Large equatorial ligand effects on C-H bond activation by nonheme iron(IV)-oxo complexes

The Unique Role of the Second Coordination Sphere to Unlock and Control Catalysis in Nonheme Fe(II)/2-Oxoglutarate Histone Demethylase KDM2A

Nonheme Fe(II) and 2-oxoglutarate (2OG)-dependent histone lysine demethylases 2A (KDM2A) catalyze the demethylation of the mono- or dimethylated lysine 36 residue in the histone H3 peptide (H3K36me1/me2), which plays a crucial role in epigenetic regulation and can be involved in many cancers. Although the overall catalytic mechanism of KDMs has been studied, how KDM2 catalysis takes place in contrast to other KDMs remains unknown. Understanding such differences is vital for enzyme redesign and can help in enzyme-selective drug design. Herein, we employed molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) to explore the complete catalytic mechanism of KDM2A, including dioxygen diffusion and binding, dioxygen activation, and substrate oxidation. Our study demonstrates that the catalysis of KDM2A is controlled by the conformational change of the second coordination sphere (SCS), specifically by a change in the orientation of Y222, which unlocks the 2OG rearrangement from off-line to in-line mode. The study demonstrates that the variant Y222A makes the 2OG rearrangement more favorable. Furthermore, the study reveals that it is the size of H3K36me3 that prevents the 2OG rearrangement, thus rendering the enzyme inactivity with trimethylated lysine. Calculations show that the SCS and long-range interacting residues that stabilize the HAT transition state in KDM2A differ from those in KDM4A, KDM7B, and KDM6A, thus providing the basics for the enzyme-selective redesign and modulation of KDM2A without influencing other KDMs.

Unravelling the Effect of Acid-Driven Electron Transfer in High-Valent FeIV =O/MnIV =O Species and Its Implications for Reactivity

The electron transfer (ET) step is one of the crucial processes in biochemical redox reactions that occur in nature and has been established as a key step in dictating the reactivity of high-valent metal-oxo species. Although metalloenzymes possessing metal-oxo units at their active site are typically associated with outer-sphere electron transfer (OSET) processes, biomimetic models, in contrast, have been found to manifest either an inner-sphere electron transfer (ISET) or OSET mechanism. This distinction is clearly illustrated through the behaviour of [(N4Py)MnIV (O)]2+ (1) and [(N4Py)FeIV (O)]2+ (2) complexes, where complex 1 showcases an OSET mechanism, while complex 2 exhibits an ISET mechanism, especially evident in their reactions involving C-H bond activation and oxygen atom transfer reactions in the presence of a Lewis/Bronsted acid. However, the precise reason for this puzzling difference remains elusive. This work unveils the origin of the perplexing inner-sphere vs outer-sphere electron transfer process (ISET vs OSET) in [(N4Py)MnIV (O)]2+ (1) and [(N4Py)FeIV (O)]2+ (2) species in the presence of Bronsted acid. The calculations indicate that when the substrate (toluene) approaches both 1 and 2 that is hydrogen bonded with two HOTf molecules (denoted as 1-HOTf and 2-HOTf, respectively), proton transfer from one of the HOTf molecules to the metal-oxo unit is triggered and a simultaneous electron transfer occurs from toluene to the metal centre. Interestingly, the preference for OSET by 1-HOTf is found to originate from the choice of MnIV =O centre to abstract spin-down (β) electron from toluene to its δ(dxy ) orbital. On the other hand, in 2-HOTf, a spin state inversion from triplet to quintet state takes place during the proton (from HOTf) coupled electron transfer (from toluene) preferring a spin-up (α) electron abstraction to its σ* (dz 2 ) orbital mediated by HOTf giving rise to ISET. In addition, 2-HOTf was calculated to possess a larger reorganisation energy, which facilitates the ISET process via the acid. The absence of spin-inversion and smaller reorganisation energy switch the mechanism to OSET for 1-HOTf. Therefore, for the first time, the significance of spin-state and spin-inversion in the electron transfer process has been identified and demonstrated within the realm of high-valent metal-oxo chemistry. This discovery holds implications for the potential involvement of high-valent Mn-oxo species in performing similar transformative processes within Photosystem II.

