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Iron porphyrin complexes are cofactors in many important proteins such as cytochromes P450, hemoglobin, heme peroxidases, etc. Many computational studies on these systems have been done over the past decade. In this study, the performance of some of the most commonly used density functional theory functionals is evaluated with regard to how they reproduce experimental structures. Seven different functionals (BP86, PBE, PBE0, TPSS, TPSSH, B3LYP, and B97-D) are used to study eight different iron porphyrin complexes. The results show that the TPSSH, PBE0, and TPSS functionals give the best results (absolute bond distance deviations of 0.015−0.016 Å), but the geometries are well-reproduced by all functionals except B3LYP. We also test four different basis sets of double-ζ quality, and we find that a combination of double-ζ basis set of Schäfer et al. on the iron atom and the 6-31G* basis set on the other atoms performs best. Finally, we remove the porphyrin side chains and increase the basis set size systematically to see if this affects the results. We show that basis sets larger than double-ζ quality are not necessary to get accurate geometries, and nonaromatic side chains do not affect the geometries. [ABSTRACT FROM AUTHOR]

The heme peroxidases have a histidine group as the axial ligand of iron. This ligand forms a hydrogen bond to an aspartate carboxylate group by the other nitrogen atom in the side chain. The aspartate is not present in the globins and it has been suggested that it gives an imidazolate character to the histidine ligand. Quantum chemical calculations have indicated that the properties of the heme site strongly depend on the position of the proton in this hydrogen bond. Therefore, we have studied the location of this proton in all intermediates in the reaction mechanism, using a set of different quantum mechanical and combined experimental and computational methods. Quantum refinements of a crystal structure of the resting FeIIIstate in yeast cytochrome cperoxidase show that the geometric differences of the two states are so small that it cannot be unambiguously decided where the proton is in the crystal structure. Vacuum calculations indicate that the position of the proton is sensitive to the surroundings and to the side chains of the porphyrin ring. Combined quantum and molecular mechanics (QM/MM) calculations indicate that the proton prefers to reside on the His ligand in all states in the reaction mechanism of the peroxidases. QM/MM free energy perturbations confirm these results, but reduce the energy difference between the two states to 12−44 kJ/mol. [ABSTRACT FROM AUTHOR]

We have studied the dynamics of water molecules in six crystal structures of four human cytochromes P450, 2A6, 2C8, 2C9, and 3A4, with molecular dynamics simulations. In the crystal structures, only a few water molecules are seen and the reported sizes of the active-site cavity vary a lot. In the simulations, the cavities are completely filled with water molecules, although with ∼20% lower density than in bulk water. The 2A6 protein differs from the other three in that it has a very small cavity with only two water molecules and no exchange with the surroundings. The other three proteins have quite big cavities, with 41 water molecules on average in 2C8 and 54−58 in 2C9 and 3A4, giving a water volume of 1500−2100 Å3. The two crystal structures of 2C9 differ quite appreciably, whereas those of 3A4 are quite similar. The active-site cavity is connected to the surroundings by three to six channels, through which there is a quite frequent exchange of water molecules (one molecule is exchanged every 30−200 ps), except in 2A6. Most of the channels are observed also in the crystal structures, but two to three channels in each protein open only during the simulations. There are no water molecules close to the heme iron ion in these simulations of the high-spin ferric state (the average distance to the closest water molecule is 3.3−5 Å), and there are few ordered water molecules in the active sites, none of which is conserved in all proteins. [ABSTRACT FROM AUTHOR]

We present a systematic investigation of how the axial ligand in heme proteins influences the geometry, electronic structure, and spin states of the active site, and the energies of the reaction cycles. Using the density functional B3LYP method and medium-sized basis sets, we have compared models with His, His+Asp, Cys, Tyr, and Tyr+Arg as found in myoglobin and hemoglobin, peroxidases, cytochrome P450, and heme catalases, respectively. We have studied 12 reactants and intermediates of the reaction cycles of these enzymes, including complexes with H 2O, OH -, O 2?, CH 3OH, O 2, H 2O 2, and HO 2 ? in various formal oxidation states of the iron ion (II to V). The results show that His gives ~0.6 V higher reduction potentials than the other ligands. In particular, it is harder to reduce and protonate the O 2 complex with His than with the other ligands, in accordance with the O 2 carrier function of globins and the oxidative chemistry of the other proteins. For most properties, the trend Cys