How bulk and surface properties of Ti4SiC3, V4SiC3, Nb4SiC3 and Zr4SiC3 tune reactivity: a computational study.

We present several in silico insights into the MAX-phase of early transition metal silicon carbides and explore how these affect carbon dioxide hydrogenation. Periodic density functional methodology is applied to models of Ti4SiC3, V4SiC3, Nb4SiC3 and Zr4SiC3. We find that silicon and carbon terminations are unstable, with sintering occurring in vacuum and significant reconstruction taking place under an oxidising environment. In contrast, the metal terminated surfaces are highly stable and very active towards CO2 reduction. However, we predict that under reaction conditions these surfaces are likely to be oxidised. These results are compared to studies on comparable materials and we predict optimal values for hydrogen evolution and CO2 reduction.

Modelling the bulk properties of ambient pressure polymorphs of zirconia.

We report a detailed survey of the calculated bulk properties of zirconia using GGA and meta-GGA functionals (PBE, PBEsol, RPBE, and TPSS), dispersion (Grimme's D2 and D3 approach), and on-site Coulomb repulsion correction (U = 2-8 eV). Structural, elastic, mechanical, and dielectric properties, as well as energetics, electronic structure, and phonon dispersion curves were computed and compared to previous investigations to identify the best DFT approach for a consistent in silico description of zirconia polymorphs. In general, inclusion of dispersion corrections led to only small changes in the calculated properties, whereas DFT+U (U = 2 or 4 eV) reduced the deviations of calculated properties from the experimental results, although deterioration of the structure and relative stabilities may be observed in some cases. Standard PBEsol, RPBE+U, and PBE+U were the best methodologies for a simultaneous description of the three polymorphs of ZrO2. RPBE+U, however, was the only functional to conserve the distinct structures and stabilities of c-, t-, and m-ZrO2 when U = 4 eV was used, resulting in the best in silico replication of the band gaps of ZrO2, whilst outperforming the other methodologies in the description of elastic, mechanical, and dielectric properties of this material. Overall, these results provide insight into the most appropriate DFT methodology for in silico investigations of ZrO2, and show that simultaneous description of all three ambient pressure zirconia polymorphs by DFT techniques with acceptable levels of accuracy can be achieved only when the correct choice of methodology is applied.

Ethylene carbonate adsorption on the major surfaces of lithium manganese oxide Li1-xMn2O4 spinel (0.000 < x < 0.375): a DFT+U-D3 study.

Understanding the surface reactivity of the commercial cathode material LiMn2O4 towards the electrolyte is important to improve the cycling performance of secondary lithium-ion batteries and to prevent manganese dissolution. In this work, we have employed spin-polarized density functional theory calculations with on-site Coulomb interactions and long-range dispersion corrections [DFT+U-D3-(BJ)] to investigate the adsorption of the electrolyte component ethylene carbonate (EC) onto the (001), (011) and (111) surfaces of the fully lithiated and partially delithiated Li1-xMn2O4 spinel (0.000 < x < 0.375). The surface interactions were investigated by evaluating the adsorption energies of the EC molecule and the surface free energies. Furthermore, we analyzed the impact of EC adsorption on the Wulff crystal morphologies, the molecular vibrational frequencies and the adsorbate/surface charge transfers. The adsorption energies indicate that the EC molecule strongly adsorbs on the (111) facet, which is attributed to a bidentate binding configuration. We found that EC adsorption enhances the stability of the (111) facet, as shown by the Wulff crystal morphologies. Although a negligible charge transfer was calculated between the spinel surfaces and the EC molecule, a large charge rearrangement takes place within the surfactant upon adsorption. The wavenumbers of the C[double bond, length as m-dash]O stretching mode for the interacting EC molecule are red-shifted with respect to the isolated adsorbate, suggesting that this bond becomes weaker. The surface free energies show that both the fully lithiated and partially delithiated forms of the LiMn2O4 surfaces are stabilized by the EC molecule.

Carbon dioxide and water co-adsorption on the low-index surfaces of TiC, VC, ZrC and NbC: a DFT study.

We present a theoretical DFT study into the activation of CO2 by TiC, VC, ZrC and NbC. Particular focus is given to the study of CO2/H2O co-adsorption and interaction on four carbide low-index surfaces: {001}, {011}, carbon-terminated {111} and metal-terminated {111}. The adsorption and activation of CO2 is shown to be most exothermic and indeed barrierless on the metal-terminated {111} surfaces, whilst adsorption on the {001} and {011} planes occurs via a small activation energy barrier. In contrast, the carbon-terminated {111} surface proves to be unstable in the presence of the adsorbates. Both water and carbon dioxide adsorb most strongly on TiC and most weakly on NbC, with the strongest co-adsorption interactions being seen in conformations that maximise hydrogen-bonding.