Deciphering the origin of million-fold reactivity observed for the open core diiron [HO-FeIII-O-FeIV[double bond, length as m-dash]O]2+ species towards C-H bond activation: role of spin-states, spin-coupling, and spin-cooperation

High-valent metal-oxo species have been characterised as key intermediates in both heme and non-heme enzymes that are found to perform efficient aliphatic hydroxylation, epoxidation, halogenation, and dehydrogenation reactions. Several biomimetic model complexes have been synthesised over the years to mimic both the structure and function of metalloenzymes. The diamond-core [Fe2(μ-O)2] is one of the celebrated models in this context as this has been proposed as the catalytically active species in soluble methane monooxygenase enzymes (sMMO), which perform the challenging chemical conversion of methane to methanol at ease. In this context, a report of open core [HO(L)FeIII-O-FeIV(O)(L)]2+ (1) gains attention as this activates C-H bonds a million-fold faster compared to the diamond-core structure and has the dual catalytic ability to perform hydroxylation as well as desaturation with organic substrates. In this study, we have employed density functional methods to probe the origin of the very high reactivity observed for this complex and also to shed light on how this complex performs efficient hydroxylation and desaturation of alkanes. By modelling fifteen possible spin-states for 1 that could potentially participate in the reaction mechanism, our calculations reveal a doublet ground state for 1 arising from antiferromagnetic coupling between the quartet FeIV centre and the sextet FeIII centre, which regulates the reactivity of this species. The unusual stabilisation of the high-spin ground state for FeIV[double bond, length as m-dash]O is due to the strong overlap of with the orbital, reducing the antibonding interactions via spin-cooperation. The electronic structure features computed for 1 are consistent with experiments offering confidence in the methodology chosen. Further, we have probed various mechanistic pathways for the C-H bond activation as well as -OH rebound/desaturation of alkanes. An extremely small barrier height computed for the first hydrogen atom abstraction by the terminal FeIV[double bond, length as m-dash]O unit was found to be responsible for the million-fold activation observed in the experiments. The barrier height computed for -OH rebound by the FeIII-OH unit is also smaller suggesting a facile hydroxylation of organic substrates by 1. A strong spin-cooperation between the two iron centres also reduces the barrier for second hydrogen atom abstraction, thus making the desaturation pathway competitive. Both the spin-state as well as spin-coupling between the two metal centres play a crucial role in dictating the reactivity for species 1. By exploring various mechanistic pathways, our study unveils the fact that the bridged μ-oxo group is a poor electrophile for both C-H activation as well for -OH rebound. As more and more evidence is gathered in recent years for the open core geometry of sMMO enzymes, the idea of enhancing the reactivity via an open-core motif has far-reaching consequences.

One-step hydroxylation of benzene to phenol over Schiff base complexes incorporated onto mesoporous organosilica in the presence of different axial ligands

Liquid-phase hydroxylation of benzene to phenol using Schiff base complexes anchored on a mesoporous organosilica support was investigated in various solvents when molecular oxygen was utilized as a green oxidant.

Reassessment of the Mechanisms of Thermal C-H Bond Activation of Methane by Cationic Magnesium Oxides: A Critical Evaluation of the Suitability of Different Density Functionals

The mechanisms of the thermal reactions of the two iconic magnesium oxide cations MgO^.+ and Mg₂ O₂ ^.+ with methane have been re-evaluated at the CCSD(T)/CBS//CCSD/def2-TZVP level of theory. For the reaction of MgO^.+ with CH₄ , only the classical hydrogen-atom transfer (HAT) was found; in contrast, for the Mg₂ O₂ ^.+ /CH₄ couple, both HAT and proton-coupled electron-transfer (PCET) exist as mechanistic variants. In order to evaluate the suitability of density functional theory (DFT) methods, the reactions were computed by using 27 density functionals. The results obtained demonstrate that the various DFT methods often deliver rather different results for both geometric and energetic features. As to the prediction of the apparent barriers, pure functionals give the largest mean absolute errors. BMK, ωB97XD, and the double-hybrid functional mPW2PLYP were confirmed to come closest to the results provided by CCSD(T)/CBS. Thus, mechanistic conclusions based on a single DFT method should be viewed with great caution. In summary, this study may assist in the selection of a suitable quantum chemical method to unravel the mechanistic details of C-H bond activation by charged metal oxides.

