Nickel-iron hydrogenases: Structural and functional properties. In: Hill HAO, Sadler PJ, Thomson AJ, editors. Metal Sites in Proteins and Models Redox Centres. Berlin: Springer Berlin Heidelberg; 1998. pp. 97-126. [DOI: 10.1007/3-540-62888-6_4]

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.

A comparison of types of catalyst: the quality of metallo-enzymes

The purpose of this review is to compare four kinds of catalyst: molecular and enzymic, both homogeneous, and non-conducting and conducting solids, both heterogeneous, in order to show the full power of metallo-enzymes. For ease of comparison we restrict ourselves to describing catalysts containing single metal atom or ion units, only briefly mentioning more complex units. Their common ground lies in the nature of their active sites for attacking the substrate, but here we stress that their differences often rest in the value of their frameworks. The frameworks contribute to activity through binding of substrate, creating selectivity, or even by directly aiding the catalytic act of transforming the substrate to the product, when there is an active region rather than a site. It may also provide limited directed motion aiding effective progress of the active groups themselves through a cycle of activity. The article highlights the difficulties in the use of other kinds of catalysts as aids to the understanding of enzymes. Part A is a general description and Part B is a set of examples of the catalysts.

Force-Field Development and Molecular Dynamics Simulations of Ferrocene–Peptide Conjugates as a Scaffold for Hydrogenase Mimics

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 micros MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 micros MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.

Synthesis, Gas-Phase Photoelectron Spectroscopic, and Theoretical Studies of Stannylated Dinuclear Iron Dithiolates

Stannylated dinuclear iron dithiolates (mu-SSnMe(2)CH(2)S)[Fe(CO)(3)](2), (mu-SCH(2)SnMe(2)CH(2)S) [Fe(CO)(3)](2), and (mu-SCH(2)SnMe(3))(2)[Fe(CO)(3)](2), which are structurally similar to the active site of iron-only hydrogenase, were synthesized and studied by gas-phase photoelectron spectroscopy. The orbital origins of ionizations were assigned by comparison of He I and He II photoelectron spectra and with the aid of hybrid density functional electronic structure calculations. Stannylation lowers the ionization energy of sulfur lone pair orbitals in these systems owing to a geometry-dependent interaction. The Fe-Fe sigma bond, which is the HOMO in all these systems, is also substantially destabilized by stannylation due to a previously unrecognized geometry-dependent interaction between axial sulfur lone pair orbitals and the Fe-Fe sigma bond. Since cleaving the Fe-Fe sigma bond is a key step in the mechanism of action of iron-only hydrogenase, these newly recognized geometry-dependent interactions may be utilized in designing biologically inspired hydrogenase catalysts.

An orientation-selected ENDOR and HYSCORE study of the Ni-C active state of Desulfovibrio vulgaris Miyazaki F hydrogenase

Electron nuclear double resonance (ENDOR) and hyperfine sublevel correlation spectroscopy (HYSCORE) are applied to study the active site of catalytic [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F in the reduced Ni-C state. These techniques offer a powerful tool for detecting nearby magnetic nuclei, including a metal-bound substrate hydrogen, and for mapping the spin density distribution of the unpaired electron at the active site. The observed hyperfine couplings are assigned via comparison with structural data from X-ray crystallography and knowledge of the complete g-tensor in the Ni-C state (Foerster et al. (2003) J Am Chem Soc 125:83-93). This is found to be in good agreement with density functional theory calculations. The two most strongly coupled protons (a(iso)=13.7, 11.8 MHz) are assigned to the beta-CH(2) protons of the nickel-coordinating cysteine 549, and a third proton (a(iso)=8.9 MHz) is assigned to a beta-CH(2) proton of cysteine 546. Using D(2)O exchange experiments, the presence of a hydride in the bridging position between the nickel and iron-recently been detected for a regulatory hydrogenase (Brecht et al. (2003) J Am Chem Soc 125:13075-13083)-is experimentally confirmed for the first time for catalytic hydrogenases. The hydride exhibits a small isotropic hyperfine coupling constant (a(iso)=-3.5 MHz) since it is bound to Ni in a direction perpendicular to the z-axis of the Ni (3d(z)(2)) orbital. Nitrogen signals that belong to the nitrogen N(epsilon) of His-88 have been identified. This residue forms a hydrogen bond with the spin-carrying Ni-coordinated sulfur of Cys-549. Comparison with other hydrogenases reveals that the active site is essentially the same in all proteins, including a regulatory hydrogenase.

