Modeling the active sites in metalloenzymes. 3. Density functional calculations on models for [Fe]-hydrogenase: structures and vibrational frequencies of the observed redox forms and the reaction mechanism at the Diiron Active Center

Probing Substrate Transport Effects on Enzymatic Hydrogen Catalysis: An Alternative Proton Transfer Pathway in Putatively Sensory [FeFe] Hydrogenase

[FeFe] hydrogenases, metalloenzymes catalyzing proton/dihydrogen interconversion, have attracted intense attention due to their remarkable catalytic properties and (bio-)technological potential for a future hydrogen economy. In order to unravel the factors enabling their efficient catalysis, both their unique organometallic cofactors and protein structural features, i.e., "outer-coordination sphere" effects have been intensively studied. These structurally diverse enzymes are divided into distinct phylogenetic groups, denoted as Group A-D. Prototypical Group A hydrogenases display high turnover rates (104-105 s-1). Conversely, the sole characterized Group D representative, Thermoanaerobacter mathranii HydS (TamHydS), shows relatively low catalytic activity (specific activity 10-1 μmol H2 mg-1 min-1) and has been proposed to serve a H2-sensory function. The various groups of [FeFe] hydrogenase share the same catalytic cofactor, the H-cluster, and the structural factors causing the diverging reactivities of Group A and D remain to be elucidated. In the case of the highly active Group A enzymes, a well-defined proton transfer pathway (PTP) has been identified, which shuttles H+ between the enzyme surface and the active site. In Group D hydrogenases, this conserved pathway is absent. Here, we report on the identification of highly conserved amino acid residues in Group D hydrogenases that constitute a possible alternative PTP. We varied two proposed key amino acid residues of this pathway (E252 and E289, TamHydS numbering) via site-directed mutagenesis and analyzed the resulting variants via biochemical and spectroscopic methods. All variants displayed significantly decreased H2-evolution and -oxidation activities. Additionally, the variants showed two redox states that were not characterized previously. These findings provide initial evidence that these amino acid residues are central to the putative PTP of Group D [FeFe] hydrogenase. Since the identified residues are highly conserved in Group D exclusively, our results support the notion that the PTP is not universal for different phylogenetic groups in [FeFe] hydrogenases.

The electrostatic potential as a descriptor for the protonation propensity in automated exploration of reaction mechanisms

We discuss the possibility of exploiting local minima of the molecular electrostatic potential for locating protonation sites in molecules in a fully automated manner. We implement and apply this concept to exploring the mechanism of proton reduction catalyzed by a hydrogenase model complex [Orthaber et al., Dalton Trans., 2014, 43, 4537]. A large number of distinct structures arising already in the early stages of the hydrogen evolution mechanism demonstrates the need for reliable, automated algorithms for the thorough analysis of catalytic processes.

Unraveling the mechanism of biomimetic hydrogen fuel production – a first principles molecular dynamics study

The Fe₂(bdt)(CO)₆ [bdt = benzenedithiolato] complex, a synthetic mimic of the [FeFe] hydrogenase enzyme can electrochemically convert protons into molecular hydrogen. The free energy landscape reveals a different mechanism for the biomimetic cycle.

Quantitative prediction of electronic absorption spectra of copper(II)-bioligand systems: Validation and applications

The visible region of the electronic absorption spectra of Cu(II) complexes was studied by time-dependent density functional theory (TD-DFT). The performance of twelve functionals in the prediction of absorption maxima (λ_max) was tested on eleven compounds with different geometry, donors and charge. The ranking of the functionals for λ_max was determined in terms of mean absolute percent deviation (MAPD) and standard deviation (SD) and it is as follows: BHandHLYP > M06 ≫ CAM-B3LYP ≫ MPW1PW91 ~ B1LYP ~ BLYP > HSE06 ~ B3LYP > B3P86 ~ ω-B97x-D ≫ TPSSh ≫ M06-2X (MAPD) and BHandHLYP > M06 ~ HSE06 > ω-B97x-D ~ CAM-B3LYP ~ MPW1PW91 > B1LYP ~ B3LYP > B3P86 > BLYP ≫ TPSSh ≫ M06-2X (SD). With BHandHLYP functional the MAPD is 3.1% and SD is 2.3%, while with M06 the MAPD is 3.7% and SD is 3.7%. The protocol validated in the first step of the study was applied to: i) calculate the number of transitions in the spectra and relate them to the geometry of Cu(II) species; ii) determine the coordination of axial water(s); iii) predict the electronic spectra of the systems where Cu(II) is bound to human serum albumin (HSA) and to the regions 94-97 and 108-112 of prion protein (PrP). The results indicate that the proposed computational protocol allows a successful prediction of the electronic spectra of Cu(II) species and to relate an experimental spectrum to a specific structure.

