Beyond S and Se: Electrocatalytic Hydrogen Production by Tellurolate-Bridged Co(III)-Mn(I) Heterodinuclear Complexes

In the pursuit of efficient electrocatalysts for the hydrogen evolution reaction (HER), a series of manganese and cobalt heterodinuclear complexes have been synthesized and characterized that have a stark resemblance with the [NiFe]-hydrogenase active site structure. Irradiation of [Mn2(CO)10] in the presence of 1.5 eq of [NaEPh] [E = S, Se, Te] followed by reaction with [Cp*CoCl]2 led to the formation of half-sandwiched trichalcogenate-bridged heterodinuclear complexes [{Mn(CO)3}(μ-EPh)3(CoCp*)] [E = S (C1); Se (C2) and Te (C3)]. The reaction of these heterodinuclear trichalcogenate-bridged complexes with [LiBH4·THF] yielded the corresponding dichalcogenate hydride-bridged heterobimetallic complexes [(CO)3Mn(μ-EPh)2(μ-H)(CoCp*)] [E = S (C5); Se (C6) and Te (C7)], which closely imitate the Ni-R intermediate of [NiFe]-hydrogenase. The resultant complexes (C5-C7) displayed impressive H2 production in DMF in the presence of HBF4, whereas the Te-based complex (C7) showcased the highest TON (184 h-1) with an impressive Faradaic efficiency of >98%. The DFT investigations revealed a unique role of bridging chalcogens in catalysis, wherein, depending on the identity of the chalcogen (S, Se, or Te), protonation could occur via two distinct routes. This study represents a rare example of the full trio of S/Se/Te-based heterodinuclear complexes whose electrocatalytic HER activity has been probed under analogous conditions.

Understanding the [NiFe] Hydrogenase Active Site Environment through Ultrafast Infrared and 2D-IR Spectroscopy of the Subsite Analogue K[CpFe(CO)(CN)2] in Polar and Protic Solvents

The [CpFe(CO)(CN)2]- unit is an excellent structural model for the Fe(CO)(CN)2 moiety of the active site found in [NiFe] hydrogenases. Ultrafast infrared (IR) pump-probe and 2D-IR spectroscopy have been used to study K[CpFe(CO)(CN)2] (M1) in a range of protic and polar solvents and as a dry film. Measurements of anharmonicity, intermode vibrational coupling strength, vibrational relaxation time, and solvation dynamics of the CO and CN stretching modes of M1 in H2O, D2O, methanol, dimethyl sulfoxide, and acetonitrile reveal that H-bonding to the CN ligands plays an important role in defining the spectroscopic characteristics and relaxation dynamics of the Fe(CO)(CN)2 unit. Comparisons of the spectroscopic and dynamic data obtained for M1 in solution and in a dry film with those obtained for the enzyme led to the conclusion that the protein backbone forms an important part of the bimetallic active site environment via secondary coordination sphere interactions.

Stepwise assembly of the active site of [NiFe]-hydrogenase

[NiFe]-hydrogenases are biotechnologically relevant enzymes catalyzing the reversible splitting of H₂ into 2e^- and 2H⁺ under ambient conditions. Catalysis takes place at the heterobimetallic NiFe(CN)₂(CO) center, whose multistep biosynthesis involves careful handling of two transition metals as well as potentially harmful CO and CN^- molecules. Here, we investigated the sequential assembly of the [NiFe] cofactor, previously based on primarily indirect evidence, using four different purified maturation intermediates of the catalytic subunit, HoxG, of the O₂-tolerant membrane-bound hydrogenase from Cupriavidus necator. These included the cofactor-free apo-HoxG, a nickel-free version carrying only the Fe(CN)₂(CO) fragment, a precursor that contained all cofactor components but remained redox inactive and the fully mature HoxG. Through biochemical analyses combined with comprehensive spectroscopic investigation using infrared, electronic paramagnetic resonance, Mössbauer, X-ray absorption and nuclear resonance vibrational spectroscopies, we obtained detailed insight into the sophisticated maturation process of [NiFe]-hydrogenase.

Understanding 2D-IR Spectra of Hydrogenases: A Descriptive and Predictive Computational Study

[NiFe] hydrogenases are metalloenzymes that catalyze the reversible cleavage of dihydrogen (), a clean future fuel. Understanding the mechanism of these biocatalysts requires spectroscopic techniques that yield insights into the structure and dynamics of the [NiFe] active site. Due to the presence of CO and ligands at this cofactor, infrared (IR) spectroscopy represents an ideal technique for studying these aspects, but molecular information from linear IR absorption experiments is limited. More detailed insights can be obtained from ultrafast nonlinear IR techniques like IRpump−IRprobe and two-dimensional (2D-)IR spectroscopy. However, fully exploiting these advanced techniques requires an in-depth understanding of experimental observables and the encoded molecular information. To address this challenge, we present a descriptive and predictive computational approach for the simulation and analysis of static 2D-IR spectra of [NiFe] hydrogenases and similar organometallic systems. Accurate reproduction of experimental spectra from a first-coordination-sphere model suggests a decisive role of the [NiFe] core in shaping the enzymatic potential energy surface. We also reveal spectrally encoded molecular information that is not accessible by experiments, thereby helping to understand the catalytic role of the diatomic ligands, structural differences between [NiFe] intermediates, and possible energy transfer mechanisms. Our studies demonstrate the feasibility and benefits of computational spectroscopy in the 2D-IR investigation of hydrogenases, thereby further strengthening the potential of this nonlinear IR technique as a powerful research tool for the investigation of complex bioinorganic molecules.

