Influence of the protein and DFT method on the broken-symmetry and spin states in nitroge
Cao, Lili LU and Ryde, Ulf LU
(2018)
In International Journal of Quantum Chemistry
118.
p.1-1
- Abstract
- The enzyme nitrogenase contains a complicated MoFe7CS9 cofactor with 35 possible broken- symmetry (BS) states. We have studied how the energies of these states depend on the geometry, the surrounding protein, the DFT functional and the basis set, studying the resting state, a one- electron reduced state and a protonated state. We find that the effect of the basis set is small, up to 11 kJ/mol. Likewise, the effect of the surrounding protein is restricted, up to 10 and 7 kJ/mol for the electrostatic and van der Waals energy terms. Single-point energies calculated on a single geom- etry give a good correlation (R2 5 0.92-0.98) to energies calculated after geometry optimization, but some BS states may be disfavored by up to 37 kJ/mol. A... (More)
- The enzyme nitrogenase contains a complicated MoFe7CS9 cofactor with 35 possible broken- symmetry (BS) states. We have studied how the energies of these states depend on the geometry, the surrounding protein, the DFT functional and the basis set, studying the resting state, a one- electron reduced state and a protonated state. We find that the effect of the basis set is small, up to 11 kJ/mol. Likewise, the effect of the surrounding protein is restricted, up to 10 and 7 kJ/mol for the electrostatic and van der Waals energy terms. Single-point energies calculated on a single geom- etry give a good correlation (R2 5 0.92-0.98) to energies calculated after geometry optimization, but some BS states may be disfavored by up to 37 kJ/mol. A change from the pure TPSS functional to the hybrid B3LYP functional may change the relative energies by up to 58 kJ/mol and the correlation between the two results is only 0.57-0.72. Both functionals agree that BS7 is the most stable BS state and that the ground spin state is the quartet for the resting state and the quintet for the reduced state. With the TPSS functional, the BS6 state is the second most stable state, always at least 21 kJ/mol less stable than the BS7 state. However, with the B3LYP functional, BS10 is the sec- ond most stable state and for the protonated state it comes close in energy. Based on these results, we suggest a procedure how to consider the 35 BS states in future investigations of the nitrogenase reaction mechanism. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/00591508-3786-45bb-a973-e156bcbe52b3
- author
- Cao, Lili
LU
and Ryde, Ulf
LU
- organization
- publishing date
- 2018-03-14
- type
- Contribution to journal
- publication status
- published
- subject
- in
- International Journal of Quantum Chemistry
- volume
- 118
- article number
- e25627
- pages
- 16 pages
- publisher
- John Wiley & Sons Inc.
- external identifiers
-
- scopus:85043719854
- ISSN
- 0020-7608
- DOI
- 10.1002/qua.25627
- project
- Computational Studies of Nitrogenase
- language
- English
- LU publication?
- yes
- id
- 00591508-3786-45bb-a973-e156bcbe52b3
- date added to LUP
- 2019-01-27 10:53:30
- date last changed
- 2023-04-09 03:11:43
@article{00591508-3786-45bb-a973-e156bcbe52b3,
abstract = {{The enzyme nitrogenase contains a complicated MoFe7CS9 cofactor with 35 possible broken- symmetry (BS) states. We have studied how the energies of these states depend on the geometry, the surrounding protein, the DFT functional and the basis set, studying the resting state, a one- electron reduced state and a protonated state. We find that the effect of the basis set is small, up to 11 kJ/mol. Likewise, the effect of the surrounding protein is restricted, up to 10 and 7 kJ/mol for the electrostatic and van der Waals energy terms. Single-point energies calculated on a single geom- etry give a good correlation (R2 5 0.92-0.98) to energies calculated after geometry optimization, but some BS states may be disfavored by up to 37 kJ/mol. A change from the pure TPSS functional to the hybrid B3LYP functional may change the relative energies by up to 58 kJ/mol and the correlation between the two results is only 0.57-0.72. Both functionals agree that BS7 is the most stable BS state and that the ground spin state is the quartet for the resting state and the quintet for the reduced state. With the TPSS functional, the BS6 state is the second most stable state, always at least 21 kJ/mol less stable than the BS7 state. However, with the B3LYP functional, BS10 is the sec- ond most stable state and for the protonated state it comes close in energy. Based on these results, we suggest a procedure how to consider the 35 BS states in future investigations of the nitrogenase reaction mechanism.}},
author = {{Cao, Lili and Ryde, Ulf}},
issn = {{0020-7608}},
language = {{eng}},
month = {{03}},
pages = {{1--1}},
publisher = {{John Wiley & Sons Inc.}},
series = {{International Journal of Quantum Chemistry}},
title = {{Influence of the protein and DFT method on the broken-symmetry and spin states in nitroge}},
url = {{https://lup.lub.lu.se/search/files/57285436/239_n2ase_bs_swap.pdf}},
doi = {{10.1002/qua.25627}},
volume = {{118}},
year = {{2018}},
}