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Computational Studies of Molybdenum and Tungsten Enzymes

Ryde, Ulf LU ; Dong, Geng LU ; Li, Jilai LU ; Feldt, Milica and Mata, Ricardo A (2016) In Molybdenum and Tungsten Enzymes: Spectroscopic and Theoretical Investigations 2017-January(7). p.275-321
Abstract

We review computational studies of three important mono-nuclear molybdenum oxo-transfer enzymes, dimethylsulfoxide reductase, sulfite oxidase and xanthine oxidase. We show that calculated energies for these reactions are very sensitive to details in the calculations, in particular to the density-functional method employed and the size of the basis set, but the treatment of dispersion and solvation effects is also crucial, as well as the definition of the reference state. We point out problems with standard quantum-mechanical (QM) cluster calculations, regarding the selection of the QM system and atomic coordinate constraints. Combined QM and molecular mechanics (QM/MM) methods also have important problems, which can be solved by... (More)

We review computational studies of three important mono-nuclear molybdenum oxo-transfer enzymes, dimethylsulfoxide reductase, sulfite oxidase and xanthine oxidase. We show that calculated energies for these reactions are very sensitive to details in the calculations, in particular to the density-functional method employed and the size of the basis set, but the treatment of dispersion and solvation effects is also crucial, as well as the definition of the reference state. We point out problems with standard quantum-mechanical (QM) cluster calculations, regarding the selection of the QM system and atomic coordinate constraints. Combined QM and molecular mechanics (QM/MM) methods also have important problems, which can be solved by calculations with very large QM systems (400-1000 atoms). Many studies have been published that reproduce experimentally measured activation energies, but for the wrong reason. We also compare the properties of molybdenum and tungsten and discuss why the active sites of the three families of molybdenum oxo-transfer enzymes are so different.

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Please use this url to cite or link to this publication:
author
organization
publishing date
type
Chapter in Book/Report/Conference proceeding
publication status
published
subject
in
Molybdenum and Tungsten Enzymes: Spectroscopic and Theoretical Investigations
editor
Hille, Russ; Schulzke, Carola; Kirk, Martin L.; ; and
volume
2017-January
issue
7
pages
47 pages
publisher
Royal Society of Chemistry
external identifiers
  • scopus:84994877351
ISSN
2045547X
ISBN
978-1-78262-884-2
978-1-78262-878-1
DOI
10.1039/9781782628842-00275
language
English
LU publication?
yes
id
2e359270-ca5e-4804-9ff1-8f45f594d4fe
date added to LUP
2017-02-04 09:46:51
date last changed
2017-11-14 09:51:53
@inbook{2e359270-ca5e-4804-9ff1-8f45f594d4fe,
  abstract     = {<p>We review computational studies of three important mono-nuclear molybdenum oxo-transfer enzymes, dimethylsulfoxide reductase, sulfite oxidase and xanthine oxidase. We show that calculated energies for these reactions are very sensitive to details in the calculations, in particular to the density-functional method employed and the size of the basis set, but the treatment of dispersion and solvation effects is also crucial, as well as the definition of the reference state. We point out problems with standard quantum-mechanical (QM) cluster calculations, regarding the selection of the QM system and atomic coordinate constraints. Combined QM and molecular mechanics (QM/MM) methods also have important problems, which can be solved by calculations with very large QM systems (400-1000 atoms). Many studies have been published that reproduce experimentally measured activation energies, but for the wrong reason. We also compare the properties of molybdenum and tungsten and discuss why the active sites of the three families of molybdenum oxo-transfer enzymes are so different.</p>},
  author       = {Ryde, Ulf and Dong, Geng and Li, Jilai and Feldt, Milica and Mata, Ricardo A},
  editor       = {Hille, Russ and Schulzke, Carola and Kirk, Martin L.},
  isbn         = {978-1-78262-884-2},
  issn         = {2045547X},
  language     = {eng},
  month        = {10},
  number       = {7},
  pages        = {275--321},
  publisher    = {Royal Society of Chemistry},
  series       = {Molybdenum and Tungsten Enzymes: Spectroscopic and Theoretical Investigations},
  title        = {Computational Studies of Molybdenum and Tungsten Enzymes},
  url          = {http://dx.doi.org/10.1039/9781782628842-00275},
  volume       = {2017-January},
  year         = {2016},
}