Metal-Oxyl Species and Their Possible Roles in Chemical Oxidations

Metal-oxyl (Mⁿ⁺-O^•) complexes having an oxyl radical ligand, which are electronically equivalent to well-known metal-oxo (M⁽ⁿ⁺¹⁾⁺═O) complexes, are surveyed as a new category of metal-based oxidants. Detection and characterization of Mⁿ⁺-O^• species have been made in some cases, although proposals and characterization of the species are mostly done on the basis of density functional theory (DFT) calculations. The reactivity of Mⁿ⁺-O^• complexes will provide a way to achieve potentially difficult oxidative conversion of substrates. This Viewpoint will provide state-of-the-art knowledge on the Mⁿ⁺-O^• species in terms of the formation, characterization, and DFT-based proposals to shed light on the characteristics of the intriguing oxidatively active species.

Advancing Fenton and photo-Fenton water treatment through the catalyst design

The review is devoted to modern Fenton, photo-Fenton, as well as Fenton-like and photo-Fenton-like reactions with participation of iron species in liquid phase and as heterogeneous catalysts. Mechanisms of these reactions were considered that include hydroxyl radical and oxoferryl species as the reactive intermediates. The barriers in the way of application of these reactions to wastewater treatment were discussed. The following fundamental problems need further research efforts: inclusion of more mechanism steps and quantum calculations of all rate constants lacking in the literature, checking the outer sphere electron transfer contribution, determination of the causes for the key changes in the homogeneous Fenton reaction mechanism with a change in the reagents concentration. The key advances for Fenton reactions implementation for the water treatment are related to tremendous hydrodynamical effects on the catalytic activity, design of ligands for high rate and completeness of mineralization in short time, and design of highly active heterogeneous catalysts. While both homogeneous and heterogeneous Fenton and photo-Fenton systems are open for further improvements, heterogeneous photo-Fenton systems are most promising for practical applications because of the inherent higher catalyst stability. Modern methods of quantum chemistry are expected to play a continuously increasing role in development of such catalysts.

Interplay Between Steric and Electronic Effects: A Joint Spectroscopy and Computational Study of Nonheme Iron(IV)-Oxo Complexes

Iron is an essential element in nonheme enzymes that plays a crucial role in many vital oxidative transformations and metabolic reactions in the human body. Many of those reactions are regio- and stereospecific and it is believed that the selectivity is guided by second-coordination sphere effects in the protein. Here, results are shown of a few engineered biomimetic ligand frameworks based on the N4Py (N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) scaffold and the second-coordination sphere effects are studied. For the first time, selective substitutions in the ligand framework have been shown to tune the catalytic properties of the iron(IV)-oxo complexes by regulating the steric and electronic factors. In particular, a better positioning of the oxidant and substrate in the rate-determining transition state lowers the reaction barriers. Therefore, an optimum balance between steric and electronic factors mediates the ideal positioning of oxidant and substrate in the rate-determining transition state that affects the reactivity of high-valent reaction intermediates.

Ta2 +-mediated ammonia synthesis from N2 and H2 at ambient temperature

In a full catalytic cycle, bare Ta₂ ⁺ in the highly diluted gas phase is able to mediate the formation of ammonia in a Haber-Bosch-like process starting from N₂ and H₂ at ambient temperature. This finding is the result of extensive quantum chemical calculations supported by experiments using Fourier transform ion cyclotron resonance MS. The planar Ta₂N₂ ⁺, consisting of a four-membered ring of alternating Ta and N atoms, proved to be a key intermediate. It is formed in a highly exothermic process either by the reaction of Ta₂ ⁺ with N₂ from the educt side or with two molecules of NH₃ from the product side. In the thermal reaction of Ta₂ ⁺ with N₂, the N≡N triple bond of dinitrogen is entirely broken. A detailed analysis of the frontier orbitals involved in the rate-determining step shows that this unexpected reaction is accomplished by the interplay of vacant and doubly occupied d-orbitals, which serve as both electron acceptors and electron donors during the cleavage of the triple bond of N≡N by the ditantalum center. The ability of Ta₂ ⁺ to serve as a multipurpose tool is further shown by splitting the single bond of H₂ in a less exothermic reaction as well. The insight into the microscopic mechanisms obtained may provide guidance for the rational design of polymetallic catalysts to bring about ammonia formation by the activation of molecular nitrogen and hydrogen at ambient conditions.

