The Interstitial Carbon of the Nitrogenase FeMo Cofactor is Far Better Stabilized than Previously Assumed

Abstract

The first quantum-mechanical calculations of all relevant potential constants in both the iron-molybdenum cofactor and the iron-vanadium cofactor of nitrogenase suggest that the carbide is bound to the center of the enzyme much more strongly than hitherto assumed. Previous studies seemed to indicate a dummy function of the interstitial carbon, with a weak force constant (ca. 0.32 N cm ). Our new investigations confirm a different picture: the central carbon atom binds the iron-sulfur cluster through six covalent C-Fe bonds. With a potential constant of more than 1.3 N cm , the interstitial carbon also appears to be dynamically persistent. According to our investigations, the values for the elasticity within the iron-sulfur cluster have to be corrected too. These new details on the mechano-chemical properties of the FeMo cofactor will be important for elucidating the catalytic cycle of nitrogen fixation. By implementing our new algorithm in the freely available COMPLIANCE program, the dependence on the coordinates during the calculation of Hesse matrices is eliminated completely.

Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities

“…Typically, smaller model systems are used to study particular active sites such as in the calculations on both the FeMo- and FeV-cofactors performed by Grunenberg in 2017 to investigate the potential force constants of the interstitial carbide atom. 384 Scott et al published a study on the effects of CO-inhibition on the Mo-nitrogenase active site using both spectroscopy and DFT. 385 Similarly, Siegbahn et al claimed that the central carbon in the FeMo-cofactor becomes protonated during the nitrogen fixing process.…”

Computational Investigations of the Chemical Mechanism of the Enzyme Nitrogenase

“… reviews this work, and, on the basis of DF calculations of Mossbauer isomer shifts, and X‐ray absorption spectroscopy, concludes that the charge z on the core cluster [CFe 7 MoS 9 ] z is −1. All recent calculations are consistent with this overall redox level . Although the value of assignment of individual oxidation states to the metal atoms of FeMo‐co is questionable, there is experimental evidence from spatially resolved diffraction refinement of the anomalous scattering of the seven Fe atoms in resting FeMo‐co that Fe1, Fe3 and Fe5 are more reduced that the other four …”

“…Benediktsson and Bjornsson discussed in detail the results of QM/MM investigations of the three BS7 states of resting FeMo‐co, concluding in favour of BS7‐1 . Thus there is general agreement that the BS7 electronic states best describe the S =3/2 resting state of FeMo‐co: BS7‐2 [+−+−++−] is generally used …”

“…The resultant force constant for the Fe−X c bond (X presumed to be N at the time) was 0.32 N cm −1 . Grunenberg used a DF calculation (BP86 functional, BS7 electronic state) of a 46 atom model of FeMo‐co to extract all of its force constants, with a substantially larger value of 1.31 N cm −1 for Fe−C c , and suggested that the Fe−C c frequency would be just below 600 cm −1 , which is beyond the range of the NRVS spectrum . The difference between the experimentally derived small force constant (0.32 N cm −1 ) and the calculated large constant (1.31 N cm −1 ) is unresolved.…”

Metal-mediated base pairs in parallel-stranded DNA

“…In the proposed base pair structure, both Hg(II) ions are coordinated by an endocyclic nitrogen atom of εA and an exocyclic oxygen atom of the thymine residue [ 80 ]. This structure ( Scheme 9 ) differs slightly from the originally proposed one containing one additional bond from the endocyclic nitrogen atom of thymine to one of the Hg(II) ions, because a calculation of the Hg···N force constant [ 81 ] had resulted in an exceptionally low value of 0.7 N cm −1 [ 80 ]. A re-inspection of the originally proposed structure indicated that it represents a local energy minimum rather than the global one.…”