We have performed a systematic computational study of the relative energies of possible protonation states of the FeMo cluster in nitrogenase in the E0-E4 states, i.e. the resting state and states with 1-4 electrons and protons added but before N2 binds. We use the combined quantum mechanics and molecular mechanics (QM/MM) approach, including the complete solvated heterotetrameric enzyme in the calculations. The QM system consisted of 112 atoms, i.e. the full FeMo cluster, as well all groups forming hydrogen bonds to it within 3.5 Å. It was treated with either the TPSS-D3 or B3LYP-D3 methods with the def2-SV(P) or def2-TZVPD basis sets. For each redox state, we calculated relative energies of at least 50 different possible positions for the proton, added to the most stable protonation state of the level with one electron less. We show quite conclusively that the resting E0 state is not protonated using quantum refinement and by comparing geometries to the crystal structure. The E1 state is protonated on S2B, in agreement with most previous computational studies. However, for the E2-E4 states, the two QM methods give diverging results, with relative energies that differ by over 300 kJ/mol for the most stable E4 states. TPSS favours hydride ions binding to the Fe ions. The first bridges Fe2 and Fe6, whereas the next two bind terminally to either Fe4, Fe5 or Fe6 with nearly equal energies. On the other hand, B3LYP disfavours hydride ions and instead suggests that 1-3 protons bind to the central carbide ion.

Nitrogenase is the only enzyme that can break the triple bond in N to form two molecules of ammonia. The enzyme has been thoroughly studied with both experimental and computational methods, but there is still no consensus regarding the atomic details of the reaction mechanism. In the most common form, the active site is a MoFeSC(homocitrate) cluster. The homocitrate ligand contains one alcohol and three carboxylate groups. In water solution, the triply deprotonated form dominates, but because the alcohol (and one of the carboxylate groups) coordinate to the Mo ion, this may change in the enzyme. We have performed a series of computational calculations with molecular dynamics (MD), quantum mechanical (QM) cluster, combined QM and molecular mechanics (QM/MM), QM/MM with Poisson-Boltzmann and surface area solvation, QM/MM thermodynamic cycle perturbations, and quantum refinement methods to settle the most probable protonation state of the homocitrate ligand in nitrogenase. The results quite conclusively point out a triply deprotonated form (net charge -3) with a proton shared between the alcohol and one of the carboxylate groups as the most stable at pH 7. Moreover, we have studied eight ionizable protein residues close to the active site with MD simulations and determined the most likely protonation states.

Nitrogenase is the only enzyme that can cleave the triple bond in N 2 , making nitrogen avaiable for other organisms. It contains a complicated MoFe 7 S 9 C(homocitrate) cluster in its active site. Many computational studies with density-functional theory (DFT) of the nitrogenase enzyme have been presented, but they do not show any consensus -they do not even agree where the first four protons should be added, forming the central intermediate E 4 . We show that the prime reason for this is that different DFT methods give relative energies that differ by almost 600 kJ mol À1 for different protonation states. This is 4-30 times more than what is observed for other systems. The reason for this is that in some structures, the hydrogens bind to sulfide or carbide ions as protons, whereas in other structures they bind to the metals as hydride ions, changing the oxidation state of the metals, as well as the Fe-C, Fe-S and Fe-Fe distances.The energies correlate with the amount of Hartree-Fock exchange in the method, indicating a variation in the amount of static correlation in the structures. It is currently unclear which DFT method gives the best results for nitrogenase. We show that non-hybrid DFT functionals and TPSSh give the most accurate structures of the resting active site, whereas B3LYP and PBE0 give the best H 2 dissociation energies.However, no DFT method indicates that a structure of E 4 with two bridging hydride ions is lowest in energy, as spectroscopic experiments indicate.

Here, the synthesis of a wafer‐scale ultrathin 2D imine polymer (2DP) film with controllable thickness from simple benzene‐1,3,5‐tricarbaldehyde (BTA) and p‐phenylenediamine (PDA) building blocks is reported using a Schiff base polycondensation reaction at the air–water interface. The synthesized freestanding 2DP films are porous, insulating, and more importantly, covalently linked, which is ideally suited for nonvolatile memristors that use a conductive filament mechanism. These devices exhibit excellent switching performance with high reliability and reproducibility, with on/off ratios in the range of 102 to 105 depending on the thickness of the film. In addition, the endurance and data retention capability of 2DP‐based nonvolatile resistive memristors are up to 200 cycles and 8 × 104 s under constant voltage stress at 0.1 V. The intrinsic flexibility of the covalent organic polymer enables the fabrication of a flexible memory device on a polyimide film, which exhibits as reliable memory performance as that on the rigid substrate. Moreover, the 2DP‐based memory device shows outstanding thermal stability and organic solvent resistance, which are desirable properties for applications in wearable devices.