Comparison of the accuracy of DFT methods for reactions with relevance to nitrogenase

Abstract

We have studied the accuracy of 16 different density functional theory methods to reproduce experimental data for bond lengths, angles, vibrational frequencies, as well as enthalpies and entropies for the binding of N2, H2, CO and hydride ions to various transition-metal complexes (with Fe, Ni, Cr, Mo and W) with relation to nitrogenase. We show that generalized gradient approximation functionals give better structure-related parameters, whereas hybrid functionals often give better energies. However, the BLYP and B97D functionals seem to give reasonably accurate results for both types of properties. Geometries and entropies are converged with split-valence basis sets, but energies and vibrational frequencies (and therefore also thermal corrections) in general require a basis set of triple-zeta quality. Dispersion corrections are important to obtain accurate energies (contributing by up to 57 kJ mol−1), as well as structures.

QM/MM Study of Partial Dissociation of S2B for the E2 Intermediate of Nitrogenase

“…On the other hand, another study indicated that pure GGA functionals, like PBE and PW91, gave the best results for structures and energies involving the binding of H 2 and N 2 to small transition-metal models with relation to nitrogenase . Yet, further studies on the latter systems with dispersion-corrected DFT functionals indicated that pure GGA functionals give better structures, whereas hybrid functionals give more reliable energetic results . Consequently, further investigation are required to decide which DFT functional gives the most reliable results for nitrogenase models.…”

“…71 Yet, further studies on the latter systems with dispersion-corrected DFT functionals indicated that pure GGA functionals give better structures, whereas hybrid functionals give more reliable energetic results. 72 Consequently, further investigation are required to decide which DFT functional gives the most reliable results for nitrogenase models. However, considering the small energy difference between the two types of structures with most methods, it is clear that both types need to be considered in investigations of the mechanism of nitrogenase.…”

The binding of reducible N2 in the reaction domain of nitrogenase

“…bonding) demonstrate that it is more accurate than other commonly used functionals when used with the numerical basis sets of DMol. 63 A similar data set was adopted in a more extensive survey of density functionals and analytical basis sets, 64 and a more recent study evaluated various functionals and analytical basis sets for calculation of distances in resting FeMo-co. 65 The dispersion components of the intermolecular interactions involved in the protein-protein and protein-N 2 contacts are treated effectively with the numerical basis sets of DMol. 56 Zhang et al showed that the combination of DNP basis sets and the PBE functional, as used here, yields excellent agreement between experimental and calculated potential energy curves for the raregas diatomics He 2 , Ne 2 , HeAr and NeAr.…”

“…59 The gradient-corrected density functional PBE 62 was used because validation tests against relevant experimental energy and geometry data (including Fe–N 2 bonding) demonstrate that it is more accurate than other commonly used functionals when used with the numerical basis sets of DMol. 63 A similar data set was adopted in a more extensive survey of density functionals and analytical basis sets, 64 and a more recent study evaluated various functionals and analytical basis sets for calculation of distances in resting FeMo-co. 65 The dispersion components of the intermolecular interactions involved in the protein–protein and protein–N 2 contacts are treated effectively with the numerical basis sets of DMol. 56 Zhang et al .…”

Analysis of the Geometric and Electronic Structure of Spin-Coupled Iron–Sulfur Dimers with Broken-Symmetry DFT: Implications for FeMoco

“…For describing energetics related to the complex mechanism of dinitrogen reduction to ammonia by the FeMoco cluster of nitrogenase, errors associated with redox energies, protonation energies, metal hydride bond formation energies, N 2 and H 2 binding energies, and metal–sulfur bond dissociation energies also need to be evaluated. Some recent studies by Dance and Ryde and co-workers have been devoted to the topic of benchmarking properties related to nitrogenase reactions, , where density functionals were compared for reactions, structures, and vibrational frequencies involving low-spin, low-valent organometallic compounds with strong-field ligands (primarily CO). We note, however, that FeMoco features high-spin Fe and Mo ions in a weak-field sulfide environment instead and that benchmarking energy errors for high-spin metal ions are likely more relevant than low-spin metal ions.…”