Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins
Jafari, Sonia ; Tavares Santos, Yakini A. ; Bergmann, Justin LU ; Irani, Mehdi LU and Ryde, Ulf LU
(2022)
In Inorganic Chemistry
61(16).
p.5991-6007
- Abstract
Redox potentials have been calculated for 12 different iron-sulfur sites of 6 different types with 1-4 iron ions. Structures were optimized with combined quantum mechanical and molecular mechanical (QM/MM) methods, and the redox potentials were calculated using the QM/MM energies, single-point QM methods in a continuum solvent or by QM/MM thermodynamic cycle perturbations. We show that the best results are obtained with a large QM system (∼300 atoms, but a smaller QM system, ∼150 atoms, can be used for the QM/MM geometry optimization) and a large value of the dielectric constant (80). For absolute redox potentials, the B3LYP density functional method gives better results than TPSS, and the results are improved with a larger basis set.... (More)
Redox potentials have been calculated for 12 different iron-sulfur sites of 6 different types with 1-4 iron ions. Structures were optimized with combined quantum mechanical and molecular mechanical (QM/MM) methods, and the redox potentials were calculated using the QM/MM energies, single-point QM methods in a continuum solvent or by QM/MM thermodynamic cycle perturbations. We show that the best results are obtained with a large QM system (∼300 atoms, but a smaller QM system, ∼150 atoms, can be used for the QM/MM geometry optimization) and a large value of the dielectric constant (80). For absolute redox potentials, the B3LYP density functional method gives better results than TPSS, and the results are improved with a larger basis set. However, for relative redox potentials, the opposite is true. The results are insensitive to the force field (charges of the surroundings) used for the QM/MM calculations or whether the protein and solvent outside the QM system are relaxed or kept fixed at the crystal structure. With the best approach for relative potentials, mean absolute and maximum deviations of 0.17 and 0.44 V, respectively, are obtained after removing a systematic error of -0.55 V. Such an approach can be used to identify the correct oxidation states involved in a certain redox reaction.
(Less)
- author
- Jafari, Sonia
; Tavares Santos, Yakini A.
; Bergmann, Justin
LU
; Irani, Mehdi
LU
and Ryde, Ulf
LU
- organization
- publishing date
- 2022
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Inorganic Chemistry
- volume
- 61
- issue
- 16
- pages
- 17 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- scopus:85128906300
- pmid:35403427
- ISSN
- 0020-1669
- DOI
- 10.1021/acs.inorgchem.1c03422
- language
- English
- LU publication?
- yes
- id
- d31b0bbc-cfa4-45cc-9491-db4cdc3b0460
- date added to LUP
- 2022-06-30 15:24:21
- date last changed
- 2024-06-13 14:40:58
@article{d31b0bbc-cfa4-45cc-9491-db4cdc3b0460,
abstract = {{<p>Redox potentials have been calculated for 12 different iron-sulfur sites of 6 different types with 1-4 iron ions. Structures were optimized with combined quantum mechanical and molecular mechanical (QM/MM) methods, and the redox potentials were calculated using the QM/MM energies, single-point QM methods in a continuum solvent or by QM/MM thermodynamic cycle perturbations. We show that the best results are obtained with a large QM system (∼300 atoms, but a smaller QM system, ∼150 atoms, can be used for the QM/MM geometry optimization) and a large value of the dielectric constant (80). For absolute redox potentials, the B3LYP density functional method gives better results than TPSS, and the results are improved with a larger basis set. However, for relative redox potentials, the opposite is true. The results are insensitive to the force field (charges of the surroundings) used for the QM/MM calculations or whether the protein and solvent outside the QM system are relaxed or kept fixed at the crystal structure. With the best approach for relative potentials, mean absolute and maximum deviations of 0.17 and 0.44 V, respectively, are obtained after removing a systematic error of -0.55 V. Such an approach can be used to identify the correct oxidation states involved in a certain redox reaction.</p>}},
author = {{Jafari, Sonia and Tavares Santos, Yakini A. and Bergmann, Justin and Irani, Mehdi and Ryde, Ulf}},
issn = {{0020-1669}},
language = {{eng}},
number = {{16}},
pages = {{5991--6007}},
publisher = {{The American Chemical Society (ACS)}},
series = {{Inorganic Chemistry}},
title = {{Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins}},
url = {{http://dx.doi.org/10.1021/acs.inorgchem.1c03422}},
doi = {{10.1021/acs.inorgchem.1c03422}},
volume = {{61}},
year = {{2022}},
}