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Fischer Projections02:18

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DFTMD studies of β-cellobiose: conformational preference using implicit solvent.

F A Momany1, U Schnupf

  • 1Plant Polymer Research, USDA, ARS, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, IL 61604, USA. frank.momany@ars.usda.gov

Carbohydrate Research
|February 22, 2011
PubMed
Summary
This summary is machine-generated.

Computational studies reveal that solvent and entropy significantly influence cellobiose conformation. Including solvation models in dynamics simulations correctly predicts the observed "syn" form as energetically favored over "anti" forms.

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Area of Science:

  • Computational Chemistry
  • Carbohydrate Chemistry
  • Molecular Dynamics

Background:

  • Previous Density Functional Theory (DFT) studies in a vacuum suggested that anti conformations of cellobiose are more stable than syn conformations.
  • Implicit solvation models like COSMO did not initially predict the observed syn conformation as the lowest energy form.
  • Explicit water molecules improved energy predictions, hinting at the importance of solvation and entropy.

Purpose of the Study:

  • To evaluate the predictive accuracy of the COSMO solvation model for carbohydrate conformational analysis.
  • To investigate the role of solvent and entropy in determining the solution-phase conformation of cellobiose.
  • To compare DFT in vacuo, COSMO, and DFT with molecular dynamics (DFTMD) simulation results.

Main Methods:

  • Performed constant energy DFT molecular dynamics (DFTMD) simulations.
  • Simulated low-energy syn and anti conformations of cellobiose.
  • Conducted simulations both with and without the COSMO solvation model included.

Main Results:

  • DFTMD simulations incorporating the COSMO model demonstrated that syn conformations become energetically favored over anti forms.
  • Analysis of dihedral angle distributions and conformational transitions confirmed the stabilization of syn forms under solvation.
  • Populations of quasi-planar, boat, and skew forms were analyzed during the simulations.

Conclusions:

  • The COSMO model, when integrated into dynamics simulations, accurately predicts the energetically favored syn conformation of cellobiose.
  • Both solvent effects and entropic contributions are crucial for understanding the observed solution-phase conformation of cellobiose.
  • DFTMD simulations offer a robust method for assessing conformational preferences of carbohydrates in solution.