bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of 3D small-angle scattering from non-spherical particles in single crystals
Authors: Fratzl P. , Langmayr F. , Paris O.
Published: July 2002

Three-dimensional small-angle scattering is discussed as a tool for investigation of anisometric particles in single-crystalline alloys. The measurement and evaluation methods take advantage of the well defined orientation relation between the precipitates and the matrix in alloys. The determination of shape, size and orientation of precipitates from the scattering in several planes of reciprocal space is discussed for the example of ellipsoids and plates. Shape and orientation of ellipsoids with small aspect ratio can be determined by deviations of the scattering intensity from spherical symmetry in certain planes of reciprocal space. Particle size is obtained from one-dimensional slices along certain directions. The small-angle scattering of plate-like particles with large aspect ratio is concentrated along radial streaks in reciprocal space. Slices along and across these streaks allow the determination of the plate thickness as well as size and aspect ratio of the plate surface. In addition, the evaluation of such `off-center' slices provides a resolution enhancement of almost one order of magnitude compared to the conventional Guinier method applied to spherically averaged data.
Determination of the Orientation of a Parent β Grain from the Orientations of the Inherited α Plates in the Phase Transformation from Body-Centred Cubic to Hexagonal Close Packed
Authors: Humbert M. , Wagner F. , Moustahfid H. , Esling C.
Published: July 2002

Knowledge of the orientations of several α plates inherited from the body-centred-cubic–hexagonal-close-packed phase transformation of a β grain allows us to determine the orientation of the latter, provided that a strict orientation relation between the two lattices exists. This contribution discusses the problem of the uniqueness of the solution and leads to the conclusion that the number of different α orientations required for that purpose is three in the less favourable case but is reduced to two in the most favourable case.
Measurement of Kinetics and Mechanisms of Phase Transitions in Lipid–Water Systems
Authors: Quinn P. J.
Published: July 2002

The lipids from biological membranes, when dispersed in aqueous media, form a variety of phases that include bilayer and nonbilayer arrangements of the molecules. Such phases have been well characterized by conventional X-ray powder diffraction and other methods. Transitions between phases are believed to underlie a number of dynamic membrane processes such as membrane fusion. Studies of the kinetics and mechanisms of phase transitions in lipid–water mixtures require high-intensity synchrotron X-ray sources to monitor the associated structural changes. Facilities at four synchrotron sources providing facilities to measure kinetics and mechanisms of phase transitions in lipid–water systems are described. Some examples are given of how these facilities have been used to measure kinetics of transitions in the dipalmitoylphosphatidylcholine–water system and how different transition mechanisms are defined.
Refinement of the Ferri- and Paramagnetic Phases of Magnetite from Neutron Multiple Diffraction Data
Authors: Mazzocchi V. L. , Parente C. B. R.
Published: July 2002

Structural parameters for the ferrimagnetic and paramagnetic phases of magnetite have been refined from neutron multiple diffraction data. Experimental neutron multiple diffraction patterns were obtained by measuring the 111 primary reflection of a natural single crystal of this compound. Measurements were made at room temperature for the ferrimagnetic phase and at 976 K for the paramagnetic phase. The corresponding simulated patterns have been calculated byMULTI, a computer program for the simulation of neutron multiple diffraction patterns. A step-by-step process was used in the refinements according to the parameter-shift method. Both isotropic and anisotropic thermal parameters were assumed for the temperature factor. Isotropic thermal parameters were considered in two different ways: an overall parameter for all ions in the structure and three different parameters for the three special positions occupied by them in the structure. The best results were found in the refinements with anisotropic thermal parameters. In this case, the values of the profileRfactor found for these refinements were 3.00 and 3.32%, respectively, for the ferrimagnetic and paramagnetic phases.
Small-angle X-ray scattering analysis of craze-fibril structures
Authors: Salomons G. J. , Singh M. A. , Bardouille T. , Foran W. A. , Capel M. S.
Published: July 2002

Load-bearing craze fibrils are fundamental to the ability of many polymer materials to support applied tensile stress. Three models of the scattering from craze-fibril structures have been compared through a rigorous analysis procedure. The results indicate that a diffuse-boundary model provides a more accurate description of scattering from the fibril structure than the standard Porod-law technique. Previously reported methods for determining fibril diameters were found to be inappropriate for high-impact polystyrene (HIPS) materials, overestimating the fibril diameters by as much as 60%. Indirect transforms using regularization theory of the fibril scattering data provide confirmation of the fibril diameters obtained from a power-law diffuse-boundary model, which is developed specifically for the craze-fibril structure of interest.
Crystalline and microstructure study of the AlN–Al2O3section in the Al–N–O system. I. Polytypes and γ-AlON spinel phase
Authors: Tabary P. , Servant C.
Published: July 2002

The crystalline structure and microstructure of some phases of the pseudo-binary system AlN–Al2O3are discussed, with special attention to the γ spinel phase. Samples with AlN content ranging between 43.3 and 3.5 mol % were studied after different thermal treatments. X-ray and neutron diffraction Rietveld peak-profile refinement allowed the determination of the cell parameters and weight fraction of the phases. By checking different hypotheses of structure, it has been shown that the positions of the anions in the γ-AlON spinel phase are not ideal and correspond to a deformed face-centred cubic (f.c.c.) structure. This deviation is not due to the presence of vacancies in the cationic sublattice. The vacancies are distributed in the octahedral sites.
Optimization and operation of a BBB X-ray interferometer
Authors: Würges J. , Rostomyan A. M. , Graeff W. , Materlik G.
Published: July 2002

