Geometric and Electronic Structures of the NiI and Methyl−NiIII Intermediates of Methyl-Coenzyme M Reductase†

ABSTRACT: Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH). The active site in MCR contains a Ni-F430 cofactor, which can exist in different oxidation states. The catalytic mechanism of methane formation has remained elusive despite intense spectroscopic and theoretical investigations. On the basis of spectroscopic and crystallographic data, the first step of the mechanism is proposed to involve a nucleophilic attack of the NiI active state (MCRred1) on Me-SCoM to form a NiIII-methyl intermediate, while computational studies indicate that the first step involves the attack of NiI on the sulfur of Me-SCoM, forming a CH3 radical and a NiII-thiolate species. In this study, a combination of Ni K-edge X-ray absorption spectroscopic (XAS) studies and density functional theory (DFT) calculations have been performed on the NiI (MCRred1), NiII (MCRred1-silent), and NiIII-methyl (MCRMe) states of MCR to elucidate the geometric and electronic structures of the different redox states. Ni K-edge EXAFS data are used to reveal a five-coordinate active site with an open upper axial coordination site in MCRred1. Ni K-pre-edge and EXAFS data and time-dependent DFT calculations unambiguously demonstrate the presence of a long Ni-C bond (∼2.04 Å) in the NiIII-methyl state of MCR. The formation and stability of this species support mechanism I, and the Ni-C bond length suggests a homolytic cleavage of the NiIII-methyl bon

A New Heterobinuclear FeIIICuII Complex with a Single Terminal FeIII–O(phenolate) Bond. Relevance to Purple Acid Phosphatases and Nucleases

A novel heterobinuclear mixed valence complex [Fe^IIICu^II(BPBPMP)(OAc)_2]ClO_4, 1, with the unsymmetrical N_5O_2 donor ligand 2-bis[{(2-pyridylmethyl)aminomethyl}-6-{(2-hydroxybenzyl)(2-pyridylmethyl)} aminomethyl]-4-methylphenol (H_2BPBPMP) has been synthesized and characterized. A combination of data from mass spectrometry, potentiometric titrations, X-ray absorption and electron paramagnetic resonance spectroscopy, as well as kinetics measurements indicates that in ethanol/water solutions an [Fe^III-(nu)OH-Cu^IIOH_2]+ species is generated which is the likely catalyst for 2,4-bis(dinitrophenyl)phosphate and DNA hydrolysis. Insofar as the data are consistent with the presence of an Fe_III-bound hydroxide acting as a nucleophile during catalysis, 1 presents a suitable mimic for the hydrolytic enzyme purple acid phosphatase. Notably, 1 is significantly more reactive than its isostructural homologues with different metal composition (Fe^IIIM^II, where M^II is Zn^II, Mn^II, Ni^II,or Fe^II). Of particular interest is the observation that cleavage of double-stranded plasmid DNA occurs even at very low concentrations of 1 (2.5 nuM), under physiological conditions (optimum pH of 7.0), with a rate enhancement of 2.7 x 10^7 over the uncatalyzed reaction. Thus, 1 is one of the most effective model complexes to date, mimicking the function of nucleases

Spin-state studies with XES and RIXS: From static to ultrafast

We report on extending hard X-ray emission spectroscopy (XES) along with resonant inelastic X-ray scattering (RIXS) to study ultrafast phenomena in a pump-probe scheme at MHz repetition rates. The investigated systems include low-spin (LS) Fe-II complex compounds, where optical pulses induce a spin-state transition to their (sub)nanosecond-lived high-spin (HS) state. Time-resolved XES clearly reflects the spin-state variations with very high signal-to-noise ratio, in agreement with HS-LS difference spectra measured at thermal spin crossover, and reference HS-LS systems in static experiments, next to multiplet calculations. The 1s2p RIXS, measured at the Fe Is pre-edge region, shows variations after laser excitation, which are consistent with the formation of the HS state. Our results demonstrate that X-ray spectroscopy experiments with overall rather weak signals, such as RIXS, can now be reliably exploited to study chemical and physical transformations on ultrafast time scales. (C) 2012 Elsevier B.V. All rights reserved

Presence of Metallic Fe Nanoclusters in r-(Al,Fe)2O3 Solid Solutions

Powders of R-(Al1-xFex)2O3 solid solutions prepared by the calcination in air of the corresponding γ-(Al1- xFex)2O3 powders were studied by several techniques including X-ray diffraction, field-emission-gun scanning electron microscopy, transmission Mössbauer spectroscopy, integral low-energy electron Mössbauer spectroscopy (ILEEMS), and Fe K-edge X-ray absorption near-edge structure (XANES) measurements. The asymmetry of the characteristic Mo¨ssbauer doublet representing Fe3+ ions substituting for Al3+ ions in the corundum lattice of R-(Al1-xFex)2O3 solid solutions was resolved and explained for the first time by using two additional subspectra, i.e., a broad second doublet characteristic of a very distorted octahedral site for Fe3+ and a singlet attributable to R-Fe, suggesting the presence of metallic iron nanoclusters consisting of only a few number of atoms within the solid solution grains. ILEEMS studies showed that the Fe nanoclusters are evenly distributed among the surface layers and the cores of the grains. Fe K-edge XANES measurements further confirmed the occurrence of metallic iron. The proportion of Fe nanoclusters increases when the total iron content is decreased, as does the proportion of distorted octahedral site, suggesting that they are located around the iron nanoclusters. The formation of the metallic Fe nanoclusters in the R-(Al1-xFex)2O3 grains is thought to be a consequence of the γ f R phase transition which implies structural rearrangement on both the cationic and anionic sublattices