Hydrogen adsorption on transition metal carbides: a DFT study.

Transition metal carbides are a class of materials widely known for both their interesting physical properties and catalytic activity. In this work, we have used plane-wave DFT methods to study the interaction with increasing amounts of molecular hydrogen on the low-index surfaces of four major carbides - TiC, VC, ZrC and NbC. Adsorption is found to be generally exothermic and occurs predominantly on the surface carbon atoms. We identify trends over the carbides and their surfaces for the energetics of the adsorption as a function of their electronic and geometrical characteristics. An ab initio thermodynamics formalism is used to study the properties of the slabs as the hydrogen coverage is increased.

Bulk and surface properties of metal carbides: implications for catalysis.

We present a comprehensive study of the bulk and surface properties of transition metal carbides with rock salt structures and discuss their formation energies and electronic structures. The bonding character of the materials is shown to be dependent on the periodic position of the transition metal as well as the surface termination, which in turn tunes the densities of states and electronic surface properties. Specific focus is given to the possible catalytic implications of the surface properties on CO2 hydrogenation.

Singlet versus Triplet Reactivity in an Mn(V)-Oxo Species: Testing Theoretical Predictions Against Experimental Evidence.

Discerning the factors that control the reactivity of high-valent metal-oxo species is critical to both an understanding of metalloenzyme reactivity and related transition metal catalysts. Computational studies have suggested that an excited higher spin state in a number of metal-oxo species can provide a lower energy barrier for oxidation reactions, leading to the conclusion that this unobserved higher spin state complex should be considered as the active oxidant. However, testing these computational predictions by experiment is difficult and has rarely been accomplished. Herein, we describe a detailed computational study on the role of spin state in the reactivity of a high-valent manganese(V)-oxo complex with para-Z-substituted thioanisoles and utilize experimental evidence to distinguish between the theoretical results. The calculations show an unusual change in mechanism occurs for the dominant singlet spin state that correlates with the electron-donating property of the para-Z substituent, while this change is not observed on the triplet spin state. Minimum energy crossing point calculations predict small spin-orbit coupling constants making the spin state change from low spin to high spin unlikely. The trends in reactivity for the para-Z-substituted thioanisole derivatives provide an experimental measure for the spin state reactivity in manganese-oxo corrolazine complexes. Hence, the calculations show that the V-shaped Hammett plot is reproduced by the singlet surface but not by the triplet state trend. The substituent effect is explained with valence bond models, which confirm a change from an electrophilic to a nucleophilic mechanism through a change of substituent.

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs.

Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.

Origin of the Regioselective Fatty-Acid Hydroxylation versus Decarboxylation by a Cytochrome P450 Peroxygenase: What Drives the Reaction to Biofuel Production?

The cytochromes P450 are heme-based mono-oxygenases or peroxygenases involved in vital reaction processes for human health. A recently described P450 per-oxygenase, OleTJE , converts long-chain fatty acids to terminal olefins and as such may have biotechnological relevance in biodiesel production. However, the reaction produces significant amounts of α- and ß-hydroxylation by-products, and their origin are poorly understood. Herein, we elucidate through a QM/MM study on the bifurcation pathways how the three possible products are generated and show how the enzyme can be further engineered for optimum desaturase activity. The studies showed that the polarity and the solvent accessibility of the substrate in the binding pocket destabilize the OH-rebound pathways and kinetically enable a thermodynamically otherwise unfavorable decarboxylation reaction. The origins of the bifurcation pathways are analyzed with valence-bond models that highlight the differences in reaction mechanism.

Origin of the proton-transfer step in the cofactor-free (1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase: effect of the basicity of an active site His residue.

Dioxygenases catalyze a diverse range of chemical reactions that involve the incorporation of oxygen into a substrate and typically use a transition metal or organic cofactor for reaction. Bacterial (1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (HOD) belongs to a class of oxygenases able to catalyze this energetically unfavorable reaction without any cofactor. In the quinaldine metabolic pathway, HOD breaks down its natural N-heteroaromatic substrate using a mechanism that is still incompletely understood. Experimental and computational approaches were combined to study the initial step of the catalytic cycle. We have investigated the role of the active site His-251/Asp-126 dyad, proposed to be involved in substrate hydroxyl group deprotonation, a critical requirement for subsequent oxygen reaction. The pH profiles obtained under steady-state conditions for the H251A and D126A variants show a strong pH effect on their kcat and kcat/Km constants, with a decrease in kcat/Km of 5500- and 9-fold at pH 10.5, respectively. Substrate deprotonation studies under transient-state conditions show that this step is not rate-limiting and yield a pKa value of ∼ 7.2 for WT HOD. A large solvent isotope effect was found, and the pKa value was shifted to ∼ 8.3 in D2O. Crystallographic and computational studies reveal that the mutations have a minor effect on substrate positioning. Computational work shows that both His-251 and Asp-126 are essential for the proton transfer driving force of the initial reaction. This multidisciplinary study offers unambiguous support to the view that substrate deprotonation, driven by the His/Asp dyad, is an essential requirement for its activation.

