Applications of Photogating and Time Resolved Spectroscopy to Mechanistic Studies of Hydrogenases

Glucose oxidase: An emerging multidimensional treatment option for diabetic wound healing

The healing of diabetic skin wounds is a complex process significantly affected by the hyperglycemic environment. In this context, glucose oxidase (GOx), by catalyzing glucose to produce gluconic acid and hydrogen peroxide, not only modulates the hyperglycemic microenvironment but also possesses antibacterial and oxygen-supplying functions, thereby demonstrating immense potential in the treatment of diabetic wounds. Despite the growing interest in GOx-based therapeutic strategies in recent years, a systematic summary and review of these efforts have been lacking. To address this gap, this review article outlines the advancements in the application of GOx and GOx-like nanozymes in the treatment of diabetic wounds, including reaction mechanisms, the selection of carrier materials, and synergistic therapeutic strategies such as multi-enzyme combinations, microneedle structures, and gas therapy. Finally, the article looks forward to the application prospects of GOx in aiding the healing of diabetic wounds and the challenges faced in translating these innovations to clinical practice. We sincerely hope that this review can provide readers with a comprehensive understanding of GOx-based diabetic treatment strategies, facilitate the rigorous construction of more robust multifunctional therapeutic systems, and ultimately benefit patients with diabetic wounds.

Light-Induced Electron Transfer in a [NiFe] Hydrogenase Opens a Photochemical Shortcut for Catalytic Dihydrogen Cleavage

[NiFe] hydrogenases catalyze the reversible cleavage of molecular hydrogen into protons and electrons. Here, we have studied the impact of temperature and illumination on an oxygen-tolerant and thermostable [NiFe] hydrogenase by IR and EPR spectroscopy. Equilibrium mixtures of two catalytic [NiFe] states, Nia-C and Nia-SR'', were found to drastically change with temperature, indicating a thermal exchange of electrons between the [NiFe] active site and iron-sulfur clusters of the enzyme. In addition, IR and EPR experiments performed under illumination revealed an unusual photochemical response of the enzyme. Nia-SR'', a fully reduced hydride intermediate of the catalytic cycle, was found to be reversibly photoconverted into another catalytic state, Nia-L. In contrast to the well-known photolysis of the more oxidized hydride intermediate Nia-C, photoconversion of Nia-SR'' into Nia-L is an active-site redox reaction that involves light-driven electron transfer towards the enzyme's iron-sulfur clusters. Omitting the ground-state intermediate Nia-C, this direct interconversion of these two states represents a potential photochemical shortcut of the catalytic cycle that integrates multiple redox sites of the enzyme. In total, our findings reveal the non-local redistribution of electrons via thermal and photochemical reaction channels and the potential of accelerating or controlling [NiFe] hydrogenases by light.

Intrinsic Defect-Driven Synergistic Synaptic Heterostructures for Gate-Free Neuromorphic Phototransistors

The optoelectronic synaptic devices based on two-dimensional (2D) materials offer great advances for future neuromorphic visual systems with dramatically improved integration density and power efficiency. The effective charge capture and retention are considered as one vital prerequisite to realizing the synaptic memory function. However, the current 2D synaptic devices are predominantly relied on materials with artificially-engineered defects or intricate gate-controlled architectures to realize the charge trapping process. These approaches, unfortunately, suffer from the degradation of pristine materials, rapid device failure, and unnecessary complication of device structures. To address these challenges, an innovative gate-free heterostructure paradigm is introduced herein. The heterostructure presents a distinctive dome-like morphology wherein a defect-rich Fe7S8 core is enveloped snugly by a curved MoS2 dome shell (Fe7S8@MoS2), allowing the realization of effective photocarrier trapping through the intrinsic defects in the adjacent Fe7S8 core. The resultant neuromorphic devices exhibit remarkable light-tunable synaptic behaviors with memory time up to ≈800 s under single optical pulse, thus demonstrating great advances in simulating visual recognition system with significantly improved image recognition efficiency. The emergence of such heterostructures foreshadows a promising trajectory for underpinning future synaptic devices, catalyzing the realization of high-efficiency and intricate visual processing applications.

