Pickett angles and Cremer–Pople coordinates as collective variables for the enhanced sampling of six-membered ring conformations

Abstract

Although completely equivalent for the description of puckered ring conformers, the two popular coordinates sets of Strauss–Pickett dihedral angles and Cremer–Pople spherical coordinates are shown to have contrasting features when employed as collective variables in free-energy calculations with accelerated sampling techniques. Results from a 100 ns molecular dynamics simulation at conformational equilibrium and from combined metadynamics/umbrella sampling calculations of glucose are exploited to elucidate these differences.

Keywords:

• puckering
• sugars
• ring conformers
• free energy

Acknowledgements

The authors thank P. Hünenberger and H. Hansen for fruitful discussions. Use of the HPC cluster Wiglaf at the Department of Physics of the University of Trento is acknowledged. The authors are member of the Interdisciplinary Laboratory of Computational Science (LISC).