What Is the Structure of the E4 Intermediate in Nitrogenase?
Cao, Lili LU and Ryde, Ulf LU
(2020)
In Journal of Chemical Theory and Computation
16.
p.1936-1952
- Abstract
- Nitrogenase is the only enzyme that can cleave the strong triple bond in
N2. The active site contains a complicated MoFe7S9C cluster. It is believed that it
needs to accept four protons and electrons, forming the E4 state, before it can bind N2.
However, there is no consensus on the atomic structure of the E4 state. Experimental
studies indicate that it should contain two hydride ions bridging two pairs of Fe ions,
and it has been suggested that both hydride ions as well as the two protons bind on the
same face of the cluster. On the other hand, density functional theory (DFT) studies
have indicated that it is energetically more favorable with either three hydride ions or with a triply protonated carbide ion,... (More) - Nitrogenase is the only enzyme that can cleave the strong triple bond in
N2. The active site contains a complicated MoFe7S9C cluster. It is believed that it
needs to accept four protons and electrons, forming the E4 state, before it can bind N2.
However, there is no consensus on the atomic structure of the E4 state. Experimental
studies indicate that it should contain two hydride ions bridging two pairs of Fe ions,
and it has been suggested that both hydride ions as well as the two protons bind on the
same face of the cluster. On the other hand, density functional theory (DFT) studies
have indicated that it is energetically more favorable with either three hydride ions or with a triply protonated carbide ion, depending on the DFT functional. We have performed a systematic combined quantum mechanical and molecular mechanical (QM/MM) study of possible E4 states with two bridging hydride ions. Our calculations suggest that the most favorable structure has hydride ions bridging the Fe2/6 and Fe3/7 ion pairs. In fact, such structures are 14 kJ/mol more stable than structures with three hydride ions, showing that pure DFT functionals give energetically most favorable structures in agreement with experiments. An important reason for this finding is that we have identified a new type of broken-symmetry state that involves only two Fe ions with minority spin, in contrast to the previously studied states with three Fe ions with minority spin. The energetically best structures have the two hydride ions on different faces of the FeMo cluster, whereas better agreement with ENDOR data is obtained if they are on the same face; such structures are only 6−22 kJ/mol less stable. (Less)
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- author
- Cao, Lili
LU
and Ryde, Ulf
LU
- organization
- publishing date
- 2020-01-31
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Journal of Chemical Theory and Computation
- volume
- 16
- pages
- 1936 - 1952
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- pmid:32003999
- scopus:85080069618
- ISSN
- 1549-9618
- DOI
- 10.1021/acs.jctc.9b01254
- language
- English
- LU publication?
- yes
- id
- d0110eea-3c48-43b3-abd2-bbb72e89465f
- date added to LUP
- 2020-09-26 10:40:13
- date last changed
- 2023-04-10 20:36:12
@article{d0110eea-3c48-43b3-abd2-bbb72e89465f,
abstract = {{Nitrogenase is the only enzyme that can cleave the strong triple bond in<br/>N2. The active site contains a complicated MoFe7S9C cluster. It is believed that it<br/>needs to accept four protons and electrons, forming the E4 state, before it can bind N2.<br/>However, there is no consensus on the atomic structure of the E4 state. Experimental<br/>studies indicate that it should contain two hydride ions bridging two pairs of Fe ions,<br/>and it has been suggested that both hydride ions as well as the two protons bind on the<br/>same face of the cluster. On the other hand, density functional theory (DFT) studies<br/>have indicated that it is energetically more favorable with either three hydride ions or with a triply protonated carbide ion, depending on the DFT functional. We have performed a systematic combined quantum mechanical and molecular mechanical (QM/MM) study of possible E4 states with two bridging hydride ions. Our calculations suggest that the most favorable structure has hydride ions bridging the Fe2/6 and Fe3/7 ion pairs. In fact, such structures are 14 kJ/mol more stable than structures with three hydride ions, showing that pure DFT functionals give energetically most favorable structures in agreement with experiments. An important reason for this finding is that we have identified a new type of broken-symmetry state that involves only two Fe ions with minority spin, in contrast to the previously studied states with three Fe ions with minority spin. The energetically best structures have the two hydride ions on different faces of the FeMo cluster, whereas better agreement with ENDOR data is obtained if they are on the same face; such structures are only 6−22 kJ/mol less stable.}},
author = {{Cao, Lili and Ryde, Ulf}},
issn = {{1549-9618}},
language = {{eng}},
month = {{01}},
pages = {{1936--1952}},
publisher = {{The American Chemical Society (ACS)}},
series = {{Journal of Chemical Theory and Computation}},
title = {{What Is the Structure of the E4 Intermediate in Nitrogenase?}},
url = {{https://lup.lub.lu.se/search/files/84188266/n2ase_e4_266.pdf}},
doi = {{10.1021/acs.jctc.9b01254}},
volume = {{16}},
year = {{2020}},
}