Selective cascade activation of polycyclic aromatic hydrocarbons in human cells: Role of enzyme's intrinsic electric field

Polycyclic aromatic hydrocarbons (PAHs) are major environmental organic pollutants. Some metabolites of PAHs show greater toxicity to humans while the others do not. It is highly important to decipher PAHs' regioselective activation mechanism and identify the major metabolites to accurately evaluate their public health risk. Here, we have performed a thorough computational study of benzo[a]anthracene (BA) metabolized by P450 1A1 by employing molecular docking, molecular dynamics simulations, quantum chemical calculation, and quantum mechanics/molecular mechanics calculations. Our findings show that highly-reactive species such as 3,4-epoxide, 8,9-epoxide, 3,4-diol-1,2-epoxide, and 8,9-diol-10,11-epoxide were major metabolites, which can efficiently react with guanine and damage DNA with extremely low energy barrier, therefore, supports the regioselective metabolism of BA. The origin of this selective activation is mainly contributed to both the oxygen‑carbon distance and previously overlooked enzyme's intrinsic electric field. Consequently, based on the resolved activation selectivity of BA. We built a high-throughput strategy to efficiently predict the metabolites of other PAHs. The accuracy of the strategy is validated by studying 16 PAHs on the priority control list. Hopefully this will aid the accurate evaluation of public health risks associated with PAH emissions.

High Affinity Electrostatic Interactions Support the Formation of CdS Quantum Dot:Nitrogenase MoFe Protein Complexes

Nitrogenase MoFe protein can be coupled with CdS nanocrystals (NCs) to enable photocatalytic N2 reduction. The nature of interactions that support complex formation is of paramount importance in intermolecular electron transfer that supports catalysis. In this work we have employed microscale thermophoresis to examine binding interactions between 3-mercaptopropionate capped CdS quantum dots (QDs) and MoFe protein over a range of QD diameters (3.4-4.3 nm). The results indicate that the interactions are largely electrostatic, with the strength of interactions similar to that observed for the physiological electron donor. In addition, the strength of interactions is sensitive to the QD diameter, and the binding interactions are significantly stronger for QDs with smaller diameters. The ability to quantitatively assess NC protein interactions in biohybrid systems supports strategies for understanding properties and reaction parameters that are important for obtaining optimal rates of catalysis in biohybrid systems.

Structural Determinants of the Catalytic Nia-L Intermediate of [NiFe]-Hydrogenase

[NiFe]-hydrogenases catalyze the reversible cleavage of H₂ into two protons and two electrons at the inorganic heterobimetallic NiFe center of the enzyme. Their catalytic cycle involves at least four intermediates, some of which are still under debate. While the core reaction, including H₂/H^- binding, takes place at the inorganic cofactor, a major challenge lies in identifying those amino acid residues that contribute to the reactivity and how they stabilize (short-lived) intermediate states. Using cryogenic infrared and electron paramagnetic resonance spectroscopy on the regulatory [NiFe]-hydrogenase from Cupriavidus necator, a model enzyme for the analysis of catalytic intermediates, we deciphered the structural basis of the hitherto elusive Ni_a-L intermediates. We unveiled the protonation states of a proton-accepting glutamate and a Ni-bound cysteine residue in the Ni_a-L1, Ni_a-L2, and the hydride-binding Ni_a-C intermediates as well as previously unknown conformational changes of amino acid residues in proximity of the bimetallic active site. As such, this study unravels the complexity of the Ni_a-L intermediate and reveals the importance of the protein scaffold in fine-tuning proton and electron dynamics in [NiFe]-hydrogenase.

