Insights into the structure of the active site of the O2-tolerant membrane bound [NiFe] hydrogenase of R. eutropha H16 by molecular modelling

Structural models for the Ni-B state of the wild-type and C81S protein variant of the membrane-bound [NiFe] hydrogenase from Ralstonia eutropha H16 were derived by applying the homology model technique combined with molecular simulations and a hybrid quantum mechanical/molecular mechanical approach. The active site structure was assessed by comparing calculated and experimental IR spectra, confirming the view that the active site structure is very similar to those of anaerobic standard hydrogenases. In addition, the data suggest the presence of a water molecule in the second coordination sphere of the active centre.     

Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site

Understanding the impact of fast dynamics upon the chemical processes occurring within the active sites of proteins and enzymes is a key challenge that continues to attract significant interest, though direct experimental insight in the solution phase remains sparse. Similar gaps in our knowledge exist in understanding the role played by water, either as a solvent or as a structural/dynamic component of the active site. In order to investigate further the potential biological roles of water, we have employed ultrafast multidimensional infrared spectroscopy experiments that directly probe the structural and vibrational dynamics of NO bound to the ferric haem of the catalase enzyme from Corynebacterium glutamicum in both H₂O and D₂O. Despite catalases having what is believed to be a solvent-inaccessible active site, an isotopic dependence of the spectral diffusion and vibrational lifetime parameters of the NO stretching vibration are observed, indicating that water molecules interact directly with the haem ligand. Furthermore, IR pump–probe data feature oscillations originating from the preparation of a coherent superposition of low-frequency vibrational modes in the active site of catalase that are coupled to the haem ligand stretching vibration. Comparisons with an exemplar of the closely-related peroxidase enzyme family shows that they too exhibit solvent-dependent active-site dynamics, supporting the presence of interactions between the haem ligand and water molecules in the active sites of both catalases and peroxidases that may be linked to proton transfer events leading to the formation of the ferryl intermediate Compound I. In addition, a strong, water-mediated, hydrogen bonding structure is suggested to occur in catalase that is not replicated in peroxidase; an observation that may shed light on the origins of the different functions of the two enzymes.     

Synthesis, characterization and some properties of mononuclear Ni and trinuclear NiFe2 complexes related to the active site of [NiFe]-hydrogenases

The [N(2)S(2)]-type ligand 1,2-(2-C(5)H(4)NCH(2)S)(2)C(6)H(4) (L) is prepared in 84% yield by a new method and its structure has been confirmed by X-ray crystallography. The new synthetic method involves sequential reaction of 1,2-phenylenedithiol with EtONa followed by treatment of the resulting disodium salt of 1,2-phenylenedithiol with in situ generated 2-(chloromethyl)pyridine from its HCl salt. Further treatment of ligand L with NiCl(2)·6H(2)O or NiI(2) affords the expected new mononuclear Ni complexes Ni[1,2-(2-C(5)H(4)NCH(2)S)(2)C(6)H(4)]Cl(2) (1) and Ni[1,2-(2-C(5)H(4)NCH(2)S)(2)C(6)H(4)]I(2) (3) in 87-88% yields, whereas reaction of L with NiBr(2) under similar conditions results in formation of the expected new mononuclear complex Ni[1,2-(2-C(5)H(4)NCH(2)S)(2)C(6)H(4)]Br(2) (2) and one unexpected new mononuclear complex Ni[1-(2-C(5)H(4)NCH(2)S)-2-(2-C(5)H(4)NCH(2)SC(6)H(4)S)C(6)H(4)]Br(2) (2*) in 82% and 5% yields, respectively. More interestingly, the ligand L-containing novel trinuclear NiFe(2) complex Ni{[1,2-(2-C(5)H(4)NCH(2)S)(2)C(6)H(4)}Fe(2)(CO)(6)(μ(3)-S)(2) (4) is found to be prepared by sequential reaction of (μ-S(2))Fe(2)(CO)(6) with Et(3)BHLi, followed by treatment of the resulting (μ-LiS)(2)Fe(2)(CO)(6) with mononuclear complex 1, 2, or 3 in 12-20% yields. The new complexes 1-4 and 2* are fully characterized by elemental analysis and various spectroscopies, and the crystal structures of 1, 2* and 3 as well as some electrochemical properties of 1-4 are also reported.     

