Evidence map›Paper›PMID 30299559›Full record

ArticleJournal of computational chemistry2019

Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin-polarized DFTB3 model.

Milena Vujović, Mioy Huynh, Sebastian Steiner, Pablo Garcia-Fernandez, Marcus Elstner, Qiang Cui, Maja Gruden

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Article in Journal of computational chemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

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6citing papers in PubMed
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1 · What the graph read from it

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3 · Its place in the literature

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6 citing papers in PubMed.

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  2. Probing the Suitability of Different CaMolecules (Basel, Switzerland) · 2021
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5 · Who and what money

Authors and funding

7 authors.

Milena VujovićCenter for Computational Chemistry and Bioinformatics, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16 11001, Belgrade, Serbia.
Mioy HuynhDepartments of Chemistry, Physics, Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts.
Sebastian SteinerInstitute of Physical Chemistry & Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Kaiserstr. 12, Karlsruhe, 76131, Germany.
Pablo Garcia-FernandezDepartamento de Ciencias de la Tierra y Fısica de la Materia Condensada, Universidad de Cantabria,Cantabria Campus Internacional, Avenida de los Castros s/n 39005, Santander, Spain.
Marcus ElstnerInstitute of Physical Chemistry & Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Kaiserstr. 12, Karlsruhe, 76131, Germany.
Qiang CuiDepartments of Chemistry, Physics, Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts.ORCID https://orcid.org/0000-0001-6214-5211
Maja GrudenCenter for Computational Chemistry and Bioinformatics, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16 11001, Belgrade, Serbia.ORCID https://orcid.org/0000-0002-0746-5754

Funding

Development and application of QM/MM methods for metalloenzymesR01GM106443 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI CUI, QIANG · 2013 to 2020
$2.3M
National Institute of General Medical Sciences R01-GM106443NIGMS NIH HHS R01 GM106443Ramón y Cajal Grant RyC-2013-12515Serbian-German collaboration project 451-03-01038/2015-09/7Serbian Ministry of Science 172035Spanish Ministry of Economy and Competitiveness FIS2015-64886-C5-2-P
6 · The paper itself

Abstract

In this work, we explore the applicability and limitations of the current third order density functional tight binding (DFTB3) formalism for treating transition metal ions using nickel as an example. To be consistent with recent parameterization of DFTB3 for copper, the parametrization for nickel is conducted in a spin-polarized formulation and with orbital-resolved Hubbard parameters and their charge derivatives. The performance of the current parameter set is evaluated based on structural and energetic properties of a set of nickel-containing compounds that involve biologically relevant ligands. Qualitatively similar to findings in previous studies of copper complexes, the DFTB3 results are more reliable for nickel complexes with neutral ligands than for charged ligands; nevertheless, encouraging agreement is noted in comparison to the reference method, B3LYP/aug-cc-pVTZ, especially for structural properties, including cases that exhibit Jahn-Teller distortions; the structures also compare favorably to available X-ray data in the Cambridge Crystallographic Database for a number of nickel-containing compounds. As to limitations, we find it is necessary to use different d shell Hubbard charge derivatives for Ni(I) and Ni(II), due to the distinct electronic configurations for the nickel ion in the respective complexes, and substantial errors are observed for ligand binding energies, especially for charged ligands, d orbital splitting energies and splitting between singlet and triplet spin states for Ni(II) compounds. These observations highlight that future improvement in intra-d correlation and ligand polarization is required to enable the application of the DFTB3 model to complex transition metal ions. © 2018 Wiley Periodicals, Inc.

Indexed as

DFTDFTB3Hubbard parametersJahn-Teller distortionnickelspin states

Identifiers

PMID30299559
PMCPMC6294695

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