Determination Of Site Occupancy Research Articles

Development of a new methodology for site distribution determination by powder diffraction with anomalous scattering using focused beam and flat shape sample geometry

A new methodology of synchrotron powder diffraction with anomalous scattering for site occupancy determination has been examined. We have been developing a new Synchrotron powder diffraction geometry with focused X-ray beam, flat shape sample and area detectors. As an application of the geometry, a new methodology for site occupancy determination has been tried. The diffraction intensity ratio change against X-ray energy near an absorption edge was observed and was compared with the calculation obtained from various site distribution crystal structure models. The methodology has been successfully applied for site distribution determination of In atom in β-(Ga,In)2O3 crystal. The new methodology can obtain diffraction intensity without approximation in absorption correction and can eliminate preferred orientation effect. By the combination of these features the new methodology can be a new application of synchrotron powder diffraction with anomalous scattering.

Determination of site occupancy of boron in 6H–SiC by multiple-wavelength neutron holography

The local structure around boron doped in 6H-type silicon carbide (SiC) was investigated using neutron holography. Three-dimensional atomic images reconstructed from multiple-wavelength holograms revealed the boron substitution for both silicon and carbon. To determine boron locations accurately, we calculated holograms with varying occupancies of six different sites and fit image intensities with those obtained from experimental holograms by the steepest descent method. As a result, it was found that boron atoms were selectively located at the Si–C-cubic site layer. Furthermore, boundaries right above the boron locations were suggested from the absence of atomic images in the upper region of reconstruction.

Enhanced magnetization of ultrathin NiFe2O4 films on SrTiO3(001) related to cation disorder and anomalous strain

NiFe$_2$O$_4$ thin films with varying thickness were grown on SrTiO$_3$(001) by reactive molecular beam epitaxy. Soft and hard x-ray photoelectron spectroscopy measurements reveal a homogeneous cation distribution throughout the whole film with stoichiometric Ni:Fe ratios of 1:2 independent of the film thickness. Low energy electron diffraction and high resolution (grazing incidence) x-ray diffraction in addition to x-ray reflectivity experiments were conducted to obtain information of the film surface and bulk structure, respectively. For ultrathin films up to 7.3 nm, lateral tensile and vertical compressive strain is observed, contradicting an adaption at the interface of NiFe$_2$O$_4$ film and substrate lattice. The applied strain is accompanied by an increased lateral defect density, which is decaying for relaxed thicker films and attributed to the growth of lateral grains. Determination of cationic site occupancies in the inverse spinel structure by analysis of site sensitive diffraction peaks reveals low tetrahedral occupancies for thin, strained NiFe$_2$O$_4$ films, resulting in partial presence of deficient rock salt like structures. These structures are assumed to be responsible for the enhanced magnetization of up to $\sim$250\% of the NiFe$_2$O$_4$ bulk magnetization as observed by superconducting quantum interference device magnetometry for ultrathin films below 7.3 nm thickness.

Interstitial hydrogen atoms in face-centered cubic iron in the Earth\u2019s core

Hydrogen is likely one of the light elements in the Earth’s core. Despite its importance, no direct observation has been made of hydrogen in an iron lattice at high pressure. We made the first direct determination of site occupancy and volume of interstitial hydrogen in a face-centered cubic (fcc) iron lattice up to 12 GPa and 1200 K using the in situ neutron diffraction method. The transition temperatures from the body-centered cubic and the double-hexagonal close-packed phases to the fcc phase were higher than reported previously. At pressures <5 GPa, the hydrogen content in the fcc iron hydride lattice (x) was small at x < 0.3, but increased to x > 0.8 with increasing pressure. Hydrogen atoms occupy both octahedral (O) and tetrahedral (T) sites; typically 0.870(±0.047) in O-sites and 0.057(±0.035) in T-sites at 12 GPa and 1200 K. The fcc lattice expanded approximately linearly at a rate of 2.22(±0.36) Å3 per hydrogen atom, which is higher than previously estimated (1.9 Å3/H). The lattice expansion by hydrogen dissolution was negligibly dependent on pressure. The large lattice expansion by interstitial hydrogen reduced the estimated hydrogen content in the Earth’s core that accounted for the density deficit of the core. The revised analyses indicate that whole core may contain hydrogen of 80(±31) times of the ocean mass with 79(±30) and 0.8(±0.3) ocean mass for the outer and inner cores, respectively.

