Investigating the Kinetic Competency of CrHydA1 [FeFe] Hydrogenase Intermediate States via Time-Resolved Infrared Spectroscopy

Indications for a universal hydrogen catalysis mechanism in [FeFe]-hydrogenases of different phylogenetic groups

[FeFe]-hydrogenases are metalloenzymes catalysing bidirectional hydrogen (H2) turnover. These enzymes are generally considered to be extremely efficient and fast catalysts. However, [FeFe]-hydrogenases constitute a very diverse enzyme family that can be divided into several distinct phylogenetic groups, denoted as groups A-G. Very little is known about the properties of [FeFe]-hydrogenases outside of the intensively studied group A, but recent studies on putatively sensory group C and D enzymes have revealed distinct differences in reactivity. The variation in structure, reactivity and physiological function observed between phylogenetic groups raises the question if all [FeFe]-hydrogenases follow the same mechanism for H2 turnover. Here, we provide the first detailed spectroscopic investigation of a slow-acting putatively sensory group D [FeFe]-hydrogenase from Thermoanaerobacter mathranii (TamHydS). Photo-reduction enabled us to characterize redox states in group D [FeFe]-hydrogenase via infrared spectroscopy under catalytic conditions. The sequential population of redox states similar to group A [FeFe]-hydrogenases supports the notion that group A and D [FeFe]-hydrogenases follow a universal catalytic mechanism. However, clear differences between enzymes from different phylogenetic groups become evident when comparing the relative stability and protonation state of suggested key catalytic intermediates. Moreover, the spectroscopic data collected on TamHydS provides new insight into the structure of the reduced active site, lending further support for the notion of a retained bridging CO ligand throughout the entire catalytic cycle.

Hydrogen Oxidation by Bioinspired Models of [FeFe]-Hydrogenase

Synthetic azadithiolate-bridged diiron clusters serve as structural analogues of the active site of [FeFe]-hydrogenases. Recently, an o-alkyl substitution of aniline-based azadithiolate bridge allowed these synthetic models to both oxidize H2 and reduce H+, i.e., bidirectional catalysis. Hydrogen oxidation by synthetic analogues of hydrogenases is rare, and even rarer is the ability of diiron hexacarbonyls to oxidize H2. A series of synthetic azadithiolate-bridged biomimetic diiron hexacarbonyl complexes are synthesized where the substitution in the para position of the ortho-methyl aniline in the azadithiolate bridge is systematically varied between electron-withdrawing and electron-donating groups to understand factors that control H2 oxidation by diiron hexacarbonyl analogues of [FeFe]-hydrogenases. The results show that the substituents in the para position of the ortho-ethyl aniline affect the electronic structure of the azadithiolate bridge as well as that of the diiron cluster. The electron-withdrawing -NO2 substituent results in faster H2 oxidation relative to that of a -OCH3 substituent.

HydE Catalytic Mechanism Is Powered by a Radical Relay with Redox-Active Fe(I)-Containing Intermediates

[FeFe]-hydrogenases are enzymes that catalyze the redox interconversion of H+ and H2 using a six-iron active site, known as the H-cluster, which consists of a structurally unique [2Fe]H subcluster linked to a [4Fe-4S]H subcluster. A set of enzymes, HydG, HydE, and HydF, are responsible for the biosynthesis of the [2Fe]H subcluster. Among them, it is well established that HydG cleaves tyrosine into CO and CN- and forms a mononuclear [Fe(II)(Cys)(CO)2(CN)] complex. Recent work using EPR spectroscopy and X-ray crystallography show that HydE uses this organometallic Fe complex as its native substrate. The low spin Fe(II) center is reduced into an adenosylated Fe(I) species, which is proposed to form an Fe(I)Fe(I) dimer within HydE. The highly unusual transformation catalyzed by HydE draws interest in both biochemistry and organometallic chemistry. Due to the instability of the substrate, the intermediates, and the proposed product, experimental characterization of the detailed HydE mechanism and its final product is challenging. Herein, the catalytic mechanism of HydE is studied using hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. A radical relay mechanism was found for the cleavage of the cysteine S-Cβ bond that is energetically favored with respect to a closed-shell mechanism involving unconventional proton transfer. In addition, we propose a pathway for the dimerization of two Fe(I) complexes within the HydE hydrophobic cavity, which is consistent with the recent experimental result that HydF can perform [FeFe]-hydrogenase maturation with a synthetic dimer complex as the substrate. These simulation results take us further down the path to a more complete understanding of these enzymes that synthesize one of Nature's most efficient energy conversion catalysts.

