Browsing by Author "Gamieldien, M R"

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    Glucose Orientation and Dynamics in α-, β-, and γ-Cyclodextrins
    (American Chemical Society, 2008) Naidoo, Kevin J; Gamieldien, M R; Chen, J Y-J; Widmalm, G; Maliniak, A
    We investigate, using molecular dynamics (MD) computer simulations, the conformational behavior of α-, β-, and γ-cyclodextrins (CDs). Our analysis of a 30 ns trajectory of CD solution dynamics reveals the underlying conformational behaviours of the CDs that explain their relative flexibility. The distributions of the torsion angles related to the glycosidic linkages, P(ϕ,ψ) were calculated for the three CDs. Most noticeable is the limited range in ϕ torsion rotations compared with ψ rotations for all the CDs. This difference between the three CDs is amplified in the motion and dynamics of their glucose monomers when we monitor their orientational and librational positions relative to the macrocyclic mean plane. The relaxation times of the monomers to their equilibrium orientations follow the pattern γ-CD > α-CD > β-CD. The root-mean-square deviations of the motion of the monomer centers of mass from the mean macrocyclic planes exhibit the same trend.
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    Optimal Configurations of “Capped” β-Cyclodextrin Dimers in Water Maximise Hydrophobic Association
    (Wiley-VCH Verlag, 2010) Gamieldien, M R; Maestre, I; Jaime, C; Naidoo, Kevin J
    Circular dichroism analysis and proton NMR experiments revealed that solutions of 3-O-(2-methylnaphthyl)-β-cyclodextrin form different dimer configurations. The exact nature of the dimer configurations were postulated to be of three types in which these capped cyclodextrins (CDs) are orientated in head-to-head and head-to-tail arrangements. Here we show from detailed computer simulations and free-energy calculations on the configurations that the head-to-head configuration in which the naphthyl groups are mutually inserted into each other’s CD cavities is the most favoured configuration. This configuration optimises the hydrophobic association of the naphthyl aromatic groups and the ring cavities as well as forming the most inter-CD hydrogen bonds of the three configurations.