Site-selective X-ray spectroscopy on an asymmetric model complex of the [FeFe] hydrogenase active site

The active site for hydrogen production in [FeFe] hydrogenase comprises a diiron unit. Bioinorganic chemistry has modeled important features of this center, aiming at mechanistic understanding and the development of novel catalysts. However, new assays are required for analyzing the effects of ligand variations at the metal ions. By high-resolution X-ray absorption spectroscopy with narrow-band X-ray emission detection (XAS/XES = XAES) and density functional theory (DFT), we studied an asymmetrically coordinated [FeFe] model complex, [(CO)(3)Fe(I)1-(bdtCl(2))-Fe(I)2(CO)(Ph(2)P-CH(2)-NCH(3)-CH(2)-PPh(2))] (1, bdt = benzene-1,2-dithiolate), in comparison to iron-carbonyl references. Kβ emission spectra (Kβ(1,3), Kβ') revealed the absence of unpaired spins and the low-spin character for both Fe ions in 1. In a series of low-spin iron compounds, the Kβ(1,3) energy did not reflect the formal iron oxidation state, but it decreases with increasing ligand field strength due to shorter iron-ligand bonds, following the spectrochemical series. The intensity of the valence-to-core transitions (Kβ(2,5)) decreases for increasing Fe-ligand bond length, certain emission peaks allow counting of Fe-CO bonds, and even molecular orbitals (MOs) located on the metal-bridging bdt group of 1 contribute to the spectra. As deduced from 3d → 1s emission and 1s → 3d absorption spectra and supported by DFT, the HOMO-LUMO gap of 1 is about 2.8 eV. Kβ-detected XANES spectra in agreement with DFT revealed considerable electronic asymmetry in 1; the energies and occupancies of Fe-d dominated MOs resemble a square-pyramidal Fe(0) for Fe1 and an octahedral Fe(II) for Fe2. EXAFS spectra for various Kβ emission energies showed considerable site-selectivity; approximate structural parameters similar to the crystal structure could be determined for the two individual iron atoms of 1 in powder samples. These results suggest that metal site- and spin-selective XAES on [FeFe] hydrogenase protein and active site models may provide a powerful tool to study intermediates under reaction conditions.     

Original design of an oxygen-tolerant [NiFe] hydrogenase: major effect of a valine-to-cysteine mutation near the active site

Hydrogenases are efficient biological catalysts of H(2) oxidation and production. Most of them are inhibited by O(2), and a prerequisite for their use in biotechnological applications under air is to improve their oxygen tolerance. We have previously shown that exchanging the residue at position 74 in the large subunit of the oxygen-sensitive [NiFe] hydrogenase from Desulfovibrio fructosovorans could impact the reaction of the enzyme with O(2) (Dementin, S.; J. Am. Chem. Soc. 2009, 131, 10156-10164; Liebgott, P. P.; Nat. Chem. Biol. 2010, 6, 63-70). This residue, a valine in the wild-type enzyme, located at the bottleneck of the gas channel near the active site, has here been exchanged with a cysteine. A thorough characterization using a combination of kinetic, spectroscopic (EPR, FTIR), and electrochemical studies demonstrates that the V74C mutant has features of the naturally occurring oxygen-tolerant membrane-bound hydrogenases (MBH). The mutant is functional during several minutes under O(2), has impaired H(2)-production activity, and has a weaker affinity for CO than the WT. Upon exposure to O(2), it is converted into the more easily reactivatable inactive form, Ni-B, and this inactive state reactivates about 20 times faster than in the WT enzyme. Control experiments carried out with the V74S and V74N mutants indicate that protonation of the position 74 residue is not the reason the mutants reactivate faster than the WT enzyme. The electrochemical behavior of the V74C mutant toward O(2) is intermediate between that of the WT enzyme from D. fructosovorans and the oxygen-tolerant MBH from Aquifex aeolicus.     

