The shape of the hexopyranose ring is an important factor which can influence the properties of carbohydrate molecules and affect their biological activity. Due to a limited availability of the experimental data, the conformational rearrangements (puckering) which occur within the pyranose rings are studied extensively by using various computational approaches. Contrary to the basic structural and energetic features characterizing the process of ring flexing, the kinetic and dynamics properties of puckering remain less recognized. We performed the first, molecular dynamics-based, systematic calculations aimed at description of the kinetic characteristics of the conformational changes in the rings of α-d- and β-d-glucopyranose molecules. The rate constants representing particular molecular events which comprise the chair-chair inversion are determined and analyzed in the context of the available experimental data. Furthermore, several various variables (e.g. transmission coefficients) and issues (e.g. memorylessness of the puckering process) are investigated and discussed. As several different parameter sets were used during the study (GROMOS 56A6CARBO, GLYCAM, GROMOS 53A6GLYC), the results provide the conclusion on the capability of the carbohydrate-dedicated force fields to describe the kinetic properties of pyranose ring flexing.
Keywords: Carbohydrate conformation; Force fields; Rare events; Ring puckering.
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