Probing the crossover in CO desorption from single crystal to nanoparticulate Ru model catalysts

cited By 10International audienceUsing model catalysts, we demonstrate that CO desorption from Ru surfaces can be switched from that typical of single crystal surfaces to one more characteristic of supported nanoparticles. First, the CO desorption behaviour from Ru nanoparticles supported on highly oriented pyrolytic graphite was studied. Both mass-selected and thermally evaporated nanoparticles were deposited. TPD spectra from the mass-selected nanoparticles exhibit a desorption peak located around 410 K with a broad shoulder extending from around 480 K to 600 K, while spectra obtained from thermally evaporated nanoparticles exhibit a single broad feature from ∼350 K to ∼450 K. A room temperature deposited 50 Å thick Ru film displays a characteristic nanoparticle-like spectrum with a broad desorption feature at ∼420 K and a shoulder extending from ∼450 K to ∼600 K. Subsequent annealing of this film at 900 K produced a polycrystalline morphology of flat Ru(001) terraces separated by monatomic steps. The CO desorption spectrum from this surface resembles that obtained on single crystal Ru(001) with two large desorption features located at 390 K and 450 K due to molecular desorption from terrace sites, and a much smaller peak at ∼530 K due to desorption of dissociatively adsorbed CO at step sites. In a second experiment, ion sputtering was used to create surface defects on a Ru(0 1 54) single crystal surface. A gradual shift away from the desorption spectrum typical of a Ru(001) surface towards one resembling desorption from supported Ru nanoparticles was observed with increasing sputter time. © 2011 the Owner Societies

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

Density functional theory

Density functional theory (DFT) finds increasing use in applications related to biological systems. Advancements in methodology and implementations have reached a point where predicted properties of reasonable to high quality can be obtained. Thus, DFT studies can complement experimental investigations, or even venture with some confidence into experimentally unexplored territory. In the present contribution, we provide an overview of the properties that can be calculated with DFT, such as geometries, energies, reaction mechanisms, and spectroscopic properties. A wide range of spectroscopic parameters is nowadays accessible with DFT, including quantities related to infrared and optical spectra, X-ray absorption and Mössbauer, as well as all of the magnetic properties connected with electron paramagnetic resonance spectroscopy except relaxation times. We highlight each of these fields of application with selected examples from the recent literature and comment on the capabilities and limitations of current methods

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