Literature DB >> 28397891

H2 binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods.

Geng Dong1, Quan Manh Phung, Simon D Hallaert, Kristine Pierloot, Ulf Ryde.   

Abstract

[NiFe] hydrogenases catalyse the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H2 as a clean fuel. In this paper, we have studied how H2 binds to the active site of this enzyme. Combined quantum mechanical and molecular mechanics (QM/MM) optimisation was performed to obtain the geometries, using both the TPSS and B3LYP density-functional theory (DFT) methods and considering both the singlet and triplet states of the Ni(ii) ion. To get more accurate energies and obtain a detailed account of the surroundings, we performed calculations with 819 atoms in the QM region. Moreover, coupled-cluster calculations with singles, doubles, and perturbatively treated triples (CCSD(T)) and cumulant-approximated second-order perturbation theory based on the density-matrix renormalisation group (DMRG-CASPT2) were carried out using three models to decide which DFT methods give the most accurate structures and energies. Our calculations show that H2 binding to Ni in the singlet state is the most favourable by at least 47 kJ mol-1. In addition, the TPSS functional gives more accurate energies than B3LYP for this system.

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Year:  2017        PMID: 28397891     DOI: 10.1039/c7cp01331k

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  6 in total

1.  Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities.

Authors:  Konstantinos D Vogiatzis; Mikhail V Polynski; Justin K Kirkland; Jacob Townsend; Ali Hashemi; Chong Liu; Evgeny A Pidko
Journal:  Chem Rev       Date:  2018-10-30       Impact factor: 60.622

Review 2.  Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase.

Authors:  Sven T Stripp; Benjamin R Duffus; Vincent Fourmond; Christophe Léger; Silke Leimkühler; Shun Hirota; Yilin Hu; Andrew Jasniewski; Hideaki Ogata; Markus W Ribbe
Journal:  Chem Rev       Date:  2022-07-18       Impact factor: 72.087

Review 3.  X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases.

Authors:  Yulia Ilina; Christian Lorent; Sagie Katz; Jae-Hun Jeoung; Seigo Shima; Marius Horch; Ingo Zebger; Holger Dobbek
Journal:  Angew Chem Int Ed Engl       Date:  2019-10-25       Impact factor: 15.336

4.  Biomimetic heterobimetallic architecture of Ni(ii) and Fe(ii) for CO2 hydrogenation in aqueous media. A DFT study.

Authors:  Bilal Ahmad Shiekh
Journal:  RSC Adv       Date:  2019-10-16       Impact factor: 4.036

5.  QM/MM Investigation of the Role of a Second Coordination Shell Arginine in [NiFe]-Hydrogenases.

Authors:  Andrés M Escorcia; Matthias Stein
Journal:  Front Chem       Date:  2018-05-15       Impact factor: 5.221

Review 6.  The Challenging in silico Description of Carbon Monoxide Oxidation as Catalyzed by Molybdenum-Copper CO Dehydrogenase.

Authors:  Anna Rovaletti; Maurizio Bruschi; Giorgio Moro; Ugo Cosentino; Claudio Greco
Journal:  Front Chem       Date:  2019-01-09       Impact factor: 5.221

  6 in total

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