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Conformational differences between alpha-cyclodextrin in aqueous solution and in crystalline form. A molecular

J E Koehler1, W Saenger, W F van Gunsteren

  • 1Institut fuer Kristallographie, Freie Universitaet Berlin, Federal Republic of Germany.

Journal of Molecular Biology
|September 5, 1988
PubMed
Summary

Molecular dynamics simulations reveal significant conformational and mobility differences for alpha-cyclodextrin in solution versus crystalline states. Solution structures show greater atomic mobility and altered hydrogen bonding compared to static crystal arrangements.

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Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Molecular Modeling

Background:

  • Molecular dynamics (MD) simulations are crucial for understanding molecular behavior in different environments.
  • Alpha-cyclodextrin exhibits distinct structures in aqueous solution and crystalline forms.

Purpose of the Study:

  • To delineate the conformational differences of alpha-cyclodextrin between aqueous solution and crystalline states using MD simulations.
  • To compare the dynamic behavior and hydrogen-bonding patterns in both environments.

Main Methods:

  • Two MD simulations were performed: one mimicking solution (90 ps, 611 water molecules) and another modeling the crystal (15 ps, 16 alpha-cyclodextrin molecules, 96 water molecules).
  • Simulations utilized a truncated octahedron box for solution and space group P2(1)2(1)2(1) for crystal modeling.

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Main Results:

  • Alpha-cyclodextrin in solution deviates by ~0.1 nm from its crystal structure and exhibits twice the atomic mobility.
  • The crystal's observed glucose unit twist is absent in solution, though ring torsion angles remain asymmetric.
  • Hydrogen-bonding patterns differ significantly between the crystal and solution states.

Conclusions:

  • Crystal structures represent a single static energy minimum, while MD simulations capture the dynamic hydrogen-bonding landscape in solution.
  • MD simulations provide a comprehensive view of alpha-cyclodextrin's conformational flexibility and hydration in different environments.