Title |
Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study)
|
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Published in |
BMC Molecular and Cell Biology, October 2001
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DOI | 10.1186/1472-6769-1-2 |
Pubmed ID | |
Authors |
Ami Lakdawala, Minmin Wang, Neysa Nevins, Dennis C Liotta, Danuta Rusinska-Roszak, Marek Lozynski, James P Snyder |
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 beta-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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