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Spatial Separation of Molecular Conformers and Clusters
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Conformational pathways of saturated six-membered rings. A static and dynamical density functional study
Andrei R Ionescu1, Attila Bérces, Marek Z Zgierski
1Steacie Institute for Molecular Sciences, National Research Council of Canada, Theory and Computation Program, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada.
The Journal of Physical Chemistry. A
|July 13, 2006
Summary
This study introduces a novel method to map carbohydrate ring conformations, revealing key inversion pathways and transition states for pyranose sugars. The findings enhance understanding of carbohydrate physical and chemical properties.
Area of Science:
- Carbohydrate Chemistry
- Computational Chemistry
- Molecular Dynamics
Background:
- The six-membered ring conformation of pyranosyl sugars significantly influences carbohydrate properties.
- Understanding these conformational dynamics is crucial for predicting chemical behavior.
Purpose of the Study:
- To develop and apply a computational method for determining potential energy surfaces and inversion pathways of six-membered rings.
- To investigate the conformational inversion pathways of model compounds and specific methylated glucopyranose anomers.
Main Methods:
- Constrained Car-Parrinello ab initio molecular dynamics using the projector augmented-wave (PAW) method.
- Utilizing normal modes of six-membered rings to derive constraints for molecular dynamics simulations.
- Employing standard quantum mechanical calculations to determine semiquantitative energies of key conformations.
Main Results:
- Successfully determined inversion pathways and transition states for model compounds like cyclohexane and tetrahydropyran.
- Identified inversion pathways for penta-O-methyl-alpha-D-glucopyranose and penta-O-methyl-beta-D-glucopyranose, revealing a transition state with five coplanar atoms.
- Demonstrated that the method accurately captures pseudorotation dynamics, aligning well with experimental data where available.
Conclusions:
- The developed constrained molecular dynamics method reliably accommodates pseudorotation in six-membered rings.
- This approach provides accurate insights into the conformational landscape and energy barriers of pyranosyl sugars.
- The findings offer a valuable tool for studying carbohydrate conformation and its impact on properties.
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