The synthesis and electronic structure of a novel [NiS4Fe2(CO)6] radical cluster: implications for the active site of the [NiFe] hydrogenases

A novel [NiS4Fe2(CO)6]cluster (1: 'S(4)'=(CH(3)C(6)H(3)S(2))(2)(CH(2))(3)) has been synthesised, structurally characterised and has been shown to undergo a chemically reversible reduction process at -1.31 V versus Fc(+)/Fc to generate the EPR-active monoanion 1(-). Multifrequency Q-, X- and S-band EPR spectra of (61)Ni-enriched 1(-) show a well-resolved quartet hyperfine splitting in the low-field region due to the interaction with a single (61)Ni (I=3/2) nucleus. Simulations of the EPR spectra require the introduction of a single angle of non-coincidence between g(1) and A(1), and g(3) and A(3) to reproduce all of the features in the S- and X-band spectra. This behaviour provides a rare example of the detection and measurement of non-coincidence effects from frozen-solution EPR spectra without the need for single-crystal measurements, and in which the S-band experiment is sensitive to the non-coincidence. An analysis of the EPR spectra of 1(-) reveals a 24 % Ni contribution to the SOMO in 1(-), supporting a delocalisation of the spin-density across the NiFe(2) cluster. This observation is supported by IR spectroscopic results which show that the CO stretching frequencies, nu(CO), shift to lower frequency by about 70 cm(-1) when 1 is reduced to 1(-). Density functional calculations provide a framework for the interpretation of the spectroscopic properties of 1(-) and suggest that the SOMO is delocalised over the whole cluster, but with little S-centre participation. This electronic structure contrasts with that of the Ni-A, -B, -C and -L forms of [NiFe] hydrogenase in which there is considerable S participation in the SOMO.     

On the studies of the vibrational spectra of cluster [Mo2O2S2(S2)2]2-

IR and Raman spectra of [Mo₂O₂S₂(S₂)₂]^2- were reported. The resonance Raman spectra and the depolarization ratios in CH₃CN solution were measured. By using the data of crystal structure, the simplified normal coordinate calculation of the stretching vibrations for anion [Mo₂O₂S₂(S₂)₂]^2- was performed. The results obtained are useful to assign the vibrational bands of some Mo-Fe-S clusters.     

An S‐Oxygenated [NiFe] Complex Modelling Sulfenate Intermediates of an O2‐Tolerant Hydrogenase

To understand the molecular details of O₂‐tolerant hydrogen cycling by a soluble NAD⁺‐reducing [NiFe] hydrogenase, we herein present the first bioinspired heterobimetallic S‐oxygenated [NiFe] complex as a structural and vibrational spectroscopic model for the oxygen‐inhibited [NiFe] active site. This compound and its non‐S‐oxygenated congener were fully characterized, and their electronic structures were elucidated in a combined experimental and theoretical study with emphasis on the bridging sulfenato moiety. Based on the vibrational spectroscopic properties of these complexes, we also propose novel strategies for exploring S‐oxygenated intermediates in hydrogenases and similar enzymes.     

Spectroscopic characterization of the key catalytic intermediate Ni-C in the O2-tolerant [NiFe] hydrogenase I from Aquifex aeolicus: evidence of a weakly bound hydride

Ni-C in the O(2)-tolerant hydrogenase I from Aquifex aeolicus binds a hydride weaker than that in O(2)-sensitive hydrogenases. This is in line with the enhanced light-sensitivity of Ni-C, greater lability of the hydride complex and increased catalytic redox potentials relevant to bio-H(2) oxidation.     

Influence of an electron-deficient bridging o-carborane on the electronic properties of an [FeFe] hydrogenase active site model

The IR carbonyl stretching frequencies of [Fe2(SRS)(CO)6] complexes correlate well with their first reduction potential; an [FeFe] hydrogenase model with a very mild reduction potential has been realized by using a strongly electron deficient carborane-dithiolate bridge.     