Extending the limits of powder diffraction analysis: Diffraction parameter space, occupancy defects, and atomic form factors.

Although the determination of site occupancies is often a major goal in Rietveld refinement studies, the accurate refinement of site occupancies is exceptionally challenging due to many correlations and systematic errors that have a hidden impact on the final refined occupancy parameters. Through the comparison of results independently obtained from neutron and synchrotron powder diffraction, improved approaches capable of detecting occupancy defects with an exceptional sensitivity of 0.1% (absolute) in the class of layered NMC (Li[NixMnyCoz]O2) Li-ion battery cathode materials have been developed. A new method of visualizing the diffraction parameter space associated with crystallographic site scattering power through the use of f* diagrams is described, and this method is broadly applicable to ternary compounds. The f* diagrams allow the global minimum fit to be easily identified and also permit a robust determination of the number and types of occupancy defects within a structure. Through a comparison of neutron and X-ray diffraction results, a systematic error in the synchrotron results was identified using f* diagrams for a series of NMC compounds. Using neutron diffraction data as a reference, this error was shown to specifically result from problems associated with the neutral oxygen X-ray atomic form factor and could be eliminated by using the ionic O2- form factor for this anion while retaining the neutral form factors for cationic species. The f* diagram method offers a new opportunity to experimentally assess the quality of atomic form factors through powder diffraction studies on chemically related multi-component compounds.

Intracrystalline “geothermometry” assessed on clino and orthopyroxene bearing synthetic rocks

Recent discussion on the application of intracrystalline “geothermometers” based on the Fe–Mg order-disorder reaction in pyroxene in natural rocks, indicates that the available calibration equations for clino and orthopyroxenes (cpx and opx), which express the equilibrium intracrystalline Fe–Mg distribution coefficient kD(Fe–Mg) as a function of temperature, require independent validation.In this paper, we tested the available experimental calibrations for clino and orthopyroxenes by determining the site occupancies of these minerals in synthetic samples grown from a hydrous nepheline basanite in a piston-cylinder apparatus at 1050 °C at 2.0 GPa to 1170 °C at 3.0 GPa, and quenched very rapidly by shutting off the power. The site occupancies were determined by single crystal X-ray diffraction (SC-XRD) and used to calculate the closure temperature, TC, of cation ordering using available calibrations of kD(Fe–Mg) vs. T. The calculated TC values of both clino and orthopyroxenes were found to be close to the temperatures at which they were quenched, in line with expected kinetic behavior, when calibrations for cpx (Murri et al., 2016) and opx (Stimpfl et al., 2005) based on SC-XRD structure refinements were used. In particular, the smallest discrepancy between calculated and actual temperature is of the order of a few degrees (12 °C for cpx and 4 °C for opx), and the largest is of the order of tens of degrees (22 °C for cpx and 55 °C for opx). On the other hand, much lower TCs were obtained when calibrations based on Mössbauer determination of site occupancies were used.These results confirm that the two methods (i.e. SC-XRD and Mössbauer) give inherently different site occupancy data and that the same methodology should thus be used for both calibration and natural samples in the determination of cooling rate of host rocks.

Carbohydrate composition and site-occupancy determination in pituitary and recombinant preparations of human thyrotropin

Carbohydrate composition and site-occupancy determination in pituitary and recombinant preparations of human thyrotropin

N-Glycoprofiling Analysis for Carbohydrate Composition and Site-Occupancy Determination in a Poly-Glycosylated Protein: Human Thyrotropin of Different Origins

