Literature DB >> 24256691

Computational modelling of oxygenation processes in enzymes and biomimetic model complexes.

Sam P de Visser1, Matthew G Quesne, Bodo Martin, Peter Comba, Ulf Ryde.   

Abstract

With computational resources becoming more efficient and more powerful and at the same time cheaper, computational methods have become more and more popular for studies on biochemical and biomimetic systems. Although large efforts from the scientific community have gone into exploring the possibilities of computational methods for studies on large biochemical systems, such studies are not without pitfalls and often cannot be routinely done but require expert execution. In this review we summarize and highlight advances in computational methodology and its application to enzymatic and biomimetic model complexes. In particular, we emphasize on topical and state-of-the-art methodologies that are able to either reproduce experimental findings, e.g., spectroscopic parameters and rate constants, accurately or make predictions of short-lived intermediates and fast reaction processes in nature. Moreover, we give examples of processes where certain computational methods dramatically fail.

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Year:  2013        PMID: 24256691     DOI: 10.1039/c3cc47148a

Source DB:  PubMed          Journal:  Chem Commun (Camb)        ISSN: 1359-7345            Impact factor:   6.222


  19 in total

1.  Calculating the geometry and Raman spectrum of physiological bis(L-histidinato)copper(II): an assessment of DFT functionals for aqueous and isolated systems.

Authors:  Jasmina Sabolović; Michael Ramek; Marijana Marković
Journal:  J Mol Model       Date:  2017-09-26       Impact factor: 1.810

2.  Properties and reactivity of μ-nitrido-bridged dimetal porphyrinoid complexes: how does ruthenium compare to iron?

Authors:  M Qadri E Mubarak; Alexander B Sorokin; Sam P de Visser
Journal:  J Biol Inorg Chem       Date:  2019-09-27       Impact factor: 3.358

Review 3.  Spectroscopic analyses of 2-oxoglutarate-dependent oxygenases: TauD as a case study.

Authors:  Denis A Proshlyakov; John McCracken; Robert P Hausinger
Journal:  J Biol Inorg Chem       Date:  2016-11-03       Impact factor: 3.358

4.  The secondary coordination sphere and axial ligand effects on oxygen reduction reaction by iron porphyrins: a DFT computational study.

Authors:  Takehiro Ohta; Perumandla Nagaraju; Jin-Gang Liu; Takashi Ogura; Yoshinori Naruta
Journal:  J Biol Inorg Chem       Date:  2016-08-09       Impact factor: 3.358

5.  Arene activation by a nonheme iron(III)-hydroperoxo complex: pathways leading to phenol and ketone products.

Authors:  Abayomi S Faponle; Frédéric Banse; Sam P de Visser
Journal:  J Biol Inorg Chem       Date:  2016-04-20       Impact factor: 3.358

6.  Singlet versus Triplet Reactivity in an Mn(V)-Oxo Species: Testing Theoretical Predictions Against Experimental Evidence.

Authors:  Tzuhsiung Yang; Matthew G Quesne; Heather M Neu; Fabián G Cantú Reinhard; David P Goldberg; Sam P de Visser
Journal:  J Am Chem Soc       Date:  2016-09-14       Impact factor: 15.419

7.  Alkyl Chain Growth on a Transition Metal Center: How Does Iron Compare to Ruthenium and Osmium?

Authors:  Mala A Sainna; Sam P de Visser
Journal:  Int J Mol Sci       Date:  2015-09-28       Impact factor: 5.923

8.  Cysteine protease inhibition by nitrile-based inhibitors: a computational study.

Authors:  Matthew G Quesne; Richard A Ward; Sam P de Visser
Journal:  Front Chem       Date:  2013-12-27       Impact factor: 5.221

9.  Dramatic influence of an anionic donor on the oxygen-atom transfer reactivity of a Mn(V) -oxo complex.

Authors:  Heather M Neu; Matthew G Quesne; Tzuhsiung Yang; Katharine A Prokop-Prigge; Kyle M Lancaster; James Donohoe; Serena DeBeer; Sam P de Visser; David P Goldberg
Journal:  Chemistry       Date:  2014-09-26       Impact factor: 5.236

10.  Nonheme iron-thiolate complexes as structural models of sulfoxide synthase active sites.

Authors:  Danushka M Ekanayake; Anne A Fischer; Maya E Elwood; Alexandra M Guzek; Sergey V Lindeman; Codrina V Popescu; Adam T Fiedler
Journal:  Dalton Trans       Date:  2020-12-22       Impact factor: 4.390

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