Neutron Refinement Research Articles

Metal Ion Roles and the Movement of Hydrogen during Reaction Catalyzed by D-Xylose Isomerase: A Joint X-Ray and Neutron Diffraction Study

Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction.

Structural variations and cation distributions in Mn 3− xCo xO 4 (0 ≤ x ≤ 3) dense ceramics using neutron diffraction data

Single phase ceramics of cobalt manganese oxide spinels Mn 3− x Co x O 4 were structurally characterized by neutron powder diffraction over the whole solid solution range. For x < 1.75, ceramics obtained at room temperature by conventional sintering techniques are tetragonal, while for x ≥ 1.75 ceramics sintered by Spark Plasma Sintering are of cubic symmetry. The unit cells, metal–metal and metal–oxygen average bonds decrease regularly with increasing cobalt content. Rietveld refinements using neutron data show that cobalt is first preferentially substituted on the tetrahedral site for x < 1, then on the octahedral site for increasing x values. Structural methods (bond valence sum computations and calculations based on Poix's work in oxide spinels) applied to our ceramics using element repartitions and [M–O] distances determined after neutron data refinements allowed us to specify the cation distributions in all phases. Mn 2+ and/or Co 2+ occupy the tetrahedral site while Mn 3+, Co 2+, Co III (cobalt in low-spin state) and Mn 4+ occupy the octahedral site. The electronic conduction mechanisms in our highly densified ceramics of pure cobalt and manganese oxide spinels are explained by the hopping of polarons between adjacent Mn 3+/Mn 4+ and Co 2+/Co III on the octahedral sites.

Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states inAspergillus flavusurate oxidase

Urate oxidase (Uox) catalyses the oxidation of urate to allantoin and is used to reduce toxic urate accumulation during chemotherapy. X-ray structures of Uox with various inhibitors have been determined and yet the detailed catalytic mechanism remains unclear. Neutron crystallography can provide complementary information to that from X-ray studies and allows direct determination of the protonation states of the active-site residues and substrate analogues, provided that large, well-ordered deuterated crystals can be grown. Here, we describe a method and apparatus used to grow large crystals of Uox (Aspergillus flavus) with its substrate analogues 8-azaxanthine and 9-methyl urate, and with the natural substrate urate, in the presence and absence of cyanide. High-resolution X-ray (1.05-1.20 A) and neutron diffraction data (1.9-2.5 A) have been collected for the Uox complexes at the European Synchrotron Radiation Facility and the Institut Laue-Langevin, respectively. In addition, room temperature X-ray data were also collected in preparation for joint X-ray and neutron refinement. Preliminary results indicate no major structural differences between crystals grown in H(2)O and D(2)O even though the crystallization process is affected. Moreover, initial nuclear scattering density maps reveal the proton positions clearly, eventually providing important information towards unravelling the mechanism of catalysis.

Synthesis, Crystal Structure, and Magnetic Properties of Sr1.31Co0.63Mn0.37O3: A Derivative of the Incommensurate Composite Hexagonal Perovskite Structure

We report the synthesis, structural investigation, and magnetic property studies of Sr1.31Co0.63Mn0.37O3 that adopts an incommensurate composite hexagonal perovskite-related structure. The crystal structure has been solved using a (3 + 1)-dimensional superspace approach from powder X-ray and neutron diffraction data (SSG R3̅m(00γ)0s, a = 9.5548(1) Å, c = 2.5599(1) Å, q = 0.65581(4)c*, RB = 0.041, RP = 0.059). The structure consists of face-sharing chains of octahedra and trigonal prisms, wherein the trigonal prismatic sites are preferentially occupied by Co with some cation disorder. A combination of electron diffraction and high-resolution electron microscopic analysis has demonstrated that the compound possesses a complicated microstructure related to the formation of domains with slightly different lengths of the modulation vector. X-ray absorption near-edge spectroscopic (XAS) studies clearly indicate the presence of Mn in the 4+ and Co in the 3+ oxidation state. While the magnetic susceptibility data indicates the presence of antiferromagnetic correlations in the system, the calculation of effective paramagnetic moment (μcal = 3.561 μB), assuming the metal oxidation states as obtained from XAS and the cation distribution as obtained from neutron refinement, is in agreement with the value obtained experimentally (μexp = 3.676 μB).

