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

J Phys Chem B. 2018 Feb 8;122(5):1608-1626. doi: 10.1021/acs.jpcb.7b11808. Epub 2018 Jan 24.

Abstract

Molecular dynamics simulations of native α-, β-, and γ-cyclodextrin in aqueous solution have been conducted with the goal to investigate the performance of the CHARMM36 force field, the AMBER-compatible q4md-CD force field, and five variants of the GROMOS force field. The properties analyzed are structural parameters derived from X-ray diffraction and NMR experiments as well as hydrogen bonds and hydration patterns, including hydration free enthalpies. Recent revisions of the torsional-angle parameters for carbohydrate systems within the GROMOS family of force fields lead to a significant improvement of the agreement between simulated and experimental NMR data. Therefore, we recommend using the variant 53A6GLYC instead of 53A6 and 56A6CARBO_R or 2016H66 instead of 56A6CARBO to simulate cyclodextrins in solution. The CHARMM36 and q4md-CD force fields show a similar performance as the three recommended GROMOS parameter sets. A significant difference is the more flexible nature of the cyclodextrins modeled with the CHARMM36 and q4md-CD force fields compared to the three recommended GROMOS parameter sets.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cyclodextrins / chemistry*
  • Molecular Dynamics Simulation*
  • Molecular Structure
  • Reproducibility of Results
  • Solutions
  • Thermodynamics*
  • Water / chemistry

Substances

  • Cyclodextrins
  • Solutions
  • Water