The missing pieces in the catalytic cycle of [FeFe] hydrogenases

Hydrogen could provide a suitable means for storing energy from intermittent renewable sources for later use on demand. However, many challenges remain regarding the activity, specificity, stability and sustainability of current hydrogen production and consumption methods. The lack of efficient catalysts based on abundant and sustainable elements lies at the heart of this problem. Nature's solution led to the evolution of hydrogenase enzymes capable of reversible hydrogen conversion at high rates using iron- and nickel-based active sites. Through a detailed understanding of these enzymes, we can learn how to mimic them to engineer a new generation of highly active synthetic catalysts. Incredible progress has been made in our understanding of biological hydrogen activation over the last few years. In particular, detailed studies of the [FeFe] hydrogenase class have provided substantial insight into a sophisticated, optimised, molecular catalyst, the active site H-cluster. In this short perspective, we will summarise recent findings and highlight the missing pieces needed to complete the puzzle.

Facile electrocatalytic proton reduction by a [Fe-Fe]-hydrogenase bio-inspired synthetic model bearing a terminal CN- ligand

An azadithiolate bridged CN- bound pentacarbonyl bis-iron complex, mimicking the active site of [Fe-Fe] H2ase is synthesized. The geometric and electronic structure of this complex is elucidated using a combination of EXAFS analysis, infrared and Mössbauer spectroscopy and DFT calculations. The electrochemical investigations show that complex 1 effectively reduces H+ to H2 between pH 0-3 at diffusion-controlled rates (1011 M-1 s-1) i.e. 108 s-1 at pH 3 with an overpotential of 140 mV. Electrochemical analysis and DFT calculations suggests that a CN- ligand increases the pKa of the cluster enabling hydrogen production from its Fe(i)-Fe(0) state at pHs much higher and overpotential much lower than its precursor bis-iron hexacarbonyl model which is active in its Fe(0)-Fe(0) state. The formation of a terminal Fe-H species, evidenced by spectroelectrochemistry in organic solvent, via a rate determining proton coupled electron transfer step and protonation of the adjacent azadithiolate, lowers the kinetic barrier leading to diffusion controlled rates of H2 evolution. The stereo-electronic factors enhance its catalytic rate by 3 order of magnitude relative to a bis-iron hexacarbonyl precursor at the same pH and potential.

A personal account on 25 years of scientific literature on [FeFe]-hydrogenase

[FeFe]-hydrogenases are gas-processing metalloenzymes that catalyze H₂ oxidation and proton reduction (H₂ release) in microorganisms. Their high turnover frequencies and lack of electrical overpotential in the hydrogen conversion reaction has inspired generations of biologists, chemists, and physicists to explore the inner workings of [FeFe]-hydrogenase. Here, we revisit 25 years of scientific literature on [FeFe]-hydrogenase and propose a personal account on 'must-read' research papers and review article that will allow interested scientists to follow the recent discussions on catalytic mechanism, O₂ sensitivity, and the in vivo synthesis of the active site cofactor with its biologically uncommon ligands carbon monoxide and cyanide. Focused on-but not restricted to-structural biology and molecular biophysics, we highlight future directions that may inspire young investigators to pursue a career in the exciting and competitive field of [FeFe]-hydrogenase research.

