Gadolinium acetylacetonate tetraphenyl monoporphyrinate complex and some of its derivatives: EXAFS study and molecular dynamics simulation

Many attempts to obtain single crystals appropriate for X-ray diffraction analysis of the Ln(tpp)(acac) derivatives (where Ln = Gd or Sm, tpp = tetraphenylporphyrin and acac = acetylacetonate) have failed so far. A suitable way to get structural parameters for these monoporphyrinates is to use extended X-ray absorption fine structure (EXAFS) spectroscopy. We recorded spectra of the monoporphyrins, Ln(tpp)(acac) and Gd(tpyp)(acac) (where tpyp = tetrapyridylporphyrin), and the bisporphyrin GdH(tpyp)2 in the solid state. We particularly focused our structural analysis on Gd(tpp)(acac), applying both molecular modeling and EXAFS, which allowed us to get accurate results about the local environment of the central atom. The Gd3+ ion of the complex at room temperature was found to be bonded to four monoporphyrin nitrogen atoms at an average distance R(Gd-N(av)) = 2.48 A and to three or four oxygen atoms at R(Gd-O(ac,w)) = 2.38 A from an acetylacetonato anion and a water molecule. The presence of the second water molecule in the coordination sphere was barely discernible by EXAFS analysis. Molecular modeling has provided further information about the coordination core geometry of the Gd(tpp)(acac) monoporphyrinate, including a bishydrated coordination sphere. Also, it has enabled the construction of a 3D structural model on which multiple scattering analyses were attempted. Monte Carlo simulation was used to validate the adjustments. EXAFS spectra analysis was carried out on the derivatives, displaying slight distortions in the lanthanide central-atom coordination geometry.     

Local atomic structure of zinc selenide films: EXAFS data

This paper presents the results of our study of the structural state and local atomic structure of zinc selenide films obtained by thermal evaporation in supervacuum at condensation temperatures of ?150°C, 0, and 150°C. Structure-sensitive methods such as X-ray diffraction, atomic force microscopy, and EXAFS spectroscopy were used. The parameters of the local atomic environment (interatomic distances, coordination numbers) of zinc and selenium atoms were obtained by Fourier transformation.     

浓度及冷冻-解冻处理对CuCl_2水溶液中Cu~(2+)区域结构的影响

应用扩展X射线吸收精细结构(EXAFS)光谱研究了CuCl2水溶液中Cu2+的区域环境结构,通过测定CuCl2水溶液在不同浓度条件下及冷冻-解冻(FT)处理前后CuK边EXAFS吸收谱,研究了浓度及冷冻-解冻处理对Cu2+第一配位层结构的影响.EXAFS实验结果表明,CuCl2水溶液中Cu2+第一配位层距离中心原子Cu最近邻原子为O原子,配位数介于3.0-4.3之间,Cu—O键长在0.192-0.198nm之间,这种结构与Cu2+的Jahn-Teller效应有关.不同浓度的CuCl2水溶液中Cu2+的区域环境结构有很大不同,随着CuCl2水溶液浓度的升高,Cu2+第一配位层配位数减小,Cu—O键伸长.结构参数拟合结果证实冷冻-解冻处理对Cu2+的区域环境结构有影响,CuCl2溶液经冷冻-解冻处理后,Cu2+第一配位层配位数变大,热无序度增加.     

A theoretical and experimental study of lead substitution in calcium hydroxyapatite

Characterization of lead substitution for calcium in hydroxyapatite (CaHA) is carried out, using experimental techniques and Density Functional theoretical (DFT) analyses. Theoretical modeling is used to obtain information of the Pb chemical environment for occupancy at either Ca(I) or Ca(II) sites of CaHA. Effects of the larger ionic radius of Pb(+2) compared to Ca(+2) are apparent in embedded cluster calculations of local chemical bonding properties. DFT periodic planewave pseudopotential studies are used to provide first-principles predictions of local structural relaxation and site preference for Pb(x)Ca(10-x)HA over the composition range x< or = 6. General characteristics of the polycrystalline material are verified by X-ray diffraction and FTIR analysis, showing the presence of a single phase of CaHA structure. A short range structure around lead is proposed in order to interpret the Pb L-edge EXAFS spectrum of the solid solution Ca(6.6)Pb(3.4)HA. In this concentration we observe that lead mainly occupies Ca(II) sites; the EXAFS fit slightly favors Pb clustering, while theory indicates the importance of Pb-Pb avoidance on site (II).     

