Conformational Pathways of Saturated Six-Membered Rings. A Static and Dynamical Density Functional Study

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DOIResolve DOI: http://doi.org/10.1021/jp052197t
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TypeArticle
Journal titleJournal of Physical Chemistry A
ISSN1089-5639
Volume109
Issue36
Pages80968105; # of pages: 10
AbstractThe conformation of the six-membered ring of pyranosyl sugars has pronounced effects on the physical and chemical properties of carbohydrates. We present a method to determine key features of the potential energy surfaces, such as transition states associated with the inversion pathways of the model compounds cyclohexane, tetrahydropyran, p-dioxane, m-dioxane, s-trioxane, and 2-oxanol. Finally, we make the first determination of the pathways for inversion of penta-O-methyl--D-glucopyranose and penta-O-methyl--D-glucopyranose. For both anomers, a transition state with five coplanar atoms with appreciable OE character was found. The method is based on constrained Car-Parrinello ab initio molecular dynamics, as implemented in the projector augmented-wave (PAW) method. The constraints are derived from the normal modes of six-membered rings and are described in terms of the canonical conformations 1C4 chair, 1,4B boat, and OS2 skew-boat. The PAW derived trajectories are in agreement with previous suggestions in the literature that pseudorotation is an important feature of such conformational interconversions. The dynamic nature as well as the internal coordinate-based constraints provide a method which can reliably accommodate pseudorotation. To determine semiquantitative energies, we recalculate key conformations using standard quantum mechanical calculations while keeping the ring dihedral angles frozen at their values found in the dynamics. In all cases where experimental barriers are known, our results are in excellent agreement.
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AffiliationNational Research Council Canada; NRC Steacie Institute for Molecular Sciences; NRC Institute for Biological Sciences
Peer reviewedNo
Identifier16891788
NPARC number12329153
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Record identifier357c916e-19e7-4437-b461-25622e976464
Record created2009-09-10
Record modified2016-05-09
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