Enzymatic mechanism of Fe-only hydrogenase: density functional study on H-H making/breaking at the diiron cluster with concerted proton and electron transfers

The mechanism of the enzymatic hydrogen bond forming/breaking (2H(+) + 2e<==>H(2)) and the plausible charge and spin states of the catalytic diiron subcluster [FeFe](H) of the H cluster in Fe-only hydrogenases are probed computationally by the density functional theory. It is found that the active center [FeFe](H) can be rationally simulated as [[H](CH(3)S)(CO)(CN(-))Fe(p)(CO(b))(mu-SRS)Fe(d)(CO)(CN(-))L], where the monovalence [H] stands for the [4Fe4S](H)(2+) subcluster bridged to the [FeFe](H) moiety, (CH(3)S) represents a Cys-S, and (CO(b)) represents a bridging CO. L could be a CO, H(2)O, H(-), H(2), or a vacant coordination site on Fe(d). Model structures of possible redox states are optimized and compared with the X-ray crystallographic structures and FTIR experimental data. On the basis of the optimal structures, we study the most favorable path of concerted proton transfer and electron transfer in H(2)-forming/breaking reactions at [FeFe](H). Previous mechanisms derived from quantum chemical computations of Fe-only hydrogenases (Cao, Z.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3734; Fan, H.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3828) involved an unidentified bridging residue (mu-SRS), which is either a propanedithiolate or dithiomethylamine. Our proposed mechanism, however, does not require such a ligand but makes use of a shuttle of oxidation states of the iron atoms and a reaction site between the two iron atoms. Therefore, the hydride H(b)(-) (bridged to Fe(p) and Fe(d)) and eta(2)-H(2) at Fe(p) or Fe(d) most possibly play key roles in the dihydrogen reversible oxidation at the [FeFe](H) active center. This suggested way of H(2) formation/splitting is reminiscent of the mechanism of [NiFe] hydrogenases and therefore would unify the mechanisms of the two related enzymes.

Heterolytic cleavage of dihydrogen promoted by sulfido-bridged tungsten-ruthenium dinuclear complexes

