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Operando soft and hard X-ray spectroscopic techniques were used in combination with plane-wave density functional theory (DFT) simulations to rationalize the enhanced activities of Zn-containing Cu nanostructured electrocatalysts in the electrocatalytic CO2 hydrogenation reaction. We show that at a potential for CO2 hydrogenation, Zn is alloyed with Cu in the bulk of the nanoparticles with no metallic Zn segregated; at the interface, low reducible Cu(I)-O species are consumed. Additional spectroscopic features are observed, which are identified as various surface Cu(I) ligated species; these respond to the potential, revealing characteristic interfacial dynamics. Similar behavior was observed for the Fe-Cu system in its active state, confirming the general validity of this mechanism; however, the performance of this system deteriorates after successive applied cathodic potentials, as the hydrogen evolution reaction then becomes the main reaction pathway. In contrast to an active system, Cu(I)-O is now consumed at cathodic potentials and not reversibly reformed when the voltage is allowed to equilibrate at the open-circuit voltage; rather, only the oxidation to Cu(II) is observed. We show that the Cu-Zn system represents the optimal active ensembles with stabilized Cu(I)-O; DFT simulations rationalize this observation by indicating that Cu-Zn-O neighboring atoms are able to activate CO2, whereas Cu-Cu sites provide the supply of H atoms for the hydrogenation reaction. Our results demonstrate an electronic effect exerted by the heterometal, which depends on its intimate distribution within the Cu phase and confirms the general validity of these mechanistic insights for future electrocatalyst design strategies.

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.

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 CO 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.

Nature employs high-energy metal-oxo intermediates embedded within enzyme active sites to perform challenging oxidative transformations with remarkable selectivity. Understanding how different local metal-oxo coordination environments control intermediate reactivity and catalytic function is a long-standing objective. However, conducting structure–activity relationships directly in active sites has proven challenging due to the limited range of amino acid substitutions achievable within the constraints of the genetic code. Here, we use an expanded genetic code to examine the impact of hydrogen bonding interactions on ferryl heme structure and reactivity, by replacing the N–H group of the active site Trp51 of cytochrome c peroxidase by an S atom. Removal of a single hydrogen bond stabilizes the porphyrin π-cation radical state of CcP W191F compound I. In contrast, this modification leads to more basic and reactive neutral ferryl heme states, as found in CcP W191F compound II and the wild-type ferryl heme-Trp191 radical pair of compound I. This increased reactivity manifests in a >60-fold activity increase toward phenolic substrates but remarkably has negligible effects on oxidation of the biological redox partner cytc. Our data highlight how Trp51 tunes the lifetimes of key ferryl intermediates and works in synergy with the redox active Trp191 and a well-defined substrate binding site to regulate catalytic function. More broadly, this work shows how noncanonical substitutions can advance our understanding of active site features governing metal-oxo structure and reactivity.

A superbase ionic liquid (IL), trihexyltetradecylphosphonium benzimidazolide ([P66614][Benzim]), is investigated for the capture of CO2 in the presence of NO2 impurities. The effect of the waste gas stream contaminant on the ability of the IL to absorb simultaneously CO2 is demonstrated using novel measurement techniques, including a mass spectrometry breakthrough method and in situ infrared spectroscopy. The findings show that the presence of an industrially relevant concentration of NO2 in a combined feed with CO2 has the effect of reducing the capacity of the IL to absorb CO2 efficiently by ∼60% after 10 absorption–desorption cycles. This finding is supported by physical property analysis (viscosity, 1H and 13C NMR, and X-ray photoelectron spectroscopy) and spectroscopic infrared characterization, in addition to density functional theory (DFT) calculations, to determine the structure of the IL-NO2 complex. The results are presented in comparison with another flue gas component, NO, demonstrating that the absorption of NO2 is more favorable, thereby hindering the ability of the IL to absorb CO2. Significantly, this work aids understanding of the effects that individual components of flue gas have on CO2 capture sorbents, through studying a contaminant that has received limited interest previously.

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.