Anaerobic Infrared Spectroelectrochemical Methods for Studying Oxygen-Sensitive [FeFe] Hydrogenases

[FeFe] hydrogenases comprise an important class of H₂ evolving enzymes; however, these proteins are often oxygen sensitive and require anaerobic environments for characterization. Understanding the electrochemical relationships between various active and inactive states of these enzymes is instrumental in uncovering the reaction mechanisms of the complex six-iron active center of [FeFe] hydrogenases called H-cluster. Since states of the H-cluster exhibit distinct fingerprint-like spectra in the mid-IR range, IR spectroelectrochemical experiments provide a powerful methodological framework for this goal. This chapter describes protocols for performing Fourier-transform infrared (FTIR) spectroelectrochemical experiments on [FeFe] hydrogenases under anaerobic conditions. Topics included experimental design, data acquisition, and data analysis.

Polymer Dots as Photoactive Membrane Vesicles for [FeFe]-Hydrogenase Self-Assembly and Solar-Driven Hydrogen Evolution

A semiartificial photosynthesis approach that utilizes enzymes for solar fuel production relies on efficient photosensitizers that should match the enzyme activity and enable long-term stability. Polymer dots (Pdots) are biocompatible photosensitizers that are stable at pH 7 and have a readily modifiable surface morphology. Therefore, Pdots can be considered potential photosensitizers to drive such enzyme-based systems for solar fuel formation. This work introduces and unveils in detail the interaction within the biohybrid assembly composed of binary Pdots and the HydA1 [FeFe]-hydrogenase from Chlamydomonas reinhardtii. The direct attachment of hydrogenase on the surface of toroid-shaped Pdots was confirmed by agarose gel electrophoresis, cryogenic transmission electron microscopy (Cryo-TEM), and cryogenic electron tomography (Cryo-ET). Ultrafast transient spectroscopic techniques were used to characterize photoinduced excitation and dissociation into charges within Pdots. The study reveals that implementation of a donor-acceptor architecture for heterojunction Pdots leads to efficient subpicosecond charge separation and thus enhances hydrogen evolution (88 460 μmol_H2·g_H2ase^-1·h^-1). Adsorption of [FeFe]-hydrogenase onto Pdots resulted in a stable biohybrid assembly, where hydrogen production persisted for days, reaching a TON of 37 500 ± 1290 in the presence of a redox mediator. This work represents an example of a homogeneous biohybrid system combining polymer nanoparticles and an enzyme. Detailed spectroscopic studies provide a mechanistic understanding of light harvesting, charge separation, and transport studied, which is essential for building semiartificial photosynthetic systems with efficiencies beyond natural and artificial systems.

Time-Resolved Infrared Spectroscopy Reveals the pH-Independence of the First Electron Transfer Step in the [FeFe] Hydrogenase Catalytic Cycle

[FeFe] hydrogenases are highly active catalysts for hydrogen conversion. Their active site has two components: a [4Fe-4S] electron relay covalently attached to the H₂ binding site and a diiron cluster ligated by CO, CN^-, and 2-azapropane-1,3-dithiolate (ADT) ligands. Reduction of the [4Fe-4S] site was proposed to be coupled with protonation of one of its cysteine ligands. Here, we used time-resolved infrared (TRIR) spectroscopy on the [FeFe] hydrogenase from Chlamydomonas reinhardtii (CrHydA1) containing a propane-1,3-dithiolate (PDT) ligand instead of the native ADT ligand. The PDT modification does not affect the electron transfer step to [4Fe-4S]_H but prevents the enzyme from proceeding further through the catalytic cycle. We show that the rate of the first electron transfer step is independent of the pH, supporting a simple electron transfer rather than a proton-coupled event. These results have important implications for our understanding of the catalytic mechanism of [FeFe] hydrogenases and highlight the utility of TRIR.

Efficient, Light-Driven Reduction of CO2 to CO by a Carbon Monoxide Dehydrogenase-CdSe/CdS Nanorod Photosystem

The solar conversion of CO₂ to low carbon fuels has been heralded as a potential solution to combat the rise in greenhouse gas emissions. Here we report the first light-driven activation of [NiFe] CODH II from Carboxydothermus hydrogenoformans for the reduction of CO₂ to CO. To accomplish this, a hybrid photosystem composed of CODH II and CdSe/CdS dot-in-rod nanocrystals was developed. By incorporating a low-potential redox mediator to assist electron transfer, quantum yields up to 19% and turnover frequencies of 9 s^-1 were achieved. These results represent a new standard in efficient CO₂ reduction by an enzyme-based photocatalytic systems. Furthermore, successful photoactivation of CODH II allows for future exploration into the enzyme's not fully understood mechanism.