Molecular Electrocatalysts for the Hydrogen Evolution Reaction: Input from Quantum Chemistry

In the pursuit of carbon-free fuels, hydrogen can be considered as an apt energy carrier. The design of molecular electrocatalysts for hydrogen production is important for the development of renewable energy sources that are abundant, inexpensive, and environmentally benign. Over the last 20 years, a large number of electrocatalysts have been developed, and considerable efforts have been directed toward the design of earth-abundant, first-row transition-metal complexes capable of promoting electrocatalytic hydrogen evolution reaction (HER). In this context, numerical approaches have emerged as powerful tools to study the catalytic performances of these complexes. This review covers some of the most significant theoretical mechanistic studies of biomimetic and bioinspired homogeneous HER catalysts. The approaches employed to study the free energy landscapes are discussed and methods used to obtain accurate estimates of relevant observables required to study the HER are presented. Furthermore, the structural and electronic parameters that govern the reactivity, and are necessary to achieve efficient hydrogen production, are discussed in view of future research directions.

Interplay of hemilability and redox activity in models of hydrogenase active sites

The hydrogen evolution reaction, as catalyzed by two electrocatalysts [M(N₂S₂)·Fe(NO)₂]⁺, [Fe-Fe]⁺ (M = Fe(NO)) and [Ni-Fe]⁺ (M = Ni) was investigated by computational chemistry. As nominal models of hydrogenase active sites, these bimetallics feature two kinds of actor ligands: Hemilabile, MN₂S₂ ligands and redox-active, nitrosyl ligands, whose interplay guides the H₂ production mechanism. The requisite base and metal open site are masked in the resting state but revealed within the catalytic cycle by cleavage of the MS-Fe(NO)₂ bond from the hemilabile metallodithiolate ligand. Introducing two electrons and two protons to [Ni-Fe]⁺ produces H₂ from coupling a hydride temporarily stored on Fe(NO)₂ (Lewis acid) and a proton accommodated on the exposed sulfur of the MN₂S₂ thiolate (Lewis base). This Lewis acid-base pair is initiated and preserved by disrupting the dative donation through protonation on the thiolate or reduction on the thiolate-bound metal. Either manipulation modulates the electron density of the pair to prevent it from reestablishing the dative bond. The electron-buffering nitrosyl's role is subtler as a bifunctional electron reservoir. With more nitrosyls as in [Fe-Fe]⁺, accumulated electronic space in the nitrosyls' π*-orbitals makes reductions easier, but redirects the protonation and reduction to sites that postpone the actuation of the hemilability. Additionally, two electrons donated from two nitrosyl-buffered irons, along with two external electrons, reduce two protons into two hydrides, from which reductive elimination generates H₂.

First-principles computation of electron transfer and reaction rate at a perovskite cathode for hydrogen production

The focus of this research is on the electron transfer and its reaction rate at the perovskite cathode of a photoelectrochemical cell for hydrogen production. By employing the density functional theory (DFT), the electron density, projected density of states (PDOS), electron distribution and electron transfer path between [Fe-Fe] hydrogenase and the perovskite cathode can be obtained. Simulation results show that the perovskite cathode is better than traditional cathodes for hydrogen production. Before transmission to the [Fe-Fe] hydrogenase, electron clouds mainly aggregate at the periphery of amine molecules. Simulations also show that the key to hydrogen production at the perovskite structure lies in the organic molecules. Electrons are transferred to the hydrocarbon structural chain before reaching the Fe atoms. The Rice, Ramsperger, Kassel and Marcus (RRKM) theory was used to predict the reaction rates at different temperatures. It was found that the reaction rates are in good agreement with the experimental results. This research provides more physical insight into the electron transfer mechanism during the hydrogen production process.

