Biomedical subjects

Frank M F de Groot

Publications and source records attributed to Frank M F de Groot.

14 recordsLinked to original sources

PubMed2006

Probing the influence of X-rays on aqueous copper solutions using time-resolved in situ combined video/X-ray absorption near-edge/ultraviolet-visible spectroscopy.

Time-resolved in situ video monitoring and ultraviolet-visible spectroscopy in combination with X-ray absorption near-edge spectroscopy (XANES) have been used for the first time in a combined manner to study the effect of synchrotron radiation on a series of homogeneous aqueous copper solutions in a microreactor. This series included both non biologically relevant (pyridine, bipyridine, neocuproine, terpyridine, dimethylpyridine, ammonia, ethylenediamine, and 1,10-phenanthroline) and biologically relevant (histidine, glycine, and imidazole) ligands. It was found that when water is present as solvent, gas bubbles are formed under the influence of the X-ray beam. At the liquid-gas interface of these bubbles, in particular cases colloidal copper nanoparticles are formed. This reduction process was found to be influenced by the type of copper precursor salt (SO(4)(2-), NO(3)(-), and Cl(-)), the ligands surrounding the copper cation, and the redox potential of the copper complexes (ranging between +594 and -360 mV). In other words, in some cases, no reduction was encountered (e.g., ammonia in the presence of SO(4)(2-) and NO(3)(-)), whereas in other cases reduction to either Cu(+) (neocuproine with SO(4)(2-)) or Cu(0) (e.g., histidine and imidazole both with SO(4)(2-), NO(3)(-), and Cl(-)) was observed. These results illustrate the added value of video spectroscopy for the interpretation of in situ XANES studies. Not only do the results give an illustration of the parameters that are important in the redox processes that occur in biological systems, they also show the potential problems associated with studying catalytic processes in aqueous solutions by XANES spectroscopy.

Journal Article↗

PubMed2006

Identification of CO adsorption sites in supported Pt catalysts using high-energy-resolution fluorescence detection X-ray spectroscopy.

High-energy-resolution fluorescence detection (HERFD) X-ray spectroscopy is presented as a new tool for the identification of the bonding sites of reactants in supported metal catalysts. The type of adsorption site of CO on an alumina-supported platinum catalyst and the orbitals involved in the bonding are identified. Because X-ray absorption spectroscopy (XAS) is element-specific and can be used under high pressures and temperatures, in situ HERFD XAS can be applied to a swathe of catalytic systems, including alloys.

Letter↗

PubMed2006

Fe L-edge XAS studies of K4[Fe(CN)6] and K3[Fe(CN)6]: a direct probe of back-bonding.

Distinct spectral features at the Fe L-edge of the two compounds K3[Fe(CN)6] and K4[Fe(CN)6] have been identified and characterized as arising from contributions of the ligand pi orbitals due to metal-to-ligand back-bonding. In addition, the L-edge energy shifts and total intensities allow changes in the ligand field and effective nuclear charge to be determined. It is found that the ligand field term dominates the edge energy shift. The results of the experimental analysis were compared to BP86 DFT calculations. The overall agreement between the calculations and experiment is good; however, a larger difference in the amount of pi back-donation between Fe(II) and Fe(III) is found experimentally. The analysis of L-edge spectral shape, energy shift, and total intensity demonstrates that Fe L-edge X-ray absorption spectroscopy provides a direct probe of metal-to-ligand back-bonding.

Algorithms↗

PubMed2006

Probing the 3d spin momentum with X-ray emission spectroscopy: the case of molecular-spin transitions.

We report X-ray emission spectra of Fe(III), Fe(II), and Co(II) spin-crossover compounds in their high-spin and low-spin forms. It is shown that all X-ray emission features are sensitive to the spin state. Variations of the Kbeta and the Kalpha emission line shapes, which are in agreement with theory, can be used as quantitative probes of the spin state; it is suggested that with appropriate reference experiments one can extract the spin momentum for a general case. Resonant X-ray emission spectra unveil details of the redistribution of electrons on the 3d levels associated with the spin-state change by revealing features at the X-ray absorption preedge not accessible through standard absorption measurements.

Journal Article↗

PubMed2006

Controlled assembly of a heterogeneous single-site ethylene trimerization catalyst as probed by X-ray absorption spectroscopy.

