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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2010

Neutron Diffraction Investigation of Langanite Crystals

The upper and lower parts of a single crystal with a nominal composition La{sub 3}Ga{sub 5.5}Nb{sub 0.5}O{sub 14}grown by the Czochralski method (Ir crucible, 99%Ar + 1%O{sub 2}, growth direction) have been studied by neutron diffraction for the first time. The compositions of the upper and lower parts are found to differ ((La{sub 2.935(2)}{open_square}{sub 0.065})(Ga{sub 0.450}Nb{sub 0.550(3)})Ga{sub 3}(Ga{sub 1.965(4)} {open_square}{sub 0.035})(O{sub 13.90(1)} {open_square}{sub 0.10}) and (La{sub 2.940(1)} {open_square}{sub 0.060})(Ga{sub 0.590}Nb{sub 0.410(2)})Ga{sub 5}(O{sub 13.82(1)} {open_square}{sub 0.18}), respectively), and microtwin formation was observed in the upper part, with two unit cells related by the translation 1/2Z. Based on a comparison of the refined crystal composition and optical transmission spectra, the absorption bands at 30 000, 24 500, and 20 500 cm{sub -1} were assigned to divacancies (2 V{sub La}{sup '''}, 3 V{sub O}{sup ..}), oxygen vacancies, and color centers, respectively. A relationship between the crystal color and oxygen content is established.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

The incommensurately modulated structures of low-temperature labradorite feldspars: a single-crystal X-ray and neutron diffraction study

Labradorite feldspars of the plagioclase solid solution series have been known for their complicated subsolidus phase relations and enigmatic incommensurately modulated structures. Characterized by the irrationally indexed e -reflections in the diffraction pattern, e -labradorite shows the largest variation in the incommensurate ordering states among the e -plagioclase structures. The strongly ordered low-temperature e -labradorite is one of the last missing pieces of the e -plagioclase puzzle. Nine plutonic and metamorphic labradorite feldspar samples from Canada, Ukraine, Minnesota (USA), Tanzania and Greenland with compositions ranging from An 52.5 to An 68 were studied with single-crystal X-ray diffraction. Two crystals from Labrador, Canada, and Duluth, MN, USA, with wide enough twin lamellae were analyzed with single-crystal neutron diffraction. The incommensurately modulated structures of e -plagioclase are refined for the first time with neutron diffraction data, which confirmed that the T—O distance modulation in the low-temperature e -plagioclase results from the Al–Si ordering in the framework. Detailed configurations of the M site are also observed in the structures refined from neutron diffraction data, which were not possible to see with X-ray diffraction data. The relation between the q -vectors and the mole% An composition is revealed for the entire compositional range of e -plagioclase, from An 25 to An 75 . The previously proposed two-trend relation depending on the cooling rate and phase transition path is confirmed. A new classification of e -plagioclase ( e α , e β and e γ ) is proposed based on the q -vector of the structure, which makes it an independent character from the presence/absence of density modulation. New parameters are proposed to quantify the ordering states of these complicated aperiodic structures of e -plagioclases, such as the difference between $\langle$T 1 o—O$\rangle$ and $\langle$T 1 m—O$\rangle$ at phase t = 0.2 or the normalized intensity of the (071\bar 1) reflection.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Cesium vacancy ordering in phase-separated C s x F e 2 - y S e 2

By simultaneously displaying magnetism and superconductivity in a single phase, the iron-based superconductors provide a model system for the study of magnetism's role in superconductivity. The class of intercalated iron selenide superconductors is unique among these in having the additional property of phase separation and coexistence of two distinct phases—one majority phase with iron vacancy ordering and strong antiferromagnetism, and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfully synthesized separate from the majority phase. In order to better understand this minority phase, a series of high-quality Cs x Fe 2–y Se 2 single crystals with (0.8 ≤ x ≤ 1;0 ≤ y ≤ 0.3) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show that the average I4/mmm structure of the minority phase is distinctly different from the high-temperature I4/mmm parent structure. Moreover, single-crystal diffraction reveals the presence of discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from three-dimensional Cs vacancy ordering. This model predicts a 25% vacancy of the Cs site in the minority phase which is consistent with the site's refined occupancy. Magnetization measurements performed in tandem with neutron single-crystal diffraction provide evidence that the minority phase is the host of superconductivity. Lastly, our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the nominal valence of iron.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Crystallization and X-ray diffraction analysis of the HMG domain of the chondrogenesis master regulator Sox9 in complex with a ChIP-Seq-identified DNA element