A special arrangement of Bonse–Hart X-ray interferometers, which uses the Bragg geometry of X-ray diffraction for the beam splitter, mirrors and the analyser (so-called BBB interferometers), has been designed and characterized both computationally and experimentally in different versions. The design includes wavelength-dependent optimization of transmission through the lamella, which is used both for beam splitting and for recombination. For characterization of the function of the instrument, interference patterns were evaluated from BBB interferograms, as well as from LLL (employing the Laue geometry for coherent beam splitting, reflecting and analysing) topograms and from interferograms resulting from a new combined geometrical layout. The influence of gravitation on the horizontally running diffraction planes was visible as a system of fringes in the interferograms, resulting from bending of the lamella under its own weight.
High-resolution electron-microscope images of crystals with correlated atomic displacements
Authors: Etheridge J.
Published: July 2002

A coordinate-space multislice description of the scattering of high-energy electrons is constructed from consecutions of differential operators acting upon atomic potentials. It is used to find expressions for the intensity distribution in high-resolution electron-microscope images of crystals whose atoms are periodically displaced relative to a reference lattice according to a modulation wave. Both static correlated displacements, such as occur in modulated structures, and time-dependent correlated displacements, as are generated by phonons, are considered. Two aspects of the image are examined in detail; its translational symmetry and its dependence upon the correlations between the atomic displacements. It is shown that the intensity distribution due to scattering from static correlated displacements has the translational symmetry of the modulated structure in that projection, as determined by the component of the modulation wavevector perpendicular to the incident beam, whereas that due to scattering from phonons has the translational symmetry of the reference lattice in that projection. The former is a consequence of higher-order Laue-zone interactions. The intensity distribution due to scattering from static displacements depends upon the absolute phase of the displacement at each scattering atomic site whereas that due to scattering from phonons depends only upon the relative phase of the displacements between different scattering sites, both within the same atomic column parallel to the beam and in adjacent columns. In both cases, the influence of the component of the correlation wavevector parallel to the incident beam is different to that perpendicular to the beam; the former affects the intensity mostly at the atomic sites whilst the latter affects the intensity mostly between the atomic sites. It is also observed that, as a consequence of the periodic nature of the polarization-vector function, the interference terms are small, both relative to the non-interference term and in an absolute sense, particularly for phonon scattering. For this reason, the contribution to the image due to scattering from correlated atomic displacements will have greater and sharper atomic contrast than that due to scattering from the reference structure without displacements. In addition, this component of the intensity distribution will not exhibit strong contrast reversal when the objective-lens defocus is changed.
Disorder, superlattice canting and chiral domains in zirconia–niobia ceramic alloys
Authors: Sellar J. R.
Published: July 2002

The structures of the zirconia-based ceramic oxide superlattice alloy phases Nb2Zr
x−2O2x+1 (x ≈ 7–12) are reviewed. It is noted that recent investigations into the alloys' structure suggest they are not strictly crystalline, with consequences for their diffraction properties. It is suggested that several aspects of their behaviour may be interpreted as proper to a frustrated two-dimensional XY model, where the distinctive planes of oxygen atoms in the alloys form a lattice of planar XY `spins'. Evidence is presented for the existence of frustration, which produces superlattice canting in the model including electron-microscope evidence for the existence of domains of staggered Ising-type chirality in the alloys, as predicted for the frustrated two-dimensional XY model by Villain [J. Phys. C (1977), 10, 1717–1734].
Quasiperiodic packings of fibres with icosahedral symmetry
Authors: Duneau Michel , Audier Marc
Published: July 2002

Different icosahedral packings of fibres have been experimentally realized. A packing construction with straight fibres of the same circular cross section, only parallel to fivefold icosahedral axes and respecting the closest packing condition, is reported. Its characteristics of point-group symmetry and related two-dimensional tilings are analysed. But for determining unambiguously all the fibre positions it appears that a mathematical construction has to be made from the cut and projection of a five-dimensional space. Through such a method, the volume fraction of fibrous reinforcement in a composite material can be calculated. The related two-dimensional tiling can be proved to be different from a Penrose tiling. Finally, the characteristics of other icosahedral packings where fibres are parallel to threefold axes or to both threefold and fivefold axes are briefly discussed and a few further experiments on their elasticity properties and photonic band-gap structure are suggested.
Frequency of Z′ values in organic and organometallic crystal structures
Authors: Steiner Thomas
Published: July 2002

The frequencies of Z′ values (formula units per asymmetric crystal unit) are documented for organic and organometallic crystal structures, using the Cambridge Structural Database. The absolute frequencies of all Z′ values reported, relative frequencies for certain substance classes, the seven crystal systems and the most abundant space groups are given. The three Z′ values ½, 1 and 2 make up 95.3% of all crystal structures. Structures with Z′ > 1 occur most frequently with nucleosides and nucleotides (20.8%), and with steroids (18.8%).
Orientational disorder as a function of temperature in the clathrate structure of hydroquinone and C60
Authors: Blanc Eric , Restori Renzo , Schwarzenbach Dieter , Bürgi Hans-Beat , Förtsch Marcel , Venugopalan Paloth , Ermer Otto
Published: July 2002