Identification of a Catalytic Iron-Hydride at the H-Cluster of [FeFe]-Hydrogenase

Hydrogenases couple electrochemical potential to the reversible chemical transformation of H₂ and protons, yet the reaction mechanism and composition of intermediates are not fully understood. In this Communication we describe the biophysical properties of a hydride-bound state (H_hyd) of the [FeFe]-hydrogenase from Chlamydomonas reinhardtii. The catalytic H-cluster of [FeFe]-hydrogenase consists of a [4Fe-4S] subcluster ([4Fe-4S]_H) linked by a cysteine thiol to an azadithiolate-bridged 2Fe subcluster ([2Fe]_H) with CO and CN^- ligands. Mössbauer analysis and density functional theory (DFT) calculations show that H_hyd consists of a reduced [4Fe-4S]_H⁺ coupled to a diferrous [2Fe]_H with a terminally bound Fe-hydride. The existence of the Fe-hydride in H_hyd was demonstrated by an unusually low Mössbauer isomer shift of the distal Fe of the [2Fe]_H subcluster. A DFT model of H_hyd shows that the Fe-hydride is part of a H-bonding network with the nearby bridging azadithiolate to facilitate fast proton exchange and catalytic turnover.

Vibrational spectroscopy reveals the initial steps of biological hydrogen evolution

[FeFe] hydrogenases are biocatalytic model systems for the exploitation and investigation of catalytic hydrogen evolution. Here, we used vibrational spectroscopic techniques to characterize, in detail, redox transformations of the [FeFe] and [4Fe4S] sub-sites of the catalytic centre (H-cluster) in a monomeric [FeFe] hydrogenase. Through the application of low-temperature resonance Raman spectroscopy, we discovered a novel metastable intermediate that is characterized by an oxidized [FeIFeII] centre and a reduced [4Fe4S]1+ cluster. Based on this unusual configuration, this species is assigned to the first, deprotonated H-cluster intermediate of the [FeFe] hydrogenase catalytic cycle. Providing insights into the sequence of initial reaction steps, the identification of this species represents a key finding towards the mechanistic understanding of biological hydrogen evolution.

Theoretical Design by First Principles Molecular Dynamics of a Bioinspired Electrode-Catalyst System for Electrocatalytic Hydrogen Production from Acidified Water

Bacterial di-iron hydrogenases produce hydrogen efficiently from water. Accordingly, we have studied by first-principles molecular-dynamics simulations (FPMD) electrocatalytic hydrogen production from acidified water by their common active site, the [FeFe]H cluster, extracted from the enzyme and linked directly to the (100) surface of a pyrite electrode. We found that the cluster could not be attached stably to the surface via a thiol link analogous to that which attaches it to the rest of the enzyme, despite the similarity of the (100) pyrite surface to the Fe4S4 cubane to which it is linked in the enzyme. We report here a systematic sequence of modifications of the structure and composition of the cluster devised to maintain the structural stability of the pyrite/cluster complex in water throughout its hydrogen production cycle, an example of the molecular design of a complex system by FPMD.

Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases

We have developed and tested molecular mechanics parameters for [FeS] clusters found in known [FeFe] hydrogenases. Bond stretching, angle bending, dihedral and improper torsion parameters for models of the oxidized and reduced catalytic H-cluster, [4Fe4S](+,2+)Cys4, [4Fe4S](+,2+)Cys3His, and [2Fe2S](+,2+)Cys4, were calculated solely from Kohn-Sham density functional theory and Natural Population Analysis. Circumsphere analysis of the cubane clusters in the energy-minimized structure of the full Clostridium pasteurianum hydrogenase I showed the resulting metallocluster structures to be similar to known cubane structures. All clusters were additionally stable in molecular dynamics simulations over the course of 1.0 ns in the fully oxidized and fully reduced enzyme models. Normal modes calculated by quasiharmonic analysis from the dynamics data show unexpected couplings among internal coordinate motions, which may reflect the effects of the protein structure on metallocluster dynamics.

A data-intensive re-evaluation of semibridging carbonyl ligands

Structural data pertaining to bimetallic complexes with semibridging carbonyl (SBCO) ligands are analyzed using a comprehensive search of the Cambridge Structural Database (CSD).