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.

Reversible or Irreversible Catalysis of H+/H2 Conversion by FeFe Hydrogenases

Studies of molecular catalysts traditionally aim at understanding how a certain mechanism allows the reaction to be fast. A distinct question, which has only recently received attention in the case of bidirectional molecular catalysts, is how much thermodynamic driving force is required to achieve fast catalysis in either direction of the reaction. "Reversible" catalysts are bidirectional catalysts that work either way in response to even a small departure from equilibrium and thus do not waste input free energy as heat; conversely, "irreversible" catalysts require a large driving force to proceed at an appreciable rate [Fourmond et al. Nat. Rev. Chem. 2021, 5, 348-360]. Numerous mechanistic rationales for these contrasting behaviors have been proposed. To understand the determinants of catalytic (ir)reversibility, we examined the steady-state, direct electron transfer voltammetry of a particular FeFe hydrogenase, from Thermoanaerobacter mathranii, which is very unusual in that it irreversibly catalyzes H₂ oxidation and production: a large overpotential is required for the reaction to proceed in either direction [Land et al. Chem. Sci. 2020, 11, 12789-12801]. In contrast to previous hypotheses, we demonstrate that in this particular enzyme catalytic irreversibility can be explained without invoking slow interfacial electron transfer or variations in the mechanism: the observed kinetics is fully consistent with the same catalytic pathway being used in both directions of the reaction.

The Nonphysiological Reductant Sodium Dithionite and [FeFe] Hydrogenase: Influence on the Enzyme Mechanism

[FeFe] hydrogenases are highly active enzymes for interconverting protons and electrons with hydrogen (H₂). Their active site H-cluster is formed of a canonical [4Fe-4S] cluster ([4Fe-4S]_H) covalently attached to a unique [2Fe] subcluster ([2Fe]_H), where both sites are redox active. Heterolytic splitting and formation of H₂ takes place at [2Fe]_H, while [4Fe-4S]_H stores electrons. The detailed catalytic mechanism of these enzymes is under intense investigation, with two dominant models existing in the literature. In one model, an alternative form of the active oxidized state H_ox, named H_oxH, which forms at low pH in the presence of the nonphysiological reductant sodium dithionite (NaDT), is believed to play a crucial role. H_oxH was previously suggested to have a protonated [4Fe-4S]_H. Here, we show that H_oxH forms by simple addition of sodium sulfite (Na₂SO₃, the dominant oxidation product of NaDT) at low pH. The low pH requirement indicates that sulfur dioxide (SO₂) is the species involved. Spectroscopy supports binding at or near [4Fe-4S]_H, causing its redox potential to increase by ∼60 mV. This potential shift detunes the redox potentials of the subclusters of the H-cluster, lowering activity, as shown in protein film electrochemistry (PFE). Together, these results indicate that H_oxH and its one-electron reduced counterpart H_red'H are artifacts of using a nonphysiological reductant, and not crucial catalytic intermediates. We propose renaming these states as the "dithionite (DT) inhibited" states H_ox-DT_i and H_red-DT_i. The broader potential implications of using a nonphysiological reductant in spectroscopic and mechanistic studies of enzymes are highlighted.