In the compound [C6H6O2]3C60, hydroquinone (C6H6O2) forms a three-dimensional hydrogen-bonded network enclosing roughly spherical cages with point symmetry \overline 3m and a diameter of 13.2 Å at 100 K. Although C60 fits tightly into these cages, it shows threefold orientational disorder, the molecular site symmetry being 2/m. The disorder has been studied with single-crystal Mo Kα X-ray data at four temperatures, 100, 200, 293 and 373 K. In the refinement, C60 was restrained to the icosahedral molecular symmetry m\overline {35} and to rigid-body translational and librational displacements including third- and fourth-order cumulants to account for curvilinear atomic movements, R(|F|) = 3.2–4.7%. At 100 K, bond lengths in C60 refine to the expected values 1.450 (1) and 1.388 (1) Å. The ratio of these values increases with increasing temperature, but the radius of the molecule remains constant at 3.537 (2) Å. The r.m.s. libration amplitudes of C60 are relatively small (5.5° at 373 K) and the probability function of orientations of C60 inside the cage shows large values only at the refined positions, indicating that the energy barrier of reorientation is large. Refinement of an ordered twinned structure was unsuccessful; the orientations of neighboring C60 appear to be uncorrelated.
Hydrated salts of 3,5-dihydroxybenzoic acid with organic diamines: hydrogen-bonded supramolecular structures in two and three dimensions
Authors: Burchell Colin J. , Ferguson George , Lough Alan J. , Gregson Richard M. , Glidewell Christopher
Published: July 2002

The trigonally trisubstituted acid 3,5-dihydroxybenzoic acid forms hydrated salt-type adducts with organic diamines. In 1,4-diazabicyclo[2.2.2]octane–3,5-dihydroxybenzoic acid–water (1/1/1) (1), where Z′ = 2 in P21/c, the constitution is [HN(CH2CH2)3N]+·[(HO)2C6H3COO]−·H2O: the anions and the water molecules are linked by six O—H...O hydrogen bonds to form two-dimensional sheets and each cation is linked to a single sheet by one O—H...N and one N—H...O hydrogen bond. Piperazine–3,5-dihydroxybenzoic acid–water (1/2/4) (2) and 1,2-diaminoethane–3,5-dihydroxybenzoic acid–water (1/2/2) (3) are also both salts with constitutions [H2N(CH2CH2)2NH2]2+·2[(HO)2C6H3COO]−·4H2O and [H3NCH2CH2NH3]2+·2[(HO)2C6H3COO]−·2H2O, respectively. Both (2) and (3) have supramolecular structures which are three-dimensional: in (2) the anions and the water molecules are linked by six O—H...O hydrogen bonds to form a three-dimensional framework enclosing large centrosymmetric voids, which contain the cations that are linked to the framework by two N—H...O hydrogen bonds; in (3) the construction of the three-dimensional framework requires the participation of cations, anions and water molecules, which are linked together by four O—H...O and three N—H...O hydrogen bonds.
Electron density in the sodium vanadium oxide bronze β-Na
x
V2O5 at 9 K
Authors: Ozerov Ruslan P. , Streltsov Victor A. , Sobolev Alexander N. , Figgis Brian N. , Volkov Victor L.
Published: July 2002

The crystal structure and electron density in sodium vanadium oxide bronze, β-Na
x
V2O5 [x = 0.282 (3)], have been studied by accurate Mo Kα X-ray diffraction measurements at 9.6 (3) K. No noticeable difference in the crystal structures at room temperature and 9.6 K has been observed. No superstructure reflections, previously found by Kanai, Kagoshima & Nagasawa [(1982), J. Phys. Soc. Jpn, 51, 697–698], have been detected at low temperature. Analysis of the deformation electron density has revealed the presence of the quasi-two-dimensional sheets of the —V—O—V—O— bonds in the structure. The electron density in the different chemical bonds within each of the three crystallographically independent VO6 polyhedra noticeably varies, although there is no clear evidence that the three crystallographically independent V atoms have different valence states.
Structure refinement of the layered composite crystal Sc2B1.1C3.2 in a five-dimensional formalism
Authors: Onoda Mitsuko , Shi Ying , Leithe-Jasper A. , Tanaka Takaho
Published: July 2002

The crystal structure of a layered compound Sc2B1.1C3.2, scandium boride carbide (M

r
= 140.43), has been re-refined as a commensurate composite crystal using 1795 single-crystal X-ray diffraction intensities with I > 2\sigma(I) collected by Shi, Leithe-Jasper, Bourgeois, Bando & Tanaka [(1999), J. Solid State Chem.
148, 442–449]. The crystal is composed of two layered subsystem structures, i.e. Sc—C—Sc sandwiches and graphite-like layers of the composition B1/3C2/3. The structure refinement was performed in a five-dimensional formalism based on the trigonal superspace group P\bar{3}m1(p00)(0p0)0m0. The unit cell and other crystal data are a = b = 3.387 (1), c = 6.703 (2) Å, V = 66.59 (1) Å3, \boldsigma_{1} = (9/7 0 0), \boldsigma_{2} = (0 9/7 0), Z = 1, D

x
= 3.501 Mg m−1. Two different three-dimensional sections through the superspace were analyzed, corresponding to two different superstructure models, one with P\bar{3}m1 and the other with P\bar{3}m1. A random distribution of B and C was assumed in the graphite-like layer and 41 structural parameters were introduced. R

F
/wR

F
} were 0.0533/0.0482 and 0.0524/0.0476, respectively, for the first and second models. Although the difference between these R

F
or wR

F
values was too fine to exclude one of the models definitely, the advantages of using a superspace group were obvious. It not only brought about better convergence of refinement cycles by virtue of fewer parameters, but also gave an insight into the problem of symmetry of the superstructure.
Z′ = 4 structure without obvious pseudosymmetry: implications for the formation of solid-state compounds
Authors: Lehmler Hans-Joachim , Robertson Larry W. , Parkin Sean , Brock Carolyn Pratt
Published: July 2002