Bioinorganic Chemistry on Electrodes: Methods to Functional Modeling

One of the major goals of bioinorganic chemistry has been to mimic the function of elegant metalloenzymes. Such functional modeling has been difficult to attain in solution, in particular, for reactions that require multiple protons and multiple electrons (nH⁺/ne^-). Using a combination of heterogeneous electrochemistry, electrode and molecule design one may control both electron transfer (ET) and proton transfer (PT) of these nH⁺/ne^- reactions. Such control can allow functional modeling of hydrogenases (H⁺ + e^- → 1/2 H₂), cytochrome c oxidase (O₂ + 4 e^- + 4 H⁺ → 2 H₂O), monooxygenases (RR'CH₂ + O₂ + 2 e^- + 2 H⁺ → RR'CHOH + H₂O) and dioxygenases (S + O₂ → SO₂; S = organic substrate) in aqueous medium and at room temperatures. In addition, these heterogeneous constructs allow probing unnatural bioinspired reactions and estimation of the inner- and outer-sphere reorganization energy of small molecules and proteins.

Enzymatic X-ray absorption spectroelectrochemistry

The ability to observe the changes that occur at an enzyme active site during electrocatalysis can provide very valuable information for understanding the mechanism and ultimately aid in catalyst design. Herein, we discuss the development of X-ray absorption spectroscopy (XAS) in combination with electrochemistry for operando studies of enzymatic systems. XAS has had a long history of enabling geometric and electronic structural insights into the catalytic active sites of enzymes, however, XAS combined with electrochemistry (XA-SEC) has been exceedingly rare in bioinorganic applications. Herein, we discuss the challenges and opportunities of applying operando XAS to enzymatic electrocatalysts. The challenges due to the low concentration of the photoabsorber and the instability of the protein in the X-ray beam are discussed. Methods for immobilizing enzymes on the electrodes, while maintaining full redox control are highlighted. A case study of combined XAS and electrochemistry applied to a [NiFe] hydrogenase is presented. By entrapping the [NiFe] hydrogenase in a redox polymer, relatively high protein concentrations can be achieved on the electrode surface, while maintaining redox control. Overall, it is demonstrated that the experiments are feasible, but require precise redox control over the majority of the absorber atoms and careful controls to discriminate between electrochemically-driven changes and beam damage. Opportunities for future applications are discussed.

Hydrogen evolution, electron-transfer, and hydride-transfer reactions in a nickel-iron hydrogenase model complex: a theoretical study of the distinctive reactivities for the conformational isomers of nickel-iron hydride

Hydrogen fuel is a promising alternative to fossil fuel. Therefore, efficient hydrogen production is crucial to elucidate the distinctive reactivities of metal hydride species, the intermediates formed during hydrogen activation/evolution in the presence of organometallic catalysts. This study uses density functional theory (DFT) to investigate the isomerizations and reactivities of three nickel-iron (NiFe) hydride isomers synthesized by mimicking the active center of NiFe hydrogenase. Hydride transfer within these complexes, rather than a chemical reaction between the complexes, converts the three hydrides internally. Their reactivities, including their electron-transfer, hydride-transfer and proton-transfer reactions, are investigated. The bridging hydride complex exhibits a higher energy level for the highest occupied molecular orbital (HOMO) than the terminal hydride during the electron-transfer reaction. This energy level indicates that the bridging hydride is more easily oxidized and is more susceptible to electron transfer than the terminal hydride. Regarding the hydride-transfer reaction between the NiFe hydride complex and methylene blue, the terminal hydrides exhibit larger hydricity and lower reaction barriers than the bridging hydride complexes. The results of energy decomposition analysis indicate that the structural deformation energy of the terminal hydride in the transition state is smaller than that of the bridging hydride complex, which lowers the reaction barrier of hydride transfer in the terminal hydride. To produce hydrogen, the rate-determining step is represented by the protonation of the hydride, and the terminal hydrides are thermodynamically and kinetically superior to the bridging ones. The differences in the reactivities of the hydride isomers ensure the precise control of hydrogen, and the theoretical calculations can be applied to design catalysts for hydrogen activation/production.

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.

Hydroxy-bridged resting states of a [NiFe]-hydrogenase unraveled by cryogenic vibrational spectroscopy and DFT computations

The catalytic mechanism of [NiFe]-hydrogenases is a subject of extensive research. Apart from at least four reaction intermediates of H₂/H⁺ cycling, there are also a number of resting states, which are formed under oxidizing conditions. Although not directly involved in the catalytic cycle, the knowledge of their molecular structures and reactivity is important, because these states usually accumulate in the course of hydrogenase purification and may also play a role in vivo during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit (HoxC) of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure resting redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, ⁵⁷Fe-labeled HoxC provided an unprecedented insight into the [NiFe] site modes, revealing their contributions in a spectral range otherwise superimposed by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data provide structural descriptions of the previously uncharacterized hydroxy- and water-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site.