Electrochemical control of [FeFe]-hydrogenase single crystals reveals complex redox populations at the catalytic site

Elucidating the distribution of intermediates at the active site of redox metalloenzymes is vital to understanding their highly efficient catalysis. Here we demonstrate that it is possible to generate, and detect, the key catalytic redox states of an [FeFe]-hydrogenase in a protein crystal. Individual crystals of the prototypical [FeFe]-hydrogenase I from Clostridium pasteurianum (CpI) are maintained under electrochemical control, allowing for precise tuning of the redox potential, while the crystal is simultaneously probed via Fourier Transform Infrared (FTIR) microspectroscopy. The high signal/noise spectra reveal potential-dependent variation in the distribution of redox states at the active site (H-cluster) according to state-specific vibrational bands from the endogeneous CO and CN- ligands. CpI crystals are shown to populate the same H-cluster states as those detected in solution, including the oxidised species Hox, the reduced species Hred/HredH+, the super-reduced HsredH+ and the hydride species Hhyd. The high sensitivity and precise redox control offered by this approach also facilitates the detection and characterisation of low abundance species that only accumulate within a narrow window of conditions, revealing new redox intermediates.

Influence of QD photosensitizers in the photocatalytic production of hydrogen with biomimetic [FeFe]-hydrogenase. Comparative performance of CdSe and CdTe

Photocatalytic systems comprising a hydrogenase-type catalyst and CdX (X = S, Se, Te) chalcogenide quantum dot (QD) photosensitizers show extraordinary hydrogen production rates under visible light excitation. What remains unknown is the mechanism of energy conversion in these systems. Here, we have explored this question by comparing the performance of two QD sensitizers, CdSe and CdTe, in photocatalytic systems featuring aqueous suspensions of a [Fe₂ (μ-1,2-benzenedithiolate) CO₆] catalyst and an ascorbic acid sacrificial agent. Overall, the hydrogen production yield for CdSe-sensitized reactions QDs was found to be 13 times greater than that of CdTe counterparts. According to emission quenching experiments, an enhanced performance of CdSe sensitizers reflected a greater rate of electron transfer from the ascorbic acid (k_Asc). The observed difference in the QD-ascorbic acid charge transfer rates between the two QD materials was consistent with respective driving forces for these systems.

Vibrational Perturbation of the [FeFe] Hydrogenase H-Cluster Revealed by 13C2H-ADT Labeling

[FeFe] hydrogenases are highly active catalysts for the interconversion of molecular hydrogen with protons and electrons. Here, we use a combination of isotopic labeling, ⁵⁷Fe nuclear resonance vibrational spectroscopy (NRVS), and density functional theory (DFT) calculations to observe and characterize the vibrational modes involving motion of the 2-azapropane-1,3-dithiolate (ADT) ligand bridging the two iron sites in the [2Fe]_H subcluster. A -¹³C²H₂- ADT labeling in the synthetic diiron precursor of [2Fe]_H produced isotope effects observed throughout the NRVS spectrum. The two precursor isotopologues were then used to reconstitute the H-cluster of [FeFe] hydrogenase from Chlamydomonas reinhardtii (CrHydA1), and NRVS was measured on samples poised in the catalytically crucial H_hyd state containing a terminal hydride at the distal Fe site. The ¹³C²H isotope effects were observed also in the H_hyd spectrum. DFT simulations of the spectra allowed identification of the ⁵⁷Fe normal modes coupled to the ADT ligand motions. Particularly, a variety of normal modes involve shortening of the distance between the distal Fe-H hydride and ADT N-H bridgehead hydrogen, which may be relevant to the formation of a transition state on the way to H₂ formation.

Ultrafast Electron Transfer from CdSe Quantum Dots to an [FeFe]-Hydrogenase Mimic

The combination of CdSe nanoparticles as photosensitizers with [FeFe]-hydrogenase mimics is known to result in efficient systems for light-driven hydrogen generation with reported turnover numbers in the order of 10⁴-10⁶. Nevertheless, little is known about the details of the light-induced charge-transfer processes. Here, we investigate the time scale of light-induced electron transfer kinetics for a simple model system consisting of CdSe quantum dots (QDs) of 2.0 nm diameter and a simple [FeFe]-hydrogenase mimic adsorbed to the QD surface under noncatalytic conditions. Our (time-resolved) spectroscopic investigation shows that both hot electron transfer on a sub-ps time scale and band-edge electron transfer on a sub-10 ps time scale from photoexcited QDs to adsorbed [FeFe]-hydrogenase mimics occur. Fast recombination via back electron transfer is observed in the absence of a sacrificial agent or protons which, under real catalytic conditions, would quench remaining holes or could stabilize the charge separation, respectively.

