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

Gökcen Savasci, Merlys Borges-Martínez, Raphael J F Berger, Christian Ochsenfeld, Raúl Mera-Adasme

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Article in Journal of molecular modeling, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

5 authors.

Gökcen SavasciMax Planck Institute (MPI) for Solid State Research, Heisenbergstr. 1, 70569, Stuttgart, Germany.

Merlys Borges-MartínezDepartamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile.

Raphael J F BergerDepartment of Chemistry and Physics of Materials, University of Salzburg, Jakob-Haringer-Str. 2a, A-5020, Salzburg, Austria. Raphael.Berger@sbg.ac.at.

Christian OchsenfeldDepartment of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, 81377, Munich, Germany.

Raúl Mera-AdasmeDepartamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile.

Funding

CONICYT-PAI 79150043CONICYT-PCHA 2015-21150093DFG BE 4632/2-1FONDECYT 11160032

6 · The paper itself

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?

Indexed as

Models, MolecularCations, DivalentComputational BiologyCoordination ComplexesQuantum TheoryThermodynamicsZincCations, DivalentCoordination ComplexesZincBenchmarkZn(II)

Identifiers

PMID31399760

DOI10.1007/s00894-019-4139-8

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