Structural refinement of neutron powder diffraction data of two-stage martensitic phase transformations in Ti50.75Ni47.75Fe1.50 shape memory alloy

Transformation behaviors of the technologically important polycrystalline Ti50.75Ni47.75Fe1.50 shape memory alloy were investigated using differential scanning calorimeter (DSC) and powder diffraction techniques. DSC revealed that there are two-stage (i.e., cubic→trigonal→monoclinic) martensitic phase transformations on cooling and a one-step transformation (monoclinic→cubic) on heating. In situ structural refinement of cubic→trigonal→monoclinic on cooling was carried out using the D1A high-resolution neutron powder diffractometer at the Institut Laue-Langevin Neutrons for Science in Grenoble, France. Results showed that the phases involved during the phase transition are consistent with the differential scanning calorimeter cooling curve, and the refined crystal structure parameters obtained from Rietveld refinements with the generalized spherical harmonic description agreed reasonably well with X-ray single-crystal data. Subsequently, a combined neutron and synchrotron structural refinement for each phase was conducted because the trial refinements initially using only the synchrotron data of trigonal phase yielded a false minimum with a somewhat high goodness-of-fit χ2. Results obtained from the combined neutron and synchrotron data of the cubic, trigonal, and monoclinic phases show that the same minimum goodness-of-fit indices were always obtained.

Protocol of Refinement in Neutron Crystallographic Analysis

The protocol of refinement in neutron protein crystallographic analysis is described in this article. During the refinement, there are several features specialized for neutron experiment:(1) the mixed chemical structure of deuterium and hydrogen atoms, (2) solvent molecules around the protein, and the deuterium exchange in the polypeptide chain. We demonstrate the example of neutron refinement steps, using rubredoxin mutant, of which neutron diffraction collected using BIX-3 diffractometer at JRR-3 in Japan Atomic Energy Agency. The X-ray refinement program of CNS was used for the present refinement. Scattering lengths, stereochemical parameters, and command input files were modified for neutron experiment. These files would be the templates for the neutron protein crystallographic analysis.

New insight into crystal chemistry of topaz: A multi-methodological study

The crystal chemistry of a natural topaz [with OH/(OH + F) < 0.5] was reinvestigated by means of laser ablation inductively coupled plasma mass spectroscopy, single-crystal X-ray diffraction (at 298 K) and neutron diffraction (at 298 and 10 K), and polarized infrared spectroscopy to define unambiguously the real symmetry of topaz, the location of the proton and its thermal displacement parameters at room and low temperatures, the hydrogen-bonding and the vibration modes (stretching and bending) of the OH dipole. X-ray and neutron structural refinements allow us to infer that the crystal structure of natural topaz with OH/(OH + F) < 0.5 can be described with the Pbnm space group. Violating reflections, found in the previous investigations and in this study, are likely due to Renninger effect (double diffraction phenomenon). The nuclear density Fourier map shows that the proton is located at Wyckoff 8d position and the refined coordinates are: x = 0.495(2), y = 0.252(1), z = 0.1629(7). The O-H bond lies on the (010)-plane and forms an angle of about 28.9° with the c-axis. Neutron structural refinements at 298 and 10 K show that the displacement ellipsoid of the proton is highly anisotropic. The H-bonding arrangement appears to be complex, with at least four potential H···O/F interactions (distances < 2.38 Å). The topological configuration of the O-H group described by the neutron structural refinements is confirmed by the infrared investigation: the OH stretching mode (at 3640 cm-1) has no component of vibration parallel to the b axis (i.e., the O-H direction is perpendicular to [010]). The OH bending mode (at 1161 cm-1) shows components along the three crystallographic axes, which appear to be more prominent along the a and b-axes. The possible distribution into the crystal structure of topaz of the minor/trace elements found (Na, Ca, Fe Cr, V, Ti, B), and the implied topological effects, is discussed.

X-ray and neutron Rietveld quantitative phase analysis of industrial Portland cement clinkers

Weight fractions of four dominant phases (C3S, C2S, C4AF, and C3A) present in five industrial clinkers were estimated by a series of neutron and X-ray Rietveld refinements. Calculated powder patterns were derived from the structural data for monoclinic and triclinic C3S, monoclinic C2S, orthorhombic C4AF, cubic C3A and MgO. Neutron diffraction data were collected with the high resolution E9 diffractometer (BENSC) using two different wavelengths, X-ray diffraction data with a high resolution transmission diffractometer. Elemental composition of the samples obtained by ESEM/EDX technique were in a good agreement with the data delivered by the producers. Convergence of the refinements was remarkably different for X-ray and for neutron data. Several refinements were not completed due to numerical instabilities. Neutron refinements were found to be more stable than X-ray, but there was not any notable difference in the final estimated phases’ compositions. Calculated absolute deviates of phases’ weight fractions were mostly within ±10%, which for the less abundant phases corresponded to relative deviations within ±50%. © 2004 International Centre for Diffraction Data.

