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1.
Rippers Y Utesch T Hildebrandt P Zebger I Mroginski MA 《Physical chemistry chemical physics : PCCP》2011,13(36):16146-16149
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. 相似文献
2.
Single crystal EPR studies of the reduced active site of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F 总被引:1,自引:0,他引:1
Foerster S Stein M Brecht M Ogata H Higuchi Y Lubitz W 《Journal of the American Chemical Society》2003,125(1):83-93
In the catalytic cycle of [NiFe] hydrogenase the paramagnetic Ni-C intermediate is of key importance, since it is believed to carry the substrate hydrogen, albeit in a yet unknown geometry. Upon illumination at low temperatures, Ni-C is converted to the so-called Ni-L state with markedly different spectroscopic parameters. It is suspected that Ni-L has lost the "substrate hydrogen". In this work, both paramagnetic states have been generated in single crystals obtained from the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F. Evaluation of the orientation dependent spectra yielded the magnitudes of the g tensors and their orientations in the crystal axes system for both Ni-C and Ni-L. The g tensors could further be related to the atomic structure by comparison with the X-ray crystallographic structure of the reduced enzyme. Although the g tensor magnitudes of Ni-C and Ni-L are quite different, the orientations of the resulting g tensors are very similar but differ from those obtained earlier for Ni-A and Ni-B (Trofanchuk et al. J. Biol. Inorg. Chem. 2000, 5, 36-44). The g tensors were also calculated by density functional theory (DFT) methods using various structural models of the active site. The calculated g tensor of Ni-C is, concerning magnitudes and orientation, in good agreement with the experimental one for a formal Ni(III) oxidation state with a hydride (H(-)) bridge between the Ni and the Fe atom. Satisfying agreement is obtained for the Ni-L state when a formal Ni(I) oxidation state is assumed for this species with a proton (H(+)) removed from the bridge between the nickel and the iron atom. 相似文献
3.
Iwasaki T Kounosu A Samoilova RI Dikanov SA 《Journal of the American Chemical Society》2006,128(7):2170-2171
The hyperfine couplings for strongly and weakly coupled 15N nuclei around a reduced Rieske [2Fe-2S] center of uniformly 15N-labeled, hyperthermostable archaeal Rieske protein at pH 13.3 were determined by hyperfine sublevel correlation (HYSCORE) spectroscopy and compared with those at physiological pH. Significant changes in the hyperfine couplings of the terminal histidine Ndelta ligands and Nepsilon nuclei were observed between them, which can be explained by not only the redistribution of the unpaired electron spin density over the ligands but also the difference in the mixed-valence state of the fully deprotonated, reduced cluster. These quantitative data can be used in theoretical analysis for the selection of an appropriate model of the mixed-valence state of the reduced Rieske center at very alkaline pH. 相似文献
4.
Marius Horch Yvonne Rippers Prof. Maria A. Mroginski Prof. Peter Hildebrandt Dr. Ingo Zebger 《Chemphyschem》2013,14(1):185-191
Hydrogenases catalyse the reversible cleavage of molecular hydrogen into protons and electrons. While most of these enzymes are inhibited under aerobic conditions, some hydrogenases are catalytically active even at ambient oxygen levels. In particular, the soluble [NiFe] hydrogenase from Ralstonia eutropha H16 couples reversible hydrogen cycling to the redox conversion of NAD(H). Its insensitivity towards oxygen has been formerly ascribed to the putative presence of additional cyanide ligands at the active site, which has been, however, discussed controversially. Based on quantum chemical calculations of model compounds, we demonstrate that spectroscopic consequences of the proposed non‐standard set of inorganic ligands are in contradiction to the underlying experimental findings. In this way, the previous model for structure and function of this soluble hydrogenase is disproved on a fundamental level, thereby highlighting the efficiency of computational methods for the evaluation of experimentally derived mechanistic proposals. 相似文献
5.