X-ray absorption spectroscopy at the Cr K- and L(2,3)-edges was used to study the assembling process of a heterogeneous Cr-based single-site catalyst. The starting point was a Phillips-type system with monochromate species anchored on a silica surface, which was first reduced to a variety of different surface Cr(II) species. The reduced sample was modified with a 1,3,5-tribenzylhexahydro 1,3,5-triazine (TAC) ligand in the presence of CH(2)Cl(2) as solvent to yield a heterogeneous single-site Cr-based catalyst active in the trimerization of ethylene. The molecular structure of the resultant catalytic material consists of distorted octahedral Cr(III) species. The extended X-ray absorption fine-structure (EXAFS) spectroscopy fitting procedure in R space up to 2.5 A showed that the synthesis leads to coordination with a TAC ligand. The fit also shows that it was possible to complete the six-fold environment around Cr(III) with two oxygen atoms and one chloride ligand. This chloride ligand is formed in a redox process from the solvent and is responsible for the oxidation of surface Cr(II) to Cr(III). The obtained geometry and the local environment of the surface complex are discussed in light of its homogeneous counterpart and confirm the single-site characteristics of the prepared catalytic material.

Journal Article↗

PubMed2006

X-ray absorption spectroscopy of Mn/Co/TiO2 Fischer-Tropsch catalysts: relationships between preparation method, molecular structure, and catalyst performance.

The effects of the addition of manganese to a series of TiO(2)-supported cobalt Fischer-Tropsch (FT) catalysts prepared by different methods were studied by a combination of X-ray diffraction (XRD), temperature-programmed reduction (TPR), transmission electron microscopy (TEM), and in situ X-ray absorption fine structure (XAFS) spectroscopy at the Co and Mn K-edges. After calcination, the catalysts were generally composed of large Co(3)O(4) clusters in the range 15-35 nm and a MnO(2)-type phase, which existed either dispersed on the TiO(2) surface or covering the Co(3)O(4) particles. Manganese was also found to coexist with the Co(3)O(4) in the form of Co(3-x)Mn(x)O(4) solutions, as revealed by XRD and XAFS. Characterization of the catalysts after H(2) reduction at 350 degrees C by XAFS and TEM showed mostly the formation of very small Co(0) particles (around 2-6 nm), indicating that the cobalt phase tends to redisperse during the reduction process from Co(3)O(4) to Co(0). The presence of manganese was found to hamper the cobalt reducibility, with this effect being more severe when Co(3-x)Mn(x)O(4) solutions were initially present in the catalyst precursors. Moreover, the presence of manganese generally led to the formation of larger cobalt agglomerates ( approximately 8-15 nm) upon reduction, probably as a consequence of the decrease in cobalt reducibility. The XAFS results revealed that all reduced catalysts contained manganese entirely in a Mn(2+) state, and two well-distinguished compounds could be identified: (1) a highly dispersed Ti(2)MnO(4)-type phase located at the TiO(2) surface and (2) a less dispersed MnO phase being in the proximity of the cobalt particles. Furthermore, the MnO was also found to exist partially mixed with a CoO phase in the form of rock-salt Mn(1-x)Co(x)O-type solid solutions. The existence of the later solutions was further confirmed by scanning transmission electron microscopy with electron energy loss spectroscopy (STEM-EELS) for a Mn-rich sample. Finally, the cobalt active site composition in the catalysts after reduction at 300 and 350 degrees C was linked to the catalytic performances obtained under reaction conditions of 220 degrees C, 1 bar, and H(2)/CO = 2. The catalysts with larger Co(0) particles ( approximately >5 nm) and lower Co reduction extents displayed a higher intrinsic hydrogenation activity and a longer catalyst lifetime. Interestingly, the MnO and Mn(1-x)Co(x)O species effectively promoted these larger Co(0) particles by increasing the C(5+) selectivity and decreasing the CH(4) production, while they did not significantly influence the selectivity of the catalysts containing very small Co(0) particles.

Journal Article↗

PubMed2006

Electronic and molecular structure of photoexcited [Ru(II)(bpy)3]2+ probed by picosecond X-ray absorption spectroscopy.

L(2,3) X-ray absorption spectra of aqueous [Ru(II)(bpy)3]2+ have been recorded in its ground and excited states, 50 ps after short pulse laser excitation. Significant changes in both the XANES (X-ray Near-Edge Absorption Structure) and the EXAFS (Extended X-ray Absorption Fine Structure) regions of the excited state complex are detected. The XANES line shapes have been quantitatively simulated using a crystal field multiplet code in trigonal symmetry. In addition, spectral changes in the EXAFS region of both ground and excited states are analyzed in order to extract structural parameters of their corresponding molecular structures. We obtain a Ru-N bond contraction by approximately 0.03 angstroms in the excited-state complex, as compared to the ground-state compound. This contraction results from electrostatic and polarization contributions, limited by steric constraints on the bpy ligands.