Sox9 is a fundamental sex-determining gene and the master regulator of chondrogenesis, and is involved in the development of various vital organs such as testes, kidney, heart and brain, and in skeletal development. Similar to other known Sox transcription factors, Sox9 recognizes and binds DNA with the consensus sequence C(T/A)TTG(T/A)(T/A) through the highly conserved HMG domain. Nonetheless, the molecular basis of the functional specificity of Sox9 in key developmental processes is still unclear. As an initial step towards a mechanistic understanding of Sox9 transcriptional regulation, the current work describes the details of the purification of the mouse Sox9 HMG domain (mSox9HMG), its crystallization in complex with a ChIP-Seq-identified FOXP2 promoter DNA element and the X-ray diffraction data analysis of this complex. The mSox9HMG–FOXP2 promoter DNA complex was crystallized by the hanging-drop vapour-diffusion method using 20% PEG 3350 in 200 m M sodium/potassium phosphate with 100 m M bis-tris propane at pH 8.5. The crystals diffracted to 2.7 Å resolution and the complex crystallized in the tetragonal space group P 4 1 2 1 2, with unit-cell parameters a = b = 99.49, c = 45.89 Å. Crystal-packing parameters revealed that asymmetric unit contained one mSox9HMG–FOXP2 promoter DNA complex with an estimated solvent content of 64%.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination

Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting of individual crystals. We validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Emergence of the isotropic Kitaev honeycomb lattice $α$–RuCl 3 and its magnetic properties

Here, we present a comprehensive investigation of the crystal and magnetic structures of the van der Waals antiferromagnet $α$–RuCl 3 using single crystal x-ray and neutron diffraction. The crystal structure at room temperature is a monoclinic (C2/m). However, with decreasing temperature, a remarkable first-order structural phase transition is observed, leading to the emergence of a rhombohedral ($R\bar3$) structure characterized by three-fold rotational symmetry forming an isotropic honeycomb lattice. On further cooling, a zigzag-type antiferromagnetic order develops below $T_{\textrm{N}} = 6\sim6.6$ K. The critical exponent of the magnetic order parameter was determined to be $\beta = 0.11(1)$, which is close to the two-dimensional Ising model. Additionally, the angular dependence of the magnetic critical field of the zigzag antiferromagnetic order for the polarized ferromagnetic phase reveals a six-fold rotational symmetry within the ab–plane. These findings reflect the symmetry associated with the Ising-like bond-dependent Kitaev spin interactions and underscore the universality of the Kitaev interaction-dominated antiferromagnetic system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2011

Investigation of modification of hydrogenation and structural properties of LaNi{sub 5} intermetallic compound induced by substitution of Ni by Pd

The hydrogenation properties of the LaNi{sub 5} (CaCu{sub 5} type, hP6, P6/mmm) and Pd substituted derivatives LaNi{sub 5-x}Pd{sub x} compounds have been studied in the whole homogeneity range of the solid solution (0.25{<=}x{<=}1.5). The pressure versus hydrogen content isotherms show several plateaus and an increase of the plateau pressure as a function of palladium concentration. The volume increase of the Pd substituted alloys should have resulted in a lowering, and not an increase, of the plateau pressure, according to the conventional models based on the size effect. In order to elucidate the origin of this anomalous behavior, both an experimental and a theoretical ab initio electronic structure investigation have been carried out. Experimentally, the nature and the structural properties of the hydrides have been studied by both in situ and ex situ neutron diffraction. The crystal structures of the three hydride phases are reported (LaNi{sub 3.5}Pd{sub 1.5}D{sub 1.96}, filled-up CaCu{sub 5} type, P6/mmm; LaNi{sub 4}PdD{sub 2.72}, LaNi{sub 2}(Ni{sub 0.75}Pt{sub 0.25}){sub 3}H{sub 2.61} type, oI128, Ibam; LaNi{sub 4.75}Pd{sub 0.25}D{sub 5.67}, partly ordered CaCu{sub 5} type, P6mm). In addition, the phase diagram of LaNi{sub 5-x}Pd{sub x}-H system has been investigated. The electronic and thermodynamic properties of both intermetallic compounds and the hydrides have been studied by ab initio electronic structure calculations. The theoretical results are in good agreement with our experimental data, and show that electronic interactions play a major role in the hydrogenation behavior of these Pd substituted intermetallic compounds, and that these effects cannot be accounted for by a simplistic model based on the size effect alone. -- Graphical abstract: Phase diagram of the system LaNi{sub 5-x}Pd{sub x}-D{sub 2} (absorption) at 25 {sup o}C and 25 bar. Display Omitted

36 MATERIALS SCIENCE↗
DOE OSTI2020

High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States

Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O 2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. Furthermore, this study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Two-dimensional image edge enhancement using two orders of Bragg diffraction