Following Electroenzymatic Hydrogen Production by Rotating Ring-Disk Electrochemistry and Mass Spectrometry*

Gas-processing metalloenzymes are of interest to future bio- and bioinspired technologies. Of particular importance are hydrogenases and nitrogenases, which both produce molecular hydrogen (H₂ ) from proton (H⁺ ) reduction. Herein, we report on the use of rotating ring-disk electrochemistry (RRDE) and mass spectrometry (MS) to follow the production of H₂ and isotopes produced from deuteron (D⁺ ) reduction (HD and D₂ ) using the [FeFe]-hydrogenase from Clostridium pasteurianum, a model hydrogen-evolving metalloenzyme. This facilitates enzymology studies independent of non-innocent chemical reductants. We anticipate that these approaches will be of value in resolving the catalytic mechanisms of H₂ -producing metalloenzymes and the design of bioinspired catalysts for H₂ production and N₂ fixation.

Microsecond-Resolved Infrared Spectroscopy on Nonrepetitive Protein Reactions by Applying Caged Compounds and Quantum Cascade Laser Frequency Combs

Infrared spectroscopy is ideally suited for the investigation of protein reactions at the atomic level. Many systems were investigated successfully by applying Fourier transform infrared (FTIR) spectroscopy. While rapid-scan FTIR spectroscopy is limited by time resolution (about 10 ms with 16 cm^-1 resolution), step-scan FTIR spectroscopy reaches a time resolution of about 10 ns but is limited to cyclic reactions that can be repeated hundreds of times under identical conditions. Consequently, FTIR with high time resolution was only possible with photoactivable proteins that undergo a photocycle. The huge number of nonrepetitive reactions, e.g., induced by caged compounds, were limited to the millisecond time domain. The advent of dual-comb quantum cascade laser now allows for a rapid reaction monitoring in the microsecond time domain. Here, we investigate the potential to apply such an instrument to the huge class of G-proteins. We compare caged-compound-induced reactions monitored by FTIR and dual-comb spectroscopy by applying the new technique to the α subunit of the inhibiting G_i protein and to the larger protein-protein complex of Gα_i with its cognate regulator of G-protein signaling (RGS). We observe good data quality with a 4 μs time resolution with a wavelength resolution comparable to FTIR. This is more than three orders of magnitude faster than any FTIR measurement on G-proteins in the literature. This study paves the way for infrared spectroscopic studies in the so far unresolvable microsecond time regime for nonrepetitive biological systems including all GTPases and ATPases.

Site-selective protonation of the one-electron reduced cofactor in [FeFe]-hydrogenase

Hydrogenases are bidirectional redox enzymes that catalyze hydrogen turnover in archaea, bacteria, and algae. While all types of hydrogenase show H2 oxidation activity, [FeFe]-hydrogenases are excellent H2 evolution catalysts as well. Their active site cofactor comprises a [4Fe-4S] cluster covalently linked to a diiron site equipped with carbon monoxide and cyanide ligands. The active site niche is connected with the solvent by two distinct proton transfer pathways. To analyze the catalytic mechanism of [FeFe]-hydrogenase, we employ operando infrared spectroscopy and infrared spectro-electrochemistry. Titrating the pH under H2 oxidation or H2 evolution conditions reveals the influence of site-selective protonation on the equilibrium of reduced cofactor states. Governed by pKa differences across the active site niche and proton transfer pathways, we find that individual electrons are stabilized either at the [4Fe-4S] cluster (alkaline pH values) or at the diiron site (acidic pH values). This observation is discussed in the context of the complex interdependence of hydrogen turnover and bulk pH.

