Probing Ferryl Reactivity in a Nonheme Iron Oxygenase Using an Expanded Genetic Code.

The ability to introduce noncanonical amino acids as axial ligands in heme enzymes has provided a powerful experimental tool for studying the structure and reactivity of their Fe=O ("ferryl") intermediates. Here, we show that a similar approach can be used to perturb the conserved Fe coordination environment of 2-oxoglutarate (2OG) dependent oxygenases, a versatile class of enzymes that employ highly-reactive ferryl intermediates to mediate challenging C-H functionalizations. Replacement of one of the cis-disposed histidine ligands in the oxygenase VioC with a less electron donating -methyl-histidine (MeHis) preserves both catalytic function and reaction selectivity.

Interfacial Chemistry in the Electrocatalytic Hydrogenation of CO over C-Supported Cu-Based Systems.

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 CO hydrogenation reaction. We show that at a potential for CO 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.

Catalytic Reduction of Carbon Dioxide on the (001), (011), and (111) Surfaces of TiC and ZrC: A Computational Study.

We present a computational study of the activity and selectivity of early transition-metal carbides as carbon dioxide reduction catalysts. We analyze the effects of the adsorption of CO and H on the (001), (011), and metal-terminated (111) surfaces of TiC and ZrC, as carbon dioxide undergoes either dissociation to CO or hydrogenation to COOH or HCOO. The relative stabilities of the three reduction intermediates and the activation energies for their formation allow the identification of favored pathways on each surface, which are examined as they lead to the release of CO, HCOOH, CHOH, and CH, thereby also characterizing the activity and selectivity of the two materials.

A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase.

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.

Combined Experimental and Theoretical Study of the Competitive Absorption of CO and NO by a Superbase Ionic Liquid.

A superbase ionic liquid (IL), trihexyltetradecylphosphonium benzimidazolide ([P][Benzim]), is investigated for the capture of CO in the presence of NO impurities. The effect of the waste gas stream contaminant on the ability of the IL to absorb simultaneously CO is demonstrated using novel measurement techniques, including a mass spectrometry breakthrough method and infrared spectroscopy. The findings show that the presence of an industrially relevant concentration of NO in a combined feed with CO has the effect of reducing the capacity of the IL to absorb CO efficiently by ∼60% after 10 absorption-desorption cycles.

How bulk and surface properties of TiSiC, VSiC, NbSiC and ZrSiC 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.

Mechanism of CO conversion to methanol over Cu(110) and Cu(100) surfaces.

Density functional methods are applied to explore the reaction mechanism for CO 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 CO 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 CO activation, which results in lower activation barriers for initial elementary processes involving CO hydrogenation and dissociation, opening up reaction pathways considered unfeasible for Cu(111).

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

Understanding the surface reactivity of the commercial cathode material LiMnO 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 LiMnO spinel (0.000 < x < 0.

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.

Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways.

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.

Mixing thermodynamics and electronic structure of the Pt Ni (0 ≤ ≤ 1) bimetallic alloy.

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 Ni solid solution.

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 CO by TiC, VC, ZrC and NbC. Particular focus is given to the study of CO/HO co-adsorption and interaction on four carbide low-index surfaces: {001}, {011}, carbon-terminated {111} and metal-terminated {111}. The adsorption and activation of CO 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.

Advances in Sustainable Catalysis: A Computational Perspective.

The enormous challenge of moving our societies to a more sustainable future offers several exciting opportunities for computational chemists. The first principles approach to "catalysis by design" will enable new and much greener chemical routes to produce vital fuels and fine chemicals. This prospective outlines a wide variety of case studies to underscore how the use of theoretical techniques, from QM/MM to unrestricted DFT and periodic boundary conditions, can be applied to biocatalysis and to both homogeneous and heterogenous catalysts of all sizes and morphologies to provide invaluable insights into the reaction mechanisms they catalyze.

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.

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 CO 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.

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 β-hydroxylation by-products, and their origin are poorly understood.

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.

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.

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.

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.

Identification and Spectroscopic Characterization of Nonheme Iron(III) Hypochlorite Intermediates.

Fe-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-hypohalite intermediates of possible relevance to iron halogenases.