浓度及冷冻鄄解冻处理对CuCl2水溶液中Cu2+区域结构的影响

应用扩展X射线吸收精细结构(EXAFS)光谱研究了CuCl2水溶液中Cu2+的区域环境结构, 通过测定CuCl2水溶液在不同浓度条件下及冷冻-解冻(FT)处理前后Cu K边EXAFS 吸收谱, 研究了浓度及冷冻-解冻处理对Cu2+第一配位层结构的影响. EXAFS实验结果表明, CuCl2水溶液中Cu2+第一配位层距离中心原子Cu最近邻原子为O原子, 配位数介于3.0-4.3之间, Cu—O键长在0.192-0.198 nm 之间, 这种结构与Cu2+的Jahn-Teller效应有关. 不同浓度的CuCl2水溶液中Cu2+的区域环境结构有很大不同, 随着CuCl2水溶液浓度的升高, Cu2+第一配位层配位数减小, Cu—O键伸长. 结构参数拟合结果证实冷冻-解冻处理对Cu2+的区域环境结构有影响, CuCl2溶液经冷冻-解冻处理后, Cu2+第一配位层配位数变大, 热无序度增加.     

Geometric and electrostatic study of the [4Fe-4S] cluster of adenosine-5'-phosphosulfate reductase from broken symmetry density functional calculations and extended X-ray absorption fine structure spectroscopy

Adenosine-5'-phosphosulfate reductase (APSR) is an iron-sulfur protein that catalyzes the reduction of adenosine-5'-phosphosulfate (APS) to sulfite. APSR coordinates to a [4Fe-4S] cluster via a conserved CC-X(~80)-CXXC motif, and the cluster is essential for catalysis. Despite extensive functional, structural, and spectroscopic studies, the exact role of the iron-sulfur cluster in APS reduction remains unknown. To gain an understanding into the role of the cluster, density functional theory (DFT) analysis and extended X-ray fine structure spectroscopy (EXAFS) have been performed to reveal insights into the coordination, geometry, and electrostatics of the [4Fe-4S] cluster. X-ray absorption near-edge structure (XANES) data confirms that the cluster is in the [4Fe-4S](2+) state in both native and substrate-bound APSR while EXAFS data recorded at ~0.1 ? resolution indicates that there is no significant change in the structure of the [4Fe-4S] cluster between the native and substrate-bound forms of the protein. On the other hand, DFT calculations provide an insight into the subtle differences between the geometry of the cluster in the native and APS-bound forms of APSR. A comparison between models with and without the tandem cysteine pair coordination of the cluster suggests a role for the unique coordination in facilitating a compact geometric structure and "fine-tuning" the electronic structure to prevent reduction of the cluster. Further, calculations using models in which residue Lys144 is mutated to Ala confirm the finding that Lys144 serves as a crucial link in the interactions involving the [4Fe-4S] cluster and APS.     

钨的原子簇化合物研究(Ⅰ)——九氯二钨酸盐的EXAFS和单晶结构分析

在实验室转靶EXAFS装置上测定了钨原子簇化合物K₃W₂Cl₉,(NHD₄)₃W₂Cl₉,(Bu₄N)₃W₂Cl₉的阴离子结构.在ENRAF-NONIUSCAD-4四圆单晶衍射仪上测定了(NH₄)₃W₂Cl₉的晶体结构。在实验误差范围内,W₂Cl₉^3-结构的EXAFS结果与单晶结果符合较好。实验结果表明,在与不同的一价阳离子结合时,阴离子W₂Cl₉^3-仍保持双共面八面体的结构。由于其中强烈的W-W金属多重键结合,使得整个阴离子的骨架和键长都没有显著变化。     

Relationships between Hg(II)-S bond distance and Hg(II) coordination in thiolates

