (1-->3)-beta-D-glucan laminaran have been investigated by means of molecular mechanics and molecular dynamics simulations in three solvents: water, dimethylformamide, and dimethyl sulfoxide. Conformational analysis of solvated laminarabiose was carried out to study the effect of specific solute-solvent interactions upon reactive hydroxyl groups. Dynamic trajectories of solvated laminarabiose have been interpreted in terms of average glycosidic-linkage conformation, hydrogen-bonding pattern, and coordination by solvent molecules. The analysis of radial distribution functions, coordination functions, mean residency times, and time correlation functions derived from the simulation trajectories furnished the necessary insight. The results have been used to assess the steric accessibility of laminaran-C4-OH and -C6-OH hydroxyl groups in the considered solvents and to rationalize corresponding earlier experimental observations. The experiments demonstrated that reaction equilibrium during chemical modification of laminaran oligomers with 2,2-dimethoxypropane involving the laminaran-C4-OH and -C6-OH hydroxyl groups significantly depended on the solvent used.
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Dipartimento di Biochimica, Biofisica e Chimica delle Macromolecole, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy.
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D002240:Carbohydrate Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D004121:Dimethyl Sulfoxide; D004126:Dimethylformamide; D005936:Glucans; D009682:Magnetic Resonance Spectroscopy; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D011134:Polysaccharides / Q000737:chemistry*; D012997:Solvents; D014867:Water
D005936:Glucans; D011134:Polysaccharides; D012997:Solvents; D014867:Water; D004126:Dimethylformamide; C008247:laminaran; D004121:Dimethyl Sulfoxide