Electronic Effects on Room-Temperature, Gas-Phase C-H Bond Activations by Cluster Oxides and Metal Carbides: The Methane Challenge

This Perspective discusses a story of one molecule (methane), a few metal-oxide cationic clusters (MOCCs), dopants, metal-carbide cations, oriented-electric fields (OEFs), and a dizzying mechanistic landscape of methane activation! One mechanism is hydrogen atom transfer (HAT), which occurs whenever the MOCC possesses a localized oxyl radical (M-O^•). Whenever the radical is delocalized, e.g., in [MgO]_n^•+ the HAT barrier increases due to the penalty of radical localization. Adding a dopant (Ga₂O₃) to [MgO]₂^•+ localizes the radical and HAT transpires. Whenever the radical is located on the metal centers as in [Al₂O₂]^•+ the mechanism crosses over to proton-coupled electron transfer (PCET), wherein the positive Al center acts as a Lewis acid that coordinates the methane molecule, while one of the bridging oxygen atoms abstracts a proton, and the negatively charged CH₃ moiety relocates to the metal fragment. We provide a diagnostic plot of barriers vs reactants' distortion energies, which allows the chemist to distinguish HAT from PCET. Thus, doping of [MgO]₂^•+ by Al₂O₃ enables HAT and PCET to compete. Similarly, [ZnO]^•+ activates methane by PCET generating many products. Adding a CH₃CN ligand to form [(CH₃CN)ZnO]^•+ leads to a single HAT product. The CH₃CN dipole acts as an OEF that switches off PCET. [MC]⁺ cations (M = Au, Cu) act by different mechanisms, dictated by the M⁺-C bond covalence. For example, Cu⁺, which bonds the carbon atom mostly electrostatically, performs coupling of C to methane to yield ethylene, in a single almost barrier-free step, with an unprecedented atomic choreography catalyzed by the OEF of Cu⁺.

Targeting of High-Valent Iron-TAML Activators at Hydrocarbons and Beyond

TAML activators of peroxides are iron(III) complexes. The ligation by four deprotonated amide nitrogens in macrocyclic motifs is the signature of TAMLs where the macrocyclic structures vary considerably. TAML activators are exceptional functional replicas of the peroxidases and cytochrome P450 oxidizing enzymes. In water, they catalyze peroxide oxidation of a broad spectrum of compounds, many of which are micropollutants, compounds that produce undesired effects at low concentrations-as with the enzymes, peroxide is typically activated with near-quantitative efficiency. In nonaqueous solvents such as organic nitriles, the prototype TAML activator gave the structurally authenticated reactive iron(V)oxo units (Fe^VO), wherein the iron atom is two oxidation equivalents above the Fe^III resting state. The iron(V) state can be achieved through the intermediacy of iron(IV) species, which are usually μ-oxo-bridged dimers (Fe^IVFe^IV), and this allows for the reactivity of this potent reactive intermediate to be studied in stoichiometric processes. The present review is primarily focused at the mechanistic features of the oxidation by Fe^VO of hydrocarbons including cyclohexane. The main topic is preceded by a description of mechanisms of oxidation of thioanisoles by Fe^VO, because the associated studies provide valuable insight into the ability of Fe^VO to oxidize organic molecules. The review is opened by a summary of the interconversions between Fe^III, Fe^IVFe^IV, and Fe^VO species, since this information is crucial for interpreting the kinetic data. The highest reactivity in both reaction classes described belongs to Fe^VO. The resting state Fe^III is unreactive oxidatively. Intermediate reactivity is typically found for Fe^IVFe^IV; therefore, kinetic features for these species in interchange and oxidation processes are also reviewed. Examples of using TAML activators for C-H bond cleavage applied to fine organic synthesis conclude the review.

Ethane C–H bond activation on the Fe(iv)–oxo species in a Zn-based cluster of metal–organic frameworks: a density functional theory study

The generation of a Fe(iv)–oxo complex and its reactivity for C–H bond activation of ethane have been theoretically unraveled.

Methane activation on nickel oxide clusters with a concerted mechanism: a density functional theory study of the effect of silica support

The support effect is an important issue in heterogeneous catalysis. A systematic density functional theory (DFT) study was performed to investigate the support effect of a silica model on the initial step of methane activation on NixOx (x =2,3) clusters with a concerted mechanism. Four reactions were examined by exploring their potential energy surfaces (PES): CH4 reacting with unsupported Ni2O2, with silica-supported Ni2O2, with unsupported Ni3O3, and with silica-supported Ni3O3. For each reaction, PES with different spin states were explored. For CH4 activation taking place via a concerted mechanism, the reaction barriers in terms of free energy and reaction free energy increased with the involvement of the model silica support. Only one PES made a major contribution to the overall reaction rate of all four reactions examined. No spin transition process was required for the reactions to undergo their most-favorable pathway from their starting reactants. These results provide a deeper insight into the support effect on C-H bond activation of small alkanes in general, and of methane in particular, on supported transition metal catalysts.