Reversible Glutamate Coordination to High-Valent Nickel Protects the Active Site of a [NiFe] Hydrogenase from Oxygen

NAD⁺-reducing [NiFe] hydrogenases are valuable biocatalysts for H₂-based energy conversion and the regeneration of nucleotide cofactors. While most hydrogenases are sensitive toward O₂ and elevated temperatures, the soluble NAD⁺-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus (HtSH) is O₂-tolerant and thermostable. Thus, it represents a promising candidate for biotechnological applications. Here, we have investigated the catalytic activity and active-site structure of native HtSH and variants in which a glutamate residue in the active-site cavity was replaced by glutamine, alanine, and aspartate. Our biochemical, spectroscopic, and theoretical studies reveal that at least two active-site states of oxidized HtSH feature an unusual architecture in which the glutamate acts as a terminal ligand of the active-site nickel. This observation demonstrates that crystallographically observed glutamate coordination represents a native feature of the enzyme. One of these states is diamagnetic and characterized by a very high stretching frequency of an iron-bound active-site CO ligand. Supported by density-functional-theory calculations, we identify this state as a high-valent species with a biologically unprecedented formal Ni(IV) ground state. Detailed insights into its structure and dynamics were obtained by ultrafast and two-dimensional infrared spectroscopy, demonstrating that it represents a conformationally strained state with unusual bond properties. Our data further show that this state is selectively and reversibly formed under oxic conditions, especially upon rapid exposure to high O₂ levels. We conclude that the kinetically controlled formation of this six-coordinate high-valent state represents a specific and precisely orchestrated stereoelectronic response toward O₂ that could protect the enzyme from oxidative damage.

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

Charge carrier dynamics and reaction intermediates in heterogeneous photocatalysis by time-resolved spectroscopies

Sunlight as the most abundant renewable energy holds the promise to make our society sustainable. However, due to its low power density and intermittence, efficient conversion and storage of solar energy as a clean fuel are crucial. Apart from solar fuel synthesis, sunlight can also be used to drive other reactions including organic conversion and air/water purification. Given such potential of photocatalysis, the past few decades have seen a surge in the discovery of photocatalysts. However, the current photocatalytic efficiency is still very moderate. To address this challenge, it is important to understand fundamental factors that dominate the efficiency of a photocatalytic process to enable the rational design and development of photocatalytic systems. Many recent studies highlighted transient absorption spectroscopy (TAS) and time-resolved infrared (TRIR) spectroscopy as powerful approaches to characterise charge carrier dynamics and reaction pathways to elucidate the reasons behind low photocatalytic efficiencies, and to rationalise photocatalytic activities exhibited by closely related materials. Accordingly, as a fast-moving area, the past decade has witnessed an explosion in reports on charge carrier dynamics and reaction mechanisms on a wide range of photocatalytic materials. This critical review will discuss the application of TAS and TRIR in a wide range of heterogeneous photocatalytic systems, demonstrating the variety of ways in which these techniques can be used to understand the correlation between materials design, charge carrier behaviour, and photocatalytic activity. Finally, it provides a comprehensive outlook for potential developments in the area of time-resolved spectroscopies with an aim to provide design strategies for photocatalysts.

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.

Inhibition of [FeFe]-hydrogenase by formaldehyde: proposed mechanism and reactivity of FeFe alkyl complexes