Unwanted N2O formation is a problem that has been noted in selective catalytic reduction (SCR) where copper zeolite catalysts are utilized. With its immense global warming potential and long-term stability, elevated atmospheric N2O has already been identified as a future challenge in the war on climate change. This paper explores the phenomenon of N2O formation during NH3-SCR over Cu-SSZ-13 catalysts, which are currently commercialized in automotive emissions control systems, and proposes a link between N2O production and the local copper environment found within the zeolite. To achieve this, a comparison is made between two Cu-SSZ-13 samples with different copper co-ordinations produced via different synthesis methods. A combination of synchrotron X-ray absorption near-edge spectroscopy, UV–vis, Raman, and density functional theory (DFT) is used to characterize the nature of copper species present within each sample. Synchrotron IR microspectroscopy is then used to compare their behavior during SCR under operando conditions and monitor the evolution of nitrate intermediates, which, along with further DFT, informs a mechanistic model for nitrate decomposition pathways. Increased N2O production is seen in the Cu-SSZ-13 sample postulated to contain a linear Cu species, providing an important correlation between the catalytic behavior of Cu-zeolites and the nature of their metal ion loading and speciation.

Density functional methods are applied to explore the reaction mechanism for CO2 hydrogenation to methanol over low-index Cu surfaces, namely Cu(110) and Cu(100). A detailed reaction network is obtained, examining several different possible mechanistic routes, including methanol formation via formate and hydrocarboxyl bound intermediates, the role of formaldehyde and formic acid as stable intermediary reaction products, as well as exploring the possibility of CO2 dissociation and subsequent hydrogenation of the resultant CO. We find that, in contrast to the dominant Cu(111) facet, the Cu(110) and Cu(100) surfaces facilitate a moderate extent of CO2 activation, which results in lower activation barriers for initial elementary processes involving CO2 hydrogenation and dissociation, opening up reaction pathways considered unfeasible for Cu(111). Consequently, a wider variety of potential mechanistic routes to achieve methanol synthesis is observed and compared to Cu(111), illustrating the essential role of the Cu surface structure in catalytic activity, and providing insights into the mechanism of CO2 hydrogenation over Cu-based catalysts. In providing a thorough and detailed exploration of all of the possible mechanistic pathways for CO2 conversion to methanol, the present work represents a reference point for future studies investigating systems representative of the industrial Cu/ZnO catalyst, enabling a clear identification of the limitations of unsupported Cu catalysts, and thus allowing a more complete understanding of the role of the support material.

DNA base repair mechanisms of alkylated DNA bases is an important reaction in chemical biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate-dependent nonheme iron dioxygenase named the AlkB repair enzyme. In this work we report a detailed computational study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases. In particular, we investigate the aliphatic hydroxylation and C[double bond, length as m-dash]C epoxidation mechanisms of alkylated DNA bases by a high-valent iron(iv)-oxo intermediate. Our computational studies use quantum mechanics/molecular mechanics methods on full enzymatic structures as well as cluster models on active site systems. The work shows that the iron(iv)-oxo species is rapidly formed after dioxygen binding to an iron(ii) center and passes a bicyclic ring structure as intermediate. Subsequent cluster models explore the mechanism of substrate hydroxylation and epoxidation of alkylated DNA bases. The work shows low energy barriers for substrate activation and consequently energetically feasible pathways are predicted. Overall, the work shows that a high-valent iron(iv)-oxo species can efficiently dealkylate alkylated DNA bases and return them into their original form.

The development of affordable bifunctional platinum alloys as electrode materials for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) remains one of the biggest challenges for the transition towards renewable energy sources. Yet, there is very little information on the optimal ratio between platinum and the transition metal used in the alloy and its impact on the electronic properties. Here, we have employed spin-polarised density functional simulations with long-range dispersion corrections [DFT–D3–(BJ)], to investigate the thermodynamics of mixing, as well as the electronic and magnetic properties of the Pt1−xNix solid solution. The Ni incorporation is an exothermic process and the alloy composition Pt0.5Ni0.5 is the most thermodynamically stable. The Pt0.5Ni0.5 solid solution is highly ordered as it is composed mainly of two symmetrically inequivalent configurations of homogeneously distributed atoms. We have obtained the atomic projections of the electronic density of states and band structure, showing that the Pt0.5Ni0.5 alloy has metallic character. The suitable electronic properties of the thermodynamically stable Pt0.5Ni0.5 solid solution shows promise as a sustainable catalyst for future regenerative fuel cells.