Journal Article↗

PubMed2006

Unusual coordination behavior of Cr3+ in microporous aluminophosphates.

A CrAPO-5 molecular sieve has been investigated with X-ray absorption spectroscopy (EXAFS-XANES) as dehydrated material and after loading with water and ammonia to unravel the coordination geometries of Cr3+ in the framework of a microporous crystalline aluminophosphate, more particularly of the AFI-type. A comparison of the XANES data, a preedge analysis with crystal field multiplet calculations and EXAFS data, pointed toward the presence of framework Cr3+ which, on dehydration, takes on a distorted tetrahedral coordination state. Due to the 3d3 configuration of Cr3+, this unusual tetrahedral coordination environment strongly tends to transform into the more stable 6-fold coordination geometry by binding two extraframework water molecules during hydration. In the presence of ammonia, tetrahedral Cr3+ readily transforms into a 5-fold coordination geometry by binding one ammonia molecule. Therefore, depending on the environmental conditions, the Cr3+ ions can occur in a 4-, 5-, or 6-fold coordination. This observation underlines the flexibility of transition metal ions, such as Cr3+, to cope with unusual coordination geometries in inorganic hosts, making them interesting as potential active sites in heterogeneous catalysis.

Journal Article↗

PubMed2005

1s2p resonant inelastic X-ray scattering of iron oxides.

1s2p resonant inelastic X-ray scattering (RIXS) spectroscopy has been measured for a series of iron oxides, including octahedral and tetrahedral Fe(II) and Fe(III) systems. Their spectral shapes have been analyzed and explained using crystal-field multiplet simulations. The RIXS planes and the K-edge and L-edge X-ray absorption spectra related to these RIXS planes will be discussed with respect to their analytical opportunities. It is concluded that the full power and possibilities of 1s2p RIXS needs an overall resolution of 0.3 eV. This will yield a technique with more detailed information than K-edge and L-edge X-ray absorption combined, obtained in a single experiment. Another major advantage is that 1s2p RIXS involves only hard X-rays, and experiments under essentially any condition and on any system are feasible.

Electrons↗

PubMed2005

LambdaO4 upside down: a new molecular structure for supported VO4 catalysts.

Vanadium oxide (1 wt %) supported on gamma-Al(2)O(3) was used to investigate the interface between the catalytically active species and the support oxide. Raman, UV-vis-NIR DRS, ESR, XANES, and EXAFS were used to characterize the sample in great detail. All techniques showed that an isolated VO(4) species was present at the catalyst surface, which implies that no V-O-V moiety is present. Surprisingly, a Raman band was present at 900 cm(-1), which is commonly assigned to a V-O-V vibration. This observation contradicts the current literature assignment. To further elucidate on potential other Raman assignments, the exact molecular structure of the VO(4) entity (1 V=O bond of 1.58 A and 3 V-O bonds of 1.72 A) together with its position relative to the support O anions and Al cation of the Al(2)O(3) support has been investigated with EXAFS. In combination with a structural model of the alumina surface, the arrangement of the support atoms in the proximity of the VO(4) entity could be clarified, leading to a new molecular structure of the interface between VO(4) and Al(2)O(3). It was found that VO(4) is anchored to the support oxide surface, with only one V-O support bond instead of three, which is commonly accepted in the literature. The structural model suggested in this paper leaves three possible assignments for the 900 cm(-1) band: a V-O-Al vibration, a V-O-H vibration, and a V-(O-O) vibration. The pros and cons of these different options will be discussed.

Journal Article↗

PubMed2005

Synchrotron radiation effects on catalytic systems as probed with a combined in-situ UV-vis/XAFS spectroscopic setup.

UV-vis spectroscopy was used in a combined in-situ UV-vis/XAFS spectroscopic setup to study the synchrotron radiation effect on aqueous homogeneous copper solutions. Two different systems were studied. In the first study, the focus was on a copper bipyridine-catalyzed oxidation of benzyl alcohol to benzaldehyde with 2,2,6,6- tetramethylpiperidinyl-1-oxy and base as cocatalysts. It was found that when the reaction mixture is exposed to the X-ray beam, the features present in the in-situ UV-vis spectrum develop differently compared to the situation when the reaction mixture is not exposed to the X-ray beam. Besides a temperature effect of the X-ray beam, both the UV-vis analysis and the XAFS analysis showed a reducing influence of the X-ray beam on the sample. To investigate this in more detail, we studied a series of dilute aqueous copper solutions from different precursor salts, viz., Cu(NO3)2.3H2O, CuSO4.5H2O, CuCl2, and CuBr2. It was found that the different aqueous copper solutions have different stabilities under the influence of the X-ray beam. Especially the solution from the CuCl2 precursor salt was found to be unstable and to be subjected to reduction. These examples illustrate the need for a second technique, such as in-situ UV-vis spectroscopy, to evaluate the effect of synchrotron radiation used to measure in-situ XAFS on catalytic systems.