On the Mechanisms of Hydrogen-Atom Transfer from Water to the Heteronuclear Oxide Cluster [Ga2 Mg2 O5 ](.+) : Remarkable Electronic Structure Effects

Mechanistic insight into the homolytic cleavage of the O-H bond of water by the heteronuclear oxide cluster [Ga2 Mg2 O5 ](.+) has been derived from state-of-the-art gas-phase experiments in conjunction with quantum chemical calculations. Three pathways have been identified computationally. In addition to the conventional hydrogen-atom transfer (HAT) to the radical center of a bridging oxygen atom, two mechanistically distinct proton-coupled electron-transfer (PCET) processes have been identified. The energetically most favored path involves initial coordination of the incoming water ligand to a magnesium atom followed by an intramolecular proton transfer to the lone-pair of the bridging oxygen atom. This step, which is accomplished by an electronic reorganization, generates two structurally equivalent OH groups either of which can be liberated, in agreement with labeling experiments.

Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations

AlkB is the title enzyme of a family of DNA dealkylases that catalyze the direct oxidative dealkylation of nucleobases. The conventional mechanism for the dealkylation of N1-methyl adenine (1-meA) catalyzed by AlkB after the formation of FeIV-oxo is comprised by a reorientation of the oxo moiety, hydrogen abstraction, OH rebound from the Fe atom to the methyl adduct, and the dissociation of the resulting methoxide to obtain the repaired adenine base and formaldehyde. An alternative pathway with hydroxide as a ligand bound to the iron atom is proposed and investigated by QM/MM simulations. The results show OH- has a small impact on the barriers for the hydrogen abstraction and OH rebound steps. The effects of the enzyme and the OH- ligand on the hydrogen abstraction by the FeIV-oxo moiety are discussed in detail. The new OH rebound step is coupled with a proton transfer to the OH- ligand and results in a novel zwitterion intermediate. This zwitterion structure can also be characterized as Fe-O-C complex and facilitates the formation of formaldehyde. In contrast, for the pathway with H2O bound to iron, the hydroxyl product of the OH rebound step first needs to unbind from the metal center before transferring a proton to Glu136 or other residue/substrate. The consistency between our theoretical results and experimental findings is discussed. This study provides new insights into the oxidative repair mechanism of DNA repair by nonheme FeII and α-ketoglutarate (α-KG) dependent dioxygenases and a possible explanation for the substrate preference of AlkB.

Benchmark study on methanol C-H and O-H bond activation by bare [Fe(IV)O](2+)

We present a high-level computational study on methanol C-H and O-H bond cleavages by bare [Fe(IV)O](2+), as well as benchmarks of various density functional theory (DFT) methods. We considered direct and concerted hydrogen transfer (DHT and CHT) pathways, respectively. The potential energy surfaces were constructed at the CCSD(T)/def2-TZVPP//B3LYP/def2-TZVP level of theory. Mechanistically, (1) the C-H bond cleavage is dominant and the O-H activation only plays minor role on the PESs; (2) the DHT from methyl should be the most practical channel; and (3) electronic structure analysis demonstrates the proton and electron transfer coupling behavior along the reaction coordinates. The solvent effect is evident and plays distinct roles in regulating the two bond activations in different mechanisms during the catalysis. The effect of optimizing the geometries using different density functionals was also studied, showing that it is not meaningful to discuss which DFT method could give the accurate prediction of the geometries, especially for transition structures. Furthermore, the gold-standard CCSD(T) method was used to benchmark 19 different density functionals with different Hartree-Fock exchange fractions. The results revealed that (i) the structural factor plays a minor role in the single point energy (SPE) calculations; (ii) reaction energy prediction is quite challenging for DFT methods; (iii) the mean absolute deviations (MADs) reflect the problematic description of the DFs when dealing with metal oxidation state change, giving a strong correlation on the HF exchange in the DFs. Knowledge from this study should be of great value for computational chemistry, especially for the de novo design of transition metal catalysts.

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.