Crystals of 4-chloro-2′-biphenylol grown at 263 K and studied at both 293 and 142 K are loosely packed and contain OH...O bonded tetramers composed of four crystallographically independent molecules (Z′ = 4). Approximate symmetry relationships between independent molecules are apparent in many, perhaps even most, structures with Z′ > 1, but are not obvious in this structure. The inefficient crystal packing, the surprisingly large value of Z′ and the absence of pseudosymmetry reflect the difficulty of finding a dense molecular arrangement that also allows for hydrogen-bond formation. Impediments to good packing are the steric congestion around the ortho hydroxyl groups and the difficulty in filling space with significantly twisted biphenyl fragments. The packing arrangement adopted is strongly reminiscent of the structure type found for eight simple 4,4′-biphenyl derivatives, but one of the four independent 4-chloro-2′-biphenylol molecules has an orientation that is significantly different from the orientations of the other three and that does not fit the 4,4′-XPhPhY pattern. It is suggested that molecules that crystallize with Z′ > 1 are good candidates for solid-state compound formation.
The Powder Diffraction File: present and future
Authors: Faber John , Fawcett Tim
Published: July 2002

The International Centre for Diffraction Data (ICDD) produces the Powder Diffraction File (PDF). This paper discusses some of the seminal events in the history of producing this primary reference for powder diffraction. Recent key events that center on collaborative initiatives have led to an enormous jump in entry population for the PDF. Collective efforts to editorialize the PDF are ongoing and provide enormous added value to the file. Recently, the ICDD has created a new series of the PDF, designated PDF-4. These relational database structures are being used to house the PDF of the future. The design and benefits of the PDF-4 are described.
Structure at 200 and 298 K and X-ray investigations of the phase transition at 242 K of [NH2(CH3)2]3Sb2Cl9 (DMACA)
Authors: Zaleski J. , Pietraszko A.
Published: July 2002

[NH2(CH3)2]3Sb2Cl9 (dimethylammonium nonachlorodiantimonate, DMACA) has, at 200 K, a monoclinic Pc space group, with a = 9.470 (3), b = 9.034 (3), c = 14.080 (4) Å, β = 95.81 (3)°, V = 1198.4 (4) Å3, Z = 2 [R = 0.024, wR = 0.025 for 4613 independent reflections with F > 4σ(F)]. At 298 K DMACA has P21/c space group with a = 9.686 (3), b = 9.037 (3), c = 14.066 (4) Å, β = 95.57 (3)°, V = 1225.3 (5) Å3, Z = 2 [R = 0.034, wR = 0.035 for 2736 reflections with F > 4σ(F)]. The anionic sublattice of DMACA consists of polyanionic (Sb2Cl9
3−), layers. In the low-temperature phase there are three crystallographically non-equivalent dimethylammonium cations in the crystal structure. One of the cations is located inside the polyanionic layers, two others – one ordered and one disordered – between the polyanionic layers. In the room-temperature phase there are two non-equivalent cations – both disordered – in the crystal structure. Temperature dependencies of lattice parameters between 200 and 300 K were determined. The occurrence of a second-order phase transition at T = 242 K was confirmed. The dependence of lengths of Sb—Cl contacts on the presence and strength of N—H...CI hydrogen bonds was discussed. It was found that lengths of Sb—Cl bonds may differ from each other by as much as 0.3 Å, because of the presence of N—H...Cl hydrogen bonds. These differences were attributed to distortion of the lone-electron pair on antimony(Ill).
Theoretical study of the deformation densities of d electrons in K2[PdCl6] and K2[PtCl6] crystals
Authors: Sakai Y. , Oshibe T. , Miyoshi E.
Published: July 2002

Aspherical distributions of the d electrons in dipotassium palladium hexachloride, K2[PdCl6], and dipotassium platinum hexachloride, K2[PtCl6], crystals were analyzed by theoretical calculations. Hartree–Fock and configuration interaction calculations were performed for [PdCl6]2− and [PtCl6]2− with and without taking into account the Madelung potentials, using a model potential method. The major relativistic effects were incorporated in the model potentials for Pd and Pt. The deformation-density maps calculated were similar to those given by the X-ray diffraction method. The theoretical result suggested that the positive peaks on the threefold axes and the negative peaks on the metal—Cl bond axis correspond to the excess d electrons (4d of Pd and 5d of Pt) in the t
2g
(dxy, dxz, dyz
) orbitals and the electron deficiency in the eg
(dz
2,dx
2−
y
2) orbitals, respectively. The positive and negative peak heights were calculated to be +1.8 and −0.8 e Å−3 for [PdCl6]2− and +1.2 and −0.6 e Å−3 for [PtCl6]2−. The effective charges and effective radii of Pd and Pt, and the number of electrons in the t
2g
, eg
and t
1u
orbitals, were calculated by direct integration. The effects of the Madelung potential and electron correlation on the charge distributions of [PdCl6]2− and [PtCl6]2− were also analyzed.
Statistical Analysis of Noncovalent Interactions of Anion Groups in Crystal Structures. III. Metal Complexes of Thiocyanate and their Hydrogen-Donor Accepting Function
Authors: Tchertanov L. , Pascard C.
Published: July 2002