The process of two-dimensional image edge enhancement with an acousto-optical spatial filter using two orders of light diffraction is studied. It is theoretically shown that the diffraction that occurs in a paratellurite crystal on a ‘slow’ acoustic wave propagating orthogonally to the optical axis of the crystal allows enhancing a two-dimensional edge of an image, transferred by optical radiation with a wavelength of 0.63 μm in a wide band of acoustic frequencies 25 – 50 MHz. Enhancement of a two-dimensional image edge at an acoustic frequency of 29 MHz is experimentally demonstrated. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2010

Field evolution of the magnetic structures in Er{sub 2}Ti{sub 2}O{sub 7} through the critical point

We have measured neutron-diffraction patterns in a single-crystal sample of the pyrochlore compound Er{sub 2}Ti{sub 2}O{sub 7} in the antiferromagnetic phase (T=0.3 K), as a function of the magnetic field, up to 6 T, applied along the [110] direction. We determine all the characteristics of the magnetic structure throughout the critical point at H{sub c}=2 T. As a main result, all Er moments align along the field at H{sub c} and their values reach a minimum. Using a four-sublattice self-consistent calculation, we show that the evolution of the magnetic structure and the value of the critical field are rather well reproduced using the same anisotropic exchange tensor as that accounting for the local paramagnetic susceptibility. In contrast, an isotropic exchange tensor does not yield the correct moment variations through the critical point. The model also accounts semiquantitatively for other experimental data obtained in previous works, such as the field dependence of the heat capacity, energy of the dispersionless inelastic modes and transition temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Identification and structural analysis of a thermophilic β-1,3-glucanase from compost

β-1,3-glucanase can specifically hydrolyze glucans to oligosaccharides and has potential applications in biotechnology. We used the metatranscriptomic technology to discover a thermophilic β-1,3-glucanase from compost. The phylogenetic study shows that it belongs to the family 16 glycoside hydrolase (GH16) and is most homologous with an enzyme from Streptomyces sioyaensis, an actinobacterium. It has the activity of 146.9 U/mg in the optimal reaction condition (75 °C and pH 5.5). Its catalytic domain was crystallized and diffracted to 1.14 Å resolution. The crystal structure shows a sandwich-like β-jelly-roll fold with two disulfide bonds. After analyzing the occurring frequencies of these cysteine residues, we designed two mutants (C160G and C180I) to study the role of these disulfide bonds. Both mutants have decreased their optimal temperature from 75 to 70 °C, which indicate that the disulfide bonds are important to maintain thermostability. Interestingly, the activity of C160G has increased ~ 17% to reach 171.4 U/mg. We speculate that the increased activity of C160G mutant is due to increased dynamics near the active site. Our studies give a good example of balancing the rigidity and flexibility for enzyme activity, which is helpful for protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing

Antibody therapeutics are one of the most important classes of drugs. Antibody structures have become an integral part of predicting the behavior of potential therapeutics, either directly or as the basis of modeling. Structures of Fab:antigen complexes have even greater value. While the crystallization and structure determination of Fabs is easy relative to many other protein classes, especially membrane proteins, broad screening and optimization of crystalline hits is still necessary. Through a comprehensive review of rabbit Fab crystal contacts and their incompatibility with human Fabs, we identified a small secondary structural element from the rabbit light chain constant domain potentially responsible for hindering the crystallization of human Fabs. Upon replacing the human kappa constant domain FG loop (HQGLSSP) with the two residue shorter rabbit loop (QGTTS), we dramatically improved the crystallization of human Fabs and Fab:antigen complexes. Our design, which we call “Crystal Kappa”, enables rapid crystallization of human fabs and fab complexes in a broad range of conditions, with less material in smaller screens or from dilute solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Neutron diffraction studies of a four-coordinated hydride in near square-planar geometry

The structure of a nanospheric polyhydrido copper cluster, [Cu 20 (H) 11 {S 2 P(O i Pr) 2 } 9 ], was determined by single-crystal neutron diffraction. Cu 20 cluster consists of an elongated triangular orthobicupola constructed from 18 Cu atoms that encapsulate a [Cu 2 H 5 } 3- ion in the center with an exceptionally short Cu-Cu distance. The eleven hydrides in the cluster display three different coordination modes to the Cu atoms: Six μ 3 -hydrides in pyramidal geometry, two μ 4 -hydrides in tetrahedral cavity, and three μ 4 -hydrides in an unprecedented near square-planar geometry. The neutron data set was collected on a small crystal of the size 0.20 mm x 0.50 mm x 0.65 mm for seven days using the Spallation Neutron Source TOPAZ single-crystal time-of-flight Laue diffractometer at the Oak Ridge National Laboratory. Furthermore, the final R-factor is 8.64% for 16014 reflections.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Femtosecond X-ray Diffraction From Two-Dimensional Protein Crystals

