Hydroxylation catalysis by mononuclear and dinuclear iron oxo catalysts: a methane monooxygenase model system versus the Fenton reagent Fe(IV)O(H2O)5(2+)

On the Nature of the Carbonyl versus Phosphoryl Binding in Uranyl Nitrate Complexes†

The electronic structure of ligands with phosphoryl and carbonyl binding sites and their complexation behavior with uranyl nitrate were investigated using density functional theory (DFT). The quantum chemical calculations indicate that the electronic charges on both phosphoryl and carbonyl groups are more polarized toward oxygen atoms in isolated ligands. This effect is predominant in the case of complexes of the former. Both P═O and C═O groups are positively charged with the exception in methylisobutylketone (MIBK), where the C=O group is virtually neutral. The fragment molecular orbital analysis suggests that during complexation, a certain amount of charge transfer occurs from the filled pπ-orbitals [π_x^(CO/PO) and π_y^(CO/PO)] of the ligand to 5f, 6d, and 7s orbitals of the uranium atom (f_σ* and ds_σ*). The NBO analysis reaffirms the charge transfer mechanism. The observed red shift in ν(C═O) and ν(P═O) identified in the simulated infrared spectrum of the corresponding complexes implies a moderate weakening of both carbonyl and phosphoryl bonds upon complexation. The atoms in molecules (AIM) analysis suggests a stronger phosphoryl binding compared to carbonyl interactions and an ionic U-O bond. The estimated complexation energies are considerable for phosphoryl ligands compared to those of the carbonyl analogue, with a reasonably large value derived for tri-n-butyl phosphate (TBP). The energy decomposition analysis marked significant stabilizing orbital interactions for phosphoryl ligands. The contributions of estimated dispersion energies are considerable in all complexes and extensively depend on the alkyl unit.

Unraveling reaction networks behind the catalytic oxidation of methane with H2O2 over a mixed-metal MIL-53(Al,Fe) MOF catalyst

Reaction paths underlying the catalytic oxidation of methane with H2O2 over an Fe containing MIL-53(Al) metal-organic framework were studied by periodic DFT calculations. Not only the activation of methane, but the full reaction network was considered, which includes the formation of the active site, the overoxidation of methane to CO2 and the decomposition of H2O2 to H2O and O2. Calculations indicate that the activation barrier for the initial activation of the Fe sites upon reaction with H2O2 is comparable to that of the subsequent C-H activation and also of the reaction steps involved in the undesirable overoxidation processes. The pronounced selectivity of the oxidation reaction over MIL-53(Al,Fe) towards the target mono-oxygenated CH3OH and CH3OOH products is attributed to the limited coordination freedom of the Fe species encapsulated in the extended octahedral [AlO6] structure-forming chains, which effectively prevents the direct overoxidation paths prior to product desorption from the active sites. Importantly, our computational analysis reveals that the active sites for the desired methane oxidation are able to much more efficiently promote the direct catalytic H2O2 decomposition reaction, rendering thus the current combination of the active site and the reactants undesirable for the prospective methane valorization process.

Complexation Behavior of the Tri-n-butyl Phosphate Ligand with Pu(IV) and Zr(IV): A Computational Study

Tri-n-butyl phosphate (TBP), used as the extractant in nuclear fuel reprocessing, shows superior extraction abilities for Pu(IV) over a large number of fission products including Zr(IV). We have applied density functional theory (DFT) calculations to explain this selectivity by investigating differences in electronic structures of Pu(NO3)4·2TBP and Zr(NO3)4·2TBP complexes. On the basis of our quantum chemical calculations, we have established the lowest energy electronic states for both complexes; the quintet is the ground state for the former, whereas the latter exists in the singlet spin state. The calculated structural parameters for the optimized geometry of the plutonium complex are in agreement with the experimental results. Atoms in Molecules analysis revealed a considerable amount of ionic character to M-O{TBP} and M-O{NO3} bonds. Additionally, we have also investigated the extraction behavior of TBP for metal nitrates and have estimated the extraction energies to be -73.1 and -57.6 kcal/mol for Pu(IV) and Zr(IV), respectively. The large extraction energy of Pu(IV) system is in agreement with the observed selectivity in the extraction of Pu.