Human thyrotropin (hTSH) is a glycoprotein with three potential glycosylation sites: two in the α-subunit and one in the β-subunit. These sites are not always occupied and occupancy is frequently neglected in glycoprotein characterization, even though it is related to folding, trafficking, initiation of inflammation and host defense, as well as congenital disorders of glycosylation (CDG). For the first time N-glycoprofiling analysis was applied to the site-occupancy determination of two native pituitary hTSH, in comparison with three recombinant preparations of hTSH, a widely used biopharmaceutical. A single methodology provided the: (i) average N-glycan mass; (ii) mass fraction of each monosaccharide and of sulfate; and (iii) percent carbohydrate. The results indicate that the occupancy (65%–87%) and carbohydrate mass (12%–19%) can be up to 34%–57% higher in recombinant hormones. The average glycan mass is 24% lower in pituitary hTSH and contains ~3-fold fewer moles of galactose (p < 0.005) and sialic acid (p < 0.01). One of the two native preparations, which had the smallest glycan mass together with the lowest occupancy and GalNAc, sulfate, Gal and sialic acid contents, also presented the lowest in vivo bioactivity and circulatory half-life. The methodology described, comparing a recombinant biopharmaceutical to its native equivalent, can be applied to any physiologically or clinical relevant glycoprotein.

Structure refinement using precession electron diffraction tomography and dynamical diffraction: tests on experimental data.

The recently published method for the structure refinement from three-dimensional precession electron diffraction data using dynamical diffraction theory [Palatinus et al. (2015). Acta Cryst. A71, 235-244] has been applied to a set of experimental data sets from five different samples - Ni2Si, PrVO3, kaolinite, orthopyroxene and mayenite. The data were measured on different instruments and with variable precession angles. For each sample a reliable reference structure was available. A large series of tests revealed that the method provides structure models with an average error in atomic positions typically between 0.01 and 0.02 Å. The obtained structure models are significantly more accurate than models obtained by refinement using kinematical approximation for the calculation of model intensities. The method also allows a reliable determination of site occupancies and determination of absolute structure. Based on the extensive tests, an optimal set of the parameters for the method is proposed.

Influence of the X-site composition on tourmaline’s crystal structure: investigation of synthetic K-dravite, dravite, oxy-uvite, and magnesio-foitite using SREF and Raman spectroscopy

The crystal structures of synthetic K-dravite [XKYMg 3 Z Al 6 T Si6O18(BO3) 3 V (OH) 3 W (OH)], dravite [XNaYMg 3 Z Al 6 T Si6O18(BO3) 3 V (OH) 3 W (OH)], oxy-uvite [XCaYMg 3 Z Al 6 T Si6O18(BO3) 3 V (OH) 3 W O], and magnesio-foitite [X☐Y(Mg2Al)ZAl 6 T Si6O18(BO3) 3 V (OH) 3 W (OH)] are investigated by polarized Raman spectroscopy, single-crystal structure refinement (SREF), and powder X-ray diffraction. The use of compositionally simple tourmalines characterized by electron microprobe analysis facilitates the determination of site occupancy in the SREF and band assignment in the Raman spectra. The synthesized K-dravite, oxy-uvite, and magnesio-foitite have significant Mg–Al disorder between their octahedral sites indicated by their respective average 〈Y–O〉 and 〈Z–O〉 bond lengths. The Y- and Z-site compositions of oxy-uvite (YMg1.52Al1.48(10) and ZAl4.90Mg1.10(15)) and magnesio-foitite (YAl1.62Mg1.38(18) and ZAl4.92Mg1.08(24)) are refined from the electron densities at each site. The Mg–Al ratio of the Y and Z sites is also determined from the relative integrated peak intensities of the Raman bands in the O–H stretching vibrational range (3250–3850 cm−1), producing values in good agreement with the SREF data. The unit cell volume of tourmaline increases from magnesio-foitite (1558.4(3) A3) to dravite (1569.5(4)–1571.7(3) A3) to oxy-uvite (1572.4(2) A3) to K-dravite (1588.1(2) A3), mainly due to lengthening of the crystallographic c-axis. The increase in the size of the X-site coordination polyhedron from dravite (Na) to K-dravite (K) is accommodated locally in the crystal structure, resulting in the shortening of the neighboring O1–H1 bond. In oxy-uvite, Ca2+ is locally associated with a deprotonated W (O1) site, whereas vacant X sites are neighbored by protonated W (O1) sites. Increasing the size of the X-site-occupying ion does not detectably affect bonding between the other sites; however, the higher charge of Ca and the deprotonated W (O1) site in oxy-uvite are correlated to changes in the lattice vibration Raman spectrum (100–1200 cm−1), particularly for bands assigned to the T 6O18 ring. The Raman spectrum of magnesio-foitite shows significant deviations from those of K-dravite, dravite, and oxy-uvite in both the lattice and O–H stretching vibrational ranges (100–1200 and 3250–3850 cm−1, respectively). The vacant X site is correlated with long- and short-range changes in the crystal structure, i.e., deformation of the T 6O18 ring and lengthening of the O1–H1 and O3–H3 bonds. However, X-site vacancies in K-dravite, dravite, and oxy-uvite result only in the lengthening of the neighboring O1–H1 bond and do not result in identifiable changes in the lattice-bonding environment.

