N2H2 binding to the nitrogenase FeMo cluster studied by QM/MM methods
Cao, Lili LU and Ryde, Ulf LU
(2020)
In Journal of Biological Inorganic Chemistry
25(3).
p.521-540
- Abstract
We have made a systematic combined quantum mechanical and molecular mechanical (QM/MM) investigation of possible structures of the N2 bound state of nitrogenase. We assume that N2 is immediately protonated to a N2H2 state, thereby avoiding the problem of determining the position of the protons in the cluster. We have systematically studied both end-on and side-on structures, as well as both HNNH and NNH2 states. Our results indicate that the binding of N2H2 is determined more by interactions and steric clashes with the surrounding protein than by the intrinsic preferences of the ligand and the cluster. The best binding mode with both the TPSS and B3LYP... (More)
We have made a systematic combined quantum mechanical and molecular mechanical (QM/MM) investigation of possible structures of the N2 bound state of nitrogenase. We assume that N2 is immediately protonated to a N2H2 state, thereby avoiding the problem of determining the position of the protons in the cluster. We have systematically studied both end-on and side-on structures, as well as both HNNH and NNH2 states. Our results indicate that the binding of N2H2 is determined more by interactions and steric clashes with the surrounding protein than by the intrinsic preferences of the ligand and the cluster. The best binding mode with both the TPSS and B3LYP density-functional theory methods has trans-HNNH terminally bound to Fe2. It is stabilised by stacking of the substrate with His-195 and Ser-278. However, several other structures come rather close in energy (within 3–35 kJ/mol) at least in some calculations: The corresponding cis-HNNH structure terminally bound to Fe2 is second best with B3LYP. A structure with HNNH2 terminally bound to Fe6 is second most stable with TPSS (where the third proton is transferred to the substrate from the homocitrate ligand). Structures with trans-HNNH, bound to Fe4 or Fe6, or cis-HNNH bound to Fe6 are also rather stable. Finally, with the TPSS functional, a structure with cis-HNNH side-on binding to the Fe3–Fe4–Fe5–Fe7 face of the cluster is also rather low in energy, but all side-on structures are strongly disfavoured by the B3LYP method.
(Less)
- author
- Cao, Lili
LU
and Ryde, Ulf
LU
- organization
- publishing date
- 2020-04-07
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Broken-symmetry DFT, E state, N binding, Nitrogenase, QM/MM
- in
- Journal of Biological Inorganic Chemistry
- volume
- 25
- issue
- 3
- pages
- 20 pages
- publisher
- Springer
- external identifiers
-
- scopus:85083360780
- pmid:32266560
- ISSN
- 0949-8257
- DOI
- 10.1007/s00775-020-01780-5
- project
- Computational Studies of Nitrogenase
- language
- English
- LU publication?
- yes
- id
- d1de0261-76ed-4091-8415-c4db72907247
- date added to LUP
- 2020-05-06 16:48:38
- date last changed
- 2024-05-15 10:20:16
@article{d1de0261-76ed-4091-8415-c4db72907247,
abstract = {{<p>We have made a systematic combined quantum mechanical and molecular mechanical (QM/MM) investigation of possible structures of the N<sub>2</sub> bound state of nitrogenase. We assume that N<sub>2</sub> is immediately protonated to a N<sub>2</sub>H<sub>2</sub> state, thereby avoiding the problem of determining the position of the protons in the cluster. We have systematically studied both end-on and side-on structures, as well as both HNNH and NNH<sub>2</sub> states. Our results indicate that the binding of N<sub>2</sub>H<sub>2</sub> is determined more by interactions and steric clashes with the surrounding protein than by the intrinsic preferences of the ligand and the cluster. The best binding mode with both the TPSS and B3LYP density-functional theory methods has trans-HNNH terminally bound to Fe2. It is stabilised by stacking of the substrate with His-195 and Ser-278. However, several other structures come rather close in energy (within 3–35 kJ/mol) at least in some calculations: The corresponding cis-HNNH structure terminally bound to Fe2 is second best with B3LYP. A structure with HNNH<sub>2</sub> terminally bound to Fe6 is second most stable with TPSS (where the third proton is transferred to the substrate from the homocitrate ligand). Structures with trans-HNNH, bound to Fe4 or Fe6, or cis-HNNH bound to Fe6 are also rather stable. Finally, with the TPSS functional, a structure with cis-HNNH side-on binding to the Fe3–Fe4–Fe5–Fe7 face of the cluster is also rather low in energy, but all side-on structures are strongly disfavoured by the B3LYP method.</p>}},
author = {{Cao, Lili and Ryde, Ulf}},
issn = {{0949-8257}},
keywords = {{Broken-symmetry DFT; E state; N binding; Nitrogenase; QM/MM}},
language = {{eng}},
month = {{04}},
number = {{3}},
pages = {{521--540}},
publisher = {{Springer}},
series = {{Journal of Biological Inorganic Chemistry}},
title = {{N<sub>2</sub>H<sub>2</sub> binding to the nitrogenase FeMo cluster studied by QM/MM methods}},
url = {{https://lup.lub.lu.se/search/files/84187549/n2ase_n2bind_267.pdf}},
doi = {{10.1007/s00775-020-01780-5}},
volume = {{25}},
year = {{2020}},
}