Matsumoto T Itakura N Nakaya Y Tatsumi K 《Chemical communications (Cambridge, England)》2011,47(3):1030-1032
A S/SH bridged hetero-dinuclear Ru/Ge complex cation reacted with H(2) to afford the μ-S/μ-H complex. The reaction was considerably slower compared to that of the μ-S/μ-OH complex. Thus, the μ-S/μ-SH and μ-S/μ-OH complexes might provide models for the unready and ready states, respectively, of [NiFe] hydrogenase. 相似文献
6.
Density functional theory (DFT) was employed to investigate the behavior of a series of catalysts used in the hydrogen evolution reaction (HER, 2H(+) + 2e(-) --> H(2)). The kinetics of the HER was studied on the [NiFe] hydrogenase, the [Ni(PS3*)(CO)](1)(-) and [Ni(PNP)(2)](2+) complexes, and surfaces such as Ni(111), Pt(111), or Ni(2)P(001). Our results show that the [NiFe] hydrogenase exhibits the highest activity toward the HER, followed by [Ni(PNP)(2)](2+) > Ni(2)P > [Ni(PS3*)(CO)](1)(-) > Pt > Ni in a decreasing sequence. The slow kinetics of the HER on the surfaces is due to the fact that the metal hollow sites bond hydrogen too strongly to allow the facile removal of H(2). In fact, the strong H-Ni interaction on Ni(2)P(001) can lead to poisoning of the highly active sites of the surface, which enhances the rate of the HER and makes it comparable to that of the [NiFe] hydrogenase. In contrast, the promotional effect of H-poisoning on the HER on Pt and Ni surfaces is relatively small. Our calculations suggest that among all of the systems investigated, Ni(2)P should be the best practical catalyst for the HER, combining the high thermostability of the surfaces and high catalytic activity of the [NiFe] hydrogenase. The good behavior of Ni(2)P(001) toward the HER is found to be associated with an ensemble effect, where the number of active Ni sites is decreased due to presence of P, which leads to moderate bonding of the intermediates and products with the surface. In addition, the P sites are not simple spectators and directly participate in the HER. 相似文献
7.
Burgdorf T Löscher S Liebisch P Van der Linden E Galander M Lendzian F Meyer-Klaucke W Albracht SP Friedrich B Dau H Haumann M 《Journal of the American Chemical Society》2005,127(2):576-592
Structure and oxidation state of the Ni-Fe cofactor of the NAD-reducing soluble hydrogenase (SH) from Ralstonia eutropha were studied employing X-ray absorption spectroscopy (XAS) at the Ni K-edge, EPR, and FTIR spectroscopy. The SH comprises a nonstandard (CN)Ni-Fe(CN)(3)(CO) site; its hydrogen-cleavage reaction is resistant against inhibition by dioxygen and carbon monoxide. Simulations of the XANES and EXAFS regions of XAS spectra revealed that, in the oxidized SH, the Ni(II) is six-coordinated ((CN)O(3)S(2)); only two of the four conserved cysteines, which bind the Ni in standard Ni-Fe hydrogenases, provide thiol ligands to the Ni. Upon the exceptionally rapid reductive activation of the SH by NADH, an oxygen species is detached from the Ni; hydrogen may subsequently bind to the vacant coordination site. Prolonged reducing conditions cause the two thiols that are remote from the Ni in the native SH to become direct Ni ligands, creating a standardlike Ni(II)(CysS)(4) site, which could be further reduced to form the Ni-C (Ni(III)-H(-)) state. The Ni-C state does not seem to be involved in hydrogen cleavage. Two site-directed mutants (HoxH-I64A, HoxH-L118F) revealed structural changes at their Ni sites and were employed to further dissect the role of the extra CN ligand at the Ni. It is proposed that the predominant coordination by (CN),O ligands stabilizes the Ni(II) oxidation state throughout the catalytic cycle and is a prerequisite for the rapid activation of the SH in the presence of oxygen. 相似文献
8.
9.