Active site vibrations of a [NiFe]-hydrogenase catalytic subunit are selectively probed by IR and NRV spectroscopy in two Ni^IIFe^II and Ni^IIIFe^II resting states, contributing in combination with DFT modeling to rationalized structural candidates.

Explicitly correlated coupled cluster method for accurate treatment of open-shell molecules with hundreds of atoms

We present a near-linear scaling formulation of the explicitly correlated coupled-cluster singles and doubles with the perturbative triples method [CCSD(T)_F12¯] for high-spin states of open-shell species. The approach is based on the conventional open-shell CCSD formalism [M. Saitow et al., J. Chem. Phys. 146, 164105 (2017)] utilizing the domain local pair-natural orbitals (DLPNO) framework. The use of spin-independent set of pair-natural orbitals ensures exact agreement with the closed-shell formalism reported previously, with only marginally impact on the cost (e.g., the open-shell formalism is only 1.5 times slower than the closed-shell counterpart for the C₁₆₀H₃₂₂ n-alkane, with the measured size complexity of ≈1.2). Evaluation of coupled-cluster energies near the complete-basis-set (CBS) limit for open-shell systems with more than 550 atoms and 5000 basis functions is feasible on a single multi-core computer in less than 3 days. The aug-cc-pVTZ DLPNO-CCSD(T)_F12¯ contribution to the heat of formation for the 50 largest molecules among the 348 core combustion species benchmark set [J. Klippenstein et al., J. Phys. Chem. A 121, 6580-6602 (2017)] had root-mean-square deviation (RMSD) from the extrapolated CBS CCSD(T) reference values of 0.3 kcal/mol. For a more challenging set of 50 reactions involving small closed- and open-shell molecules [G. Knizia et al., J. Chem. Phys. 130, 054104 (2009)], the aug-cc-pVQ(+d)Z DLPNO-CCSD(T)_F12¯ yielded a RMSD of ∼0.4 kcal/mol with respect to the CBS CCSD(T) estimate.

The large subunit of the regulatory [NiFe]-hydrogenase from Ralstonia eutropha - a minimal hydrogenase?

Chemically synthesized compounds that are capable of facilitating the reversible splitting of dihydrogen into protons and electrons are rare in chemists' portfolio. The corresponding biocatalysts – hydrogenases – are, however, abundant in the microbial world. [NiFe]-hydrogenases represent a major subclass and display a bipartite architecture, composed of a large subunit, hosting the catalytic NiFe(CO)(CN)₂ cofactor, and a small subunit whose iron–sulfur clusters are responsible for electron transfer. To analyze in detail the catalytic competence of the large subunit without its smaller counterpart, we purified the large subunit HoxC of the regulatory [NiFe]-hydrogenase of the model H₂ oxidizer Ralstonia eutropha to homogeneity. Metal determination and infrared spectroscopy revealed a stoichiometric loading of the metal cofactor. This enabled for the first time the determination of the UV-visible extinction coefficient of the NiFe(CO)(CN)₂ cofactor. Moreover, the absence of disturbing iron–sulfur clusters allowed an unbiased look into the low-spin Fe²⁺ of the active site by Mössbauer spectroscopy. Isolated HoxC was active in catalytic hydrogen–deuterium exchange, demonstrating its capacity to activate H₂. Its catalytic activity was drastically lower than that of the bipartite holoenzyme. This was consistent with infrared and electron paramagnetic resonance spectroscopic observations, suggesting that the bridging position between the active site nickel and iron ions is predominantly occupied by water-derived ligands, even under reducing conditions. In fact, the presence of water-derived ligands bound to low-spin Ni²⁺ was reflected by the absorption bands occurring in the corresponding UV-vis spectra, as revealed by time-dependent density functional theory calculations conducted on appropriate in silico models. Thus, the isolated large subunits indeed represent simple [NiFe]-hydrogenase models, which could serve as blueprints for chemically synthesized mimics. Furthermore, our data point to a fundamental role of the small subunit in preventing water access to the catalytic center, which significantly increases the H₂ splitting capacity of the enzyme.

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

pH Dependent Reversible Formation of a Binuclear Ni2 Metal-Center Within a Peptide Scaffold

A disulfide-bridged peptide containing two Ni2+ binding sites based on the nickel superoxide dismutase protein, {Ni2(SODmds)}, has been prepared. At physiological pH (7.4) it was found that the metal sites are mononuclear with a square planar NOS2 coordination environment with the two sulfur-based ligands derived from cysteinate residues, the nitrogen ligand derived from the amide backbone and a water ligand. Furthermore, S K-edge X-ray absorption spectroscopy indicated that the two cysteinate sulfur atoms ligated to nickel are each protonated. Elevation of the pH to 9.6 results in the deprotonation of the cysteinate sulfur atoms, and yields a binuclear, cysteinate bridged Ni22+ center with each nickel contained in a distorted square planar geometry. At both pH = 7.4 and 9.6 the nickel sites are moderately air sensitive, yielding intractable oxidation products. However, at pH = 9.6 {Ni2(SODmds)} reacts with O2 at an ~3.5-fold faster rate than at pH = 7.4. Electronic structure calculations indicate the reduced reactivity at pH = 7.4 is a result of a reduction in S(3p) character and deactivation of the nucleophilic frontier molecular orbitals upon cysteinate sulfur protonation.

Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities

Computational chemistry provides a versatile toolbox for studying mechanistic details of catalytic reactions and holds promise to deliver practical strategies to enable the rational in silico catalyst design. The versatile reactivity and nontrivial electronic structure effects, common for systems based on 3d transition metals, introduce additional complexity that may represent a particular challenge to the standard computational strategies. In this review, we discuss the challenges and capabilities of modern electronic structure methods for studying the reaction mechanisms promoted by 3d transition metal molecular catalysts. Particular focus will be placed on the ways of addressing the multiconfigurational problem in electronic structure calculations and the role of expert bias in the practical utilization of the available methods. The development of density functionals designed to address transition metals is also discussed. Special emphasis is placed on the methods that account for solvation effects and the multicomponent nature of practical catalytic systems. This is followed by an overview of recent computational studies addressing the mechanistic complexity of catalytic processes by molecular catalysts based on 3d metals. Cases that involve noninnocent ligands, multicomponent reaction systems, metal-ligand and metal-metal cooperativity, as well as modeling complex catalytic systems such as metal-organic frameworks are presented. Conventionally, computational studies on catalytic mechanisms are heavily dependent on the chemical intuition and expert input of the researcher. Recent developments in advanced automated methods for reaction path analysis hold promise for eliminating such human-bias from computational catalysis studies. A brief overview of these approaches is presented in the final section of the review. The paper is closed with general concluding remarks.

A low-valent dinuclear ruthenium diazadiene complex catalyzes the oxidation of dihydrogen and reversible hydrogenation of quinones

The dinuclear ruthenium complex [Ru2H(μ-H)(Me2dad)(dbcot)2] contains a 1,4-dimethyl-diazabuta-1,3-diene (Me2dad) as a non-innocent bridging ligand between the metal centers to give a [Ru2(Me2dad)] core. In addition, each ruthenium is bound to one dibenzo[a,e]cyclooctatetraene (dbcot) ligand. This Ru dimer converts H2 to protons and electrons. It also catalyzes reversibly under mild conditions the selective hydrogenation of vitamins K2 and K3 to their corresponding hydroquinone equivalents without affecting the C[double bond, length as m-dash]C double bonds. Mechanistic studies suggest that the [Ru2(Me2dad)] moiety, like hydrogenases, reacts with H2 and releases electrons and protons stepwise.

Comprehensive reaction mechanisms at and near the Ni-Fe active sites of [NiFe] hydrogenases

[NiFe] hydrogenase (H2ase) catalyzes the oxidation of dihydrogen to two protons and two electrons and/or its reverse reaction. For this simple reaction, the enzyme has developed a sophisticated but intricate mechanism with heterolytic cleavage of dihydrogen (or a combination of a hydride and a proton), where its Ni-Fe active site exhibits various redox states. Recently, thermodynamic parameters of the acid-base equilibrium for activation-inactivation, a new intermediate in the catalytic reaction, and new crystal structures of [NiFe] H2ases have been reported, providing significant insights into the activation-inactivation and catalytic reaction mechanisms of [NiFe] H2ases. This Perspective provides an overview of the reaction mechanisms of [NiFe] H2ases based on these new findings.

Hydrogen evolution from water catalyzed by cobalt-mimochrome VI*a, a synthetic mini-protein

The folding of a synthetic mini-hydrogenase is shown to enhance catalyst efficiency and longevity.

A synthetic enzyme is reported that electrocatalytically reduces protons to hydrogen (H₂) in water near neutral pH under aerobic conditions. Cobalt mimochrome VI*a (CoMC6*a) is a mini-protein with a cobalt deuteroporphyrin active site within a scaffold of two synthetic peptides covalently bound to the porphyrin. Comparison of the activity of CoMC6*a to that of cobalt microperoxidase-11 (CoMP11-Ac), a cobalt porphyrin catalyst with a single “proximal” peptide and no organized secondary structure, reveals that CoMC6*a has significantly enhanced longevity, yielding a turnover number exceeding 230 000, in comparison to 25 000 for CoMP11-Ac. Furthermore, comparison of cyclic voltammograms of CoMC6*a and CoMP11-Ac indicates that the trifluoroethanol-induced folding of CoMC6*a lowers the overpotential for catalytic H₂ evolution by up to 100 mV. These results demonstrate that even a minimal polypeptide matrix can enhance longevity and efficiency of a H₂-evolution catalyst.

A new near-linear scaling, efficient and accurate, open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory

The Coupled-Cluster expansion, truncated after single and double excitations (CCSD), provides accurate and reliable molecular electronic wave functions and energies for many molecular systems around their equilibrium geometries. However, the high computational cost, which is well-known to scale as O(N⁶) with system size N, has limited its practical application to small systems consisting of not more than approximately 20-30 atoms. To overcome these limitations, low-order scaling approximations to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The production level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell unrestricted Hartree-Fock reference wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few shortcomings of UHF-LPNO-CCSD were noticed that required a redesign of the method, which is the subject of this paper. To this end, we employ the high-spin open-shell variant of the N-electron valence perturbation theory formalism to define the initial guess wave function, and consequently also the open-shell PNOs. The new PNO ansatz properly converges to the closed-shell limit since all truncations and approximations have been made in strict analogy to the closed-shell case. Furthermore, given the fact that the formalism uses a single set of orbitals, only a single PNO integral transformation is necessary, which offers large computational savings. We show that, with the default PNO truncation parameters, approximately 99.9% of the total CCSD correlation energy is recovered for open-shell species, which is comparable to the performance of the method for closed-shells. UHF-DLPNO-CCSD shows a linear scaling behavior for closed-shell systems, while linear to quadratic scaling is obtained for open-shell systems. The largest systems we have considered contain more than 500 atoms and feature more than 10 000 basis functions with a triple-ζ quality basis set.