Extended X-ray absorption fine structure (EXAFS) spectroscopy is a sensitive structural probe of the coordination environments of Hg(II) with thiol (sulfhydryl) groups, and is equally applicable to solid and aqueous organic or inorganic matter. Information on the number and geometric arrangement of S ligands can be derived from metal-ligand distances because the distances vary with Hg stereochemistry and can be accurately measured by the EXAFS technique. To improve the reliability of determining coordination structures of Hg with thiol groups, correlations among Hg-S bond distance, Hg coordination, and S-Hg-S angle in homoleptic Hg(II)-thiolates were calculated from analysis of the structures of the 162 Hg(SR)n motifs (n = 2, 3, 4) contained in the Cambridge Structural Database v. 5.28. Graphical correlations of bond distance with coordination number and with bond angle show distinct ranges of values characteristic of specific structural configurations.     

X-Ray Absorption Spectroscopy of Strontium(II) Coordination

Detailed analyses of crystalline, hydrated, and precipitated strontium compounds and an aqueous strontium solution by synchrotron extended X-ray absorption fine structure (EXAFS) were used to quantify local thermal and static disorder and to characterize strontium coordination in a variety of oxygen-ligated bonding environments. Analysis of anharmonic vibrational disorder (i.e., significant contribution from a third cumulant term (C(3)) in the EXAFS phase-shift function) in compounds with low and high static disorder around strontium showed that first-shell anharmonic contributions were generally not significant above experimental error in the EXAFS fits (R+/-0.02 ? with and without C(3)). The only case in which a significant apparent decrease in Sr-O distance was observed with increasing temperature, and for which a third cumulant term was significant, was for dilute strontium in aqueous solution. Empirical parameterization of Debye-Waller factor (sigma(2)) for strontium compounds as a function of backscatterer atomic number (Z), interatomic Sr-Z distance, and temperature of spectral data collection showed systematic increases in sigma(2) as a function of increasing temperature and Sr-Z bond length. At values of sigma(2) greater than approximately 0.025 ?(2) (for N<12 and R(Sr)-Z>3 ?), backscattering was generally not significant above noise levels in spectra of compounds of known crystal structure. Comparison of the EXAFS spectra of freshly precipitated SrCO(3) (spectra collected wet) to that of dry, powdered strontianite (SrCO(3)(s)) indicated no significant differences in the local atomic structure around strontium. Analysis of partially hydrated strontium in natural Ca-zeolite (heulandite) showed that strontium is substituted only in the calcium (Ca2) site. Backscattering from aluminum and silicon atoms in the zeolite framework were apparent in the EXAFS spectra at low and room temperature at distances from central strontium of <4.2 ?. Comparison of strontium structural coordination determined in this and previous studies suggests that previous EXAFS determinations of hydrated strontium may have underestimated first-shell interatomic distances and coordination numbers because minor contributions to the EXAFS phase-shift and amplitude functions were not accounted for, either theoretically or empirically. Copyright 2000 Academic Press.     

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.     

Structure and temperature behavior of metallo-supramolecular assemblies

A detailed structural analysis of a Langmuir-Blodgett (LB) multilayer composed of a polyelectrolyte-amphiphile complex (PAC) is presented. The PAC is self-assembled from metal ions, ditopic bis-terpyridines, and amphiphiles. The vertical structure of the LB multilayer is investigated by X-ray reflectometry. The multilayer has a periodicity of 57 A, which corresponds to an architecture of flat lying metallo-supramolecular coordination polyelectrolyte (MEPE) rods and upright-standing amphiphiles (dihexadecyl phosphate, DHP). In-plane diffraction reveals hexagonal packing of the DHP molecules. Using extended X-ray absorption fine structure (EXAFS) experiments, we prove that the central metal ion is coordinated to the terpyridine moieties in a pseudo-octahedral coordination environment. The Fe-N bond distances are 1.82 and 2.0 A, respectively. Temperature resolved measurements indicate a reversible phase transition in a temperature range up to 55 degrees C. EXAFS measurements indicate a lengthening of the average Fe-N bond distance from 1.91 to 1.95 A. The widening of the coordination cage upon heating is expected to lower the ligand field stabilization, thus giving rise to spin transitions in these composite materials.     

