A revised potential-energy surface for molecular mechanics studies of carbohydrates

Carbohydr Res. 1988 Sep 15;180(2):207-21. doi: 10.1016/0008-6215(88)80078-8.

Abstract

A revised CHARMM-type molecular mechanics potential-energy function has been developed for use in the dynamical simulation of simple carbohydrates in aqueous solution. Atomic charges used in this parameterization were taken to be those previously determined to be appropriate for hydrogen-bonded systems, and the various force-constants were selected by the nonlinear least-squares matching of the calculated normal-mode frequencies and minimum-energy structure to experiment as a function of the parameter set. The new function was found to represent the vibrational spectrum and ring pucker of alpha-D-glucopyranose as well as previously studied potentials, while incorporating the charges necessary for the simulation of condensed phases. Molecular dynamics simulations of the motions of alpha-D-glucopyranose in vacuo in both the 1C4 and 4C1 conformation were conducted, and compared to the results of previous simulations using another potential-energy function. The revised potential function was found to produce a D-glucose molecule less flexible in vacuo than had been previously observed.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Carbohydrates*
  • Computer Simulation
  • Electrochemistry
  • Hydrogen Bonding
  • Models, Chemical
  • Solutions
  • Water

Substances

  • Carbohydrates
  • Solutions
  • Water