The mechanism for inhibition of [FeFe]-hydrogenases by formaldehyde is examined with model complexes. Key findings: (i) CH2 donated by formaldehyde covalently link Fe and the amine cofactor, blocking the active site and (ii) the resulting Fe-alkyl is a versatile electrophilic alkylating agent. Solutions of Fe2[(μ-SCH2)2NH](CO)4(PMe3)2 (1) react with a mixture of HBF4 and CH2O to give three isomers of [Fe2[(μ-SCH2)2NCH2](CO)4(PMe3)2]+ ([2]+). X-ray crystallography verified the NCH2Fe linkage to an octahedral Fe(ii) site. Although [2]+ is stereochemically rigid on the NMR timescale, spin-saturation transfer experiments implicate reversible dissociation of the Fe-CH2 bond, allowing interchange of all three diastereoisomers. Using 13CH2O, the methylenation begins with formation of [Fe2[(μ-SCH2)2N13CH2OH](CO)4(PMe3)2]+. Protonation converts this hydroxymethyl derivative to [2]+, concomitant with 13C-labelling of all three methylene groups. The Fe-CH2N bond in [2]+ is electrophilic: PPh3, hydroxide, and hydride give, respectively, the phosphonium [Fe2[(μ-SCH2)2NCH2PPh3](CO)4(PMe3)2]+, 1, and the methylamine Fe2[(μ-SCH2)2NCH3](CO)4(PMe3)2. The reaction of [Fe2[(μ-SCH2)2NH](CN)2(CO)4]2- with CH2O/HBF4 gave [Fe2[(μ-SCH2)2NCH2CN](CN)(CO)5]- ([4]-), the result of reductive elimination from [Fe2[(μ-SCH2)2NCH2](CN)2(CO)4]-. The phosphine derivative [Fe2[(μ-SCH2)2NCH2CN](CN)(CO)4(PPh3)]- ([5]-) was characterized crystallographically.

The crystalline state as a dynamic system: IR microspectroscopy under electrochemical control for a [NiFe] hydrogenase

Controlled formation of catalytically-relevant states within crystals of complex metalloenzymes represents a significant challenge to structure-function studies. Here we show how electrochemical control over single crystals of [NiFe] hydrogenase 1 (Hyd1) from Escherichia coli makes it possible to navigate through the full array of active site states previously observed in solution. Electrochemical control is combined with synchrotron infrared microspectroscopy, which enables us to measure high signal-to-noise IR spectra in situ from a small area of crystal. The output reports on active site speciation via the vibrational stretching band positions of the endogenous CO and CN- ligands at the hydrogenase active site. Variation of pH further demonstrates how equilibria between catalytically-relevant protonation states can be deliberately perturbed in the crystals, generating a map of electrochemical potential and pH conditions which lead to enrichment of specific states. Comparison of in crystallo redox titrations with measurements in solution or of electrode-immobilised Hyd1 confirms the integrity of the proton transfer and redox environment around the active site of the enzyme in crystals. Slowed proton-transfer equilibria in the hydrogenase in crystallo reveals transitions which are only usually observable by ultrafast methods in solution. This study therefore demonstrates the possibilities of electrochemical control over single metalloenzyme crystals in stabilising specific states for further study, and extends mechanistic understanding of proton transfer during the [NiFe] hydrogenase catalytic cycle.

Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies

Vibrational spectroscopy and in particular, resonance Raman (RR) spectroscopy, can provide molecular details on metalloproteins containing multiple cofactors, which are often challenging for other spectroscopies. Due to distinct spectroscopic fingerprints, RR spectroscopy has a unique capacity to monitor simultaneously and independently different metal cofactors that can have particular roles in metalloproteins. These include e.g., (i) different types of hemes, for instance hemes c, a and a3 in caa3-type oxygen reductases, (ii) distinct spin populations, such as electron transfer (ET) low-spin (LS) and catalytic high-spin (HS) hemes in nitrite reductases, (iii) different types of Fe-S clusters, such as 3Fe-4S and 4Fe-4S centers in di-cluster ferredoxins, and (iv) bi-metallic center and ET Fe-S clusters in hydrogenases. IR spectroscopy can provide unmatched molecular details on specific enzymes like hydrogenases that possess catalytic centers coordinated by CO and CN- ligands, which exhibit spectrally well separated IR bands. This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.