Crystal growth of a novel oxygen-deficient layered perovskite: Ba 7Li 3Ru 4O 20

Single crystals of both Ba 7Li 3Ru 4O 20 and Ba 4NaRu 3O 12 were grown from reactive molten hydroxide fluxes. Ba 7Li 3Ru 4O 20 is a 7L-layer perovskite-related phase resulting from the stacking of six [AO 3] layers and one oxygen deficient [AO 2] layer, thereby creating LiO 4 tetrahedra in addition to the LiO 6 octahedra and face-sharing Ru 2O 9 bi-octahedra formed from the [AO 3] layers. The compound crystallizes in the space group R 3 ̄ m with a=5.7927(1) Å and c=50.336(2) Å, Z=3. Ba 4NaRu 3O 12 crystallizes in the space group P6 3 mc with lattice parameters of a=5.8014(2) Å and c=19.2050(9) Å, Z=2. Ba 4NaRu 3O 12 is identical to a previously reported neutron refinement structure. The magnetic properties of Ba 7Li 3Ru 4O 20 are also reported.

Crystal structure, magnetic properties, and Mössbauer studies ofLa0.6Sr0.4FeO3−δprepared by quenching in different atmospheres

Samples of ${\mathrm{La}}_{0.6}{\mathrm{Sr}}_{0.4}{\mathrm{FeO}}_{3\ensuremath{-}\ensuremath{\delta}}$ compounds prepared by quenching in different gaseous environments were studied by x-ray diffraction, neutron diffraction, magnetization measurements, and M\ossbauer spectroscopy (MS). All materials are single phase and crystallize in the rhombohedral perovskite structure. Samples prepared in flowing air, ${\mathrm{N}}_{2},$ and ${\mathrm{O}}_{2}$ yielded oxygen vacancies ranging from 0% to 1%. The oxygen vacancy concentration increases from 6.8% to 9.6% as the ratio of ${\mathrm{C}\mathrm{O}/\mathrm{C}\mathrm{O}}_{2}$ changes from 10:90 to 90:10. The air-, ${\mathrm{N}}_{2}\ensuremath{-},$ and ${\mathrm{O}}_{2}$-quenched samples have a magnetic ordering temperature in the range of 300--325 K. The magnetic ordering temperature increases for all the samples subjected to the reducing ${\mathrm{C}\mathrm{O}/\mathrm{C}\mathrm{O}}_{2}$ atmosphere. The neutron data refinements and magnetization data indicate that the Fe sublattice of ${\mathrm{La}}_{0.6}{\mathrm{Sr}}_{0.4}{\mathrm{FeO}}_{3\ensuremath{-}\ensuremath{\delta}}$ has an antiferromagnetic structure below the magnetic ordering temperature. The Fe atoms possess a magnetic moment of $3.8{\ensuremath{\mu}}_{B}$ and a hyperfine field of 53 T in the ${\mathrm{C}\mathrm{O}/\mathrm{C}\mathrm{O}}_{2}$-quenched samples. It is found that the heat treatment in the ${\mathrm{C}\mathrm{O}/\mathrm{C}\mathrm{O}}_{2}$ atmosphere creates more oxygen vacancies, changes the Fe valence states, and increases the unit cell volume. In the meantime, the Fe-O-Fe bond angle increases. These dramatically affect the Fe-O-Fe superexchange coupling. The change of the Fe-O-Fe bond angle and the change of the Fe valence states in the ${\mathrm{C}\mathrm{O}/\mathrm{C}\mathrm{O}}_{2}$ heat treatment play a key role in the increase of the magnetic ordering temperatures and the magnetic moment. Therefore by creating oxygen vacancies or having excess oxygen, the exchange interaction of Fe-O and the valence state of Fe ions are affected, and lead to large changes in the magnetic properties, such as the magnetic ordering temperature, the magnetic moments, and the hyperfine interactions in the pervoskite structure.

