DFT Calculations of Isomer Shifts and Quadrupole Splitting Parameters in Synthetic Iron−Oxo Complexes:  Applications to Methane Monooxygenase and Ribonucleotide Reductase

Abstract

To predict isomer shifts and quadrupole splitting parameters of Fe atoms in the protein active sites of methane monooxygenase and ribonucleotide reductase, a correlation between experimental isomer shifts ranging 0.1-1.5 mm s(-)(1) for Fe atoms in a training set with the corresponding density functional theory (DFT) calculated electron densities at the Fe nuclei in those complexes is established. The geometries of the species in the training set, consisting of synthetic polar monomeric and dimeric iron complexes, are taken from the Cambridge structural database. A comparison of calculated Mössbauer parameters for Fe atoms from complexes in the training set with their corresponding experimental values shows very good agreement (standard deviation of 0.11 mm/s, correlation coefficient of -0.94). However, for the Fe atoms in the active sites of the structurally characterized proteins of methane monooxygenase and ribonucleotide reductase, the calculated Mössbauer parameters deviate more from their experimentally measured values. The high correlation that exists between calculated and observed quadrupole splitting and isomer shift parameters for the synthetic complexes leads us to conclude that the main source of the error arising for the protein active sites is due to the differing degrees of atomic-level resolution for the protein structural data, compared to the synthetic complexes in the training set. Much lower X-ray resolutions associated with the former introduce uncertainty in the accuracy of several bond lengths. This is ultimately reflected in the calculated isomer shifts and quadrupole splitting parameters of the Fe sites in the proteins. For the proteins, the closest correspondence between predicted and observed Mössbauer isomer shifts follows the order MMOH(red), RNR(red), MMOH(ox), and RNR(ox), with average deviations from experiment of 0.17, 0.17, 0.17-0.20, and 0.32 mm/s, but this requires DFT geometry optimization of the iron-oxo dimer complexes.

First principles calculation of Mössbauer isomer shift

“…(7), (17), and (19), depends of the choice of the atomic orbital basis set and on the choice of density functional employed [58,77,81,82,[90][91][92][124][125][126][127][128][129][130]. It has been suggested that, for every combination of basis set and approximate density functional, an individual value of the calibration constant should be obtained [81,82].…”

“…In the calculations on iron (as well as on some other elements), the non-relativistic quantum chemical formalism is usually employed in connection with the cluster approach [77,[80][81][82]85,86,88,89,103,104,[124][125][126][127][128][129][130]. The so-obtained contact densities are corrected for relativistic effects with the use of scaling factor S (Z).…”

The Density Functional Theory

“…Thus, it can be determined to good accuracy (often better than 0.1 mm s -1 ) from ground-state DFT calculations using a suitable method-specific calibration procedure on the basis of a linear correlation between the calculated electron density at the nucleus versus the measured d Liu et al 2003;Neese 2002;Sinnecker et al 2005;Zhang et al 2002). The predicted d is in good agreement with experimental data when using B3LYP-calibrated curves in combination with basis sets that are flexible in the core region and extensively polarized (Berry et al 2008;Schoneboom et al 2005;Sinnecker et al 2005).…”

A Mössbauer study on iron(II) complex of 2-acetyl-1,3-indandione ⎼ spin-crossover or structural changes

“…Han and Noodleman have proposed several correlation formula by doing linear regression fit of the calculated ρ(0) and δexp isomer shift, IS, as well as for the quadrupole splitting, QS, on large sets of experimentally availble data and using different theoretical models [14][15][16]. By using some of the proposed correlations, we attempted to find explanation of the experimentally observed Mössbauer spectral features and propose the most probable structure of the Fe(II) complex of 2AID.…”