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A theoretical study of the copper–cysteine bond in blue copper proteins

Ryde, Ulf LU ; Olsson, Mats H. M.; Roos, Björn LU and Borin-Carlos, Antonio (2001) In Theoretical Chemistry Accounts 105(6). p.452-462
Abstract
The accuracy of theoretical calculations on models of the blue copper proteins is investigated using density functional theory (DFT) Becke's three-parameter hybrid method with the Lee–Yang–Parr correlation functional (B3LYP) and medium-sized basis sets. Increasing the basis set to triple-zeta quality with f-type functions on all heavy atoms and enlarging the model [up to Cu(imidazole-CH3)2(SC2H5) (CH3SC2H5)0/+] has only a limited influence on geometries and relative energies. Comparative calculations with more accurate wave-function–based methods (second-order Møller–Plesset perturbation theory, complete-active-space second-order perturbation theory, coupled-cluster method, including single and double replacement amplitudes and in addition... (More)
The accuracy of theoretical calculations on models of the blue copper proteins is investigated using density functional theory (DFT) Becke's three-parameter hybrid method with the Lee–Yang–Parr correlation functional (B3LYP) and medium-sized basis sets. Increasing the basis set to triple-zeta quality with f-type functions on all heavy atoms and enlarging the model [up to Cu(imidazole-CH3)2(SC2H5) (CH3SC2H5)0/+] has only a limited influence on geometries and relative energies. Comparative calculations with more accurate wave-function–based methods (second-order Møller–Plesset perturbation theory, complete-active-space second-order perturbation theory, coupled-cluster method, including single and double replacement amplitudes and in addition triple replacement perturbatively) and a variety of basis sets on smaller models indicate that the DFT/B3LYP approach gives reliable results with only a small basis set dependence, whereas the former methods strongly depend on the size of the basis sets. The effect of performing the geometry optimizations in a continuum solvent is quite small, except for the flexible Cu-SMet bond. The results of this study confirm the earlier results that neither the oxidized nor the reduced copper site in the blue proteins is strained to any significant degree (in energy terms) by the protein surrounding. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Theoretical Chemistry Accounts
volume
105
issue
6
pages
452 - 462
publisher
Springer
external identifiers
  • scopus:0035633658
ISSN
1432-881X
DOI
10.1007/s002140000242
language
English
LU publication?
yes
id
e833e587-b288-4e16-943a-517b0628c21c (old id 2275887)
date added to LUP
2012-01-04 11:40:18
date last changed
2018-06-10 04:40:37
@article{e833e587-b288-4e16-943a-517b0628c21c,
  abstract     = {The accuracy of theoretical calculations on models of the blue copper proteins is investigated using density functional theory (DFT) Becke's three-parameter hybrid method with the Lee–Yang–Parr correlation functional (B3LYP) and medium-sized basis sets. Increasing the basis set to triple-zeta quality with f-type functions on all heavy atoms and enlarging the model [up to Cu(imidazole-CH3)2(SC2H5) (CH3SC2H5)0/+] has only a limited influence on geometries and relative energies. Comparative calculations with more accurate wave-function–based methods (second-order Møller–Plesset perturbation theory, complete-active-space second-order perturbation theory, coupled-cluster method, including single and double replacement amplitudes and in addition triple replacement perturbatively) and a variety of basis sets on smaller models indicate that the DFT/B3LYP approach gives reliable results with only a small basis set dependence, whereas the former methods strongly depend on the size of the basis sets. The effect of performing the geometry optimizations in a continuum solvent is quite small, except for the flexible Cu-SMet bond. The results of this study confirm the earlier results that neither the oxidized nor the reduced copper site in the blue proteins is strained to any significant degree (in energy terms) by the protein surrounding.},
  author       = {Ryde, Ulf and Olsson, Mats H. M. and Roos, Björn and Borin-Carlos, Antonio},
  issn         = {1432-881X},
  language     = {eng},
  number       = {6},
  pages        = {452--462},
  publisher    = {Springer},
  series       = {Theoretical Chemistry Accounts},
  title        = {A theoretical study of the copper–cysteine bond in blue copper proteins},
  url          = {http://dx.doi.org/10.1007/s002140000242},
  volume       = {105},
  year         = {2001},
}