Here we present femtosecond x-ray diffraction patterns from two-dimensional (2-D) protein crystals using an x-ray free electron laser (XFEL). To date it has not been possible to acquire x-ray diffraction from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permits a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy methodology at the Linac Coherent Light Source, we observed Bragg diffraction to better than 8.5 Å resolution for two different 2-D protein crystal samples that were maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Crystal and electronic structures of the new quaternary RCr₃Si₂C (R=Y, Gd–Tm, Lu, U) compounds

Nine new quaternary intermetallic RCr₃Si₂C (R=Y, Gd–Tm, Lu, U) compounds have been synthesized and characterized by both powder and single-crystal X-ray diffraction. These compounds crystallize in the hexagonal system with space group P6/mmm and lattice parameters a~9 Å and c~4 Å. Single-crystal X-ray diffraction refinement evidences a new type-structure closely related to the YCo₃Ga₂-type. Electronic structure properties and crystal stability of real YCr₃Si₂C against hypothetical YCr₃Si₂ are discussed in view of the Korringa–Kohn–Rostoker calculations, accounting for models with different atomic occupancy on selected sites as well as emphasizing the role of carbon in stabilization of YCr₃Si₂C compound. Highlights: • Crystal structure determination of the new intermetallic YCr₃Si₂C compound. • New type-structure closely related to the YCo₃Ga₂-type. • Theoretical study of the structural stability by electronic structure calculations. • Crystal structure characterization of the entire RCr₃Si₂C series.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Surface Curvatures and Diffraction Profiles of Sagittaly Bent Laue Crystals

The performance of a bent Laue crystal monochromator crucially depends on the sagittal and meridional bending curvatures of the crystal. To optimize the design of monochromator crystals, the surface curvatures and diffraction profiles of a set of sagittally bent Laue crystals with different aspect ratios have been studied experimentally by optical metrology and X-ray measurements. The results were confirmed with finite-element analysis using large-deformation theory. The nonlinear relationship between the curvatures necessitates an experimentally determined parameter in the theoretical modeling of the diffraction profiles. By taking into account the local stress and the aspect ratio of the sagittally bent Laue crystal, the modified analytical approach successfully predicts the rocking-curve width and the integrated reflecting power. The effect of extreme sagittal bending on the rocking curve is also discussed. To retain high reflectivity, the bending curvature should not exceed its critical value for the specified crystal geometry. Furthermore, the uniformity of the bending curvatures across the crystal surface has been examined, which suggests that the minimum crystal dimension should be approximately twice the size of the beam footprint.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

In-situ neutron diffraction of LaCoO₃ perovskite under uniaxial compression. I. Crystal structure analysis and texture development

The dynamics of texture formation, changes in crystal structure, and stress accommodation mechanisms have been studied in perovskite-type R3⁻c rhombohedral LaCoO₃ during uniaxial compression using in-situ neutron diffraction. The in-situ neutron diffraction revealed the complex crystallographic changes causing the texture formation and significant straining along certain crystallographic directions during compression, which are responsible for the appearance of hysteresis and non-linear ferroelastic deformation in the LaCoO₃ perovskite. The irreversible strain after the first loading was connected with the appearance of non-recoverable changes in the intensity ratio of certain crystallographic peaks, causing non-reversible texture formation. However, in the second loading/unloading cycle, the hysteresis loop was closed and no further irrecoverable strain appeared after deformation. The significant texture formation is responsible for an increase in the Young's modulus of LaCoO₃ at high compressive stresses, ranging from 76 GPa at the very beginning of the loading to 194 GPa at 900 MPa at the beginning of the unloading curve.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Peculiarities of Laue Diffraction of Neutrons in Strongly Absorbing Crystals

Well-known Kato’s theory of the Laue diffraction of spherical X-ray waves is generalized to the case of the neutron diffraction in strongly absorbing crystals, taking into consideration both the potential and the resonant scattering of neutrons by nuclei as well as a realistic angular dispersion of incident neutrons. The saddle-point method is applied for estimation of the angular integrals, being more adequate in the case of strongly absorbing crystals than the commonly used stationary-phase approximation. It is found that the intensity distribution of the diffracted and refracted beams along the basis of the Borrmann triangle significantly depends on the deviation of the neutron energy from the nuclear resonant level. When comparing our calculations with the Shull’s experimental data on neutron diffraction in silicon, we also regard the role of finite width of the collimating and scanning slits.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