A series of sulfido-bridged tungsten-ruthenium dinuclear complexes Cp*W(mu-S)(3)RuX(PPh(3))(2) (4a; X = Cl, 4b; X = H), Cp*W(O)(mu-S)(2)RuX(PPh(3))(2) (5a; X = Cl, 5b; X = H), and Cp*W(NPh)(mu-S)(2)RuX(PPh(3))(2) (6a; X = Cl, 6b; X = H) have been synthesized by the reactions of (PPh(4))[Cp*W(S)(3)] (1), (PPh(4))[Cp*W(O)(S)(2)] (2), and (PPh(4))[Cp*W(NPh)(S)(2)] (3), with RuClX(PPh(3))(3) (X = Cl, H). The heterolytic cleavage of H(2) was found to proceed at room temperature upon treating 5a and 6a with NaBAr(F)(4) (Ar(F) = 3, 5-C(6)H(3)(CF(3))(2)) under atmospheric pressure of H(2), which gave rise to [Cp*W(OH)(mu-S)(2)RuH(PPh(3))(2)](BAr(F)(4)) (7a) and [Cp*W(NHPh)(mu-S)(2)RuH(PPh(3))(2)](BAr(F)(4)) (8), respectively. When Cp*W(O)(mu-S)(2)Ru(PPh(3))(2)H (5b) was treated with a Brønstead acid, [H(OEt(2))(2)](BAr(F)(4)) or HOTf, protonation occurred exclusively at the terminal oxide to give [Cp*W(OH)(mu-S)(2)RuH(PPh(3))(2)](X) (7a; X = BAr(F)(4), 7b; X = OTf), while the hydride remained intact. The analogous reaction of Cp+W(mu-S)(3)Ru(PPh(3))(2)H (4b) led to immediate evolution of H(2). Selective deprotonation of the hydroxyl group of 7a or 7b was induced by NEt(3) and 4b, generating Cp*W(O)(mu-S)(2)Ru(PPh(3))(2)H (5b). Evolution of H(2) was also observed for the reactions of 7a or 7b with CH(3)CN to give [Cp*W(O)(mu-S)(2)Ru(CH(3)CN)(PPh(3))(2)](X) (11a; X = BAr(F)(4), 11b; X = OTf). We examined the H/D exchange reactions of 4b, 5b, and 7a with D(2) and CH(3)OD, and found that facile H/D scrambling over the W-OH and Ru-H sites occurred for 7a. Based on these experimental results, the mechanism of the heterolytic H(2) activation and the reverse H(2) evolution reactions are discussed.

Kinetic evidence for intramolecular proton transfer between nickel and coordinated thiolate

The complexes [Ni(YR)(triphos)]BPh(4) (Y = S, R = Ph or Et or Y = Se, R = Ph; triphos = (Ph(2)PCH(2)CH(2))(2)PPh) have been prepared and characterized, and the X-ray crystal structure of [Ni(SPh)(triphos)]BPh(4) has been solved. In MeCN, [Ni(YR)(triphos)](+) are protonated by [lutH](+) (lut = 2,6-dimethylpyridine) to give [Ni(YHR)(triphos)](2+). Studies on the kinetics of these equilibrium reactions reveal an unexpected difference in the reactivities of [Ni(SPh)(triphos)](+) and [Ni(SEt)(triphos)](+). In both cases, the reactions exhibit a first-order dependence on the concentration of complex. When R = Ph, the dependence on the concentrations of [lutH(+)] and lut is given by k(obs) = k(1)(Ph)[lutH(+)] + k(-1)(Ph)[lut], which is typical of an equilibrium reaction where k(1)(Ph) and k(-1)(Ph) correspond to the forward and back reactions, respectively. Analogous behavior is observed for [Ni(SePh)(triphos)](+). However, for [Ni(SEt)(triphos)](+), the kinetics are more complicated, and k(obs) = (k(1)k(2)[lutH(+)] + (k(-2) + k(2)))/(k(1)[lutH(+)] + k(-1)[lut]), which is indicative of a mechanism involving two coupled equilibria in which the initial protonation of the thiolate is followed by a unimolecular equilibrium reaction that is assumed to involve the formation of an eta(2)-EtS-H ligand. The difference in reactivity between the complexes with alkyl and aryl thiolate ligands is a consequence of the (Ni(triphos))(2+) site "leveling" the basicities of these ligands. The pK(a)'s of the PhSH and EtSH constituents coordinated to the (Ni(triphos))(2+) are 16.0 and 14.6, respectively, whereas the difference in pK(a)'s of free PhSH and EtSH differ by ca. 4 units. The pK(a) of [Ni(SeHPh)(triphos)](+) is 14.4. The more strongly sigma-donating EtS ligand makes the (Ni(triphos))(2+) core sufficiently electron-rich that the basicities of the sulfur and nickel in [Ni(SEt)(triphos)](+) are very similar; therefore, the proton serves as a bridge between the two sites. The relevance of these observations to the proposed mechanisms of nickel-based hydrogenases is discussed.

