biostudies-literatureJiang HChina Scholarship CouncilVetenskapsr?detLunds Universitet19433-19445https://www.ebi.ac.uk/biostudies/studies/S-EPMC10698722biostudies-literatureUnknown62(48)Nitrogenase is the only enzyme that can cleave the strong triple bond in N₂, making nitrogen available for biological life. There are three isozymes of nitrogenase, differing in the composition of the active site, viz., Mo, V, and Fe-nitrogenase. Recently, the first crystal structure of Fe-nitrogenase was presented. We have performed the first combined quantum mechanical and molecular mechanical (QM/MM) study of Fe-nitrogenase. We show with QM/MM and quantum-refinement calculations that the homocitrate ligand is most likely protonated on the alcohol oxygen in the resting E₀ state. The most stable broken-symmetry (BS) states are the same as for Mo-nitrogenase, i.e., the three Noodleman BS7-type states (with a surplus of β spin on the eighth Fe ion), which maximize the number of nearby antiferromagnetically coupled Fe-Fe pairs. For the E₁ state, we find that protonation of the S2B μ₂ belt sulfide ion is most favorable, 14-117 kJ/mol more stable than structures with a Fe-bound hydride ion (the best has a hydride ion on the Fe2 ion) calculated with four different density-functional theory methods. This is similar to what was found for Mo-nitrogenase, but it does not explain the recent EPR observation that the E₁ state of Fe-nitrogenase should contain a photolyzable hydride ion. For the E₁ state, many BS states are close in energy, and the preferred BS state differs depending on the position of the extra proton and which density functional is used.Inorganic chemistryProtonation of Homocitrate and the E₁ State of Fe-Nitrogenase Studied by QM/MM Calculations.PMC106987222022-049782018-059732018-05003Lundgren KJMJiang HRyde UfalseProtonation of Homocitrate and the E₁ State of Fe-Nitrogenase Studied by QM/MM Calculations.Nitrogenase is the only enzyme that can cleave the strong triple bond in N₂, making nitrogen available for biological life. There are three isozymes of nitrogenase, differing in the composition of the active site, viz., Mo, V, and Fe-nitrogenase. Recently, the first crystal structure of Fe-nitrogenase was presented. We have performed the first combined quantum mechanical and molecular mechanical (QM/MM) study of Fe-nitrogenase. We show with QM/MM and quantum-refinement calculations that the homocitrate ligand is most likely protonated on the alcohol oxygen in the resting E₀ state. The most stable broken-symmetry (BS) states are the same as for Mo-nitrogenase, i.e., the three Noodleman BS7-type states (with a surplus of β spin on the eighth Fe ion), which maximize the number of nearby antiferromagnetically coupled Fe-Fe pairs. For the E₁ state, we find that protonation of the S2B μ₂ belt sulfide ion is most favorable, 14-117 kJ/mol more stable than structures with a Fe-bound hydride ion (the best has a hydride ion on the Fe2 ion) calculated with four different density-functional theory methods. This is similar to what was found for Mo-nitrogenase, but it does not explain the recent EPR observation that the E₁ state of Fe-nitrogenase should contain a photolyzable hydride ion. For the E₁ state, many BS states are close in energy, and the preferred BS state differs depending on the position of the extra proton and which density functional is used.2023-01-01T00:00:00Z2023 Dec2025-04-26T11:46:50.079Z2025-04-06T13:48:14.51ZS-EPMC106987223798762410.1021/acs.inorgchem.3c02329