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Journal of Molecular Modeling

, Volume 18, Issue 3, pp 843–849 | Cite as

Problems with molecular mechanics implementations on the example of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide

  • Agata SiwekEmail author
  • Katarzyna Świderek
  • Stefan Jankowski
Original Paper

Abstract

Results from force fields implemented in HyperChem, a program frequently used in studies of bioactive compounds, have been compared using the example of the conformational analysis of a 1-carbonylthiosemicarbazide that exhibits strong antibacterial activity. By comparing these results with the original force fields and the experimental NMR ROESY spectrum, it was shown that these implementations can lead to erroneous results.

Figure

The most stable conformations of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide obtained with the Amber, CHARMM, and OPLS force fields; note that—confusingly—the most stable conformations obtained with these three force fields are very different

Keywords

Molecular mechanics Amber CHARMM OPLS Conformational search 1-Carbonylthiosemicarbazide HyperChem 

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Agata Siwek
    • 1
    Email author
  • Katarzyna Świderek
    • 2
  • Stefan Jankowski
    • 3
  1. 1.Department of Organic Chemistry, Faculty of PharmacyMedical UniversityLublinPoland
  2. 2.Institute of Applied Radiation ChemistryTechnical University of LodzLodzPoland
  3. 3.Institute of Organic ChemistryTechnical University of LodzLodzPoland

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