[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation

The [FeFe]- and [NiFe]-hydrogenases catalyze the formal interconversion between hydrogen and protons and electrons, possess characteristic non-protein ligands at their catalytic sites and thus share common mechanistic features. Despite the similarities between these two types of hydrogenases, they clearly have distinct evolutionary origins and likely emerged from different selective pressures. [FeFe]-hydrogenases are widely distributed in fermentative anaerobic microorganisms and likely evolved under selective pressure to couple hydrogen production to the recycling of electron carriers that accumulate during anaerobic metabolism. In contrast, many [NiFe]-hydrogenases catalyze hydrogen oxidation as part of energy metabolism and were likely key enzymes in early life and arguably represent the predecessors of modern respiratory metabolism. Although the reversible combination of protons and electrons to generate hydrogen gas is the simplest of chemical reactions, the [FeFe]- and [NiFe]-hydrogenases have distinct mechanisms and differ in the fundamental chemistry associated with proton transfer and control of electron flow that also help to define catalytic bias. A unifying feature of these enzymes is that hydrogen activation itself has been restricted to one solution involving diatomic ligands (carbon monoxide and cyanide) bound to an Fe ion. On the other hand, and quite remarkably, the biosynthetic mechanisms to produce these ligands are exclusive to each type of enzyme. Furthermore, these mechanisms represent two independent solutions to the formation of complex bioinorganic active sites for catalyzing the simplest of chemical reactions, reversible hydrogen oxidation. As such, the [FeFe]- and [NiFe]-hydrogenases are arguably the most profound case of convergent evolution. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

Computational investigation of [FeFe]-hydrogenase models: characterization of singly and doubly protonated intermediates and mechanistic insights

The [FeFe]-hydrogenase enzymes catalyze hydrogen oxidation and production efficiently with binuclear Fe metal centers. Recently the bioinspired H₂-producing model system Fe₂(adt)(CO)₂(dppv)₂ (adt=azadithiolate and dppv=diphosphine) was synthesized and studied experimentally. In this system, the azadithiolate bridge facilitates the formation of a doubly protonated ammonium-hydride species through a proton relay. Herein computational methods are utilized to examine this system in the various oxidation states and protonation states along proposed mechanistic pathways for H₂ production. The calculated results agree well with the experimental data for the geometries, CO vibrational stretching frequencies, and reduction potentials. The calculations illustrate that the NH···HFe dihydrogen bonding distance in the doubly protonated species is highly sensitive to the effects of ion-pairing between the ammonium and BF₄^– counterions, which are present in the crystal structure, in that the inclusion of BF₄^– counterions leads to a significantly longer dihydrogen bond. The non-hydride Fe center was found to be the site of reduction for terminal hydride species and unsymmetric bridging hydride species, whereas the reduced symmetric bridging hydride species exhibited spin delocalization between the Fe centers. According to both experimental measurements and theoretical calculations of the relative pK_a values, the Fe_d center of the neutral species is more basic than the amine, and the bridging hydride species is more thermodynamically stable than the terminal hydride species. The calculations implicate a possible pathway for H₂ evolution that involves an intermediate with H₂ weakly bonded to one Fe, a short H₂ distance similar to the molecular bond length, the spin density delocalized over the two Fe centers, and a nearly symmetrically bridged CO ligand. Overall, this study illustrates the mechanistic roles of the ammonium-hydride interaction, flexibility of the bridging CO ligand, and intramolecular electron transfer between the Fe centers in the catalytic cycle. Such insights will assist in the design of more effective bioinspired catalysts for H₂ production.

Theoretical calculations in conjunction with supporting experimental data are used to analyze the mechanistic pathway for hydrogen evolution catalyzed by the bioinspired model Fe₂(adt)(CO)₂(dppv)₂. This study elucidates the site of reduction and the pK_a values associated with formation of the singly and doubly protonated species, as well as the roles of the ammonium-hydride interaction, flexibility of the bridging CO ligand, and intramolecular electron transfer between the Fe centers in the catalytic cycle for H₂ production.

