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Validation and Comparison of Force Fields for Native Cyclodextrins in Aqueous Solution.

Julia Gebhardt1, Catharina Kleist2, Sven Jakobtorweihen2

  • 1Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart , D-70569 Stuttgart, Germany.

The Journal of Physical Chemistry. B
|December 30, 2017
PubMed
Summary

Molecular dynamics simulations show that revised GROMOS force fields (53A6GLYC, 56A6CARBO_R, 2016H66) accurately model cyclodextrins. CHARMM36 and q4md-CD offer more flexible simulations.

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Area of Science:

  • Computational chemistry and molecular modeling
  • Biomolecular simulations
  • Carbohydrate chemistry

Background:

  • Cyclodextrins (CDs) are crucial in various applications, necessitating accurate simulation methods.
  • Molecular dynamics (MD) simulations rely on force fields to predict molecular behavior.
  • Evaluating and refining force fields for carbohydrates is essential for reliable simulation outcomes.

Purpose of the Study:

  • To assess the performance of CHARMM36, q4md-CD, and GROMOS force fields for native cyclodextrins (α-, β-, γ-CD).
  • To compare simulation results with experimental data, including structural parameters, hydrogen bonding, and hydration.
  • To identify optimal force field parameters for accurate cyclodextrin simulations in aqueous solution.

Main Methods:

  • Performed molecular dynamics simulations of α-, β-, and γ-cyclodextrins in aqueous solution.
  • Utilized CHARMM36, AMBER-compatible q4md-CD, and five GROMOS force field variants.
  • Analyzed structural parameters, hydrogen bonds, hydration patterns, and hydration free enthalpies against experimental data (X-ray, NMR).

Main Results:

  • Revised GROMOS force fields (53A6GLYC, 56A6CARBO_R, 2016H66) show improved agreement with experimental NMR data.
  • CHARMM36 and q4md-CD force fields yield more flexible cyclodextrin models compared to recommended GROMOS sets.
  • All tested force fields provide comparable results for hydration patterns and free enthalpies.

Conclusions:

  • Recommends GROMOS variants 53A6GLYC, 56A6CARBO_R, and 2016H66 for accurate cyclodextrin simulations.
  • CHARMM36 and q4md-CD are suitable for studies requiring a more flexible representation of cyclodextrins.
  • Force field selection impacts the simulated flexibility of cyclodextrins in aqueous environments.