Hydrogen bonding effect between active site and protein environment on catalysis performance in H2-producing [NiFe] hydrogenases

The interaction between the active site and the surrounding protein environment plays a fundamental role in the hydrogen evolution reaction (HER) in [NiFe] hydrogenases. Our density functional theory (DFT) findings demonstrate that the reaction Gibbs free energy required for the rate determining step decreases by 7.1 kcal mol^-1 when the surrounding protein environment is taken into account, which is chiefly due to free energy decreases for the two H⁺/e^- addition steps (the so-called Ni-SIa to I1, and Ni-C to Ni-R), being the largest thermodynamic impediments of the whole reaction. The variety of hydrogen bonds (H-bonds) between the amino acids and the active site is hypothesised to be the main reason for such stability: H-bonds not only work as electrostatic attractive forces that influence the charge redistribution, but more importantly, they act as an electron 'pull' taking electrons from the active site towards the amino acids. Moreover, the electron 'pull' effect through H-bonds via the S^- in cysteine residues shows a larger influence on the energy profile than that via the CN^- ligands on Fe.

Equilibrium between inactive ready Ni-SIr and active Ni-SIa states of [NiFe] hydrogenase studied by utilizing Ni-SIr-to-Ni-SIa photoactivation

Previously, the Ni-SI_r state of [NiFe] hydrogenase was found to convert to the Ni-SI_a state by light irradiation. Herein, large activation energies and a large kinetic isotope effect were obtained for the reconversion of the Ni-SI_a state to the Ni-SI_r state after the Ni-SI_r-to-Ni-SI_a photoactivation, suggesting that the Ni-SI_a state reacts with H₂O and leaves a bridging hydroxo ligand for the Ni-SI_r state.

Photoactivation of the Ni-SIr state to the Ni-SIa state in [NiFe] hydrogenase: FT-IR study on the light reactivity of the ready Ni-SIr state and as-isolated enzyme revisited

The Ni-SIr state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F was photoactivated to its Ni-SIa state by Ar(+) laser irradiation at 514.5 nm, whereas the Ni-SL state was light induced from a newly identified state, which was less active than any other identified state and existed in the "as-isolated" enzyme.

The oxygen reduction reaction on [NiFe] hydrogenases

Oxygen tolerance capacity is critical for hydrogen oxidation/evolution catalysts.

Diiron Dithiolate Hydrides Complemented with Proton-Responsive Phosphine-Amine Ligands

The reaction of Fe₂(pdt)(CO)₆ with two equivalents of Ph₂PC₆H₄NH₂ (PNH₂) affords the amido hydride HFe₂(pdt)(CO)₂(PNH₂)(PNH) {[H1H]⁰, pdt^2- = CH₂(CH₂S^-)₂}. Isolated intermediates in this conversion include Fe₂(pdt)(CO)₅-(κ¹-PNH₂) and Fe₂(pdt)(CO)₄(κ²-PNH₂). X-ray crystallographic analysis of [H1H]⁰ shows that the chelating amino/amido-phosphine ligands occupy trans-dibasal positions. The ³¹P NMR spectrum indicates that [H1H]⁰ undergoes rapid proton exchange between the amido and amine centers. No exchange was observed for the hydride. Protonation of [H1H]⁰ gives [HFe₂(pdt)(CO)₂(PNH₂)₂]⁺ ([H₂1H]⁺), which contains two equivalent amino-phosphine ligands. Single-crystal X-ray crystallographic analysis of [H₂1H]⁺ also reveals hydrogen bonds between the exo amine protons with a THF molecule and BF₄. Deprotonation of [H1H]⁰ with potassium tert-butoxide gave [HFe₂(pdt)(CO)₂(PNH)₂]^- ([1H]^-), which was characterized spectroscopically. The complex has time-averaged C₂ symmetry with two amido-phosphine ligands. FTIR spectroscopic measurements show that υ_CO shifts by approximately 20 cm^-1 in the series [1H]^-, [H1H]⁰, and [H₂1H]⁺. These shifts are comparable to those seen for the S-protonation of the (NC)₂(CO)Fe-(μ-Scys)₂Ni(Scys)₂ site in the [NiFe]-hydrogenases.^[1].