Molecular basis of [FeFe]-hydrogenase function: an insight into the complex interplay between protein and catalytic cofactor

The precise electrochemical features of metal cofactors that convey the functions of redox enzymes are essentially determined by the specific interaction pattern between cofactor and enclosing protein environment. However, while biophysical techniques allow a detailed understanding of the features characterizing the cofactor itself, knowledge about the contribution of the protein part is much harder to obtain. [FeFe]-hydrogenases are an interesting class of enzymes that catalyze both, H2 oxidation and the reduction of protons to molecular hydrogen with significant efficiency. The active site of these proteins consists of an unusual prosthetic group (H-cluster) with six iron and six sulfur atoms. While H-cluster architecture and catalytic states during the different steps of H2 turnover have been thoroughly investigated during the last 20 years, possible functional contributions from the polypeptide framework were only assumed according to the level of conservancy and X-ray structure analyses. Due to the recent development of simpler and more efficient expression systems the role of single amino acids can now be experimentally investigated. This article summarizes, compares and categorizes the results of recent investigations based on site directed and random mutagenesis according to their informative value about structure function relationships in [FeFe]-hydrogenases. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.

Inhibition of [FeFe]-hydrogenases by formaldehyde and wider mechanistic implications for biohydrogen activation

Formaldehyde-a rapid and reversible inhibitor of hydrogen evolution by [FeFe]-hydrogenases-binds with a strong potential dependence that is almost complementary to that of CO. Whereas exogenous CO binds tightly to the oxidized state known as H(ox) but very weakly to a state two electrons more reduced, formaldehyde interacts most strongly with the latter. Formaldehyde thus intercepts increasingly reduced states of the catalytic cycle, and density functional theory calculations support the proposal that it reacts with the H-cluster directly, most likely targeting an otherwise elusive and highly reactive Fe-hydrido (Fe-H) intermediate.

Comparison of chemical properties of iron, cobalt, and nickel porphyrins, corrins, and hydrocorphins

Density functional calculations have been used to compare the geometric, electronic, and functional properties of the three important tetrapyrrole systems in biology, heme, coenzyme B 12, and coenzyme F430, formed from iron porphyrin ( Por ), cobalt corrin ( Cor ), and nickel hydrocorphin ( Hcor ). The results show that the flexibility of the ring systems follows the trend Hcor > Cor > Por and that the size of the central cavity follows the trend Cor < Por < Hcor . Therefore, low-spin Co I, Co II, and Co III fit well into the Cor ring, whereas Por seems to be more ideal for the higher spin states of iron, and the cavity in Hcor is tailored for the larger Ni ion, especially in the high-spin Ni II state. This is confirmed by the thermodynamic stabilities of the various combinations of metals and ring systems. Reduction potentials indicate that the +I and +III states are less stable for Ni than for the other metal ions. Moreover, Ni – C bonds are appreciably less stable than Co - C bonds. However, it is still possible that a Ni – CH 3 bond is formed in F 430 by a heterolytic methyl transfer reaction, provided that the donor is appropriate, e.g. if coenzyme M is protonated. This can be facilitated by the adjacent SO 3− group in this coenzyme and by the axial glutamine ligand, which stabilizes the Ni III state. Our results also show that a Ni III– CH 3 complex is readily hydrolysed to form a methane molecule and that the Ni III hydrolysis product can oxidize coenzyme B and M to a heterodisulphide in the reaction mechanism of methyl coenzyme M reductase.

Predicting Nuclear Resonance Vibrational Spectra of [Fe(OEP)(NO)]