M. Guiral-Brugna M. -T. Giudici-Orticoni M. Bruschi P. Bianco 《Journal of Electroanalytical Chemistry》2001,510(1-2)
Hydrogenases are enzymes which catalyze hydrogen production/consumption reactions. In this paper, the [Fe] hydrogenase from Desulfovibrio vulgaris Hildenborough is shown to catalyze the direct hydrogen production from protons, in the absence of any promoter, at a basal pyrolytic graphite electrode using cyclic voltammetry techniques. The effect of several parameters upon catalytic current is investigated: pH, hydrogenase concentration, ionic strength, competition with another protein (bovine serum albumin), cycling repetition, mode of electrode polishing. The extent and efficiency of the hydrogenase electroactivity are examined in the presence of either an artificial electron carrier (methylviologen) or a physiological partner cytochrome c3 isolated from the same bacterial strain. Results suggest that the electron-transfer process is essentially controlled by a complex between both hydrogenase and cytochrome c3. Electrocatalysis appears to be largely governed by the adsorption of hydrogenase on the electrode surface very likely involving hydrophobic interactions. 相似文献
10.
Kim SH Xing G Bollinger JM Krebs C Hoffman BM 《Journal of the American Chemical Society》2006,128(32):10374-10375
myo-Inositol oxygenase (MIOX) is a non-heme diiron oxygenase that cleaves cyclohexane-(1,2,3,5/4,6-hexa)-ol (myo-inositol, MI) to d-glucuronate. Here, we use 2H ENDOR spectroscopy to demonstrate that MI binds to the diiron(II/III) cofactor of MIOX via an alkoxide bridge, most likely involving O1. Analysis shows that MI adopts a symmetrical geometry in which the O-C-2H plane of the bridge is approximately orthogonal to the Fe-O-Fe plane. 相似文献
11.
Facile H2 heterolysis was found to be mediated by coordinatively unsaturated Cp*Ir and Cp*Rh thiolate complexes. The reaction of iridium complex is reversible, and the formation of an intermediary Ir-H/thiol complex was detected. The reversible conversion between thiolate complex+H2 and hydride complex+thiol provides an intriguing functional model of [NiFe] hydrogenase. 相似文献
12.
13.
Pandelia ME Infossi P Stein M Giudici-Orticoni MT Lubitz W 《Chemical communications (Cambridge, England)》2012,48(6):823-825
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. 相似文献
14.
Lyon EJ Shima S Boecher R Thauer RK Grevels FW Bill E Roseboom W Albracht SP 《Journal of the American Chemical Society》2004,126(43):14239-14248
The iron-sulfur-cluster-free hydrogenase Hmd (H(2)-forming methylenetetrahydromethanopterin dehydrogenase) from methanogenic archaea has recently been found to contain one iron associated tightly with an extractable cofactor of yet unknown structure. We report here that Hmd contains intrinsic CO bound to the Fe. Chemical analysis of Hmd revealed the presence of 2.4 +/- 0.2 mol of CO/mol of iron. Fourier transform infrared spectra of the native enzyme showed two bands of almost equal intensity at 2011 and 1944 cm(-)(1), interpreted as the stretching frequencies of two CO molecules bound to the same iron in an angle of 90 degrees . We also report on the effect of extrinsic (12)CO, (13)CO, (12)CN(-), and (13)CN(-) on the IR spectrum of Hmd. 相似文献
15.
The currently presumed assignment of CO/CN ligands in the structure of the active cluster in CO-inactivated [FeFe] hydrogenase is shown to be inconsistent with the available IR data in the enzyme from Clostridium pasteurianum I. A different arrangement has the correct qualitative and quantitative features, reproducing the observed line spacing and intensities and the observed line shift consequent to inactivation with labeled 13CO instead of 12CO. The new assignment is also consistent with the observed change from rhombic to axial symmetry of the electron paramagnetic resonance g tensor upon inactivation. 相似文献
16.
[formula: see text] The synthesis of (R)-[2-2H]isopentenyl diphosphate from D-mannitol 1,2:5,6-bis-acetonide in 10 steps is reported. Stereospecific incorporation of the label is achieved by a BF3-catalyzed NaCNBD3 reduction of the enantiomerically pure (S)-isopropylidene oxirane intermediate. The enantiomeric excess of the penultimate precursor [2-2H]isopentenyl tosylate (> 95% ee) was determined by 2H NMR spectroscopy in a poly-gamma-benzyl-L-glutamate/CH2Cl2 liquid crystal at -50 degrees C. 相似文献
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18.