Proton Transfer in the Catalytic Cycle of [NiFe] Hydrogenases: Insight from Vibrational Spectroscopy

Catalysis of H₂ production and oxidation reactions is critical in renewable energy systems based around H₂ as a clean fuel, but the present reliance on platinum-based catalysts is not sustainable. In nature, H₂ is oxidized at minimal overpotential and high turnover frequencies at [NiFe] catalytic sites in hydrogenase enzymes. Although an outline mechanism has been established for the [NiFe] hydrogenases involving heterolytic cleavage of H₂ followed by a first and then second transfer of a proton and electron away from the active site, details remain vague concerning how the proton transfers are facilitated by the protein environment close to the active site. Furthermore, although [NiFe] hydrogenases from different organisms or cellular environments share a common active site, they exhibit a broad range of catalytic characteristics indicating the importance of subtle changes in the surrounding protein in controlling their behavior. Here we review recent time-resolved infrared (IR) spectroscopic studies and IR spectroelectrochemical studies carried out in situ during electrocatalytic turnover. Additionally, we re-evaluate the significant body of IR spectroscopic data on hydrogenase active site states determined through more conventional solution studies, in order to highlight mechanistic steps that seem to apply generally across the [NiFe] hydrogenases, as well as steps which so far seem limited to specific groups of these enzymes. This analysis is intended to help focus attention on the key open questions where further work is needed to assess important aspects of proton and electron transfer in the mechanism of [NiFe] hydrogenases.

Experimental and DFT Investigations Reveal the Influence of the Outer Coordination Sphere on the Vibrational Spectra of Nickel-Substituted Rubredoxin, a Model Hydrogenase Enzyme

Nickel-substituted rubredoxin (NiRd) is a functional enzyme mimic of hydrogenase, highly active for electrocatalytic and solution-phase hydrogen generation. Spectroscopic methods can provide valuable insight into the catalytic mechanism, provided the appropriate technique is used. In this study, we have employed multiwavelength resonance Raman spectroscopy coupled with DFT calculations on an extended active-site model of NiRd to probe the electronic and geometric structures of the resting state of this system. Excellent agreement between experiment and theory is observed, allowing normal mode assignments to be made on the basis of frequency and intensity analyses. Both metal-ligand and ligand-centered vibrational modes are enhanced in the resonance Raman spectra. The latter provide information about the hydrogen bonding network and structural distortions due to perturbations in the secondary coordination sphere. To reproduce the resonance enhancement patterns seen for high-frequency vibrational modes, the secondary coordination sphere must be included in the computational model. The structure and reduction potential of the Ni^IIIRd state have also been investigated both experimentally and computationally. This work begins to establish a foundation for computational resonance Raman spectroscopy to serve in a predictive fashion for investigating catalytic intermediates of NiRd.

H2binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods

CCSD(T) and DMRG-CASPT2 calculations show that H₂prefers to bind to Ni rather than to Fe in [NiFe] hydrogenase.

Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides

Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.

Structure and function of [NiFe] hydrogenases

Hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons via a heterolytic splitting mechanism. The active sites of [NiFe] hydrogenases comprise a dinuclear Ni-Fe center carrying CO and CN^- ligands. The catalytic activity of the standard (O₂-sensitive) [NiFe] hydrogenases vanishes under aerobic conditions. The O₂-tolerant [NiFe] hydrogenases can sustain H₂ oxidation activity under atmospheric conditions. These hydrogenases have very similar active site structures that change the ligand sphere during the activation/catalytic process. An important structural difference between these hydrogenases has been found for the proximal iron-sulphur cluster located in the vicinity of the active site. This unprecedented [4Fe-3S]-6Cys cluster can supply two electrons, which lead to rapid recovery of the O₂ inactivation, to the [NiFe] active site.

Models of the Ni-L and Ni-SIa States of the [NiFe]-Hydrogenase Active Site

A new class of synthetic models for the active site of [NiFe]-hydrogenases are described. The Ni(I/II)(SCys)2 and Fe(II)(CN)2CO sites are represented with (RC5H4)Ni(I/II) and Fe(II)(diphos)(CO) modules, where diphos = 1,2-C2H4(PPh2)2(dppe) or cis-1,2-C2H2(PPh2)2(dppv). The two bridging thiolate ligands are represented by CH2(CH2S)2(2-) (pdt(2-)), Me2C(CH2S)2(2-) (Me2pdt(2-)), and (C6H5S)2(2-). The reaction of Fe(pdt)(CO)2(dppe) and [(C5H5)3Ni2]BF4 affords [(C5H5)Ni(pdt)Fe(dppe)(CO)]BF4 ([1a]BF4). Monocarbonyl [1a]BF4 features an S = 0 Ni(II)Fe(II) center with five-coordinated iron, as proposed for the Ni-SIa state of the enzyme. One-electron reduction of [1a](+) affords the S = 1/2 derivative [1a](0), which, according to density functional theory (DFT) calculations and electron paramagnetic resonance and Mössbauer spectroscopies, is best described as a Ni(I)Fe(II) compound. The Ni(I)Fe(II) assignment matches that for the Ni-L state in [NiFe]-hydrogenase, unlike recently reported Ni(II)Fe(I)-based models. Compound [1a](0) reacts with strong acids to liberate 0.5 equiv of H2 and regenerate [1a](+), indicating that H2 evolution is catalyzed by [1a](0). DFT calculations were used to investigate the pathway for H2 evolution and revealed that the mechanism can proceed through two isomers of [1a](0) that differ in the stereochemistry of the Fe(dppe)CO center. Calculations suggest that protonation of [1a](0) (both isomers) affords Ni(III)-H-Fe(II) intermediates, which represent mimics of the Ni-C state of the enzyme.

Why is a proton transformed into a hydride by [NiFe] hydrogenases? An intrinsic reactivity analysis based on conceptual DFT

The hydrogen evolution reaction (HER) catalysed by [NiFe] hydrogenases entails a series of chemical events involving great mechanistic interest.

