Lytic polysaccharide monooxygenases (LPMOs) are Cu-containing enzymes that facilitate the degradation of recalcitrant polysaccharides by the oxidative cleavage of glycosidic bonds. They are gaining rapidly increasing attention as key players in biomass conversion, especially for the production of second-generation biofuels. Elucidation of the detailed mechanism of the LPMO reaction is a major step toward the assessment and optimization of LPMO efficacy in industrial biotechnology, paving the way to utilization of sustainable fuel sources. Here, we used density functional theory calculations to study the reaction pathways suggested to date, exploiting a very large active-site model for a fungal AA9 LPMO and using a celloheptaose unit as a substrate mimic. We identify a copper oxyl intermediate as being responsible for H-atom abstraction from the substrate, followed by a rapid, water-assisted hydroxyl rebound, leading to substrate hydroxylation.

Spectroscopic investigation of an isolated [NiFe]-hydrogenase large subunit enables a unique view of the NiFe(CO)(CN)2 cofactor.

The apparently simple dihydrogen formation from protons and electrons (2H + + 2e − ⇄ H 2 ) is one of the most challenging reactions in nature. It is catalyzed by metalloenzymes of amazing complexity, called hydrogenases. A better understanding of the chemistry of these enzymes, especially that of the [NiFe]-hydrogenases subgroup, has important implications for production of H 2 as alternative sustainable fuel. In this work, reactivation mechanism of the oxidized and inactive Ni−B and Ni−A states of the [NiFe]hydrogenases active site has been investigated using density functional theory. Results obtained from this study show that one-electron reduction and protonation of the active site promote the removal of the bridging hydroxide ligand contained in Ni−B and Ni−A. However, this process is sufficient to activate only the Ni−B state. H 2 binding to the active site is required to convert Ni−A to the active Ni−SI a state. Here, we also propose a reasonable structure for the spectroscopically well-characterized Ni−SI r and Ni−SU species, formed respectively from the one-electron reduction of Ni−B and Ni−A. Ni−SI r , depending on the pH at which the reaction occurs, features a bridging hydroxide ligand or a water molecule terminally coordinated to the Ni atom, whereas in Ni−SU a water molecule is terminally coordinated to the Fe atom, and the Cys64 residue is oxidized to sulfenate. The sulfenate oxygen atom in the Ni−A state affects the stereoelectronic properties of the binuclear cluster by modifying the coordination geometry of Ni, and consequently, by switching the regiochemistry of H 2 O and H 2 binding from the Ni to the Fe atom. This effect is predicted to be at the origin of the different reactivation kinetics of the oxidized and inactive Ni−B and Ni−A states.

This perspective aims at illustrating a computational viewpoint on some specific issues concerning structure-activity relationships related to [FeFe]-hydrogenase ([FeFe]-H2ase) biomimicry. Most of research outlined herein have been addressed by means...

In view of the depletion of fossil fuel reserves and climatic effects of greenhouse gas emissions, Ni,Fe-containing carbon monoxide dehydrogenase (Ni-CODH) enzymes have attracted increasing interest in recent years for their capability to selectively catalyze the reversible reduction of CO 2 to CO (CO 2 + 2H + + 2e – CO + H 2 O). The possibility of converting the greenhouse gas CO 2 into useful materials that can be used as synthetic building blocks or, remarkably, as carbon fuels makes Ni-CODH a very promising target for reverse-engineering studies. In this context, in order to provide insights into the chemical principles underlying the biological catalysis of CO 2 activation and reduction, quantum mechanics calculations have been carried out in the framework of density functional theory (DFT) on different-sized models of the Ni-CODH active site. With the aim of uncovering which stereoelectronic properties of the active site (known as the C-cluster) are crucial for the efficient binding and release of CO 2 , different coordination modes of CO 2 to different forms and redox states of the C-cluster have been investigated. The results obtained from this study highlight the key role of the protein environment in tuning the reactivity and the geometry of the C-cluster. In particular, the protonation state of His93 is found to be crucial for promoting the binding or the dissociation of CO 2 . The oxidation state of the C-cluster is also shown to be critical. CO 2 binds to C red2 according to a dissociative mechanism (i.e., CO 2 binds to the C-cluster after the release of possible ligands from Fe u ) when His93 is doubly protonated. CO 2 can also bind noncatalytically to C red1 according to an associative mechanism (i.e., CO 2 binding is preceded by the binding of H 2 O to Fe u ). Conversely, CO 2 dissociates when His93 is singly protonated and the C-cluster is oxidized at least to the C int redox state.