Exploring Structure and Function of Redox Intermediates in [NiFe]-Hydrogenases by an Advanced Experimental Approach for Solvated, Lyophilized and Crystallized Metalloenzymes

To study metalloenzymes in detail, we developed a new experimental setup allowing the controlled preparation of catalytic intermediates for characterization by various spectroscopic techniques. The in situ monitoring of redox transitions by infrared spectroscopy in enzyme lyophilizate, crystals, and solution during gas exchange in a wide temperature range can be accomplished as well. Two O2 -tolerant [NiFe]-hydrogenases were investigated as model systems. First, we utilized our platform to prepare highly concentrated hydrogenase lyophilizate in a paramagnetic state harboring a bridging hydride. This procedure proved beneficial for 57 Fe nuclear resonance vibrational spectroscopy and revealed, in combination with density functional theory calculations, the vibrational fingerprint of this catalytic intermediate. The same in situ IR setup, combined with resonance Raman spectroscopy, provided detailed insights into the redox chemistry of enzyme crystals, underlining the general necessity to complement X-ray crystallographic data with spectroscopic analyses.

Covalent Organic Frameworks Enabling Site Isolation of Viologen-Derived Electron-Transfer Mediators for Stable Photocatalytic Hydrogen Evolution

Electron transfer is the rate-limiting step in photocatalytic water splitting. Viologen and its derivatives are able to act as electron-transfer mediators (ETMs) to facilitate the rapid electron transfer from photosensitizers to active sites. Nevertheless, the electron-transfer ability often suffers from the formation of a stable dipole structure through the coupling between cationic-radical-containing viologen-derived ETMs, by which the electron-transfer process becomes restricted. Herein, cyclic diquats, a kind of viologen-derived ETM, are integrated into a 2,2'-bipyridine-based covalent organic framework (COF) through a post-quaternization reaction. The content and distribution of embedded diquat-ETMs are elaborately controlled, leading to the favorable site-isolated arrangement. The resulting materials integrate the photosensitizing units and ETMs into one system, exhibiting the enhanced hydrogen evolution rate (34600 μmol h^-1  g^-1 ) and sustained performances when compared to a single-module COF and a COF/ETM mixture. The integration strategy applied in a 2D COF platform promotes the consecutive electron transfer in photochemical processes through the multi-component cooperation.

In Vitro Assembly as a Tool to Investigate Catalytic Intermediates of [NiFe]-Hydrogenase

[NiFe]-hydrogenases catalyze the reversible reaction H2 ⇄ 2H+ + 2e-. Their basic module consists of a large subunit, coordinating the NiFe(CO)(CN)2 center, and a small subunit that carries electron-transferring iron-sulfur clusters. Here, we report the in vitro assembly of fully functional [NiFe]-hydrogenase starting from the isolated large and small subunits. Activity assays complemented by spectroscopic measurements revealed a native-like hydrogenase. This approach was used to label exclusively the NiFe(CO)(CN)2 center with 57Fe, enabling a clear view of the catalytic site by means of nuclear resonance vibrational spectroscopy. This strategy paves the way for in-depth studies of [NiFe]-hydrogenase catalytic intermediates.

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.

Defining Intermediates of Nitrogenase MoFe Protein during N2 Reduction under Photochemical Electron Delivery from CdS Quantum Dots

Coupling the nitrogenase MoFe protein to light-harvesting semiconductor nanomaterials replaces the natural electron transfer complex of Fe protein and ATP and provides low-potential photoexcited electrons for photocatalytic N₂ reduction. A central question is how direct photochemical electron delivery from nanocrystals to MoFe protein is able to support the multielectron ammonia production reaction. In this study, low photon flux conditions were used to identify the initial reaction intermediates of CdS quantum dot (QD):MoFe protein nitrogenase complexes under photochemical activation using EPR. Illumination of CdS QD:MoFe protein complexes led to redox changes in the MoFe protein active site FeMo-co observed as the gradual decline in the E₀ resting state intensity that was accompanied by an increase in the intensity of a new "g_eff = 4.5" EPR signal. The magnetic properties of the g_eff = 4.5 signal support assignment as a reduced S = 3/2 state, and reaction modeling was used to define it as a two-electron-reduced "E₂" intermediate. Use of a MoFe protein variant, β-188^Cys, which poises the P cluster in the oxidized P⁺ state, demonstrated that the P cluster can function as a site of photoexcited electron delivery from CdS to MoFe protein. Overall, the results establish the initial steps for how photoexcited CdS delivers electrons into the MoFe protein during reduction of N₂ to ammonia and the role of electron flux in the photochemical reaction cycle.