The bidentate function of the thiocyanate anion was studied using the Cambridge Structural Database System. Complexing properties (metal–thiocyanate interactions) with respect to metal cations were analysed. Two main classes were distinguished: (a) alkali and alkaline earth metals, and (b) metals of Zn and Cu groups and transition metals (group VIII). Good correlations were found between the nature of the metal (radius, oxidation state and charge) and its position relative to the thiocyanate unit. Hydrogen-bond acceptor properties of discrete and complexed SCN units were compared. The extraordinarily active hydrogen-bonding behaviour allows this anion to act as a powerful bridge between different molecular fragments. In metal complexes the cation provokes a redistribution of anionic charge in SCN and the distribution of electron density, in turn, controls the hydrogen-bonding properties of the terminal acceptor atom. Binding properties of thiocyanate in biological systems were illustrated using the Brookhaven Protein Data Bank. A comparison of anion binding in small-molecule structures and in macromolecular structures shows good agreement.
Temperature-Dependent Phase Transitions in Two Crystalline Host–Guest Complexes Derived from Mandelic Acid
Authors: Hager O. , Foces-Foces C. , Llamas-Saiz A. L. , Weber E.
Published: July 2002

The supramolecular inclusion complexes of two mandelic acid-based chiral host compounds with dimethylformamide (DMF), (1) and (2), show reversible solid–solid state phase transitions upon lowering the temperature. For both inclusion complexes, the low- [(1a) and (2a) at 170 K] and the high- [(1b) at 250 and (2b) at 270 K] temperature structures were solved. (R)-1,1-Bis(4-tert-butylphenyl)-2-phenylethan-1,2-diol–dimethylformamide (1/1), C28H34O2.C3H7NO (1a), T = 170 K, monoclinic, P21, a = 14.4530 (14), b = 6.0540 (2), c = 16.1117 (14) Å, β = 105.332 (7)°, V = 1359.6 (2) Å3, Z = 2,
D

x

= 1.162 g cm−3; (1b), T = 250 K, monoclinic, P21, a = 24.8110 (20), b = 6.0739 (2), c = 18.8645 (10) Å, β = 98.100 (6)°, V = 2814.5 (3) Å3, Z = 4,
D

x

= 1.123 g cm−3. (R)-1,1-Bis(4-tert-butylphenyl)-2-(4-methylphenyl)ethan-1,2-diol–dimethylformamide (1/1), C29H36O2.C3H7NO (2a), T = 170 K, monoclinic, P21, a = 24.4457 (38), b = 5.9519 (6), c = 20.4609 (38) Å, β = 101.95 (1)°, V = 2912.5 (8) Å3, Z = 4,
D

x

= 1.117 g cm−3; (2b), T = 270 K, triclinic, P1, a = 14.4172 (28), b = 6.0303 (4), c = 17.5636 (56) Å, α = 88.74 (1), β = 101.43 (2), γ = 93.13 (1)°, V = 1494.4 (6) Å3, Z = 2,
D

x

= 1.088 g cm−3. The low-temperature forms have the higher crystallographic symmetry. In (1b) half of the DMF guests are twisted by 45.0° with respect to those in (1a). A comparative discussion of the four crystal packings is presented.
Intermolecular Force-Field Parameters for Boron Hydrides
Authors: Williams D. E. , Gao D.
Published: July 2002

Intermolecular atom–atom force-field parameters of the (exp-6-1) type for B and H atoms in boron hydrides were determined. They were obtained by full-weighted least-squares minimization of 116 forces in 15 observed crystal structures of boranes, the heat of sublimation of B10H14 and data from ab initio wavefunction calculations for diborane. Net atomic charges were obtained by fitting them to molecular electric potentials calculated from ab initio wavefunctions. Charges of terminal hydrogens were usually negative and those of bridging hydrogens usually positive. Repulsion-energy calculations for the B2H6 dimer provided the exponential dependence of H...H repulsion. Using the resulting force field, minimum-energy crystal structures were found with structural parameter values close to those of the observed structures. For diborane, energy minimization beginning with randomly oriented molecules placed initially in an 8 × 8 × 8 body-centered orthogonal cell led to the observed crystal structure and monoclinic space group.
Multicomponent Polyanions. 53. Structure of Tetrakis(trimethylammonium) Tetra-μ-oxo-bis(triaquahexadecaoxo(trioxophenylphosphato)hexamolybdate) Dihydrate, [NH(CH3)3]4[{(C6H5P)Mo6O21(H2O)3}2].2H2O
Authors: Lyxell D.-G. , Boström D. , Hashimoto M. , Pettersson L.
Published: July 2002

The title compound crystallized in the monoclinic space group P21/n (No. 14) [a = 11.211 (5), b = 12.862 (3), c = 23.05 (1) Å, β = 94.37 (3)°, V = 3314 (2) Å3, Z = 2]. The polyanion can be regarded as a dimer of a phenylphosphonatohexamolybdate, (C6H5P)Mo6O23(H2O)3, linked by four O atoms. In this monomeric unit the six molybdenum octahedra are grouped into two parts consisting of four and two edge-sharing octahedra, respectively. These two parts are connected by two corner-sharing O atoms to form a bent Mo6 ring. The phenylphosphonate group coordinates to the Mo6 ring from the narrow side as a tripodal ligand. The {(C6H5P)Mo6O21(H2O)3}2 units form layers parallel to (001) and the structure is stabilized by hydrogen bonds between water and neighboring anions. The monomeric unit has been shown to be a key structure in the process of deducing the aqueous solution structures of the (C6H5P)Mo_6^{2-} and (C6H5P)Mo_7^{4-} species found in a previous equilibrium study of the H+–MoO_4^{2-}–(C6H5P)O_3^{2-} system.
Superstructure Ordering of Intermetallics: B8 Structures in the Pseudo-Cubic Regime
Authors: Lidin S.
Published: July 2002