The development of affordable bifunctional platinum alloys as electrode materials for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) remains one of the biggest challenges for the transition towards renewable energy sources. Yet, there is very little information on the optimal ratio between platinum and the transition metal used in the alloy and its impact on the electronic properties. Here, we have employed spin-polarised density functional simulations with long-range dispersion corrections [DFT-D3-(BJ)], to investigate the thermodynamics of mixing, as well as the electronic and magnetic properties of the Pt

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.

International audience; The effect of acidic gases present in flue gas, specifically NO, on the capture of CO2 by the superbase ionic liquid, trihexyltetradecylphosphonium benzimidazolide ([P66614][Benzim]), is reported. An online mass spectrometry technique was utilized to study the CO2 uptake of the ionic liquid during multiple absorption and desorption cycles of a gas feed containing NO and CO2 at realistic flue gas concentrations, and it was found that while NO alone could bind irreversibly, the CO2 capacity of the IL was largely unaffected by the presence of NO in a cofeed of the gases. In situ attenuated total reflection infrared was employed to probe the competitive absorption of CO2 and NO by [P66614][Benzim], in which carbamate and NONOate species were observed to cobind to different sites of the benzimidazolide anion. These effects were further characterized by analyzing changes in physical properties (viscosity and nitrogen content) and other spectroscopic changes (1H NMR, 13C NMR and XPS). Density functional theory computations were used to calculate binding energies and infrared frequencies of the absorption products, which were shown to corroborate the results and explain the reaction pathways.

Enzymes are versatile oxidants in Nature that catalyze a range of reactions very efficiently. Experimental studies on the mechanism of enzymes are sometimes difficult due to the short lifetime of catalytic cycle intermediates. Theoretical modeling can assist and guide experiment and elucidate mechanisms for fast reaction pathways. Two key computational approaches are in the literature, namely quantum mechanics/molecular mechanics (QM/MM) on complete enzyme structures and QM cluster models on active site structures only. These two approaches are reviewed here. We give examples where the QM cluster approach worked well and, for instance, enabled the bioengineering of an enzyme to change its functionality. In addition, several examples are given, where QM cluster models were insufficient and full QM/MM structures were needed to establish regio-, chemo-, and stereoselectivities.

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.

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 CO

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.

Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum (opium poppy), which belongs to the non-heme 2-oxoglutarate/Fe(II)-dependent dioxygenases (ODD) family, is a key enzyme in the morphine biosynthesis pathway. Initially, T6ODM was characterized as an enzyme catalyzing O-demethylation of thebaine to neopinone and oripavine to morphinone. However, the substrate range of T6ODM was recently expanded to a number of various benzylisoquinoline alkaloids. Here, we present crystal structures of T6ODM in complexes with 2-oxoglutarate (T6ODM:2OG, PDB: 5O9W) and succinate (T6ODM:SIN, PDB: 5O7Y). Both metal and 2OG binding sites display similarity to other proteins from the ODD family, but T6ODM is characterized by an exceptionally large substrate binding cavity, whose volume can partially explain the promiscuity of this enzyme. Moreover, the size of the cavity allows for binding of multiple molecules at once, posing a question about the substrate-driven specificity of the enzyme.

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.

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 ≈ nitratecyanateazidefluoride ≪ 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.

Background: The mechanism of cofactor-free dioxygenases has not been clearly elucidated. Results: Mutation of the His/Asp dyad in (1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase strongly affects substrate deprotonation and overall catalysis. Conclusion: Base mechanism is demonstrated where His-251 acts as catalytic base and Asp-126 modulates basicity. Significance: Many dioxygenases activate their substrates via deprotonation, which is an essential step for later reaction with oxygen., 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.

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N(1) -methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)-oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ- and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.

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.

