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Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study)

Authors
Journal
BMC Chemical Biology
1472-6769
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Volume
1
Issue
1
Identifiers
DOI: 10.1186/1472-6769-1-2
Keywords
  • Research Article
Disciplines
  • Biology
  • Chemistry
  • Physics

Abstract

Background Molecular mechanics (MM) and quantum chemical (QM) calculations are widely applied and powerful tools for the stereochemical and conformational investigations of molecules. The same methods have been extensively used to probe the conformational profile of Taxol (Figure 1) both in solution and at the β-tubulin protein binding site. Results In the present work, the relative energies of seven conformations of Taxol derived from NMR and X-ray analyses were compared with a set of widely used force fields and semiempirical MO methods coupled to a continuum solvent treatment. The procedures not only diverge significantly in their assessment of relative conformational energies, but none of them provide satisfactory agreement with experiment. Conclusions For Taxol, molecular mechanics and semiempirical QM methods are unable to provide a consistent energetic ranking of side-chain conformations. For similar highly polar organic structures, "energy-free" conformational search methods are advised.

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