Towards a black‐box for biological EXAFS data analysis. II. Automatic BioXAS Refinement and Analysis (ABRA)

In biological systems, X‐ray absorption spectroscopy (XAS) can determine structural details of metal binding sites with high resolution. Here a method enabling an automated analysis of the corresponding EXAFS data is presented, utilizing in addition to least‐squares refinement the prior knowledge about structural details and important fit parameters. A metal binding motif is characterized by the type of donor atoms and their bond lengths. These fit results are compared by bond valance sum analysis and target distances with established structures of metal binding sites. Other parameters such as the Debye–Waller factor and shift of the Fermi energy provide further insights into the quality of a fit. The introduction of mathematical criteria, their combination and calibration allows an automated analysis of XAS data as demonstrated for a number of examples. This presents a starting point for future applications to all kinds of systems studied by XAS and allows the algorithm to be transferred to data analysis in other fields.     

Osteopontin: A Uranium Phosphorylated Binding‐Site Characterization

Herein, we describe the structural investigation of one possible uranyl binding site inside a nonstructured protein. This approach couples spectroscopy, thermodynamics, and theoretical calculations (DFT) and studies the interaction of uranyl ions with a phosphopeptide, thus mimicking a possible osteopontin (OPN) hydroxyapatite growth‐inhibition site. Although thermodynamical aspects were investigated by using time‐resolved laser fluorescence spectroscopy (TRLFS) and isothermal titration calorimetry (ITC), structural characterization was performed by extended X‐ray absorption fine structure (EXAFS) at the U L_III‐edge combined with attenuated total reflection Fourier transform infrared (ATR‐FTIR) spectroscopy. From the vibrational and fluorescence spectra, several structural models of a UO₂²⁺/peptide complex were developed and subsequently refined by using theoretical calculations to fit the experimental EXAFS obtained. The structural effect of the pH value was also considered under acidic to moderately acidic conditions (pH 1.5–5.5). Most importantly, the uranyl/peptide coordination environment was similar to that of the native protein.     

Microstructural properties and local atomic structures of cobalt oxide nanoparticles synthesised by mechanical ball-milling process

In this study, facile preparation of pure and nano-sized cobalt oxides particles was achieved using low-cost mechanical ball-milling synthesis route. Microstructural and morphological properties of synthesised products were characterised by X-ray diffraction (XRD) and transmission electron microscopy (TEM) techniques. XRD results indicated that the fabricated samples composed of cubic pure phase CoO and Co₃O₄ nanocrystalline particles with an average crystallite size of 37.2 and 31.8 nm, respectively. TEM images showed that the resulting samples consisted of agglomerates of particles with average diameter of about 37.6 nm for CoO and 31.9 nm for Co₃O₄. Phase purity of the prepared samples was further investigated due to their promising technological applications. Local atomic structure properties of the prepared nanoparticles were probed using synchrotron radiation-based X-ray absorption spectroscopy (XAS) including X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). EXAFS data analysis further confirmed the formation of single-phase CoO and Co₃O₄ nanoparticles. In addition, structural properties of cobalt oxide nanoparticles were investigated by performing density functional theory calculations at B3LYP/TZVP level and Born–Oppenheimer molecular dynamics. Theoretical calculations for both prepared samples were found to be consistent with the experimental results derived from EXAFS analysis. Obtained results herein reveals that highly crystalline and pure phase CoO and Co₃O₄ nanoparticles can be synthesised using simple, inexpensive and eco-friendly ball-milling method for renewable energy applications involving fuel cells and water splitting devices.     

Extended X‐ray absorption fine structure and multiple‐scattering simulation of nickel dithiolene complexes Ni[S2C2(CF3)2]2n (n = −2, −1, 0) and an olefin adduct Ni[S2C2(CF3)2]2(1‐hexene)