硅胶担载四核羰基钴催化剂的EXAFS和IR研究

本文以透射法EXAFS和IR等手段研究了四核羰基钴金属簇Co_4(CO)_(10)(PPh)_2担载在SiO_2上以后及用于烯烃醛化反应前后的变化,确定了相应的结构参数并探讨了催化活性与结构的关系。     

Modeling Heterogeneity in UO2 Nanoparticles Using X-ray Absorption Spectroscopy

EXAFS provides the capability to interrogate nanoparticle (NP) structure in atomistic detail without relying on long-range crystallinity. There is a limitation in that EXAFS provides averaged structural information, making it difficult to separate a small amount of heterogeneous structure from bulk. In this work, models were developed to extract surface-specific information from conventional EXAFS measurements collected on UO₂ NPs of varying size. Specifically, the surface terminating species of UO₂ NPs was determined from comparison of coordination numbers with geometric models while the origin of static disorder was interrogated from user-defined simulations. Results show that the degree of oxygenation on the NP surface does not significantly deviate from bulk surface and that static disorder is highly enhanced in NP surface layers but cannot be attributed to surface relaxation effects alone. The approach described herein has the potential to be adapted to a range of inorganic NP systems to interrogate surface structure.     

Temperature Driven Transformation of the Flexible Metal–Organic Framework DUT-8(Ni)

DUT-8(Ni) metal–organic framework (MOF) belongs to the family of flexible pillared layer materials. The desolvated framework can be obtained in the open pore form (op) or in the closed pore form (cp), depending on the crystal size regime. In the present work, we report on the behaviour of desolvated DUT-8(Ni) at elevated temperatures. For both, op and cp variants, heating causes a structural transition, leading to a new, crystalline compound, containing two interpenetrated networks. The state of the framework before transition (op vs. cp) influences the transition temperature: the small particles of the op phase transform at significantly lower temperature in comparison to the macroparticles of the cp phase, transforming close to the decomposition temperature. The new compound, confined closed pore phase (ccp), was characterized by powder X-ray diffraction and spectroscopic techniques, such as IR, EXAFS, and positron annihilation lifetime spectroscopy (PALS). Thermal effects of structural transitions were studied using differential scanning calorimetry (DSC), showing an overall exothermic effect of the process, involving bond breaking and reformation. Theoretical calculations reveal the energetics, driving the observed temperature induced phase transition.     

Identification of molecules in inorganic compounds from X-ray or neutron diffraction data and correction of their structures on the basis of vibrational spectroscopy data

A method of identification of molecules in inorganic crystals with asymmetric M-X...M bridges has been suggested on the basis of analysis of interatomic distances in the structure unit M (−X...M) _n , which includes the atoms of the first and second coordination spheres. This analysis makes it possible to discern molecules (complex anions or cations) as a groups of atoms linked with each other by short M-X bonds, whereas the atoms of neighboring groups are linked by long M...X bonds. The symmetry of such a group is often lower than it follows from X-ray or neutron diffraction data. Studying vibrational spectra affords information on the true symmetry of a molecule. The use of the method is exemplified by the rhombohedral BaTiO₃ phase.     

Spectroscopic characterization of cobalt-containing mesoporous materials

Cobalt-containing mesoporous materials that have been prepared using different procedures have been comparatively characterized by transmission electron microscopy/energy-dispersive X-ray spectroscopy (TEM/EDS), extended X-ray absorption fine structure spectroscopy (EXAFS), X-ray absorption near edge spectroscopy (XANES), and ultraviolet-visible (UV-vis), near-infrared (NIR), and mid-infrared (mid-IR) spectroscopies, and the results provide new insights into the local environment and properties of cobalt in this type of material. TEM/EDS analyses have shown that tetraethyl orthosilicate (TEOS) may be less appropriate as a silicon source during the syntheses of cobalt-containing mesoporous materials, because the distribution of cobalt throughout the framework may become uneven. EXAFS has been determined to be the most suitable method for direct verification of framework incorporation, by identifying silicon as the backscatterer in the second shell. Such a direct verification may not be obtained using UV-vis spectroscopy. From EXAFS analyses, it is also possible to distinguish between surface-bound and framework-incorporated cobalt. There is a good agreement between the results obtained from XANES and UV-vis regarding the coordination symmetry of cobalt in the samples. The presence of cobalt in the silica framework has been determined to create Lewis acid sites, and these acid sites are suggested to be located at tetrahedral cobalt sites at the surface.     

