PM3-compatible zinc parameters optimized for metalloenzyme active sites

Edward N. Brothers, Dimas Suarez, David W. Deerfield, Kenneth M. Merz

Research output: Contribution to journalArticle

31 Citations (Scopus)


Recent studies have shown that semiempirical methods (e.g., PM3 and AM1) for zinc-containing compounds are unreliable for modeling structures containing zinc ions with ligand environments similar to those observed in zinc metalloenzymes. To correct these deficiencies a reparameterization of zinc at the PM3 level was undertaken. In this effort we included frequency corrected B3LYP/6-311G* zinc metalloenzyme ligand environments along with previously utilized experimental data. Average errors for the heats of formation have been reduced from 46.9 kcal/mol (PM3) to 14.2 kcal/mol for this new parameter set, termed ZnB for "Zinc, Biological." In addition, the new parameter sets predict geometries for the Bacillus fragilis active site model and other zinc metalloenzyme mimics that are qualitatively in agreement with high-level ab initio results, something existing parameter sets failed to do.

Original languageEnglish
Pages (from-to)1677-1692
Number of pages16
JournalJournal of Computational Chemistry
Issue number14
Publication statusPublished - 15 Nov 2004


  • Metalloenzyme active sites
  • Zinc parameters

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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