Hydrogen evolution in [NiFe] hydrogenases and related biomimetic systems: similarities and differences

Schematic overview of the orbitals that play a role in the cycle of reversible hydrogen oxidation in [NiFe] hydrogenases.

[NiFeSe]-hydrogenase chemistry

The development of technology for the inexpensive generation of the renewable energy vector H2 through water splitting is of immediate economic, ecological, and humanitarian interest. Recent interest in hydrogenases has been fueled by their exceptionally high catalytic rates for H2 production at a marginal overpotential, which is presently only matched by the nonscalable noble metal platinum. The mechanistic understanding of hydrogenase function guides the design of synthetic catalysts, and selection of a suitable hydrogenase enables direct applications in electro- and photocatalysis. [FeFe]-hydrogenases display excellent H2 evolution activity, but they are irreversibly damaged upon exposure to O2, which currently prevents their use in full water splitting systems. O2-tolerant [NiFe]-hydrogenases are known, but they are typically strongly biased toward H2 oxidation, while H2 production by [NiFe]-hydrogenases is often product (H2) inhibited. [NiFeSe]-hydrogenases are a subclass of [NiFe]-hydrogenases with a selenocysteine residue coordinated to the active site nickel center in place of a cysteine. They exhibit a combination of unique properties that are highly advantageous for applications in water splitting compared with other hydrogenases. They display a high H2 evolution rate with marginal inhibition by H2 and tolerance to O2. [NiFeSe]-hydrogenases are therefore one of the most active molecular H2 evolution catalysts applicable in water splitting. Herein, we summarize our recent progress in exploring the unique chemistry of [NiFeSe]-hydrogenases through biomimetic model chemistry and the chemistry with [NiFeSe]-hydrogenases in semiartificial photosynthetic systems. We gain perspective from the structural, spectroscopic, and electrochemical properties of the [NiFeSe]-hydrogenases and compare them with the chemistry of synthetic models of this hydrogenase active site. Our synthetic models give insight into the effects on the electronic properties and reactivity of the active site upon the introduction of selenium. We have utilized the exceptional properties of the [NiFeSe]-hydrogenase from Desulfomicrobium baculatum in a number of photocatalytic H2 production schemes, which are benchmark systems in terms of single site activity, tolerance toward O2, and in vitro water splitting with biological molecules. Each system comprises a light-harvesting component, which allows for light-driven electron transfer to the hydrogenase in order for it to catalyze H2 production. A system with [NiFeSe]-hydrogenase on a dye-sensitized TiO2 nanoparticle gives an enzyme-semiconductor hybrid for visible light-driven generation of H2 with an enzyme-based turnover frequency of 50 s(-1). A stable and inexpensive polymeric carbon nitride as a photosensitizer in combination with the [NiFeSe]-hydrogenase shows good activity for more than 2 days. Light-driven H2 evolution with the enzyme and an organic dye under high O2 levels demonstrates the excellent robustness and feasibility of water splitting with a hydrogenase-based scheme. This has led, most recently, to the development of a light-driven full water splitting system with a [NiFeSe]-hydrogenase wired to the water oxidation enzyme photosystem II in a photoelectrochemical cell. In contrast to the other systems, this photoelectrochemical system does not rely on a sacrificial electron donor and allowed us to establish the long sought after light-driven water splitting with an isolated hydrogenase.

Rates and Routes of Electron Transfer of [NiFe]-Hydrogenase in an Enzymatic Fuel Cell

Hydrogenase enzymes are being used in enzymatic fuel cells immobilized on a graphite or carbon electrode surface, for example. The enzyme is used for the anodic oxidation of molecular hydrogen (H2) to produce protons and electrons. The association and orientation of the enzyme at the anode electrode for a direct electron transfer is not completely resolved. The distal FeS-cluster in [NiFe]-hydrogenases contains a histidine residue which is known to play a critical role in the intermolecular electron transfer between the enzyme and the electrode surface. The [NiFe]-hydrogenase graphite electrode association was investigated using Brownian Dynamics simulations. Residues that were shown to be in proximity to the electrode surface were identified (His184, Ser196, Glu461, Glu464), and electron transfer routes connecting the distal FeS-cluster with the surface residues were investigated. Several possible pathways for electron transfer between the distal FeS-cluster and the terminal amino acid residues were probed in terms of their rates of electron transfer using DFT methods. The reorganization energies λ of the distal iron-sulfur cluster and coronene as a molecular model for graphite were calculated. The reorganization energy of the distal (His)(Cys)3 cluster was found to be not very different from that of a standard cubane clusters with a (Cys)4 coordination. Electronic coupling matrix elements and rates of electron transfer for the different pathways were calculated according to the Marcus equation. The rates for glutamate-mediated electrode binding were found to be incompatible with experimental data. A direct electron transfer from the histidine ligand of the distal FeS-cluster to the electrode yielded rates of electron transfer in excellent agreement with experiment. A second pathway, however, from the distal FeS-cluster to the Ser196 residue was found to be equally efficient and feasible.