Determination of solute site occupancies within γ′ precipitates in nickel-base superalloys via orientation-specific atom probe tomography

The analytical limitations in atom probe tomography such as resolving a desired set of atomic planes, for solving complex materials science problems, have been overcome by employing a well-developed unique and reproducible crystallographic technique, involving synergetic coupling of orientation microscopy with atom probe tomography. The crystallographic information in atom probe reconstructions has been utilized to determine the solute site occupancies in Ni–Al–Cr based superalloys accurately. The structural information in atom probe reveals that both Al and Cr occupy the same sub-lattice within the L12-ordered γ′ precipitates to form Ni3(Al,Cr) precipitates in a Ni–14Al–7Cr (at%) alloy. Interestingly, the addition of Co, which is a solid solution strengthener, to a Ni–14Al–7Cr alloy results in the partial reversal of Al site occupancy within γ′ precipitates to form (Ni,Al)3(Al,Cr,Co) precipitates. This unique evidence of reversal of Al site occupancy, resulting from the introduction of other solutes within the ordered structures, gives insights into the relative energetics of different sub-lattice sites when occupied by different solutes.

The SNO/SOH TMT strategy for combinatorial analysis of reversible cysteine oxidations.

SNO/SOH TMT strategy outperforms other available strategies for cysteine oxidation analysis. It provides quantitative profiling of S-nitrosylation and S-sulfenylation changes simultaneously in two experimental conditions. It allows correction of modification levels by protein abundance changes and determination of relative modification site occupancy - all in a single nLC-MSMS experiment based on commercially available reagents. The method has proven precise and sensitive enough to detect and quantify endogenous levels of oxidative stress on proteome-wide scale.

Determination of deuterium site occupancy in ZrCoD3 and its role in improved durability of Zr–Co–Ni deuterides against disproportionation

In the present study, we have for the first time reported the occupancy of deuterium in a new interstitial site of ZrCoD3 which explain the hydrogen induced disproportionation behavior of ZrCo alloy. We have also reported the effect of Ni substitution on interstitial site occupancy of deuterium in ZrCo1−xNixD3, which in turn explains the improved durability of these Ni substituted deuterides against disproportionation. The crystal structure of the ZrCo1−xNix (x = 0.0, 0.1, 0.2, 0.3) deuterides was investigated by X-ray powder diffraction and neutron diffraction methods. The XRD data reveals a single phase formation for all deuterides with varying Ni content (x). The neutron diffraction study shows that deuterium occupies a new site 8e in addition to 4c2 and 8f1. Additionally, the Zr–D distance in 8e site is shorter than that in ZrD2. Therefore, increase in 8e site occupancy will in turn decreases the durability against disproportionation and vice-versa. Furthermore, the neutron diffraction reveals that occupancy of new 8e site decreases and its Zr–D distance increases with increase in Ni content, which explicate the higher durability against disproportionation for Ni rich compound.

State-Dependent Etomidate Occupancy of Its Allosteric Agonist Sites Measured in a Cysteine-Substituted GABAA Receptor