[Bu~4N]~3[Mo~2FeS~8O].(CH~2OH)~2簇合物的合成, 结构和性质研究

(NH4)2MoS~4、FeCl~3与乙二醇钠在乙二醇溶液中反应, 再与Bu~4NBr作用可得到一种M0-Fe-S簇合物[Bu~4N]~3[Mo~2FeS~8O].HOCH~2OH。其结构经X光晶体结构分析确定。并测定其红外光谱、紫外光谱、Mossbauer谱和电化学性质。该化合物可催化KBH~4转化乙炔还原为乙烯的反应。     

High-nuclearity Ce/Mn and Th/Mn cluster chemistry: preparation of complexes with [Ce4Mn10O10(OMe)6]18+ and [Th6Mn10O22(OH)2]18+ cores

The syntheses, structures, and magnetic properties are reported of the mixed-metal complexes [Ce4Mn10O10(OMe)6(O2CPh)16(NO3)2(MeOH)2(H2O)2] (1) and [Th6Mn10O22(OH)2(O2CPh)16-(NO3)2(H2O)8] (2), which were both prepared by the reaction of (NBun4)[Mn4O2(O2CPh)9(H2O)] (3) with a source of the heterometal in MeCN/MeOH. Complexes 1 and 2 crystallize in the monoclinic space group C2/c and the triclinic space group P, respectively. Complex 1 consists of 10 MnIII, 2 CeIII, and 2 CeIV atoms and possesses a very unusual tubular [Ce4Mn10O10(OMe)6]18+ core. Complex 2 consists of 10 MnIV and 6 ThIV atoms and possesses a [Th6Mn10O22(OH)2]18+ core with the metal atoms arranged in layers with a 2:3:6:3:2 pattern. Peripheral ligation around the cores is provided by 16 bridging benzoates, 2 chelating nitrates, and either (i) 2 each of terminal H2O and MeOH groups in 1 or (ii) 8 terminal H2O groups in 2. Complex 1 is the largest mixed-metal Ce/Mn cluster and the first 3d/4f cluster with mixed-valency in its lanthanide component, while complex 2 is the first Th/Mn cluster and the largest mixed transition metal/actinide cluster to date. Solid-state dc and ac magnetic susceptibility measurements on 1 and 2 establish that they possess S = 4 and 3 ground states, respectively. Ac susceptibility studies on 1 revealed nonzero frequency-dependent out-of-phase (chiM' ') signals at temperatures below 3 K; complex 2 displays no chiM' ' signals. However, single-crystal magnetization vs dc field scans at variable temperatures and variable sweep-rates down to 0.04 K on 1 revealed no noticeable hysteresis loops, except very minor ones at 0.04 K assignable to weak intermolecular interactions propagated by hydrogen bonds involving CeIII-bound ligands. Complex 1 is thus concluded not to be a single-molecule magnet (SMM), and the combined results thus represent a caveat against taking such ac signals as sufficient proof of a SMM.     

超分子化合物[CO(bppdca)_2(HL)_2(H_2O)_2]·2H_2O]的晶体结构和性质

以N,N′-二(3-吡啶基)-吡啶-3,5-二甲酰胺(bppdca)和1,4-环己烷二羧酸(H2L)为混合配体,利用水热合成方法获得了一个三维的超分子化合物[CO(bppdca)2(HL)2(H2O)2]·2H2O],并通过元素分析、IR和单晶X射线衍射技术确定了该化合物晶体结构.结构分析表明该化合物属单斜晶系,P21/n空间群,晶胞参数a=0.820 65(6)nm,b=1.259 76(9)nm,c=2.479 11(18)nm,β=98.061 0(10)°,Z=2,V=2.537 6(3)nm3,Mr=1 111.98,Dc=1.455g/cm3,F(000)=116 2,μ=0.421mm-1,S=1.018,R=0.041 7,wR=0.102 3.晶体结构分析表明,配合物中的CoⅡ与2个bppdca配体、2个HL阴离子以及2个配位水分子形成单金属配合物.相邻的配合物通过氢键作用拓展成三维超分子框架.另外,也研究了该化合物的热稳定性、荧光性质以及光催化性质.