Nuclear Resonance Vibrational Spectroscopy (NRVS) is a sensitive vibrational probe for biologically important heme complexes. The exquisite sensitivity of the NRVS data to the electronic structure provides detailed insights into the nature of these interesting compounds, but requires highly accurate computational methods for the mode assignments. To determine the best combinations of density functionals and basis sets, a series of benchmark DFT calculations on the previously characterized complex [Fe(OEP)NO] (OEP(2-)=octaethylporphyrinatio dianion) were performed. A test set of 21 methodology combinations including 8 functionals (BP86, mPWPW91, B3LYP, PBE1PBE, M062X, M06L, LC-BP86 and ωB97X-D) and 5 basis set (VTZ, TZVP, Lanl2DZ for iron and 6-31G*, 6-31+G* for other atoms) was carried out to calculate electronic structures and vibrational frequencies. We also implemented the conversion of frequency calculations into orientation-selective mode composition factors (e(2)), which can used to simulate the Vibrational Density Of States (VDOS) using Gaussian normal distribution functions. These use a series of user-friendly scripts for their application to NRVS. The structures as well as the isotropic and anisotropic NRVS of [Fe(OEP)NO] obtained with the M06L functional with a variety of basis sets are found to best reproduce the available experimental data, followed by B3LYP/LanL2DZ calculations. Other density functionals and basis sets do not produce the same level of accuracy. The noticeably worse agreement between theory and experiment for the out-plane NRVS compared with the excellent performance of the M06L functional for the in-plane prediction is attributed to deficiencies of the physical model rather than the computational methodology.

Metal-metal bonds in biology

Nickel-containing carbon monoxide dehydrogenases, acetyl-CoA synthases, nickel-iron hydrogenases, and diron hydrogenases are distinct metalloenzymes yet they share a number of important characteristics. All are O(2)-sensitive, with active-sites composed of iron and/or nickel ions coordinated primarily by sulfur ligands. In each case, two metals are juxtaposed at the "heart" of the active site, within range of forming metal-metal bonds. These active-site clusters exhibit multielectron redox abilities and must be reductively activated for catalysis. Reduction potentials are milder than expected based on formal oxidation state changes. When reductively activated, each cluster attacks an electrophilic substrate via an oxidative addition reaction. This affords a two-electron-reduced substrate bound to one or both metals of an oxidized cluster. M-M bonds have been established in hydrogenases where they serve to initiate the oxidative addition of protons and perhaps stabilize active sites in multiple redox states. The same may be true of the CODH and ACS active sites-Ni-Fe and Ni-Ni bonds in these sites may play critical roles in catalysis, stabilizing low-valence states and initiating oxidative addition of CO(2) and methyl group cations, respectively. In this article, the structural and functional commonalities of these metalloenzyme active sites are described, and the case is made for the formation and use of metal-metal bonds in each enzyme mentioned. As a post-script, the importance of Fe-Fe bonds in the nitrogenase FeMoco active site is discussed.

Insights into [FeFe]-hydrogenase structure, mechanism, and maturation

Hydrogenases are metalloenzymes that are key to energy metabolism in a variety of microbial communities. Divided into three classes based on their metal content, the [Fe]-, [FeFe]-, and [NiFe]-hydrogenases are evolutionarily unrelated but share similar nonprotein ligand assemblies at their active site metal centers that are not observed elsewhere in biology. These nonprotein ligands are critical in tuning enzyme reactivity, and their synthesis and incorporation into the active site clusters require a number of specific maturation enzymes. The wealth of structural information on different classes and different states of hydrogenase enzymes, biosynthetic intermediates, and maturation enzymes has contributed significantly to understanding the biochemistry of hydrogen metabolism. This review highlights the unique structural features of hydrogenases and emphasizes the recent biochemical and structural work that has created a clearer picture of the [FeFe]-hydrogenase maturation pathway.

Importance of the protein framework for catalytic activity of [FeFe]-hydrogenases

The active center (H-cluster) of [FeFe]-hydrogenases is embedded into a hydrophobic pocket within the protein. We analyzed several amino acids, located in the vicinity of this niche, by site-directed mutagenesis of the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1). These amino acids are highly conserved and predicted to be involved in H-cluster coordination. Characterization of two hydrogenase variants confirmed this hypothesis. The exchange of residues CrHydA1Met(415) and CrHydA1Lys(228) resulted in inactive proteins, which, according to EPR and FTIR analyses, contain no intact H-cluster. However, [FeFe]-hydrogenases in which CpIMet(353) (CrHydA1Met(223)) and CpICys(299) (CrHydA1Cys(169)) were exchanged to leucine and serine, respectively, showed a structurally intact H-cluster with catalytic activity either absent (CpIC299S) or strongly diminished (CpIM353L). In the case of CrHydA1C169S, the H-cluster was trapped in an inactive state exhibiting g values and vibrational frequencies that resembled the H(trans) state of DdH from Desulfovibrio desulfuricans. This cysteine residue, interacting with the bridge head nitrogen of the di(methyl)amine ligand, seems therefore to represent an essential contribution of the immediate protein environment to the reaction mechanism. Exchanging methionine CpIM(353) (CrHydA1M(223)) to leucine led to a strong decrease in turnover without affecting the K(m) value of the electron donor. We suggest that this methionine constitutes a "fine-tuning" element of hydrogenase activity.