A series of Ni dithiolene complexes Ni[S₂C₂(CF₃)]₂ⁿ (n = ?2, ?1, 0) ( 1 , 2 , 3 ) and a 1‐hexene adduct Ni[S₂C₂(CF₃)₂]₂(C₆H₁₂) ( 4 ) have been examined by Ni K‐edge X‐ray absorption near‐edge structure (XANES) and extended X‐ray absorption fine‐structure (EXAFS) spectroscopies. Ni XANES for 1 – 3 reveals clear pre‐edge features and approximately +0.7 eV shift in the Ni K‐edge position for `one‐electron' oxidation. EXAFS simulation shows that the Ni—S bond distances for 1 , 2 and 3 (2.11–2.16 Å) are within the typical values for square planar complexes and decrease by ～0.022 Å for each `one‐electron' oxidation. The changes in Ni K‐edge energy positions and Ni—S distances are consistent with the `non‐innocent' character of the dithiolene ligand. The Ni—C interactions at ～3.0 Å are analyzed and the multiple‐scattering parameters are also determined, leading to a better simulation for the overall EXAFS spectra. The 1‐hexene adduct 4 presents no pre‐edge feature, and its Ni K‐edge position shifts by ?0.8 eV in comparison with its starting dithiolene complex 3 . Consistently, EXAFS also showed that the Ni—S distances in 4 elongate by ～0.046 Å in comparison with 3 . The evidence confirms that the neutral complex is `reduced' upon addition of olefin, presumably by olefin donating the π‐electron density to the LUMO of 3 as suggested by UV/visible spectroscopy in the literature.     

X-ray absorption spectroscopy study and photocatalyst application of CuO and Cu0.9Ti0.1O nanoparticles

We report detailed investigations on the electronic structure and photocatalyst application of CuO and Cu_0.9Ti_0.1O nanoparticles (NPs). The NPs were prepared by co-precipitation method and subsequent annealing. Crystal structure and morphology of the NPs were investigated by synchrotron X-ray diffraction and high resolution transmission electron microscope, respectively. The local atomic structure around the Cu atoms was investigated by the extended X-ray absorption fine structure (EXAFS) at the Cu K-edge. Electronic structure determination was done using near edge X-ray absorption fine structure (NEXAFS) at the O K-edge, Cu L-edge, Cu K-edge and Ti L-edge. From the structural and electronic structure investigations, it is inferred that the Ti substitutes the Cu in CuO lattice without forming any secondary phases and the valence state of Cu is not affected by the Ti substitution; however the Cu – O bond length is found to be shorten in the Ti doped sample. As prepared NPs exhibit excellent photocatalyst application toward the degradation of methyl orange (MO) and potassium dichromate (PD) pollutant dyes under the visible light irradiation. The mechanism of the photodegradation of MO and PD pollutants, by the smaller sized CuO and larger sized Cu_0.9Ti_0.1O NPs, is briefly discussed.     

Sr(NO_3)_2·DCH18C6配合物晶体结构与辐射稳定性

二环己基-18-冠-6(DCH18C6)可以有效地从高放废液中分离90Sr,对于减小放射性废物的危害和实现高放废物的减容有重要意义.由于在实际应用中DCH18C6处于射线照射下,其结构可能会被破坏并引起络合能力的变化,因此有必要对该配合物的辐射稳定性进行研究.本文合成了Sr(NO3)2?DCH18C6配合物晶体,并通过单晶X射线衍射(XRD)与扩展X射线吸收精细结构谱(EXAFS)等方法进行了表征,确定Sr2+与周围氧原子的配位数为10,Sr―O平均键长约为0.268 nm/0.266 nm(XRD/EXAFS).配位原子来自DCH18C6的六个氧原子以及两个作为双齿配体的硝酸根的四个氧原子.对该配合物晶体在空气中进行γ辐照,EXAFS结果表明吸收剂量为400 kGy时,Sr―O键长及配位数没有发生变化,配位结构没有被破坏,具有很好的耐辐照稳定性.显微红外光谱(Micro-FTIR)结果进一步证明辐照后冠醚环的部分C―H键氧化为羟基或羰基,但并不影响DCH18C6与Sr2+的配位结构.     

