Multiscale Modeling of the Active Site of [Fe] Hydrogenase: The H2Binding Site in Open and Closed Protein Conformations

Enzymatic and Bioinspired Systems for Hydrogen Production

The extraordinary potential of hydrogen as a clean and sustainable fuel has sparked the interest of the scientific community to find environmentally friendly methods for its production. Biological catalysts are the most attractive solution, as they usually operate under mild conditions and do not produce carbon-containing byproducts. Hydrogenases promote reversible proton reduction to hydrogen in a variety of anoxic bacteria and algae, displaying unparallel catalytic performances. Attempts to use these sophisticated enzymes in scalable hydrogen production have been hampered by limitations associated with their production and stability. Inspired by nature, significant efforts have been made in the development of artificial systems able to promote the hydrogen evolution reaction, via either electrochemical or light-driven catalysis. Starting from small-molecule coordination compounds, peptide- and protein-based architectures have been constructed around the catalytic center with the aim of reproducing hydrogenase function into robust, efficient, and cost-effective catalysts. In this review, we first provide an overview of the structural and functional properties of hydrogenases, along with their integration in devices for hydrogen and energy production. Then, we describe the most recent advances in the development of homogeneous hydrogen evolution catalysts envisioned to mimic hydrogenases.

Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research

Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.

Heterologous Hydrogenase Overproduction Systems for Biotechnology-An Overview

Hydrogenases are complex metalloenzymes, showing tremendous potential as H2-converting redox catalysts for application in light-driven H2 production, enzymatic fuel cells and H2-driven cofactor regeneration. They catalyze the reversible oxidation of hydrogen into protons and electrons. The apo-enzymes are not active unless they are modified by a complicated post-translational maturation process that is responsible for the assembly and incorporation of the complex metal center. The catalytic center is usually easily inactivated by oxidation, and the separation and purification of the active protein is challenging. The understanding of the catalytic mechanisms progresses slowly, since the purification of the enzymes from their native hosts is often difficult, and in some case impossible. Over the past decades, only a limited number of studies report the homologous or heterologous production of high yields of hydrogenase. In this review, we emphasize recent discoveries that have greatly improved our understanding of microbial hydrogenases. We compare various heterologous hydrogenase production systems as well as in vitro hydrogenase maturation systems and discuss their perspectives for enhanced biohydrogen production. Additionally, activities of hydrogenases isolated from either recombinant organisms or in vivo/in vitro maturation approaches were systematically compared, and future perspectives for this research area are discussed.

Dioxygen Sensitivity of [Fe]-Hydrogenase in the Presence of Reducing Substrates

Mono-iron hydrogenase ([Fe]-hydrogenase) reversibly catalyzes the transfer of a hydride ion from H₂ to methenyltetrahydromethanopterin (methenyl-H₄ MPT⁺ ) to form methylene-H₄ MPT. Its iron guanylylpyridinol (FeGP) cofactor plays a key role in H₂ activation. Evidence is presented for O₂ sensitivity of [Fe]-hydrogenase under turnover conditions in the presence of reducing substrates, methylene-H₄ MPT or methenyl-H₄ MPT⁺ /H₂ . Only then, H₂ O₂ is generated, which decomposes the FeGP cofactor; as demonstrated by spectroscopic analyses and the crystal structure of the deactivated enzyme. O₂ reduction to H₂ O₂ requires a reductant, which can be a catalytic intermediate transiently formed during the [Fe]-hydrogenase reaction. The most probable candidate is an iron hydride species; its presence has already been predicted by theoretical studies of the catalytic reaction. The findings support predictions because the same type of reduction reaction is described for ruthenium hydride complexes that hydrogenate polar compounds.