The structural chemistry of the intermetallic B8-type compounds is reviewed.
Oxime–Carboxyl Hydrogen Bonds: the Preferred Interaction Determining Crystal Packing of `Carboxyoximes'
Authors: Maurin J. K.
Published: July 2002

The statistical analysis of hydrogen-bond interactions formed by oximes and carboxylic acids has been performed. Ab initio quantum-chemical calculations have been used to rationalize the observed preference for the oxime–carboxyl interaction compared with homologous binding (carboxyl–carboxyl and oxime–oxime). The crystal packing observed in the structure of pyruvic acid oxime (hydroxyiminopyruvic acid) has been explained as the consequence of a combination of the energetically optimal structure of the isolated molecule and the optimal interaction of monomers forming a dimer.
Electrostatic lattice energy in ionic crystals: optimization of the convergence of Ewald series
Authors: Catti M.
Published: July 2002

Ewald's method is reconsidered to express the dependence of Madelung energy on the ionic charges explicitly, also taking into account the space-group symmetry of the structure. Upper bounds for the residues of the two partial series have been calculated by integral approximation; that relative to the direct-lattice series is shown to depend on the cube root of the unit-cell volume. The optimum value of the parameter A, which equalizes the rates of convergence of the two sums and minimizes the total number of terms, has been determined numerically for a given termination error and for a range of unit-cell dimensions. Theoretical results are tested by calculations on some specific crystal structures.
Resolution measurement in structures derived from single particles
Authors: Grigorieff Nikolaus
Published: July 2002

Analytical expressions are derived and computer simulations are presented to assess the accuracy of procedures commonly used to estimate the resolution of three-dimensional (3D) structures derived from images of single protein molecules or complexes. It is shown that in the case of a low signal-to-noise ratio in the images, the Fourier ring correlation between two structures, each calculated using one half of the data, significantly overestimates the resolution when the two half data sets were aligned against the same reference structure. The overestimate arises because of a correlation between the noise components present in the images. The correlation is introduced by the alignment and becomes more serious as the signal-to-noise ratio is reduced. A reliable resolution measure is only obtained when the two half data sets are aligned against two independent reference structures. It is further shown that the noise correlation also significantly affects the spectral signal-to-noise ratio and the Q factor, making them unreliable measures of signal present in a 3D structure and in the original images, respectively. It is concluded that the alignment of images is always accompanied by a correlation of the noise and that this correlation is indistinguishable from a correlation arising from a signal.
Fitting atomic models into electron-microscopy maps
Authors: Rossmann Michael G.
Published: July 2002

Combining X-ray crystallographically determined atomic structures of component domains or subunits with cryo-electron microscopic three-dimensional images at around 22 Å resolution can produce structural information that is accurate to about 2.2 Å resolution. In an initial step, it is necessary to determine accurately the absolute scale and absolute hand of the cryo-electron microscopy map, the former of which can be off by up to 5%. It is also necessary to determine the relative height of density by using a suitable scaling function. Difference maps can identify, for instance, sites of glycosylation, the position of which helps to fit the component structures into the EM density maps. Examples are given from the analysis of alphaviruses, rhinovirus–receptor interactions and poliovirus–receptor interactions.
Structure of Human Apolactoferrin at 2.0 Å Resolution. Refinement and Analysis of Ligand-Induced Conformational Change
Authors: Jameson Geoffrey B. , Anderson Bryan F. , Norris Gillian E. , Thomas David H. , Baker Edward N.
Published: July 2002

The three-dimensional structure of a form of human apolactoferrin, in which one lobe (the N-lobe) has an open conformation and the other lobe (the C-lobe) is closed, has been refined at 2.0 Å resolution. The refinement, by restrained least-squares methods, used synchrotron radiation X-ray diffraction data combined with a lower resolution diffractometer data set. The final refined model (5346 protein atoms from residues 1–691, two Cl− ions and 363 water molecules) gives a crystallographic R factor of 0.201 (R
free = 0.286) for all 51305 reflections in the resolution range 10.0–2.0 Å. The conformational change in the N-lobe, which opens up the binding cleft, involves a 54° rotation of the N2 domain relative to the N1 domain. This also results in a small reorientation of the two lobes relative to one another with a further ∼730 Å2 of surface area being buried as the N2 domain contacts the C-lobe and the inter-lobe helix. These new contacts also involve the C-terminal helix and provide a mechanism through which the conformational and iron-binding status of the N-lobe can be signalled to the C-lobe. Surface-area calculations indicate a fine balance between open and closed forms of lactoferrin, which both have essentially the same solvent-accessible surface. Chloride ions are bound in the anion-binding sites of both lobes, emphasizing the functional significance of these sites. The closed configuration of the C-lobe, attributed in part to weak stabilization by crystal packing interactions, has important implications for lactoferrin dynamics. It shows that a stable closed structure, essentially identical to that of the iron-bound form, can be formed in the absence of iron binding.
1.7 Å structure of the stabilized REIv mutant T39K. Application of local NCS restraints
Authors: Usón Isabel , Pohl Ehmke , Schneider Thomas R. , Dauter Zbigniew , Schmidt Arno , Fritz Hans-Joachim , Sheldrick George M.
Published: July 2002