A high-temperature Fourier transform infrared study of the interlayer and Si–O-stretching region in phengite-2M1

AbstractA natural phengite-2M1 of composition (K0.95Na0.05)(Al0.76Fe0.14Mg0.10)2 (Si3.25Al0.75)O10(OH1.96F0.04) [a= 5.2173(1) Å, b= 9.0493(2) Å, c= 19.989 (1) Å and β = 95.734(4)°] was studied using in situ high-temperature FTIR. Correlations to structural changes were made using previously-reported neutron diffraction data from the same sample. Correlations have been made between the microscopic atomic displacements (arising from thermal effects) and analogous macroscopic properties, such as bond strain and ditrigonal distortions. Spectra were collected in the far-infrared region to study the behaviour of the interlayer (K+) cation and also in the mid-infrared region to distinguish the Si–O stretching modes. We found anisotropic thermal expansion of the interlayer site. The K O bond length is divided into K Oouter and K Oinner, and the K–Oinner bond length is correlated with the far-infrared spectra. The thermal dependence of the correlation between K–O bond length and corresponding far-infrared stretching frequency is different from the effect of the chemical composition. We also found that the K–O bond strain could be successfully resolved into the sum of inner strain and lattice strain. The Si–O stretching mode, obtained from the mid-infrared measurements, showed only weak changes. However, the neutron refinement data showed different thermal behaviour for distinct crystallographic T-sites.

Structure and magnetic properties of the MnBi low temperature phase

High purity MnBi low temperature phase has been prepared and analyzed using magnetic measurements and neutron diffraction. The low-temperature phase of the MnBi alloy has a coercivity μ0iHc of 2.0 T at 400 K, and exhibits a positive temperature coefficient from 0 to at least 400 K. The neutron data refinement indicated that the Mn atom changes its spin direction from c axis above room temperature to nearly perpendicular to the c axis at 50 K. A canted magnetic structure has been observed below 200 K. The anisotropy field increases with increasing temperature which gives rise to a high coercivity at the higher temperatures. The anisotropic bonded magnets have maximum energy products (BH)max of 7.7 and 4.6 MGOe at room temperature and 400 K, respectively.

Neutron Diffraction, Mössbauer Spectrum, and Magnetic Behavior of Ag2FeMn2(PO4)3 with Alluaudite-like Structure

The new compound Ag2FeMn2(PO4)3 has been synthesized using solid state reactions, and characterized by X-ray and neutron diffraction. It crystallizes in the monoclinic space group C2/c with the parameters a=12.1466(3) Å, b=12.7328(4) Å, c=6.4999(5) Å, and β=114.53(3)°. Its structure is formed by [FeMn2O12]∞ chains of edge-sharing FeO6 and MnO6 octahedra. The chains are interconnected by the PO4 tetrahedra giving rise to layers parallel to the ac plane and exhibiting a three-dimensional channel-like structure where the silver cations are located. The distribution of the FeO6 and MnO6 octahedra along the chains was determined by the neutron refinements. The Mössbauer spectral parameters indicate the presence of only Fe(III) octahedral sites. The reciprocal susceptibility variation shows a deviation from the Curie–Weiss law below 19 K, which can be attributed to a weakly ferromagnetic component owing to probable canting of antiferromagnetically coupled spins along the [FeMn2O12]∞ chains.

Thermal response of structure and hydroxyl ion of phengite-2M1: an in situ neutron diffraction and FTIR study

The thermal dependence of the structure of natural phengite-2M 1 with chemical formula (K 0.95 Na 0.05 )(Al 0.76 Fe 0.14 Mg 0.10 2 (Si 3.25 Al 0.75 )O 10 (OH 1.96 F 0.04 ) has been studied by in situ neutron diffraction. The short-range correlated behaviour of the hydroxyl group was probed by FTIR spectroscopy while the long-range correlated hydroxyl structure was studied by neutron diffraction. Changes in long-range ordering of Si and Al on the tetrahedral sites were not observed from neutron diffraction. Structure refinement of the neutron diffraction data by the Rietveld method suggested that the apparent average hydroxyl bond length decreases on heating. The infrared data show a decrease in the stretching frequency of hydroxyl group, however. Possible explanations for these results are explored. It seems most likely that the apparent shortening of the hydroxyl bond length may be an artefact due to an increase in its vibrational amplitude. The anisotropic vibration of the hydroxyl bond as revealed by the anisotropic displacement parameters of H, increases so much that the average length (shown by the neutron refinement) appears to decrease at high temperatures while the local length of the bond, as indicated by FTIR results, increases.

Neutron refinement of the crystal structure of partially exchanged taurine, (ND 3 + )0.65(NH 3 + )0.35(CH2)2SO 3 −

Refinement of neutron-diffraction data from a partially deuteriated single crystal of taurine, 2-aminoethylsulfonic acid, confirms the zwitterion structure, ND 3 + (CH2)2SO 3 − , at room temperature; the S−C−C−N torsion angle of thegauche configuration in the solid state is −69.40. Hydrogen positions have been located more precisely than in the earlier X-ray analysis to yield apparent bond lengths N−D/H=1.02(1) A and C−H=1.08(1) A.