The activation strain model and molecular orbital theory

The activation strain model is a powerful tool for understanding reactivity, or inertness, of molecular species. This is done by relating the relative energy of a molecular complex along the reaction energy profile to the structural rigidity of the reactants and the strength of their mutual interactions: ΔE(ζ) = ΔE_strain(ζ) + ΔE_int(ζ). We provide a detailed discussion of the model, and elaborate on its strong connection with molecular orbital theory. Using these approaches, a causal relationship is revealed between the properties of the reactants and their reactivity, e.g., reaction barriers and plausible reaction mechanisms. This methodology may reveal intriguing parallels between completely different types of chemical transformations. Thus, the activation strain model constitutes a unifying framework that furthers the development of cross-disciplinary concepts throughout various fields of chemistry. We illustrate the activation strain model in action with selected examples from literature. These examples demonstrate how the methodology is applied to different research questions, how results are interpreted, and how insights into one chemical phenomenon can lead to an improved understanding of another, seemingly completely different chemical process. WIREs Comput Mol Sci 2015, 5:324-343. doi: 10.1002/wcms.1221.

Computational electrochemistry: prediction of liquid-phase reduction potentials

This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.

Demonstration of the heterolytic O-O bond cleavage of putative nonheme iron(II)-OOH(R) complexes for Fenton and enzymatic reactions

One-electron reduction of mononuclear nonheme iron(III) hydroperoxo (Fe(III)-OOH) and iron(III) alkylperoxo (Fe(III)-OOR) complexes by ferrocene (Fc) derivatives resulted in the formation of the corresponding iron(IV) oxo complexes. The conversion rates were dependent on the concentration and oxidation potentials of the electron donors, thus indicating that the reduction of the iron(III) (hydro/alkyl)peroxo complexes to their one-electron reduced iron(II) (hydro/alkyl)peroxo species is the rate-determining step, followed by the heterolytic O-O bond cleavage of the putative iron(II) (hydro/alkyl)peroxo species to give the iron(IV) oxo complexes. Product analysis supported the heterolytic O-O bond-cleavage mechanism. The present results provide the first example showing the one-electron reduction of iron(III) (hydro/alkyl)peroxo complexes and the heterolytic O-O bond cleavage of iron(II) (hydro/alkyl)peroxo species to form iron(IV) oxo intermediates which occur in nonheme iron enzymatic and Fenton reactions.

Applications of density functional theory to iron-containing molecules of bioinorganic interest

The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.

DFT study of the mechanism for methane hydroxylation by soluble methane monooxygenase (sMMO): effects of oxidation state, spin state, and coordination number

The exact structure of the active site of intermediate Q, the methane-oxidizing species of soluble methane monooxygenase (sMMO), and the reaction mechanism of Q with methane molecule are still not fully clear. To gain further insights into the structure and reaction mechanism, five diiron models of Q that differ in shape, oxidation state, spin state, and coordination number of the two iron centers are studied. Different mechanisms in different spin states were explored. Density functional theory (DFT) calculations show that Fe(III)Fe(IV)(μ-O)(μ-OH) is more reactive than Fe(IV)(2)(μ-O)(2) in the oxygen-rich environment and that the reactivity of the active core of sMMO-Q is not enhanced by converting its oxo bridge into a terminal ligand. A four-coordinated diiron model is the most effective for methane hydroxylation. Both radical and non-radical intermediates are involved in the reactions for the four-coordinated diiron model.

MRI evaluation of hepatic iron overload: Recent advances

Many studies show that hepatic iron overload has a close association with hepatitis, hepatic fibrosis, cirrhosis, and hepatic tumors. Methods currently used for detection of hepatic iron overload, such as plasma ferritin detection, liver biopsy, and superconducting quantum interface device, have some limitations. Improvement in software and hardware has enabled MRI to become a safe, noninvasive and accurate method for detecting hepatic iron overload. This article aims to summarize the performance and application of MRI in the evaluation of hepatic iron overload.