Hiromichi Kurosu Mizuyo Kikuchi Isao Ando 《Journal of Polymer Science.Polymer Physics》1995,33(5):769-775
The solid-state 15N CP/MAS NMR spectra and 15N spin-lattice relaxation times (T1) of doped and dedoped 15N-labeled polypyrroles prepared by electrochemical polymerization, have been measured by means of high-resolution solid-state 15N NMR. The 15N signal of polypyrrole consists of four peaks decomposed by line shape analysis. The four peaks obtained have been assigned to the various structures of polypyrrole. Further, the half-width of the 15N NMR spectra of polypyrroles is discussed as related to the electrical conductivity. © 1995 John Wiley & Sons, Inc. 相似文献
19.
Groenewold GS Gianotto AK Cossel KC Van Stipdonk MJ Moore DT Polfer N Oomens J de Jong WA Visscher L 《Journal of the American Chemical Society》2006,128(14):4802-4813
The gas-phase infrared spectra of discrete uranyl ([UO2]2+) complexes ligated with acetone and/or acetonitrile were used to evaluate systematic trends of ligation on the position of the O=U=O stretch and to enable rigorous comparison with the results of computational studies. Ionic uranyl complexes isolated in a Fourier transform ion cyclotron resonance mass spectrometer were fragmented via infrared multiphoton dissociation using a free electron laser scanned over the mid-IR wavelengths. The asymmetric O=U=O stretching frequency was measured at 1017 cm(-1) for [UO2(CH3COCH3)2]2+ and was systematically red shifted to 1000 and 988 cm(-1) by the addition of a third and fourth acetone ligand, respectively, which was consistent with increased donation of electron density to the uranium center in complexes with higher coordination number. The values generated computationally using LDA, B3LYP, and ZORA-PW91 were in good agreement with experimental measurements. In contrast to the uranyl frequency shifts, the carbonyl frequencies of the acetone ligands were progressively blue shifted as the number of ligands increased from two to four and approached that of free acetone. This observation was consistent with the formation of weaker noncovalent bonds between uranium and the carbonyl oxygen as the extent of ligation increases. Similar trends were observed for [UO2(CH3CN)n]2+ complexes, although the uranyl asymmetric stretching frequencies were greater than those measured for acetone complexes having equivalent coordination, which is consistent with the fact that acetonitrile is a weaker nucleophile than is acetone. This conclusion was confirmed by the uranyl stretching frequencies measured for mixed acetone/acetonitrile complexes, which showed that substitution of one acetone for one acetonitrile produced a modest red shift of 3-6 cm(-1). 相似文献
20.
Variable temperature 2H NMR experiments (line shape analysis, relaxation studies) were carried out on the pyridine-d5-tris-(1,2-dioxyphenyl)-cyclotriphosphazene inclusion compound in the temperature range between 110-300 K. It is found that the pyridine guests are highly mobile throughout the whole temperature range covered here. The observation of three superimposed 2H NMR signals can be understood in terms of a particular (motionally averaged) orientation of the pyridine molecules, which is a consequence of the molecular symmetry of the pyridine guests and the imposed channel restrictions. The experimental data are consistent with a combined rotation on cone-small angle fluctuation model, which assumes a fast molecular reorientation between two superimposed cones with an opening angle for the inner cone between 59-73 degrees (angle of fluctuation between 1-3 degrees ). On the basis of this model assumption it is possible to reproduce both the experimental 2H NMR line shapes and the spin-lattice relaxation data in a quantitative way. The analysis of the partially relaxed spectra (inversion recovery experiments) yields the correlation times for this overall motional process. They follow an Arrhenius behavior from which an activation energy of 8.7 +/- 0.4 kJ mol(-1) is derived. The results are discussed in the framework of the published data for related systems. 相似文献