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Molecular dynamics simulation of crystalline β-cyclodextrin dodecahydrate at 293 K and 120 K

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Abstract

Molecular dynamics (MD) simulations for crystalline β-cyclodextrin dodecahydrate (β-CD) at two different temperatures, 293 K and 120 K, have been performed using the GROMOS program package. The calculated structural properties are compared to those obtained from neutron diffraction studies of this system at the quoted temperatures. The simulation was carried out over a period of 20 ps on four unit cells containing 8 β-CD molecules and 96 water molecules, whereby all atoms were allowed to move.

At room temperature, the experimental positions of the (non-hydrogen) glucose atoms are reproduced within 0.034 nm, a value which is smaller than the experimental (0.041 nm) or simulated (0.049 nm) overall root mean square (rms) positional fluctuation. The corresponding numbers for the low temperature study are 0.046 nm, 0.019 nm and 0.022 nm. At both temperatures the experimentally observed degree of anisotropy of the atomic motions is also found in the simulations.

The comparison of a variety of structural properties leads to the conclusion that the molecular model and force field used are able to simulate the cyclodextrin system very well. Experimentally observed differences in properties as a function of number of glucose units in the CD molecule (α-CD, 6 versus β-CD, 7) and as a function of temperature are qualitatively reproduced by the simulations.

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Koehler, J.E.H., Saenger, W. & van Gunsteren, W.F. Molecular dynamics simulation of crystalline β-cyclodextrin dodecahydrate at 293 K and 120 K. Eur Biophys J 15, 211–224 (1987). https://doi.org/10.1007/BF00577069

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Key words

  • β-cyclodextrin dodecahydrate
  • molecular dynamics simulation
  • hydrogen bonds
  • empirical force field
  • water molecule diffusion
  • positional disorder