(NEt(4))(2)[Fe(CN)(2)(CO)('S(3)')]: an iron thiolate complex modeling the [Fe(CN)(2)(CO)(S-Cys)(2)] site of [NiFe] hydrogenase centers

In the search for complexes modeling the [Fe(CN)(2)(CO)(cysteinate)(2)] cores of the active centers of [NiFe] hydrogenases, the complex (NEt(4))(2)[Fe(CN)(2)(CO)('S(3)')] (4) was found ('S(3)'(2-)=bis(2-mercaptophenyl)sulfide(2-)). Starting complex for the synthesis of 4 was [Fe(CO)(2)('S(3)')](2) (1). Complex 1 formed from [Fe(CO)(3)(PhCH=CHCOMe)] and neutral 'S(3)'-H(2). Reactions of 1 with PCy(3) or DPPE (1,2-bis(diphenylphosphino)ethane) yielded diastereoselectively [Fe(CO)(2)(PCy(3))('S(3)')] (2) and [Fe(CO)(dppe)('S(3)')] (3). The diastereoselective formation of 2 and 3 is rationalized by the trans influence of the 'S(3)'(2-) thiolate and thioether S atoms which act as pi donors and pi acceptors, respectively. The trans influence of the 'S(3)'(2-) sulfur donors also rationalizes the diastereoselective formation of the C(1) symmetrical anion of 4, when 1 is treated with four equivalents of NEt(4)CN. The molecular structures of 1, 3 x 0.5 C(7)H(8), and (AsPh(4))(2)[Fe(CN)(2)(CO)('S(3)')] x acetone (4 a x C(3)H(6)O) were determined by X-ray structure analyses. Complex 4 is the first complex that models the unusual 2:1 cyano/carbonyl and dithiolate coordination of the [NiFe] hydrogenase iron site. Complex 4 can be reversibly oxidized electrochemically; chemical oxidation of 4 by [Fe(Cp)(2)PF(6)], however, led to loss of the CO ligand and yielded only products, which could not be characterized. When dissolved in solvents of increasing proton activity (from CH(3)CN to buffered H(2)O), complex 4 exhibits drastic nu(CO) blue shifts of up to 44 cm(-1), and relatively small nu(CN) red shifts of approximately 10 cm(-1). The nu(CO) frequency of 4 in H(2)O (1973 cm(-1)) is higher than that of any hydrogenase state (1952 cm(-1)). In addition, the nu(CO) frequency shift of 4 in various solvents is larger than that of [NiFe] hydrogenase in its most reduced or oxidized state. These results demonstrate that complexes modeling properly the nu(CO) frequencies of [NiFe] hydrogenase probably need a [Ni(thiolate)(2)] unit. The results also demonstrate that the nu(CO) frequency of [Fe(CN)(2)(CO)(thiolate)(2)] complexes is more significantly shifted by changing the solvent than the nu(CO) frequency of [NiFe] hydrogenases by coupled-proton and electron-transfer reactions. The "iron-wheel" complex [Fe(6)[Fe('S(3)')(2)](6)] (6) resulting as a minor by-product from the recrystallization of 2 in boiling toluene could be characterized by X-ray structure analysis.

Coordination sphere flexibility of active-site models for Fe-only hydrogenase: studies in intra- and intermolecular diatomic ligand exchange