Aim of this contribution is to review some recent quantum mechanical approaches used to compute the redox potentials of transition metal complexes, with the emphasis on copper and iron species, which are particularly relevant in inorganic biochemistry and in synthetic chemistry of biomimetic compounds. The paper presents also new DFT results obtained on Cu and Fe aquo ions in the framework of the Thermodynamic Integration and Grand Canonical Ensemble approaches.Such results show that without explicit inclusion of water molecules in the external solvation shells (even using a continuum solvation model) also very advanced methodologies fail to predict the redox potential in an acceptable manner. This is a confirmation of some previous studies which however never addressed this specific problem along the aforementioned approaches. Better Parkinson and Alzheimer diseases. [2][3][4] As a consequence, the disclosure of the catalytic mechanism of Fe and Cu enzymes, as well as of related bio-mimetic or bio-inspired compounds, is crucial to understand such processes at the molecular level. In this context, the role of computational chemistry, and more specifically of quantum mechanical (QM) methods, cannot be underestimated. These methods, when giving reliable predictions, may nicely complement the experimental investigations, especially to elucidate the catalytic mechanisms of Fe and Cu enzymes, and of related bio-mimetic coordination compounds. [5,6] In fact, most QM studies have been focused on the chemical steps of the catalytic cycles, [7] that is, steps characterized by covalent bond formation and/or cleavage, disclosing the structure and relative energy of key intermediate species and corresponding transition states connecting them, whereas the energetics of redox steps has been often neglected. Indeed, the proper description of electron transfer in coordination compounds implies the accurate calculation of standard reduction potentials, which can be more or less tricky, depending on the coordination compound under investigation. When considering Fe and Cu biologically relevant compounds, several considerations are in order. While iron is often bound to proteins as a cofactor (e.g., the heme group), copper is usually Int.

[NiFe]-hydrogenases catalyse the relevant H → 2H + 2e reaction. Aerobic oxidation or anaerobic oxidation of this enzyme yields two inactive states called Ni-A and Ni-B. These states differ for the reactivation kinetics which are slower for Ni-A than Ni-B. While there is a general consensus on the structure of Ni-B, the nature of Ni-A is still controversial. Indeed, several crystallographic structures assigned to the Ni-A state have been proposed, which, however, differ for the nature of the bridging ligand and for the presence of modified cysteine residues. The spectroscopic characterization of Ni-A has been of little help due to small differences of calculated spectroscopic parameters, which does not allow to discriminate among the various forms proposed for Ni-A. Here, we report a DFT investigation on the nature of the Ni-A state, based on systematic explorations of conformational and configurational space relying on accurate energy calculations, and on comparisons of theoretical geometries with the X-ray structures currently available. The results presented in this work show that, among all plausible isomers featuring various protonation patterns and oxygenic ligands, the one corresponding to the crystallographic structure recently reported by Volbeda et al. (J Biol Inorg Chem 20:11-22, 19)-featuring a bridging hydroxide ligand and the sulphur atom of Cys64 oxidized to bridging sulfenate-is the most stable. However, isomers with cysteine residues oxidized to terminal sulfenate are very close in energy, and modifications in the network of H-bond with neighbouring residues may alter the stability order of such species.

The extraordinary capability of [NiFe]-hydrogenases to catalyse the reversible interconversion of protons and electrons into dihydrogen (H) has stimulated numerous experimental and theoretical studies addressing the direct utilization of these enzymes in H production processes. Unfortunately, the introduction of these natural H-catalysts in biotechnological applications is limited by their inhibition under oxidising (aerobic and anaerobic) conditions. With the aim of contributing to overcome this limitation, we studied the oxidative inactivation mechanism of [NiFe]-hydrogenases by performing Density Functional Theory (DFT) calculations on a very large model of their active site in which all the amino acids forming the first and second coordination spheres of the NiFe cluster have been explicitly included. We identified an O molecule and two HO molecules as sources of the two oxygen atoms that are inserted at the active site of the inactive forms of the enzyme (Ni-A and Ni-B) under aerobic and anaerobic conditions, respectively. Furthermore, our results support the experimental evidence that the Ni-A-to-Ni-B ratio strongly depends on the number of reducing equivalents available for the process and on the oxidizing conditions under which the reaction takes place.