Quantum cluster size and solvent polarity effects on the geometries and Mössbauer properties of the active site model for ribonucleotide reductase intermediate X: a density functional theory study

摘要

In studying the properties of metalloproteins using ab initio quantum mechanical methods, one has to focus on the calculations on the active site. The bulk protein and solvent environment is often neglected, or is treated as a continuum dielectric medium with a certain dielectric constant. The size of the quantum cluster of the active site chosen for calculations can vary by including only the first-shell ligands which are directly bound to the metal centers, or including also the second-shell residues which are adjacent to and normally have H-bonding interactions with the first-shell ligands, or by including also further hydrogen bonding residues. It is not well understood how the size of the quantum cluster and the value of the dielectric constant chosen for the calculations will influence the calculated properties. In this paper, we have studied three models (A, B, and C) of different sizes for the active site of the ribonucleotide reductase intermediate X, using density functional theory (DFT) OPBE functional with broken-symmetry methodology. Each model is studied in gas-phase and in the conductor-like screening (COSMO) solvation model with different dielectric constants ε = 4, 10, 20, and 80, respectively. All the calculated Fe-ligand geometries, Heisenberg J coupling constants, and the Mössbauer isomer shifts, quadrupole splittings, and the ⁵⁷Fe, ¹H, and ¹⁷O hyperfine tensors are compared. We find that the calculated isomer shifts are very stable. They are virtually unchanged with respect to the size of the cluster and the dielectric constant of the environment. On the other hand, certain Fe-ligand distances are sensitive to both the size of the cluster and the value of ε. ε = 4, which is normally used for the protein environment, appears too small when studying the diiron active site geometry with only the first-shell ligands as seen by comparisons with larger models.