A central axiom of ligand-receptor theory is that agonists bind more tightly to active than to inactive receptors. However, measuring agonist affinity in inactive receptors is confounded by concomitant activation. We identified a cysteine substituted mutant γ-aminobutyric acid type A (GABAA) receptor with unique characteristics allowing the determination of allosteric agonist site occupancy in both inactive and active receptors. Etomidate, the allosteric agonist, is an anesthetic that activates or modulates α1β2γ2L GABAA receptors via transmembrane sites near β2M286 residues in M3 domains. Voltage-clamp electrophysiology studies of α1β2M286Cγ2L receptors show that GABA is an efficacious agonist and that etomidate modulates GABA-activated activity, but direct etomidate agonism is absent. Quantitative analysis of mutant activity using an established Monod-Wyman-Changeux (MWC) allosteric model indicates that the intrinsic efficacy of etomidate, defined as its relative affinity for active versus inactive receptors, is lower than in wild-type receptors. Para-chloromercuribenzene sulfonate covalently modifies β2M286C side-chain sulfhydryls, irreversibly altering GABA-induced currents. Etomidate concentration dependently reduces the apparent rate of β2M286C-pCMBS bond formation, tracked electrophysiologically. High etomidate concentrations completely protect the β2M286C suflhydryl from covalent modification, suggesting close steric interactions. The 50% protective etomidate concentration (PC50) is 14 μM in inactive receptors and 1.1 to 2.2 μM during GABA-activation, experimentally demonstrating that activated receptors bind etomidate more avidly than do inactive receptors. The experimental PC50 values are remarkably close to, and therefore validate, MWC model predictions for etomidate dissociation constants in both inactive and active receptors. Our results support MWC models as valid frameworks for understanding the agonism, coagonism, and modulation of ligand-gated ion channels.

Site occupancy determination of Eu/Y doped in Ca 2SnO 4 phosphor by electron channeling microanalysis

Energy-dispersive X-ray analysis based on electron channeling effects in transmission electron microscopy (TEM) was performed on Ca 2SnO 4 phosphor materials doped with Eu 3+/Y 3+ at various concentrations, which showed red photoluminescence associated with the Eu 3+ 5D 0– 7F 2 electric dipole transition. The method provided direct information on which host element site impurity elements occupy. The local atomic configurations and chemical bonding states associated with dopant impurities with different ionic radii were also examined by TEM–electron energy-loss spectroscopy (TEM–EELS).

Quantitative determination of site occupancy of multi-rare-earth elements doped into Ca 2SnO 4 phosphor by electron channeling microanalysis

[Display omitted] The composition of Ca 1.8Eu 0.2Y 0.2Sn 0.8O 4 determined by electron channeling microanalysis is graphically shown, where the rare-earth dopants, Eu and Y preferentially occupy the Ca and Sn sites, respectively, to maintain the local charge neutrality.

Determination of site occupancies by the intermeasurement minimization method. I. Anomalous scattering usage for noncentrosymmetric crystals

New methods for the determination of site occupancy factors are described. The methods are based on the analysis of differences between intensities of Friedel reflections in noncentrosymmetric crystals. In the first method (Anomalous-Expert) the site occupancy factor is determined by the condition that it is identical for two data sets: (1) initial data without averaging of Friedel intensities and (2) data that are averaged on Friedel pairs after the reduction of the anomalous scattering contribution. In the second method (anomalous anisotropic intermeasurement minimization method, Anomalous-AniMMM) the site occupancy factor is refined to satisfy the condition that the differences between the intensities of Friedel reflections that are reduced on the anomalous scattering contribution must be minimal. The methods were checked for three samples of RbTi1−xZrxOPO4crystals (A,BandC) with KTiOPO4structure, at 295 and 105 K (five experimental data sets). Microprobe measurements yield compositionsxA,B= 0.034 (5) andxC= 0.022 (4). The corresponding site occupancy factors areQA,B= 0.932 (10) andQC= 0.956 (8). Using Anomalous-AniMMM and three independent refinements for the first and second samples, the initial occupancy factor ofQA,B= 0.963 (15) was improved toQA,B= 0.938 (7). Of the three room-temperature data sets, one was improved toQA,B= 0.934 (2). For the third sample and one data set, the initial occupancy factor ofQC= 1.000 was improved toQC= 0.956 (1). The methods improve the Hirshfeld rigid-bond test. It is discussed how the description of chemical bonding influences the site occupancy factor.