Gnxas, A Multiple-scattering Approach To Exafs Analysis - Methodology and Applications To Iron Complexes

GNXAS, a recently developed integrated approach to the analysis of EXAFS data is presented in detail. GNXAS provides for the direct fitting of theoretical signals (calculated by utilizing the Hedin-Lundqvist complex exchange and correlation potential and spherical wave propagators) to the experimental data. GNXAS is able to calculate all the signals related to two-, three-, and four-atom correlation functions with the proper treatment of correlated distances and Debye-Waller factors. The technique is particularly well-suited for the analysis of multiple-scattering effects and thus allows for accurate determination of bond distance and angular information of second and third neighbors. Herein we report the application of GNXAS to several chemical systems of known structure. The reliability of GNXAS was evaluated on a well-ordered inorganic complex, Fe(acac)(3), as well as a lower-symmetry coordination complex with mixed ligation, Na[Fe(OH2)EDTA]. The total EXAFS signal generated by GNXAS matches closely the experimental data for both complexes, especially when all the multiple-scattering contributions were included in the theoretical signal. First neighbor distances obtained from refinement using GNXAS, as well as distances and angles for further neighbors, compared very well with crystallographic values. The angle dependence of the Fe-C-N multiple-scattering contribution in K3Fe(CN)(6) was also examined. The results indicate that GNXAS can be used to determine angles relatively accurately for Fe-C-N configurations with angles greater than about 150 degrees. These results establish the utility and reliability of the GNXAS approach and provide a reliable means to determine additional structural information from EXAFS analysis of structures of chemical interest

Determination of the Fe-n-o Angle In (feno)(7) Complexes Using Multiple-scattering Exafs Analysis By Gnxas

The Fe-N-O bond angle in a series of {FeNO}(7) complexes has been probed by EXAFS, utilizing a new theoretical data analysis package, GNXAS. This package provides an integrated approach to the analysis of EXAFS data based on a full curved-wave, multiple-scattering theoretical treatment incorporating least-squares refinement. Since GNXAS is able to calculate all the signals relating to two-, three-, and four-atom correlation functions with the proper treatment of correlated distances and Debye-Waller factors, it is particularly well-suited for analysis of multiple-scattering effects and bond angle determination. EXAFS data were obtained on a series of crystallographically characterized {FeNO}(7) inorganic complexes with varying Fe-N-O angles to examine the sensitivity of the GNXAS fit to this angle. The compounds studied were Fe(TMC)NO (where TMC = 1,4,8,1 l-tetramethyl-l,4,8,11-tetraazacyclotetradecane) which has an Fe-N-O bond angle of 177.5(5)degrees, Fe(TACN)(N-3)(2)NO (where TACN = N,N',N''-trimethyl-1,4,7-triazacyclononane) which has an angle of 156(1)degrees, and Fe(salen)NO (where salen = N,N'-ethylenebis(salicylideneiminato)) which has a bond angle of 127(6)degrees at 175 degrees C and 147(5)degrees at 23 degrees C. EXAFS data for FeEDTA-NO (whose crystal structure has not been determined and thus the angle is unknown) were also obtained and analyzed using GNXAS to determine the Fe-N-O bond angle. Results are presented which indicate that it is possible to determine whether the Fe-N-O unit is bent or linear, with the GNXAS analysis being extremely sensitive when the angle is between 150 degrees and 180 degrees. Using this method the Fe-N-O angle in FeEDTA-NO is found to be 156(5)degrees. The results of this study establish that EXAFS analysis using GNXAS can provide reliable angular information for small molecules coordinated to transition metals with rather complex coordination environments. This study thus provides the basis for the determination of the coordination geometry of molecules like NO and O-2 to metalloprotein active sites

Using Gnxas, A Multiple-scattering Exafs Analysis, For Determination of the Fe-n-o Angle In (feno)(7) Complexes

The Fe-N-O bond angle in a series of {FeNO}(7) complexes has been probed by EXAFS, utilizing a new theoretical data analysis package, GNXAS. This package provides an integrated approach to the analysis of EXAFS data based on a full curved-wave, multiple-scattering theoretical treatment incorporating least squares refinement. EXAFS data were obtained on two crystallographically-characterized {FeNO}(7) inorganic complexes with varying Fe-N-O angles to examine the sensitivity of the GNXAS fit to this angle. Results are presented which indicate that it is possible to determine whether the Fe-N-O unit is bent or linear, with the GNXAS analysis being extremely sensitive when the angle is between 150 degrees and 180 degrees. This study thus provides the basis for the determination of the coordination geometry of molecules like NO and O-2 to metalloprotein active sites