The X-ray structure of the T39K mutant of the variable domain of a human immunoglobulin κ light chain has been determined at room temperature to 1.7 Å resolution with a conventional R factor of 0.182. T39K crystallizes in the triclinic space group P1 [a = 35.4 (1), b = 40.1 (1), c = 43.1 (1) Å, α = 66.9 (1), β = 85.4 (1), γ = 73.8 (1)°]. The unit-cell contains two monomers, related by a non-crystallographic twofold axis. The use of a novel type of local non-crystallographic symmetry restraints on related isotropic displacement parameters and 1–4 distances as incorporated in the refinement program SHELXL improves the model and quality of the maps, but local differences between both monomers in areas subject to different packing contacts can still be observed. 12 overall anisotropic scaling parameters were refined. These may have compensated for the difficulties in accurately scaling single rotation axis image-plate data from a triclinic crystal, because of the scarcity of common equivalent reflections. The final model has been used to perform a number of tests on anisotropic scaling, non-crystallographic symmetry, anisotropic refinement, determination of standard uncertainties and bulk solvent correction. It is remarkable that removal of the NCS restraints from the final model caused R
free to increase. These tests clarify the strategies for optimum use of SHELXL for refinement at medium as opposed to atomic resolution.
Preliminary crystallographic studies of a protease-resistant botulinum neurotoxin associated protein Hn-33
Authors: Hadfield Andrea T. , Petsko Greg , Lindo Paul , Singh Bal-Ram
Published: July 2002

Botulinum neurotoxin (BoNT) is one of the most potent toxins known. BoNT is also a food poison, which means that the toxin must survive the protease action and acidity of the gut. A group of neurotoxin-associated proteins which are only beginning to be identified and characterized are believed to be responsible for this protection. Hn-33 is a 33 kDa polypeptide which is a major component of the type A botulinum neurotoxin complex. Crystals of Hn-33 have been grown by vapour-diffusion techniques. They belong to a primitive orthorhombic space group and diffract to a resolution of 2.6 Å, with unit-cell parameters a = 130.3, b = 122.2, c = 37.2 Å.
Crystallization and preliminary diffraction data analysis of both single and pseudo-merohedrally twinned crystals of rubredoxin oxygen oxidoreductase from Desulfovibrio gigas
Authors: Frazão C. , Sieker L. , Coelho R. , Morais J. , Pacheco I. , Chen L. , LeGall J. , Dauter Z. , Wilson K. , Carrondo M. A.
Published: July 2002

Crystals of rubredoxin oxygen oxidoreductase have been obtained and characterized. They belong to space group P21212, with unit-cell dimensions a = 88.24 (15), b = 101.25 (7), c = 90.80 (3) Å. The homodimer (86 kDa) in the asymmetric unit is related by a non-crystallographic twofold rotation axis parallel to the ab `diagonal' direction, as shown by the self-rotation maximum in the section with χ = 180°. This pseudo-crystallographic symmetry element was also found to be the twinning axis of pseudo-merohedrally twinned crystals, leading to apparent pseudo-tetragonal P4212 crystal symmetry.
Crystallization and preliminary X-ray studies of flavocetin-A, a platelet glycoprotein Ib-binding protein from the habu snake venom
Authors: Fukuda Kouichi , Mizuno Hiroshi , Atoda Hideko , Morita Takashi
Published: July 2002

Flavocetin-A (FL-A) is a platelet glycoprotein Ib-binding protein, a high molecular mass oligomer (149 kDa) of C-type lectin-like subunits α and β isolated from the habu snake venom. Purified FL-A crystallized in the tetragonal space group I4 with unit-cell dimensions a = b = 121.0, c = 63.2 Å. The crystals diffract to at least 2.4 Å resolution. The structure has been solved by molecular replacement using the crystal structure of factors IX/X-binding protein (PDB code 1ixx) as a search model. The asymmetric unit contains one heterodimer, showing that FL-A is a novel tetradimer (αβ)4 composed of four heterodimers related by a crystallographic fourfold axis.
Theory of resonant X-ray emission spectroscopy
Authors: Kotani A.
Published: July 2002

A short review is presented of recent topics in resonant X-ray emission spectroscopy (RXES), especially of the polarization dependence of RXES in d and f electron systems. Polarization-dependent RXES provides important information on the symmetry of electronic states. A scattering-angle dependence in the fluorescence yield of rare-earth metals, RXES in polarized and depolarized configurations of TiO2, and the magnetic circular dichroism in RXES of ferromagnetic systems are discussed together with typical experimental data.
A study of uranium speciation in acetate solutions at temperatures from 25 to 250°C
Authors: Mosselmans J. Frederick , Bailey Elizabeth , Schofield Paul
Published: July 2002

We report U L3-edge XAS analysis results from a study of the speciation of U(VI) in acetate solutions between 25 and 250°C, at pH's between 1.82 and 2.57 and [acetate]:[U] ratios of 0.5 to 50. At 25°C in excess acetate there are at least two acetate ligands in the equatorial plane with a U-O bond distance of 2.44 Å. At elevated temperatures with excess acetate, acetate is still coordinated but the speciation mixture appears more complicated. Less evidence exists for acetate coordination when [acetate]:[U] ratio is unity or below. pH within this limited range appears to have little effect on the uranyl speciation. Keywords: , Uranium, high-temperature solutions
Glancing-angle diffraction anomalous fine structure of InAs quantum dots and quantum wires
Authors: Grenier S. , Proietti M. G. , Renevier H. , Gonzalez L. , García J. M. , Gérard J. M. , García J.
Published: July 2002