Magnetism in BaCoS2

BaCoS 2 is a layered Mott–Hubbard insulator that orders antiferromagnetically near 300 K. We report magnetic susceptibility measurements on polycrystalline BaCoS2 from 77 to 800 K, and in- and out-of-plane measurements on single crystals from 2 to 350 K. We also report a powder neutron refinement of the magnetic structure of BaCoS2. The neutron measurements indicate that the moments lie in the plane, and that the magnetic unit cell is the same as the (orthorhombic) chemical cell. The ordered moment obtained from the neutron refinement is close to 3 μB, indicating that the Co ions are in the high-spin (S=3/2) configuration. The effective moment inferred from the high temperature susceptibility, p=5.26μB, is also consistent with high-spin Co+2.

New group V κ-phases

New κ-phases (P. Rautala and J.T. Norton, Trans. AIME, 194 (1952) 1045; A. Harsta and S. Rundqvist, J. Solid State Chem., 70 (1987) 210) were discovered and crystallographically characterized in the Zr Ta S, Zr Nb S, Zr V S, Hf Nb S, and Hf V S systems, A κ-phase was also identified in the Hf Ta S system through Guinier powder diffraction. These compounds are the first examples of the κ-phase structure containing the Group V transition metals, Ta, Nb, and V. The Ta and Nb κ-phases exhibit the largest volumes (by about 13%) and the largest amounts of second row nonmetal per formula unit of the known κ-phases. X-ray single-crystal diffraction experiments were used to determine metal site occupancies in these κ-phases, and it was found that statistical mixing of the metals primarily on one site occurred for the Ta and Nb compounds. Refinements of the X-ray intensity data indicated that the octahedral nonmetal sites (denoted X2) are less than fully occupied by sulfur in the Ta and Nb κ-phases and less than fully occupied by oxygen in the V κ-phases. Combined neutron and X-ray powder refinements reliably determined that these nonmetal X2 sites are occupied by a mixture of sulfur, oxygen, and vacancies in the Zr Nh S and Zr Ta S κ-phases. The κ-phases in the Zr Nb S (G. Marking et al., Phys. Rev. B, 48 (1993) 16630) and Hf Nb S systems were found to be superconductors with T 2s of 10.35 K and between 6 and 7 K respectively.

Synthesis, crystal structure and magnetism of Sr 3Sb 2NiO 9—A ferrimagnetic perovskite

A new nickel(II) oxide, Sr 3Sb 2NiO 9, has been synthesised at 1200 °C. Rietveld fits to the powder synchrotron X-ray diffraction pattern show that this compound has orthorhombic symmetry [ a = 5.6237(1), b = 5.6442(1), c = 7.9574(1) A ̊ at 300 K ] and adopts a pseudo-double perovskite structure with Sb:Ni ratios of 40:60 and 93:7 at alternate cation sites. Powder neutron refinements demonstrate that space group symmetry is Pnnm between 1.5 and 300 K due to partly disordered rotations of the Sb/NiO 6 octahedra. Sr 3Sb 2NiO 9 behaves as a Curie-Weiss paramagnet at high temperatures with μ eff = 3.25(1) BM per Ni 2+ ion and ⊖ = − 119(1) K reflecting dominant antiferromagnetic spin-spin interactions, but a weak ferromagnetic component observed below the ordering temperature of 20 K suggests overall ferrimagnetic behaviour.

Powder X-Ray and Neutron Diffraction Studies of the (Ba 1- xSr x)2(Sr 0.67Bi 0.33)(Pb 1- yBi y)O 6-δ Compounds with the (NH 4) 3FeF 6 Structure Type

A new series of compounds of composition (Ba 1- x Sr x ) 2(Sr 0.67Bi 0.33)(Pb 1- y Bi y )O 6-δ has been prepared and characterized by powder X-ray and neutron diffraction studies. The phases adopt the cubic (NH 4) 3FeF 6 type structure (space group Fm3 m) with Sr 2+ ions occupying the B sites. TGA and neutron refinements show oxygen vacancies and a large anisotropy associated with the O atoms. The anisotropy is discussed in terms of a vacancy model.

Simultaneous neutron and x-ray refinement of Ortho-II superstructure in YBa 2Cu 3O 6.5

Clearly defined Lorentzian-like profiles of the Ortho-II superstructure diffraction peaks have been observed with neutrons for the first time. The superstructure has been refined by simultaneously fitting neutron and x-ray measurements on the same crystal. The combination of both x-ray and neutron information is important since the formation of the Ortho-II phase is driven by oxygen ordering which can be most clearly seen by the neutrons whilst the x-rays are more sensitive to the heavy ion displacements.