Electrochemical, Spectroscopic, and Density Functional Theory Characterization of Redox Activity in Nickel-Substituted Azurin: A Model for Acetyl-CoA Synthase

Nickel-containing enzymes are key players in global hydrogen, carbon dioxide, and methane cycles. Many of these enzymes rely on Ni(I) oxidation states in critical catalytic intermediates. However, due to the highly reactive nature of these species, their isolation within metalloenzymes has often proved elusive. In this report, we describe and characterize a model biological Ni(I) species that has been generated within the electron transfer protein, azurin. Replacement of the native copper cofactor with nickel is shown to preserve the redox activity of the protein. The Ni(II/I) couple is observed at -590 mV versus NHE, with an interfacial electron transfer rate of 70 s(-1). Chemical reduction of Ni(II)Az generates a stable species with strong absorption features at 350 nm and a highly anisotropic, axial EPR signal with principal g-values of 2.56 and 2.10. Density functional theory calculations provide insight into the electronic and geometric structure of the Ni(I) species, suggesting a trigonal planar coordination environment. The predicted spectroscopic features of this low-coordinate nickel site are in good agreement with the experimental data. Molecular orbital analysis suggests potential for both metal-centered and ligand-centered reactivity, highlighting the covalency of the metal-thiolate bond. Characterization of a stable Ni(I) species within a model protein has implications for understanding the mechanisms of complex enzymes, including acetyl coenzyme A synthase, and developing scaffolds for unique reactivity.

Structural differences between the active sites of the Ni-A and Ni-B states of the [NiFe] hydrogenase: an approach by quantum chemistry and single crystal ENDOR spectroscopy

The two resting forms of the active site of [NiFe] hydrogenase, Ni-A and Ni-B, have significantly different activation kinetics, but reveal nearly identical spectroscopic features which suggest the two states exhibit subtle structural differences. Previous studies have indicated that the states differ by the identity of the bridging ligand between Ni and Fe; proposals include OH(-), OOH(-), H2O, O(2-), accompanied by modified cysteine residues. In this study, we use single crystal ENDOR spectroscopy and quantum chemical calculations within the framework of density functional theory (DFT) to calculate vibrational frequencies, (1)H and (17)O hyperfine coupling constants and g values with the aim to compare these data to experimental results obtained by crystallography, FTIR and EPR/ENDOR spectroscopy. We find that the Ni-A and Ni-B states are constitutional isomers that differ in their fine structural details. Calculated vibrational frequencies for the cyano and carbonyl ligands and (1)H and (17)O hyperfine coupling constants indicate that the bridging ligand in both Ni-A and Ni-B is indeed an OH(-) ligand. The difference in the isotropic hyperfine coupling constants of the β-CH2 protons of Cys-549 is sensitive to the orientation of Cys-549; a difference of 0.5 MHz is observed experimentally for Ni-A and 1.9 MHz for Ni-B, which results from a rotation of 7 degrees about the Cα-Cβ-Sγ-Ni dihedral angle. Likewise, the difference of the intermediate g value is correlated with a rotation of Cys-546 of about 10 degrees.

Cofactor composition and function of a H2-sensing regulatory hydrogenase as revealed by Mössbauer and EPR spectroscopy

The regulatory hydrogenase (RH) from Ralstonia eutropha H16 acts as a sensor for the detection of environmental H₂ and regulates gene expression related to hydrogenase-mediated cellular metabolism. In marked contrast to prototypical energy-converting [NiFe] hydrogenases, the RH is apparently insensitive to inhibition by O₂ and CO. While the physiological function of regulatory hydrogenases is well established, little is known about the redox cycling of the [NiFe] center and the nature of the iron-sulfur (FeS) clusters acting as electron relay. The absence of any FeS cluster signals in EPR had been attributed to their particular nature, whereas the observation of essentially only two active site redox states, namely Ni-SI and Ni-C, invoked a different operant mechanism. In the present work, we employ a combination of Mössbauer, FTIR and EPR spectroscopic techniques to study the RH, and the results are consistent with the presence of three [4Fe-4S] centers in the small subunit. In the as-isolated, oxidized RH all FeS clusters reside in the EPR-silent 2+ state. Incubation with H₂ leads to reduction of two of the [4Fe-4S] clusters, whereas only strongly reducing agents lead to reduction of the third cluster, which is ascribed to be the [4Fe-4S] center in 'proximal' position to the [NiFe] center. In the two different active site redox states, the low-spin Fe^II exhibits distinct Mössbauer features attributed to changes in the electronic and geometric structure of the catalytic center. The results are discussed with regard to the spectral characteristics and physiological function of H₂-sensing regulatory hydrogenases.

Modulation of active site electronic structure by the protein matrix to control [NiFe] hydrogenase reactivity

Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere ligands that act to modify the geometry and physical properties of the active site metal centers. We carried out a combined set of classical molecular dynamics and quantum/classical mechanics calculations to provide quantitative estimates of how dynamic fluctuations of the active site within the protein matrix modulate the electronic structure at the catalytic center. Specifically we focused on the dynamics of the inner and outer coordination spheres of the cysteinate-bound Ni-Fe cluster in the catalytically active Ni-C state. There are correlated movements of the cysteinate ligands and the surrounding hydrogen-bonding network, which modulate the electron affinity at the active site and the proton affinity of a terminal cysteinate. On the basis of these findings, we hypothesize a coupling between protein dynamics and electron and proton transfer reactions critical to dihydrogen production.