Direct determination of cation site occupancies in natural ferrite spinels by L2,3 X-ray absorption spectroscopy and X-ray magnetic circular dichroism

Cation distributions in natural ferrite spinels, some containing large amounts of Mg, Ti, Mn, and Zn, have been investigated using the element-, site-, and symmetry-selective spectroscopic techniques of L 2,3 X-ray absorption spectroscopy (XAS) and X-ray magnetic circular dichroism (XMCD). By comparing XMCD data with calculated spectra, the site occupancies of the Fe cations have been determined. From the analysis of natural ferrite spinels with formulae very close to that of pure magnetite (Fe 3 O 4 ), a standard XMCD spectrum for natural magnetite is proposed. Magnetites with small numbers of cation vacancies due to oxidation (solid solutions with maghemite, γ-Fe 2 O 3 ) show that all the vacancies occur in octahedral sites. Ti L 2,3 XAS of oxidized Ti-bearing magnetites (hereafter referred to titanomagnetites) shows that Ti is tetravalent occurring on the octahedral site with 10Dq ~2eV; Fe L 2,3 XMCD spectra indicate that the vacancies occur in both tetrahedral and octahedral sites. Mn L 2,3 XAS of the Mn-rich ferrite spinels shows that Mn is predominantly ordered onto the tetrahedral site with an Mn 2+ :Mn 3+ ratio of 0.85:0.15. Mn- and Zn-rich ferrite spinels have an excess of cations over 3.0 per 4-oxygen formula unit. The sign of the XMCD for Mn corresponds to a parallel alignment of the Mn moments with the Fe 3+ moments in the tetrahedral sublattice. This work demonstrates clearly that combined XAS and XMCD provides direct information on the distribution of multivalent cations in chemically complex magnetic spinels.

SITE OCCUPANCY OF Co AND Ni IN ERYTHRITE ANNABERGITE SOLID SOLUTIONS DEDUCED BY VIBRATIONAL SPECTROSCOPY

Members of the solid-solution series between erythrite [Co3(AsO4)2·8H2O] and annabergite [Ni3(AsO4)2·8H2O] were synthesized and studied by a combination of X-ray diffraction, scanning electron microscopy, and Raman and infrared spectroscopy. The solid solution is complete, with the space group C2/m (monoclinic) being retained throughout. The unit-cell parameters decrease in size along all crystallographic directions as the amount of Ni increases. The β angle in the unit cell also decreases from 105.05(1)° (erythrite) to 104.90(1)° (annabergite). Crystals of annabergite and samples with a high Ni content are elongate along the a axis, and contrast with crystals of erythrite and Co-rich samples, which are elongate along c. In the Raman and infrared spectra of the synthetic samples, the band positions shift in accordance with the increase in bond strength associated with the decrease in the unit-cell parameters. Trends in positions of the antisymmetric arsenate stretching vibrations in the Raman spectra are sensitive to the site occupancy of metal ions in the structure. Changes in the crystal morphology, unit-cell parameters and vibrational spectra have been rationalized in terms of the site occupancy of Co and Ni in the structure. Substitution of Ni is directed to metal site 1 (C 2h site symmetry), whereas Co is directed to metal site 2 (C 2 site symmetry). Raman spectroscopy has proved to be useful for the determination of site occupancy of metal ions in solid solutions of minerals.

Analysis of O‐glycosylation site occupancy in bovine κ‐casein glycoforms separated by two‐dimensional gel electrophoresis

The ability of two-dimensional gel electrophoresis (2-DE) to separate glycoproteins was exploited to separate distinct glycoforms of kappa-casein that differed only in the number of O-glycans that were attached. To determine where the glycans were attached, the individual glycoforms were digested in-gel with pepsin and the released glycopeptides were identified from characteristic sugar ions in the tandem mass spectrometry (MS) spectra. The O-glycosylation sites were identified by tandem MS after replacement of the glycans with ammonia / aminoethanethiol. The results showed that glycans were not randomly distributed among the five potential glycosylation sites in kappa-casein. Rather, glycosylation of the monoglycoform could only be detected at a single site, T152. Similarly the diglycoform appeared to be modified exclusively at T152 and T163, while the triglycoform was modified at T152, T163 and T154. While low levels of glycosylation at other sites cannot be excluded the hierarchy of site occupation between glycoforms was clearly evident and argues for an ordered addition of glycans to the protein. Since all five potential O-glycosylation sites can be glycosylated in vivo, it would appear that certain sites remain latent until other sites are occupied. The determination of glycosylation site occupancy in individual glycoforms separated by 2-DE revealed a distinct pattern of in vivo glycosylation that has not been recognized previously.