Targeting intermediates of [FeFe]-hydrogenase by CO and CN vibrational signatures

In this work, we employ density functional theory to assign vibrational signatures of [FeFe]-hydrogenase intermediates to molecular structures. For this purpose, we perform an exhaustive analysis of structures and harmonic vibrations of a series of CN and CO containing model clusters of the [FeFe]-hydrogenase enzyme active site considering also different charges, counterions, and solvents. The pure density functional BP86 in combination with a triple-ζ polarized basis set produce reliable molecular structures as well as harmonic vibrations. Calculated CN and CO stretching vibrations are analyzed separately. Scaled vibrational frequencies are then applied to assign intermediates in [FeFe]-hydrogenase's reaction cycle. The results nicely complement the previous studies of Darensbourg and Hall, and Zilberman et al. The infrared spectrum of the H(ox) form is in very good agreement with the calculated spectrum of the Fe(I)Fe(II) model complex featuring a free coordination site at the distal Fe atom, as well as, with the calculated spectra of the complexes in which H(2) or H(2)O are coordinated at this site. The spectrum of H(red) measured from Desulfovibrio desulfuricans is compatible with a mixture of a Fe(I)Fe(I) species with all terminal COs, and a Fe(I)Fe(I) species with protonated dtma ligand, while the spectrum of H(red) recently measured from Chlamydomonas reinhardtii is compatible with a mixture of a Fe(I)Fe(I) species with a bridged CO, and a Fe(II)Fe(II) species with a terminal hydride bound to the Fe atom.

Favorable Protonation of the (μ-edt)[Fe(2)(PMe(3))(4)(CO)(2)(H-terminal)](+) Hydrogenase Model Complex Over Its Bridging μ-H Counterpart: A Spectroscopic and DFT Study

The mechanism of hydrogen production in [FeFe] hydrogenase remains elusive. However, a species featuring a terminal hydride bound to the distal Fe is thought to be the key intermediate leading to hydrogen production. In this study, density functional theory (DFT) calculations on the terminal (H-term) and bridging (μ-H) hydride isomers of (μ-edt)-[Fe(2)(PMe(3))(4)(CO)(2)H](+) are presented in order to understand the factors affecting their propensity for protonation. Relative to H-term, μ-H is 12.7 kcal/mol more stable, which contributes to its decreased reactivity towards an acid. Potential energy surface (PES) calculations for the reaction of the H-term isomer with 4-nitropyridinium, a proton source, further reveal a lower activation energy barrier (14.5 kcal/mol) for H-term than for μ-H (29 kcal/mol). Besides these energetic considerations, the H-term isomer displays a key molecular orbital (MO <139>) that has a relatively strong hydride (1s) contribution (23%), which is not present in the μ-H isomer. This indicates a potential orbital control of the reaction of the hydride complexes with acid. The lower activation energy barrier and this key MO together control the overall catalytic activity of (μ-edt)[Fe(2)(PMe(3))(4)(CO)(2)(H-term)](+). Lastly, Raman and IR spectroscopy were performed in order to probe the ν(Fe-H) stretching mode of the two isomers and their deuterated counterparts. A ν(Fe-H) stretching mode was observed for the μ-H complex at 1220 cm(-1). However, the corresponding mode is not observed for the less stable H-term isomer.

