Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations
Journal Article
2010
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Authors
Journal Title
J. Phys. Chem. B.
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Publisher
American Chemical Society
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University of Cape Town
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Abstract
The puckered conformations of furanose and pyranose carbohydrate rings are central to analyzing the action
of enzymes on carbohydrates. Enzyme reaction mechanisms are generally inaccessible to experiments and so
have become the focus of QM(semiempirical)/MM simulations. We show that the complete free energy of
puckering is required to evaluate the accuracy of semiempirical methods used to study reactions involving
carbohydrates. Interestingly, we find that reducing the free energy space to lower dimensions results in near
meaningless minimum energy pathways. We analyze the furanose and pyranose free energy pucker surfaces
and volumes using AM1, PM3, PM3CARB-1, and SCC-DFTB. A comparison with DFT optimized
structures and a HF free energy surface reveals that SCC-DFTB provides the best semiempirical description
of five- and six-membered carbohydrate ring deformation.
Description
Reference:
Barnett, C. B., & Naidoo, K. J. (2010). Ring puckering: a metric for evaluating the accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB carbohydrate QM/MM simulations. The Journal of Physical Chemistry B, 114(51), 17142-17154.