A Beginner’s Guide to Thermodynamic Modelling of [FeFe] Hydrogenase

[FeFe] hydrogenases, which are considered the most active naturally occurring catalysts for hydrogen oxidation and proton reduction, are extensively studied as models to learn the important features for efficient H2 conversion catalysis. Using infrared spectroscopy as a selective probe, the redox behaviour of the active site H-cluster is routinely modelled with thermodynamic schemes based on the Nernst equation for determining thermodynamic parameters, such as redox midpoint potentials and pKa values. Here, the thermodynamic models usually applied to [FeFe] hydrogenases are introduced and discussed in a pedagogic fashion and their applicability to additional metalloenzymes and molecular catalysts is also addressed.

Experimental insight into enzyme catalysis and dynamics: A review on applications of state of art spectroscopic methods

Enzymes are dynamic in nature and understanding their activity depends on exploring their overall structural fluctuation as well as transformation at the active site in free state as well as turnover conditions. In this chapter, the application of several different spectroscopy techniques viz. single molecule spectroscopy, ultrafast spectroscopy and Raman spectroscopy in the context of enzyme dynamics and catalysis are discussed. The importance of such studies are significant in the understanding of new discoveries of drugs, cure for some lethal diseases, gene modification as well as in industrial applications.

Proton Transfer Mechanisms in Bimetallic Hydrogenases

Hydrogenases are metalloenzymes that catalyze proton reduction and H₂ oxidation with outstanding efficiency. They are model systems for bioinorganic chemistry, including low-valent transition metals, hydride chemistry, and proton-coupled electron transfer. In this Account, we describe how photochemistry and infrared difference spectroscopy can be used to identify the dynamic hydrogen-bonding changes that facilitate proton transfer in [NiFe]- and [FeFe]-hydrogenase.[NiFe]-hydrogenase binds a heterobimetallic nickel/iron site embedded in the protein by four cysteine ligands. [FeFe]-hydrogenase carries a homobimetallic iron/iron site attached to the protein by only a single cysteine. Carbon monoxide and cyanide ligands in the active site facilitate detailed investigations of hydrogenase catalysis by infrared spectroscopy because of their strong signals and redox-dependent frequency shifts. We found that specific redox-state transitions in [NiFe]- and [FeFe]-hydrogenase can be triggered by visible light to record extremely sensitive "light-minus-dark" infrared difference spectra monitoring key amino acid residues. As these transitions are coupled to protonation changes, our data allowed investigation of dynamic hydrogen-bonding changes that go well beyond the resolution of protein crystallography.In [NiFe]-hydrogenase, photolysis of the bridging hydride ligand in the Ni-C state was followed by infrared difference spectroscopy. Our data clearly indicate the formation of a protonated cysteine residue as well as hydrogen-bonding changes involving a glutamic acid residue and a "dangling water" molecule. These findings are in excellent agreement with crystallographic analyses of [NiFe]-hydrogenase. In [FeFe]-hydrogenase, an external redox dye was used to accumulate the Hred state. Infrared difference spectra indicate hydrogen-bonding changes involving two glutamic acid residues and a conserved arginine residue. While crystallographic analyses of [FeFe]-hydrogenase in the oxidized state failed to explain the rapid proton transfer because of a breach in the succession of residues, our findings facilitated a precise molecular model of discontinued proton transfer.Comparing both systems, our data emphasize the role of the outer coordination sphere in bimetallic hydrogenases: we suggest that protonation of a nickel-ligating cysteine in [NiFe]-hydrogenase causes the notable preference toward H₂ oxidation. On the contrary, proton transfer in [FeFe]-hydrogenase involves an adjacent cysteine as a relay group, promoting both H₂ oxidation and proton reduction. These observations may guide the design of organometallic compounds that mimic the catalytic properties of hydrogenases.

[FeFe]-Hydrogenases: maturation and reactivity of enzymatic systems and overview of biomimetic models

[FeFe]-hydrogenases recieved increasing interest in the last decades. This review summarises important findings regarding their enzymatic reactivity as well as inorganic models applied as electro- and photochemical catalysts.

Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis

Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.

