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Journal of Molecular Modeling

, 25:258 | Cite as

A comparison of computational methodologies for the structural modelling of biologically relevant zinc complexes

  • Gökcen Savasci
  • Merlys Borges-Martínez
  • Raphael J. F. BergerEmail author
  • Christian Ochsenfeld
  • Raúl Mera-Adasme
Original Paper
  • 82 Downloads

Abstract

The impact of a variety of modern computational methods on the structure of biologically relevant zinc complexes is studied. Different density functionals and a Hartree-Fock-based method, scalar-relativistic effects, and basis set integration grid choices, among others, are assessed for set of high-resolution crystallographic structures. While a previous study recommends incorporating relativistic effects into density functional theory calculations in order to improve the accuracy of obtained geometries for small Zn(II) coordination compounds, we show that, for the set in study, relativistic effects do not affect the geometries to a significant extent. The PBEh-3c composite method emerges as good alternative for the treatment of Zn(II) complexes, while the HF-3c method can be employed when computational efficiency is important.

Graphical Abstract

Which methods are best suited for the computation of Zn(II) bioligand complexes?

Keywords

Zn(II) Benchmark 

Notes

Acknowledgments

The authors thank Dr. Jörg Kussmann (LMU Munich) for fruitful discussions and helpful comments on the manuscript. R.M.-A. thanks Prof. Dr. Moisés Dominguez for useful discussion.

Funding information

This study was funded by the CONICYT–Chile FONDECYT no. 11160032 and PAI no. 79150043, SPP 1807 “Control of London dispersion interactions in molecular chemistry” (BE 4632/2-1) of the DFG, and CONICYT-PCHA/Doctorado Nacional/2015-21150093 (for a PhD scholarship).

Supplementary material

894_2019_4139_MOESM1_ESM.pdf (3.9 mb)
(PDF 3.87 MB)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Gökcen Savasci
    • 1
    • 2
    • 3
  • Merlys Borges-Martínez
    • 3
  • Raphael J. F. Berger
    • 4
    Email author
  • Christian Ochsenfeld
    • 2
    • 5
  • Raúl Mera-Adasme
    • 3
  1. 1.Max Planck Institute (MPI) for Solid State ResearchStuttgartGermany
  2. 2.Department of ChemistryUniversity of Munich (LMU)MunichGermany
  3. 3.Departamento de Ciencias del Ambiente, Facultad de Química y BiologíaUniversidad de Santiago de Chile (USACH)SantiagoChile
  4. 4.Department of Chemistry and Physics of MaterialsUniversity of SalzburgSalzburgAustria
  5. 5.Department of Chemistry, Center for Integrated Protein Science (CIPSM)University of Munich (LMU)MunichGermany

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