On understanding proton transfer to the biocatalytic [Fe-Fe](H) sub-cluster in [Fe-Fe]H(2)ases: QM/MM MD simulations

Proton transfer to the [Fe-Fe](H) sub-cluster in the Desulfovibrio desulfuricans (DdH) and Clostridium pasteurianum (CpI) [Fe-Fe] hydrogenases was investigated by a combination of first principles and empirical molecular dynamics simulations. Pathways that can be inferred from the X-ray crystal structures of DdH and CpI, i.e., (Glu159→Ser198→Glu156→water460→Cys178→DTMA([Fe-Fe](H)) and (Glu282→Ser319→Glu279→water612→Cys299), respectively, were considered. Proton transfer from Cys178 to DTMA in the [Fe-Fe](H) sub-cluster in DdH was readily observed in our results, specifically when [Fe-Fe](H) was in the reduced state ([Fe(I)-Fe(I)]) or in the mixed valence state for the protonated distal iron Fe(d) ([Fe(I)-Fe(II)-H(-)](H)). A concerted mechanism is proposed, where proton transfer in DdH from Glu159 to Glu156 via Ser198 and Glu156 to Cys178 via water460 readily occurred, as well as from Glu282 to Glu279 via Ser319 and Glu279 to Cys299 via water612 in CpI. The theoretical prediction of the proton transfer characteristics is consistent with the assumed biocatalytic mechanism of the [Fe-Fe] hydrogenases in which the proton binds at Fe(d), providing confirmation that has not been explored so far. The computational results were qualitatively validated by the agreement with experimental hydrogen production activity data for mutated CpI enzymes, relative to the wild-type protein. Finally, the insight provided by the simulations, combined, in part, with experimental validation, are important for establishing an approach in future exploration of proton transfer to the active site in this class of enzymes, and possibly also for biomimetic analogs.

[Fe-Fe]-hydrogenase Reactivated by Residue Mutations as Bridging Carbonyl Rearranges: A QM/MM Study

In the current work, we found aqueous enzyme phase reaction pathways for the reactivation of the exogenously inhibited [Fe-Fe]-hydrogenases by O2, or OH-, which metabolizes to H2O1,2. We used the hybrid quantum mechanics/molecular mechanics (QM/MM) method to study the reactivation pathways of the exogenously inhibited enzyme matrix. The ONIOM calculations performed on the enzyme agree with experimental results3, i.e., wild-type [Fe-Fe]-hydrogenase H-cluster is inhibited by oxygen metabolites. An enzyme spherical region with a radius of 8 Å (from the distal iron, Fed) has been screened for residues that prevent H2O from leaving the catalytic site and reactivate the [Fe-Fe]-hydrogenase H-cluster. In the screening process, polar residues were removed, one at a time, and frequency calculations provided the change in the Gibbs' energy for the dissociation of water (due to their deletion). When residue deletion resulted in significant Gibbs' energy decrease, further residue substitutions have been carried out. Following each substitution, geometry optimization and frequency calculations have been performed to assess the change in the Gibbs' energy for the elimination H2O. Favorable thermodynamic results have been obtained for both single residue removal (ΔGΔGlu374 = -1.6 kcal/mol), single substitution (ΔGGlu374His = -3.1 kcal/mol), and combined residue substitutions (ΔGArg111Glu;Thr145Val;Glu374His;Tyr375Phe = -7.5 kcal/mol). Because the wild-type enzyme has only an endergonic step to overcome, i.e., for H2O removal, by eliminating several residues, one at a time, the endergonic step was made to proceed spontaneously. Thus, the most promising residue deletions which enhance H2O elimination are ΔArg111, ΔThr145, ΔSer177, ΔGlu240, ΔGlu374, and ΔTyr375. The thermodynamics and electronic structure analyses show that the bridging carbonyl (COb) of the H-cluster plays a concomitant role in the enzyme inhibition/reactivation. In gas phase, COb shifts towards Fed to compensate for the electron density donated to oxygen upon the elimination of H2O. However, this is not possible in the wild-type enzyme because the protein matrix hinders the displacement of COb towards Fed, which leads to enzyme inhibition. However, enzyme reactivation can be achieved by means of appropriate amino acid substitutions.

A unifying structural and electronic concept for Hmd and [FeFe] hydrogenase active sites

The hydrogenases [FeFe] and Hmd feature at first sight rather different active sites. A closer inspection reveals striking similarities, which allow us to define swapped ligand spheres in such a way that the single active iron center of Hmd functions in a first-shell ligand environment resembling the reacting iron atom in [FeFe] hydrogenase and vice versa. These redesigned ligand environments can be conveniently studied with quantum chemical methods and point to general reactivity principles for iron centers with hydrogenase activity.