Synthesis, Reactivity, and Catalytic Transfer Hydrogenation Activity of Ruthenium Complexes Bearing NNN Tridentate Ligands: Influence of the Secondary Coordination Sphere

By the introduction of -OH group(s) into different position(s) of 6-(pyridin-2-ylmethyl)-2,2'-bipyridine, several NNN-type ligands were synthesized and then introduced to ruthenium (Ru) centers by reactions with RuCl2(PPh3)3. In the presence of PPh3 or CO, these ruthenium complexes reacted with NH4PF6 in CH2Cl2 or CH3OH to give a series of ionic products 5-9. The reaction of Ru(L2)(PPh3)Cl2 (2) with CO generated a neutral complex [Ru(L2)(CO)Cl2] (10). In the presence of CH3ONa, 10 was further converted into complex [Ru(L2)(HOCH3)(CO)Cl] (11), in which there was a methanol molecule coordinating with ruthenium, as suggested by density functional theory calculations. The catalytic transfer hydrogenation activity of all of these new bifunctional metal-ligand complexes was tested. Dichloride complex 2 exhibits best activity, whereas carbonyl complexes 10 and 11 are efficient for selectively reducing 5-hexen-2-one, suggesting different hydrogenation mechanisms. The results reveal the dramatic influence for the reactivity and catalytic activity of the secondary coordination sphere in transition metal complexes.

Multiscale Modelling of Lytic Polysaccharide Monooxygenases

Lytic polysaccharide monooxygenase (LPMO) enzymes have attracted considerable attention owing to their ability to enhance polysaccharide depolymerization, making them interesting with respect to production of biofuel from cellulose. LPMOs are metalloenzymes that contain a mononuclear copper active site, capable of activating dioxygen. However, many details of this activation are unclear. Some aspects of the mechanism have previously been investigated from a computational angle. Yet, either these studies have employed only molecular mechanics (MM), which are inaccurate for metal active sites, or they have described only the active site with quantum mechanics (QM) and neglected the effect of the protein. Here, we employ hybrid QM and MM (QM/MM) methods to investigate the first steps of the LPMO mechanism, which is reduction of Cu^II to Cu^I and the formation of a Cu^II-superoxide complex. In the latter complex, the superoxide can bind either in an equatorial or an axial position. For both steps, we obtain structures that are markedly different from previous suggestions, based on small QM-cluster calculations. Our calculations show that the equatorial isomer of the superoxide complex is over 60 kJ/mol more stable than the axial isomer because it is stabilized by interactions with a second-coordination-sphere glutamine residue, suggesting a possible role for this residue. The coordination of superoxide in this manner agrees with recent experimental suggestions.

Applications of large-scale density functional theory in biology

Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.

Brønsted-Lowry Acid Strength of Metal Hydride and Dihydrogen Complexes

Transition metal hydride complexes are usually amphoteric, not only acting as hydride donors, but also as Brønsted-Lowry acids. A simple additive ligand acidity constant equation (LAC for short) allows the estimation of the acid dissociation constant Ka(LAC) of diamagnetic transition metal hydride and dihydrogen complexes. It is remarkably successful in systematizing diverse reports of over 450 reactions of acids with metal complexes and bases with metal hydrides and dihydrogen complexes, including catalytic cycles where these reactions are proposed or observed. There are links between pKa(LAC) and pKa(THF), pKa(DCM), pKa(MeCN) for neutral and cationic acids. For the groups from chromium to nickel, tables are provided that order the acidity of metal hydride and dihydrogen complexes from most acidic (pKa(LAC) -18) to least acidic (pKa(LAC) 50). Figures are constructed showing metal acids above the solvent pKa scales and organic acids below to summarize a large amount of information. Acid-base features are analyzed for catalysts from chromium to gold for ionic hydrogenations, bifunctional catalysts for hydrogen oxidation and evolution electrocatalysis, H/D exchange, olefin hydrogenation and isomerization, hydrogenation of ketones, aldehydes, imines, and carbon dioxide, hydrogenases and their model complexes, and palladium catalysts with hydride intermediates.

Ruthenium complexes bearing an unsymmetrical pincer ligand with a 2-hydroxypyridylmethylene fragment: active catalysts for transfer hydrogenation of ketones

The synthesis, reactivity and catalytic transfer hydrogenation activity of three metal–ligand cooperative ruthenium(ii) complexes (3–5) with a 2-hydroxypyridylmethylene fragment are reported.