Several nonheme iron enzymes and biomimetic model complexes catalyze a substrate halogenation reaction. Recent computational studies (Borowski et al. J Am Chem Soc 132:12887-12898, 2010) on α-ketoglutarate dependent halogenase proposed an initial isomerization reaction that is important to give halogenated products. We present here a series of density functional theory calculations on a biomimetic model complex-[Fe(IV)(O)(TPA)Cl](+), where TPA is tris(2-pyridylmethyl)amine-and investigate the mechanisms of substrate halogenation versus hydroxylation using the reactant and its isomer where the oxo and chloro groups have changed positions. We show here that the reactions occur on a dominant quintet spin state surface, although the reactants are in a triplet state. Despite the fact that the reactants can exist in two stable isomers with the oxo group either trans or cis to the axial ligand, they react differently with substrates, where one gives dominant hydroxylation and the other gives dominant chlorination of substrates. The ligand in the cis position of the oxo group is found to be active in the reaction mechanism and donated to the substrate during the reaction. A detailed thermochemical analysis of possible reaction mechanisms reveals that the strengths of the Fe-OH and Fe-Cl bonds in the radical intermediates are the key reasons for this regioselectivity switch of hydroxylation over halogenation. This study highlights the differences between enzymatic and biomimetic halogenases, where the former only react after an essential isomerization step, which is not necessary in model complexes.

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.

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 β-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.

Iron-containing metalloenzymes are found throughout the natural world and are vital catalysts in many crucial metabolic and biosynthetic biological pathways. In nature, the major classes of metallo-heme-proteins are the monooxygenases, containing a protoporphyrin IX center, the catalases and the peroxidases. The cytochromes P450 (P450s) are a superfamily of heme-containing, structurally and functionally diverse enzymes that are ubiquitous to most biochemical systems; as such they have attracted interest of many researchers. The huge array of often evolutionarily unrelated proteins that fall into this super class of enzymes means that it is more useful to subdivide nonheme iron enzymes into classes based on the ligands that coordinate their iron cores. The largest of these classes belongs to a group of nonheme iron dioxygenases which have a structural motif that coordinates the iron through two histidine and one aspartate amino acid creating a facial 2-His-1-Asp ligand system.

The review focus is a comparison of QM and QM/MM modeling techniques applied to study of metalloenzymes. The chapter aim is to highlight many of the advantages and potential pitfalls of the exciting and revolutionary QM/MM techniques using both large QM/MM systems and QM-only modeling as references. The review is illustrated by case studies for isopenicillin N synthase, ethylbenzene dehydrogenase, cytochrome P450 enzyme, AlkB DNA repair enzyme as well as 4-hydroxyphenylpyruvate dioxygenase. We find many advantages in various QM/MM techniques, over the more traditional QM cluster approaches, while at the same time offering some advice about how to avoid potential complications arising from some of these approaches’ most notable drawbacks. We conclude that while there will always be an important role for QM cluster models, in computational studies, the revolutionary developments in QM/MM techniques open a bright and exciting future of new research.

Aquest mateix article està publicat a l'edició en alemany de la revista 'Angewandte Chemie' ISSN 0044-8249, EISSN 1521-3757), 2015, vol. 127, núm. 14, p. 4431–4435 http://dx.doi.org/10.1002/ange.201411995 FeIII-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 FeIII-hypohalite intermediates of possible relevance to iron halogenases. We show that FeIII-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 FeIII-OCl, and ultimately FeIV=O, species and provide indirect evidence for a short-lived FeII-OCl intermediate. The species observed and the pathways involved offer insight into and, importantly, a spectroscopic database for the investigation of iron halogenases Financial support comes from the European Research Council (ERC-2011-StG-279549 to W.R.B.; ERC-2009-StG-239910 to M.C.), the Netherlands Fund for Technology and Science STW (11059, to W.R.B.) the Ministry of Education, Culture and Science (Gravity program 024.001.035 to A.D. and W.R.B.) and the Ubbo Emmius Fund of the University of Groningen (A.D.). The BBSRC is thanked for a studentship to M.G.Q. and COST action CM1003 “Biological oxidation reactions—mechanism and design of new catalyst” for funding of a short-term scientific mission to A.D. and D.A. The National (UK) Service of Computational Chemistry Software is acknowledged for providing CPU time (S.P.d.V.)

With computational resources becoming more efficient and more powerful and at the same time cheaper, computational methods have become more and more popular for studies on biochemical and biomimetic systems. Although large efforts from the scientific community have gone into exploring the possibilities of computational methods for studies on large biochemical systems, such studies are not without pitfalls and often cannot be routinely done but require expert execution. In this review we summarize and highlight advances in computational methodology and its application to enzymatic and biomimetic model complexes. In particular, we emphasize on topical and state-of-the-art methodologies that are able to either reproduce experimental findings, e.g., spectroscopic parameters and rate constants, accurately or make predictions of short-lived intermediates and fast reaction processes in nature. Moreover, we give examples of processes where certain computational methods dramatically fail.