Catalytic mechanism of cofactor-free dioxygenases and how they circumvent spin-forbidden oxygenation of their substrates.

Dioxygenases catalyze a diverse range of biological reactions by incorporating molecular oxygen into organic substrates. Typically, they use transition metals or organic cofactors for catalysis. Bacterial 1-H-3-hydroxy-4-oxoquinaldine-2,4-dioxygenase (HOD) catalyzes the spin-forbidden transfer of dioxygen to its N-heteroaromatic substrate in the absence of any cofactor. We combined kinetics, spectroscopic and computational approaches to establish a novel reaction mechanism. The present work gives insight into the rate limiting steps in the reaction mechanism, the effect of first-coordination sphere amino acids as well as electron-donating/electron-withdrawing substituents on the substrate. We highlight the role of active site residues Ser101/Trp160/His251 and their involvement in the reaction mechanism. The work shows, for the first time, that the reaction is initiated by triplet dioxygen and its binding to deprotonated substrate and only thereafter a spin state crossing to the singlet spin state occurs. As revealed by steady- and transient-state kinetics the oxygen-dependent steps are rate-limiting, whereas Trp160 and His251 are essential residues for catalysis and contribute to substrate positioning and activation, respectively. Computational modeling further confirms the experimental observations and rationalizes the electron transfer pathways, and the effect of substrate and substrate binding pocket residues. Finally, we make a direct comparison with iron-based dioxygenases and explain the mechanistic and electronic differences with cofactor-free dioxygenases. Our multidisciplinary study confirms that the oxygenation reaction can take place in absence of any cofactor by a unique mechanism in which the specially designed fit-for-purpose active-site architecture modulates substrate reactivity toward oxygen.

Differences and comparisons of the properties and reactivities of iron(III)-hydroperoxo complexes with saturated coordination sphere.

Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high-valent iron(IV)-oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)-hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)-hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)-hydroperoxo reacted directly with substrates or that an initial O-O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)-hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)-hydroperoxo complex with pentadentate ligand system (L5(2)). Direct C-O bond formation by an iron(III)-hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L5(2))Fe(III)(OOH)](2+) should be able to initiate an aromatic hydroxylation process, although a low-energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)-hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O-O bond, whereas a heterolytic O-O bond breaking in heme iron(III)-hydroperoxo is found.

Drug metabolism by cytochrome p450 enzymes: what distinguishes the pathways leading to substrate hydroxylation over desaturation?

Cytochrome P450 enzymes are highly versatile biological catalysts in our body that react with a broad range of substrates. Key functions in the liver include the metabolism of drugs and xenobiotics. One particular metabolic pathway that is poorly understood relates to the P450 activation of aliphatic groups leading to either hydroxylation or desaturation pathways. A DFT and QM/MM study has been carried out on the factors that determine the regioselectivity of aliphatic hydroxylation over desaturation of compounds by P450 isozymes. The calculations establish multistate reactivity patterns, whereby the product distributions differ on each of the spin-state surfaces; hence spin-selective product formation was found. The electronic and thermochemical factors that determine the bifurcation pathways were analysed and a model that predicts the regioselectivity of aliphatic hydroxylation over desaturation pathways was established from valence bond and molecular orbital theories. Thus, the difference in energy of the OH versus the OC bond formed and the π-conjugation energy determines the degree of desaturation products. In addition, environmental effects of the substrate binding pocket that affect the regioselectivities were identified. These studies imply that bioengineering P450 isozymes for desaturation reactions will have to include modifications in the substrate binding pocket to restrict the hydroxylation rebound reaction.

Hydrogen-bonding interactions trigger a spin-flip in iron(III) porphyrin complexes.

A key step in cytochrome P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure of a five-coordinate iron(III) octaethyltetraarylporphyrin chloride. The spin state of the metal was found to switch reversibly between high (S=5/2) and intermediate spin (S=3/2) with hydrogen bonding. Our study highlights the possible effects and importance of hydrogen-bonding interactions in heme proteins. This is the first example of a synthetic iron(III) complex that can reversibly change its spin state between a high and an intermediate state through weak external perturbations.