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds

Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.

Electron Transfer from Semiconductor Nanocrystals to Redox Enzymes

This review summarizes progress in understanding electron transfer from photoexcited nanocrystals to redox enzymes. The combination of the light-harvesting properties of nanocrystals and the catalytic properties of redox enzymes has emerged as a versatile platform to drive a variety of enzyme-catalyzed reactions with light. Transfer of a photoexcited charge from a nanocrystal to an enzyme is a critical first step for these reactions. This process has been studied in depth in systems that combine Cd-chalcogenide nanocrystals with hydrogenases. The two components can be assembled in close proximity to enable direct interfacial electron transfer or integrated with redox mediators to transport charges. Time-resolved spectroscopy and kinetic modeling have been used to measure the rates and efficiencies of the electron transfer. Electron transfer has been described within the framework of Marcus theory, providing insights into the factors that can be used to control the photochemical activity of these biohybrid systems. The range of potential applications and reactions that can be achieved using nanocrystal-enzyme systems is expanding, and numerous fundamental and practical questions remain to be addressed.

Unifying Activity, Structure, and Spectroscopy of [NiFe] Hydrogenases: Combining Techniques To Clarify Mechanistic Understanding

Achieving a unified understanding of the mechanism of a multicenter redox enzyme such as [NiFe] hydrogenase is complicated by difficulties in reconciling information obtained by using different techniques and on samples in different physical forms. Measurements of the activity of the enzyme, and of factors which perturb activity, are generally carried out using biochemical assays in solution or with electrode-immobilized enzymes using protein film electrochemistry (PFE). Conversely, spectroscopy aimed at reporting on features of the metalloclusters in the enzyme, such as electron paramagnetic resonance (EPR) or X-ray absorption spectroscopy (XAS), is often conducted on frozen samples and is thus difficult to relate to catalytically relevant states as information about turnover and activity has been lost. To complicate matters further, most of our knowledge of the atomic-level structure of metalloenzymes comes from X-ray diffraction studies in the solid, crystalline state, which are again difficult to link to turnover conditions. Taking [NiFe] hydrogenases as our case study, we show here how it is possible to apply infrared (IR) spectroscopic sampling approaches to unite direct spectroscopic study with catalytic turnover. Using a method we have named protein film IR electrochemistry (PFIRE), we reveal the steady-state distribution of intermediates during catalysis and identify catalytic "bottlenecks" introduced by site-directed mutagenesis. We also show that it is possible to study dynamic transitions between active site states of enzymes in single crystals, uniting solid state and solution spectroscopic information. In all of these cases, the spectroscopic data complement and enhance interpretation of purely activity-based measurements by providing direct chemical insight that is otherwise hidden. The [NiFe] hydrogenases possess a bimetallic [NiFe] active site, coordinated by CO and CN^- ligands, linked to the protein via bridging and terminal cysteine sulfur ligands, as well as an electron relay chain of iron sulfur clusters. Infrared spectroscopy is ideal for probing hydrogenases because the CO and CN^- ligands are strong IR absorbers, but the suite of IR-based approaches we describe here will be equally valuable in studying substrate- or intermediate-bound states of other metalloenzymes where key mechanistic questions remain open, such as nitrogenase, formate dehydrogenase, or carbon monoxide dehydrogenase. We therefore hope that this Account will encourage future studies which unify information from different techniques across bioinorganic chemistry.