A series of dinuclear complexes, (mu-SRS)Fe(2)(CO)(6) (R = -CH(2)CH(2)-, -CH(2)CH(2)CH(2)-, -CH(2)-C(6)H(4)-CH(2)-; edt, pdt, and o-xyldt, respectively) has been examined for specific characteristics that might relate to structural similarity with the active site of Fe-only hydrogenases. Variable-temperature proton NMR studies display the fluxionality of the iron-dithiocyclohexane unit in (mu-pdt)Fe(2)(CO)(6) while in the (mu-o-xyldt)Fe(2)(CO)(6) compound, the bridge is fixed. Temperature-dependent (13)C NMR spectral studies establish intramolecular CO site exchange localized on discrete Fe(CO)(3) units in all complexes, which is influenced by steric effects of the mu-SRS unit. Kinetic studies of intermolecular CO/CN(-) ligand-exchange reactions establish associative or I(a) mechanisms in sequential steps to form the dicyano dianion, (mu-SRS)[Fe(CO)(2)(CN)](2)(=) with 100% selectivity. Theoretical calculations (DFT) of transition states in the intramolecular site-exchange processes lead to a rationale for the interesting cooperativity in the CN(-)/CO intermolecular ligand-exchange process. The hinge motion of the three light atom S-to-S bridge is related to a possible heterolytic H(2) activation/production process in the enzyme.

Kinetic characterization of Desulfovibrio gigas hydrogenase upon selective chemical modification of amino acid groups as a tool for structure-function relationships

The effect of amino acid residues modification of Desulfovibrio gigas hydrogenase on different activity assays is reported. The first method consisted in the modification of glutamic and aspartic acid residues of the enzyme with ethylenediamine in order to change the polarity of certain regions of the protein surface. The second method consisted in the modification of histidine residues with a Ru complex in order to change the acid-base properties of the histidine residues. The implication of these modifications in the enzyme kinetics has been studied by measuring in parallel the activities of para/ortho hydrogen conversion, deuterium/hydrogen exchange and dyes reduction with hydrogen. Our experimental data support some hypothesis based on the three-dimensional structure of this enzyme: (a) electrostactic interactions between the hydrogenase and the redox partner play an essential role in the kinetics; (b) the histidine ligand and the surrounding acidic residues of the distal [4Fe4S] cluster form the recognition site of the redox partner of the hydrogenase; and (c) histidine residues are involved in the hydron transfer pathway of the hydrogenase.

Positive transcriptional feedback controls hydrogenase expression in Alcaligenes eutrophus H16

The protein HoxA is the central regulator of the Alcaligenes eutrophus H16 hox regulon, which encodes two hydrogenases, a nickel permease and several accessory proteins required for hydrogenase biosynthesis. Expression of the regulatory gene hoxA was analyzed. Screening of an 8-kb region upstream of hoxA with a promoter probe vector localized four promoter activities. One of these was found in the region immediately 5' of hoxA; the others were correlated with the nickel metabolism genes hypA1, hypB1, and hypX. All four activities were independent of HoxA and of the minor transcription factor sigma(54). Translational fusions revealed that hoxA is expressed constitutively at low levels. In contrast to these findings, immunoblotting studies revealed a clear fluctuation in the HoxA pool in response to conditions which induce the hox regulon. Quantitative transcript assays indicated elevated levels of hyp mRNA under hydrogenase-derepressing conditions. Using interposon mutagenesis, we showed that the activity of a remote promoter is required for hydrogenase expression and autotrophic growth. Site-directed mutagenesis revealed that P(MBH), which directs transcription of the structural genes of the membrane-bound hydrogenase, contributes to the expression of hoxA under hydrogenase-derepressing conditions. Thus, expression of the hox regulon is governed by a positive feedback loop mediating amplification of the regulator HoxA. These results imply the existence of an unusually large (ca. 17,000-nucleotide) transcript.

Active sites of transition-metal enzymes with a focus on nickel

Since 1995, crystal structures have been determined for many transition-metal enzymes, in particular those containing the rarely used transition metals vanadium, molybdenum, tungsten, manganese, cobalt and nickel. Accordingly, our understanding of how an enzyme uses the unique properties of a specific transition metal has been substantially increased in the past few years. The different functions of nickel in catalysis are highlighted by describing the active sites of six nickel enzymes - methyl-coenyzme M reductase, urease, hydrogenase, superoxide dismutase, carbon monoxide dehydrogenase and acetyl-coenzyme A synthase.