N(2)H(2) binding to the nitrogenase FeMo cluster studied by QM/MM methods

We have made a systematic combined quantum mechanical and molecular mechanical (QM/MM) investigation of possible structures of the N(2) bound state of nitrogenase. We assume that N(2) is immediately protonated to a N(2)H(2) 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(2) states. Our results indicate that the binding of N(2)H(2) 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(2) 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00775-020-01780-5) contains supplementary material, which is available to authorized users.