The Laser-Induced Potential Jump: A Method for Rapid Electron Injection into Oxidoreductase Enzymes

Oxidoreductase enzymes often perform technologically useful chemical transformations using abundant metal cofactors with high efficiency under ambient conditions. The understanding of the catalytic mechanism of these enzymes is, however, highly dependent on the availability of well-characterized and optimized time-resolved analytical techniques. We have developed an approach for rapidly injecting electrons into a catalytic system using a photoactivated nanomaterial in combination with a range of redox mediators to produce a potential jump in solution, which then initiates turnover via electron transfer (ET) to the catalyst. The ET events at the nanomaterial-mediator-catalyst interfaces are, however, highly sensitive to the experimental conditions such as photon flux, relative concentrations of system components, and pH. Here, we present a systematic optimization of these experimental parameters for a specific catalytic system, namely, [FeFe] hydrogenase from Chlamydomonas reinhardtii (CrHydA1). The developed strategies can, however, be applied in the study of a wide variety of oxidoreductase enzymes. Our potential jump system consists of CdSe/CdS core-shell nanorods as a photosensitizer and a series of substituted bipyridinium salts as mediators with redox potentials in the range from -550 to -670 mV (vs SHE). With these components, we screened the effect of pH, mediator concentration, protein concentration, photosensitizer concentration, and photon flux on steady-state photoreduction and hydrogen production as well as ET and potential jump efficiency. By manipulating these experimental conditions, we show the potential of simple modifications to improve the tunability of the potential jump for application to study oxidoreductases.

The roles of long-range proton-coupled electron transfer in the directionality and efficiency of [FeFe]-hydrogenases

As paradigms for proton-coupled electron transfer in enzymes and benchmarks for a fully renewable H₂ technology, [FeFe]-hydrogenases behave as highly reversible electrocatalysts when immobilized on an electrode, operating in both catalytic directions with minimal overpotential requirement. Using the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1) we have conducted site-directed mutagenesis and protein film electrochemistry to determine how efficient catalysis depends on the long-range coupling of electron and proton transfer steps. Importantly, the electron and proton transfer pathways in [FeFe]-hydrogenases are well separated from each other in space. Variants with conservative substitutions (glutamate to aspartate) in either of two positions in the proton-transfer pathway retain significant activity and reveal the consequences of slowing down proton transfer for both catalytic directions over a wide range of pH and potential values. Proton reduction in the variants is impaired mainly by limiting the turnover rate, which drops sharply as the pH is raised, showing that proton capture from bulk solvent becomes critical. In contrast, hydrogen oxidation is affected in two ways: by limiting the turnover rate and by a large overpotential requirement that increases as the pH is raised, consistent with the accumulation of a reduced and protonated intermediate. A unique observation having fundamental significance is made under conditions where the variants still retain sufficient catalytic activity in both directions: An inflection appears as the catalytic current switches direction at the 2H⁺/H₂ thermodynamic potential, clearly signaling a departure from electrocatalytic reversibility as electron and proton transfers begin to be decoupled.

Spectroscopic and Computational Evidence that [FeFe] Hydrogenases Operate Exclusively with CO-Bridged Intermediates

[FeFe] hydrogenases are extremely active H₂-converting enzymes. Their mechanism remains highly controversial, in particular, the nature of the one-electron and two-electron reduced intermediates called H_redH⁺ and H_sredH⁺. In one model, the H_redH⁺ and H_sredH⁺ states contain a semibridging CO, while in the other model, the bridging CO is replaced by a bridging hydride. Using low-temperature IR spectroscopy and nuclear resonance vibrational spectroscopy, together with density functional theory calculations, we show that the bridging CO is retained in the H_sredH⁺ and H_redH⁺ states in the [FeFe] hydrogenases from Chlamydomonas reinhardtii and Desulfovibrio desulfuricans, respectively. Furthermore, there is no evidence for a bridging hydride in either state. These results agree with a model of the catalytic cycle in which the H_redH⁺ and H_sredH⁺ states are integral, catalytically competent components. We conclude that proton-coupled electron transfer between the two subclusters is crucial to catalysis and allows these enzymes to operate in a highly efficient and reversible manner.