XAS study on copper red in ancient glass beads from Thailand

Glass has been used in ornaments and decorations in Thailand for thousands of years, being discovered in several archeological sites and preserved in museums throughout the country. To date only a few of them have been examined by conventional methods for their compositions and colorations. In this work we report for the first time an advanced structural analysis of Thai ancient glass beads using synchrotron X-ray absorption spectroscopy (XAS) and energy-dispersive X-ray (EDX) spectrometry. Four samples of ancient glass beads were selected from four different archeological sites in three southern provinces (Ranong, Krabi and Pang-nga) of Thailand. Archaeological dating indicated that they were made more than 1,300 years ago. A historically known method for obtaining a red color is to add compounds containing transition elements such as gold, copper, and chromium. For our samples, EDX spectrometry data revealed existing fractions of iron, copper, zinc, and chromium in ascending order. Thus, copper was selectively studied by XAS as being potentially responsible for the red color in the glass beads. K-shell X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) of copper were recorded in fluorescence mode using an advanced 13-element germanium detector. Comparisons with XANES spectra of reference compounds identified two major forms of copper, monovalent copper and a metallic cluster, dispersed in the glass matrix. The cluster dimension was approximated on the basis of structural modeling and a theoretical XANES calculation. As a complement, EXAFS spectra were analyzed to determine the first-shell coordination around copper. XAS was proven to be an outstanding, advanced technique that can be applied to study nondestructively archaeological objects to understand their characteristics and how they were produced in ancient times.     

cis—Mo(DMF)_3Br_3异构体的晶体和分子结构

制得了cis—Mo(DMF)_3Br_3(DMF指N,N—二甲基甲酰胺)的一种异构体并用X射线三维衍射数据进行了晶体结构测定。晶体的空间群属Pca2_1。晶胞大小为a=20.157(4),b=13.950(4),c=13.142(4)。晶体的测量密度为2.02g/cm~3,与Z=8相符。结构用直接法-Fourier合成法解得,最终R因子为0.060。结构分析表明,晶体仍为cis-Mo(DMF)_3Br_3,分子中Mo周围的三个Br原子和三个DMF配位基的O原子仍按顺式排列成近八面体,但DMF的取向不规则。分子不再具有对称性。     

Metal Ion Coordination at the Water-Manganite (gamma-MnOOH) Interface

The local structure of Zn(II) adsorbed at the water-manganite (gamma-MnOOH) interface has been investigated by extended X-ray absorption fine structure (EXAFS) spectroscopy. Adsorption experiments were carried out within the pH range 6.17-9.87 and surface coverages of 0.9 to 9.7 μmol/m(2)cZn(II) coordination was observed to change from six to four as pH was increased. This was indicated by a change in Zn-O distance from 2.04 to 1.96 ? and by a decrease in the obtained coordination numbers. Two higher shells were detected at about 3.08 and 3.33 ?, at all pH values and surface coverage investigated. As the backscattering phase and amplitude functions of Mn and Zn are similar, we used structural and chemical considerations to assign the backscattering at 3.08 ? to Mn neighbors, and the one at 3.33 ? to Zn atoms. Indeed the size of the Zn polyhedra, especially of ZnO(4), does not quite match the structure of the manganite surface. We conclude that Zn(II) forms multinuclear hydroxo-complexes or a zinc hydroxide phase at the surface, as it might be easier for an additional Zn(II) to bond to an already sorbed Zn. These results were compared to our previous EXAFS study of Cd(II) adsorption onto manganite, where mononuclear inner-sphere complexes bound to the surface via edges were found. Copyright 2000 Academic Press.