Investigation of polynuclear Zr(IV) hydroxide complexes by nanoelectrospray mass-spectrometry combined with XAFS

Polynuclear species of zirconium in acidic aqueous solution are investigated by combining X-ray absorption spectroscopy (XAFS) and nanoelectrospray mass spectrometry (ESI-MS). Species distributions are measured between pH_C 0 and pH_C 3 for [Zr] = 1.5–10 mM. While the monomer remains a minor species, with increasing pH the degree of polymerization increases and the formation of tetramers, pentamers, octamers, and larger polymers is observed. The high resolution of the mass spectrometer permits the unambiguous determination of polynuclear zirconium hydroxide complexes by means of their isotopic patterns. The relative abundances of mononuclear and polynuclear species present simultaneously in solution are measured, even if one of the species contributes only 0.1% of the Zr concentration. For the first time it has been directly observed that the hydrolysis of polynuclear Zr species is a continuous process which leads to charge compensation through the sequential substitution of water molecules by hydroxide ligands until doubly charged polymers dominate at conditions (H⁺ and Zr concentrations) close to the solubility of Zr(OH)₄(am). The invasiveness of the electrospray process was minimized by using very mild declustering conditions, leaving the polynuclear species within a solvent shell of approximately 20 water molecules. Figure Schematic Diagram of Multiplexed Measurement of 9 Anti-Nuclear Antibodies Using the AtheNa Multilyte Assay     

镨叶绿素a分子结构的确定

通过合成镨叶绿素a(Pr-Chla)研究了稀土在叶绿素中的结合方式.Pr-Chla的紫外可见光谱(UV-Vis)、红外光谱(FTIR)证实镨离子已配位到叶绿素a的卟啉环上.其磁圆二色谱(MCD)在Soret带具有双层夹心卟啉的特征结构;通过扩展X射线吸收精细结构谱(EXAFS),采用双层夹心结构模型拟合,确定了Pr周围的近邻结构.表明合成镨叶绿素a具有双层夹心结构.Pr(Ⅲ)夹于两个卟啉环之间,与上下卟啉环上共8个N原子配位,Pr-N键平均键长0.242nm.     

Xas study of actinide solvent extraction compounds. ii: UO(NO)(L) (with L=tri-isobutylphosphate, tri-n-butylphosphate, trimethylphosphate and triphenylphosphate)

In the back-end of the nuclear fuel cycle, liquid–liquid extraction is the selected separation method. For an improved design of new extracting agent, the knowledge of the coordination polyhedra of the metal ions is important. In this paper, we investigated the coordination sphere of a series of uranyl complexes with selected organophosphorus extracting molecules: UO₂(NO₃)₂L₂ (with L=tri-iso-butylphosphate, tri-n-butylphosphate, trimethylphosphate and triphenylphosphate) using X-ray absorption spectroscopy. FEFF7 calculations of the EXAFS spectra corresponding to the model compound UO₂(NO₃)₂(TiBP)₂ (with TiBP=tri-iso-butylphosphate) for which the crystal structure is known led to a multiple scattering approach of the data fitting. EXAFS results show subtle U–O(P) bond distance differences between the different complexes that are discussed in terms of both electronic and steric effects of L. These results are discussed with regards to the extraction ability of L. In the same time, exploratory work has been attempted in order to evaluate U–O–P bond angle variations as a function of L using multiple photon-scattering paths. Satisfactory values have been obtained compared to the crystallographic data.     

MoCo/Y, MoNi/Y氮化物催化剂的结构和CH4+CO2重整反应性能

采用氨气还原法制备了NaY分子筛负载的MoCo/Y、MoNi／Y双组氮化物催化剂，用XRD和EXAFS方法征了样品的结构，并测定了其在CH4＋CO2重整反应中的活性，在氧化态时，MoCo/Y样品中主要存在CoMoO4和Co3O4两种物相，Mo的配位状态接近于CoMoO4，而Co的配位状态更接近于Co3O4，MoNi／Y样品中主要有NiMoO4和NiO两种物相，Mo的配位状态接近于MiMoO4，而Ni的配位状态可能是NiMoO4和NiO两种化合物中Ni配位状态的平均效果，Ni-Mo之间的朴素作用似乎比Co-Mo相对较强，在氮化态时，两种样品中Mo的配位状态较为相似，但即不同于MoO3，也不同于单组分γ－Mo2N.Co和Ni的配位状态都不同于各在氧化态下的状态，且都在相同的位置出现一个新强峰，这似乎表明MoCo和MoNi生成了结构相似的氮化物，在CH4＋CO2重整反应中，氮化态MoCO/Y和MoNi/Y的活性大大超过非负载单组分γ－Mo2N催化剂，其中MoNi/Y的活性相对更好一些，且活性随Ni含量增加而提高。