Journal Article↗

PubMed2004

The electronic structure of Mn in oxides, coordination complexes, and the oxygen-evolving complex of photosystem II studied by resonant inelastic X-ray scattering.

Resonant inelastic X-ray scattering (RIXS) was used to collect Mn K pre-edge spectra and to study the electronic structure in oxides, molecular coordination complexes, as well as the S1 and S2 states of the oxygen-evolving complex (OEC) of photosystem II (PS II). The RIXS data yield two-dimensional plots that can be interpreted along the incident (absorption) energy or the energy transfer axis. The second energy dimension separates the pre-edge (predominantly 1s to 3d transitions) from the main K-edge, and a detailed analysis is thus possible. The 1s2p RIXS final-state electron configuration along the energy transfer axis is identical to conventional L-edge absorption spectroscopy, and the RIXS spectra are therefore sensitive to the Mn spin state. This new technique thus yields information on the electronic structure that is not accessible in conventional K-edge absorption spectroscopy. The line splittings can be understood within a ligand field multiplet model, i.e., (3d,3d) and (2p,3d) two-electron interactions are crucial to describe the spectral shapes in all systems. We propose to explain the shift of the K pre-edge absorption energy upon Mn oxidation in terms of the effective number of 3d electrons (fractional 3d orbital population). The spectral changes in the Mn 1s2p(3/2) RIXS spectra between the PS II S1 and S2 states are small compared to that of the oxides and two of the coordination complexes (Mn(III)(acac)3 and Mn(IV)(sal)2(bipy)). We conclude that the electron in the step from S1 to S2 is transferred from a strongly delocalized orbital.

Electrons↗

PubMed2003

L-edge X-ray absorption spectroscopy of non-heme iron sites: experimental determination of differential orbital covalency.

X-ray absorption spectroscopy has been utilized to obtain the L-edge multiplet spectra for a series of non-heme ferric and ferrous complexes. Using these data, a methodology for determining the total covalency and the differential orbital covalency (DOC), that is, differences in covalency in the different symmetry sets of the d orbitals, has been developed. The integrated L-edge intensity is proportional to the number of one-electron transition pathways to the unoccupied molecular orbitals as well as to the covalency of the iron site, which reduces the total L-edge intensity and redistributes intensity, producing shake-up satellites. Furthermore, differential orbital covalency leads to differences in intensity for the different symmetry sets of orbitals and, thus, further modifies the experimental spectra. The ligand field multiplet model commonly used to simulate L-edge spectra does not adequately reproduce the spectral features, especially the charge transfer satellites. The inclusion of charge transfer states with differences in covalency gives excellent fits to the data and experimental estimates of the different contributions of charge transfer shake-up pathways to the t(2g) and e(g) symmetry orbitals. The resulting experimentally determined DOC is compared to values calculated from density functional theory and used to understand chemical trends in high- and low-spin ferrous and ferric complexes with different covalent environments. The utility of this method toward problems in bioinorganic chemistry is discussed.

Absorptiometry, Photon↗

PubMed2002

Site-selective EXAFS in mixed-valence compounds using high-resolution fluorescence detection: a study of iron in Prussian Blue.

A quantitative analysis is presented for the site-selective Fe K-edge absorption spectra of Prussian Blue: Fe(4)[Fe(CN)(6)](3) x xH(2)O (x = 14-16). The site-selective spectra were recorded using high-resolution fluorescence detection of the K beta emission from a polycrystalline sample. The K beta fluorescence lines arising from the high-spin and low-spin sites are shifted in energy. Since the emission features partially overlap, fluorescence-detected absorption spectra using different emission energies represent different linear combinations of the pure high-spin and low-spin EXAFS. A numerical method was used to extract the individual site EXAFS spectra from the experimental data. The analysis yields a range of solutions. A unique solution can be obtained if homovalent model compounds are used to simulate the K beta fluorescence emission from the two Fe sites in Prussian Blue. EXAFS analysis of the range of spectra obtained in the numerical method yields almost identical interatomic distances for the different spectra while the Debye-Waller factors vary considerably. The distances obtained in the EXAFS fit correspond to the crystallographic distances.

Crystallography, X-Ray↗