Identification and spectroscopic characterization of nonheme iron(III) hypochlorite intermediates.

Fe(III)-hypohalite complexes have been implicated in a wide range of important enzyme-catalyzed halogenation reactions including the biosynthesis of natural products and antibiotics and post-translational modification of proteins. The absence of spectroscopic data on such species precludes their identification. Herein, we report the generation and spectroscopic characterization of nonheme Fe(III)-hypohalite intermediates of possible relevance to iron halogenases. We show that Fe(III)-OCl polypyridylamine complexes can be sufficiently stable at room temperature to be characterized by UV/Vis absorption, resonance Raman and EPR spectroscopies, and cryo-ESIMS. DFT methods rationalize the pathways to the formation of the Fe(III)-OCl, and ultimately Fe(IV)=O, species and provide indirect evidence for a short-lived Fe(II)-OCl intermediate. The species observed and the pathways involved offer insight into and, importantly, a spectroscopic database for the investigation of iron halogenases.

Oxygen-atom transfer reactivity of axially ligated Mn(V)-oxo complexes: evidence for enhanced electrophilic and nucleophilic pathways.

Addition of anionic donors to the manganese(V)-oxo corrolazine complex Mn(V)(O)(TBP8Cz) has a dramatic influence on oxygen-atom transfer (OAT) reactivity with thioether substrates. The six-coordinate anionic [Mn(V)(O)(TBP8Cz)(X)](-) complexes (X = F(-), N3(-), OCN(-)) exhibit a ∼5 cm(-1) downshift of the Mn-O vibrational mode relative to the parent Mn(V)(O)(TBP8Cz) complex as seen by resonance Raman spectroscopy. Product analysis shows that the oxidation of thioether substrates gives sulfoxide product, consistent with single OAT. A wide range of OAT reactivity is seen for the different axial ligands, with the following trend determined from a comparison of their second-order rate constants for sulfoxidation: five-coordinate ≈ thiocyanate ≈ nitrate < cyanate < azide < fluoride ≪ cyanide. This trend correlates with DFT calculations on the binding of the axial donors to the parent Mn(V)(O)(TBP8Cz) complex. A Hammett study was performed with p-X-C6H4SCH3 derivatives and [Mn(V)(O)(TBP8Cz)(X)](-) (X = CN(-) or F(-)) as the oxidant, and unusual "V-shaped" Hammett plots were obtained. These results are rationalized based upon a change in mechanism that hinges on the ability of the [Mn(V)(O)(TBP8Cz)(X)](-) complexes to function as either an electrophilic or weak nucleophilic oxidant depending upon the nature of the para-X substituents. For comparison, the one-electron-oxidized cationic Mn(V)(O)(TBP8Cz(•+)) complex yielded a linear Hammett relationship for all substrates (ρ = -1.40), consistent with a straightforward electrophilic mechanism. This study provides new, fundamental insights regarding the influence of axial donors on high-valent Mn(V)(O) porphyrinoid complexes.

Direct observation of a nonheme iron(IV)-oxo complex that mediates aromatic C-F hydroxylation.

The synthesis of a pentadentate ligand with strategically designed fluorinated arene groups in the second coordination sphere of a nonheme iron center is reported. The oxidatively resistant fluorine substituents allow for the trapping and characterization of an Fe(IV)(O) complex at -20 °C. Upon warming of the Fe(IV)(O) complex, an unprecedented arene C-F hydroxylation reaction occurs. Computational studies support the finding that substrate orientation is a critical factor in the observed reactivity. This work not only gives rare direct evidence for the participation of an Fe(IV)(O) species in arene hydroxylation but also provides the first example of a high-valent iron-oxo complex that mediates aromatic C-F hydroxylation.

Experimental and computational evidence for the mechanism of intradiol catechol dioxygenation by non-heme iron(III) complexes.

Catechol intradiol dioxygenation is a unique reaction catalyzed by iron-dependent enzymes and non-heme iron(III) complexes. The mechanism by which these systems activate dioxygen in this important metabolic process remains controversial. Using a combination of kinetic measurements and computational modelling of multiple iron(III) catecholato complexes, we have elucidated the catechol cleavage mechanism and show that oxygen binds the iron center by partial dissociation of the substrate from the iron complex. The iron(III) superoxide complex that is formed subsequently attacks the carbon atom of the substrate by a rate-determining C-O bond formation step.