Cysteine SH and Glutamate COOH Contributions to [NiFe] Hydrogenase Proton Transfer Revealed by Highly Sensitive FTIR Spectroscopy

A [NiFe] hydrogenase (H₂ ase) is a proton-coupled electron transfer enzyme that catalyses reversible H₂ oxidation; however, its fundamental proton transfer pathway remains unknown. Herein, we observed the protonation of Cys546-SH and Glu34-COOH near the Ni-Fe site with high-sensitivity infrared difference spectra by utilizing Ni-C-to-Ni-L and Ni-C-to-Ni-SI_a photoconversions. Protonated Cys546-SH in the Ni-L state was verified by the observed SH stretching frequency (2505 cm^-1 ), whereas Cys546 was deprotonated in the Ni-C and Ni-SI_a states. Glu34-COOH was double H-bonded in the Ni-L state, as determined by the COOH stretching frequency (1700 cm^-1 ), and single H-bonded in the Ni-C and Ni-SI_a states. Additionally, a stretching mode of an ordered water molecule was observed in the Ni-L and Ni-C states. These results elucidate the organized proton transfer pathway during the catalytic reaction of a [NiFe] H₂ ase, which is regulated by the H-bond network of Cys546, Glu34, and an ordered water molecule.

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.

The Molecular Proceedings of Biological Hydrogen Turnover

Over the past two decades, the bioinorganic chemistry of hydrogenases has attracted much interest from basic and applied research. Hydrogenases are highly efficient metalloenzymes that catalyze the reversible reduction of protons to molecular hydrogen (H₂) in all domains of life. Their iron- and nickel-based cofactors represent promising blueprints for the design of biomimetic, synthetic catalysts. In this Account, we address the molecular proceedings of hydrogen turnover with [FeFe]-hydrogenases. The active site cofactor of [FeFe]-hydrogenases ("H-cluster") comprises a unique diiron complex linked to a [4Fe-4S] cluster via a single cysteine. Since it was discovered that a synthetic analogue of the diiron site can be incorporated into apoprotein in vitro to yield active enzyme, significant progress has been made toward a comprehensive understanding of hydrogenase catalysis. The diiron site carries three to four carbon monoxide (CO) and two cyanide (CN^-) ligands that give rise to intense infrared (IR) absorption bands. These bands are sensitive reporters of the electron density across the H-cluster, which can be addressed by infrared spectroscopy to follow redox and protonation changes at the cofactor. Synthetic variation of the metal-bridging dithiolate ligand at the diiron site, as well as site-directed mutagenesis of amino acids, provides access to the proton pathways toward the cofactor. Quantum chemical calculations are employed to specifically assign IR bands to vibrational modes of the diatomic ligands and yield refined H-cluster geometries. Here, we provide an overview of recent research on [FeFe]-hydrogenases with emphasis on experimental and computational IR studies. We describe advances in attenuated total reflection Fourier transform infrared spectroscopy (ATR FTIR) and protein film electrochemistry, as well as density functional theory (DFT) calculations. Key cofactor species are discussed in terms of molecular geometry, redox state, and protonation. Isotope editing is introduced as a tool to evaluate the cofactor geometry beyond the limits of protein crystallography. In particular, the role of proton-coupled electron transfer (PCET) in the generation of catalytically relevant redox species is addressed. We propose that site-selective protonation of the H-cluster biases surplus electrons either to the [4Fe-4S] cluster or to the diiron site. Protonation of the [4Fe-4S] cluster prevents premature reduction at the diiron site and stabilizes a reactive, terminal hydride. The observed H-cluster species are assigned to rapid H₂ conversion or to reactions possibly involved in activity regulation and cellular H₂ sensing. In the catalytic cycle of [FeFe]-hydrogenases, an H-cluster geometry is preserved that features a bridging CO ligand. PCET levels the redox potential for two steps of sequential cofactor reduction. The concept of consecutive PCET at a geometrically inert cofactor with tight control of electron and proton localization may inspire the design of a novel generation of biomimetic catalysts for the production of H₂ as a fuel.

[FeFe]-Hydrogenases: recent developments and future perspectives

[FeFe]-Hydrogenases are the most efficient enzymes for catalytic hydrogen turnover.