With computational resources becoming more efficient and more powerful and at the same time cheaper, computational methods have become more and more popular for studies on biochemical and biomimetic systems. Although large efforts from the scientific community have gone into exploring the possibilities of computational methods for studies on large biochemical systems, such studies are not without pitfalls and often cannot be routinely done but require expert execution. In this review we summarize and highlight advances in computational methodology and its application to enzymatic and biomimetic model complexes. In particular, we emphasize on topical and state-of-the-art methodologies that are able to either reproduce experimental findings, e.g., spectroscopic parameters and rate constants, accurately or make predictions of short-lived intermediates and fast reaction processes in nature. Moreover, we give examples of processes where certain computational methods dramatically fail.

The new biomimetic ligands N4Py(2Ph) (1) and N4Py(2Ph,amide) (2) were synthesized and yield the iron(II) complexes [Fe(II)(N4Py(2Ph))(NCCH3)](BF4)2 (3) and [Fe(II)(N4Py(2Ph,amide))](BF4)2 (5). Controlled orientation of the Ph substituents in 3 leads to facile triplet spin reactivity for a putative Fe(IV)(O) intermediate, resulting in rapid arene hydroxylation. Addition of a peripheral amide substituent within hydrogen-bond distance of the iron first coordination sphere leads to stabilization of a high-spin Fe(III)OOR species which decays without arene hydroxylation. These results provide new insights regarding the impact of secondary coordination sphere effects at nonheme iron centers.

Density functional theory (DFT) calculations are presented on biomimetic model complexes of cysteine dioxygenase and focus on the effect of axial and equatorial ligand placement. Recent studies by one of us [Y. M. Badiei, M. A. Siegler and D. P. Goldberg, J. Am. Chem. Soc. 2011, 133, 1274] gave evidence of a nonheme iron biomimetic model of cysteine dioxygenase using an i-propyl-bis(imino)pyridine, equatorial tridentate ligand. Addition of thiophenol, an anion – either chloride or triflate – and molecular oxygen, led to several possible stereoisomers of this cysteine dioxygenase biomimetic complex. Moreover, large differences in reactivity using chloride as compared to triflate as the binding anion were observed. Here we present a series of DFT calculations on the origin of these reactivity differences and show that it is caused by the preference of coordination site of anion versus thiophenol binding to the chemical system. Thus, stereochemical interactions of triflate and the bulky iso-propyl substituents of the ligand prevent binding of thiophenol in the trans position using triflate. By contrast, smaller anions, such as chloride, can bind in either cis or trans ligand positions and give isomers with similar stability. Our calculations help to explain the observance of thiophenol dioxygenation by this biomimetic system and gives details of the reactivity differences of ligated chloride versus triflate.

There is a major controversy in cytochrome P450 chemistry regarding the nature of the active oxidant responsible for substrate monoxygenation. Part of this controversy originates from the fact that the later stages in the catalytic cycle of P450 enzymes proceed so fast that little experimental evidence is available. Early studies suggested an iron(IV)- oxo heme cation radical ([heme((+•))-Fe(IV)=O] or Compound I) as the active species able to abstract a hydrogen atom from a substrate and rebind the hydroxyl group to form an alcohol product. Such simplistic early models involving a single active species have subsequently been invalidated by several experimental studies which clearly indicates that there must be at least two active species of some description. Based on these and other data, a two-oxidant hypothesis was put forward where Compound I and its precursor in the catalytic cycle ([heme-Fe(III)-OOH]- or Compound 0) are competitive oxidants. Density functional theory studies, however, suggest an alternative hypothesis involving a two-state-reactivity scenario where Compound I has two close-lying spin states that react differently with substrates and masquerade as two distinct oxidants. These theoretical studies show that the two spin states of Compound I react with substrates via aliphatic and aromatic C-H hydroxylation, C=C epoxidation and sulfoxidation reactions, and explain experimentally observed product distributions and kinetic isotope effects. This review will give an overview of recent studies on the two-oxidant versus two-state-reactivity hypotheses and how theory contributes to the understanding of enzymatic reaction processes.