We have performed Diffraction Anomalous Fine Structure measurements at the As K-edge of self-growth InAs/InP(001) Quantum Wires and InAs/GaAs(001) Quantum Dots. The samples have been grown by Molecular Beam Epitaxy and their equivalent thickness is of 2.5 monolayers. We have measured the (440) and (420) Bragg reflections in glancing-angle scattering geometry, at incidence angles close to the substrate critical angle. We demonstrate the feasibility of the experiment reporting, for the first time, Diffraction Anomalous Fine Structure spectra of such low coverage epitaxial layers, and we show that the analysis of the Diffraction Anomalous Fine Structure lineshape together with the analysis of oscillatory part of the signal, can provide information about composition and strain of the nanostructures.
Photon-stimulated ion desorption from molybdenum oxides following Mo 2p
3/2 excitation
Authors: Wu Guohua , Baba Yuji , Sekiguchi Tetsuhiro , Shimoyama Iwao
Published: July 2002

Photon-stimulated ion desorption from solid MoO3 following the Mo 2p3/2 resonant transition has been investigated. In the XANES spectrum, Mo 2p3/2 peak is split into two components corresponding to the excitations from Mo 2p3/2 into the t2g and eg orbitals. It was observed that the desorption yield of O+ ions at the Mo 2p3/2 ⇒ eg resonance is higher than that at the Mo 2p3/2 ⇒ t2g resonance. The Auger decay spectra reveal that there exist two kinds of spectator Auger decays. The high desorption yield at the 2p3/2 ⇒ eg resonance is interpreted by the fast breaking of the Mo-O bond due to the localization of the electrons in the highly antibonding eg.
Manganese, iron and sulfur K edge XAFS of promoted sulfated zirconia catalysts
Authors: Jentoft Rolf E. , Hahn Alexander , Jentoft Friederike C. , Ressler Thorsten
Published: July 2002

Promoted sulfated zirconia samples were prepared by the incipient wetness technique to produce isomerization catalysts which were active for the conversion of n-butane to isobutane at 338K (up to 10% conversion of 1% n-butane, 1atm., 0.25 h−1 WHSV). The local structure of Fe and Mn in promoted sulfated zirconia was investigated using fluorescence yield XAS. Spectra were taken of calcined samples, activated samples, and samples after reaction with n-butane (maximum activity and deactivated). Factor analysis reveals that the Mn K edge XANES can be described by a linear combination of the spectra of two separate components, and that the ratio of these components changes with activation of the catalyst, and during use in the n-butane isomerization reaction. The change in ratio of the Mn species during activation and reaction results in a reduction of the average Mn valence from 2.4 to 2.2. The Fe K edge XANES was not similarly affected by activation and reaction with n-butane.
Investigations on the local structure of Ag+/ZSM-5 catalysts and their photocatalytic reactivities for the decomposition of N2O at 298 K
Authors: Matsuoka Masaya , Ju Woo-Sung , Yamashita Hiromi , Anpo Masakazu
Published: July 2002

Ag+/ZSM-5 catalysts were prepared by an ion-exchange method and UV-irradiation of the catalysts in the presence of N2O led to the photocatalytic decomposition of N2O into N2 and O2 at 298 K. Investigations on the effective wavelength of irradiated UV-light for the reaction as well as the in-situ characterization of the catalysts by means of XAFS, UV-Vis, photoluminescence and FT-IR spectroscopies revealed that the photoexcitation of the Ag+-N2O complexes formed between gaseous N2O and the isolated Ag+ ions play a significant role in this reaction.
Tuning of X-ray phase retarder for magnetic EXAFS spectroscopy in helicity modulation mode
Authors: Suzuki Motohiro , Kawamura Naomi , Ishikawa Tetsuya
Published: July 2002

A technique for polarization tuning over a wide energy range has been developed for magnetic EXAFS spectroscopies using a diamond x-ray phase retarder in helicity modulation mode. A quick rocking scan using a piezo stage enabled us to tune the angle of retarder crystal with the precision of ±2 arcsecond within 1 s. Available energy range of circular dichroism measurements has been extended to 6-16 keV by adopting not only undulator gap scan but also the present tuning technique. This technique has been applied to magnetic EXAFS measurements in pure iron at the Fe K-edge. Higher signal-to-noise ratio was obtained in reduced data acquisition time.
Quantitative analysis of L-edge white line intensities: the influence of saturation and transverse coherence
Authors: Hahlin Anders , Karis Olof , Brena Barbara , Hunter Dunn Jonathan , Arvanitis Dimitri
Published: July 2002

We have performed x-ray absorption spectroscopy at the Fe, Ni, and Co L
2,3 edges of in situ grown thin magnetic films. We compare electron yield measurements performed at SSRL and BESSY-I. Differences in the L
2,3 white line intensities are found for all three elements, comparing data from the two facilities. We propose a correlation between spectral intensities and the degree of spatial coherence of the exciting radiation. The electron yield saturation effects are stronger for light with a higher degree of spatial coherence. Therefore the observed, coherence related, intensity variations are due to an increase in the absorption coefficient, and not to secondary channel related effects.
X-ray magnetic circular dichroism in cobalt–iron spinels and electronic states of Co ions
Authors: Kita Naonori , Shibuichi Naoto , Sasaki Satoshi
Published: July 2002

Synchrotron X-ray experiments on magnetic circular dichroism (XMCD) have been performed at Co K and Fe K absorption edges for CoFe2O4, Fe1.5Co1.5O4 and FeCo2O4 with the spinel structure. The XANES studies have clarified that only Fe3+ exists in all compounds and Co2+ and Co3+ coexist in the latter two cobaltites. A systematic change in XMCD spectra has concluded that the Co2+ ions in the B sites of FeCo2O4 are in the low-spin state. Since the Co2+ ions in CoFe2O4 are in the high-spin state, the spectra of the intermediate cobaltite may be explained as a mixture of low-spin and high-spin states.
Determination of parameters of valence states by using XANES
Authors: Migal Yu. F. , Kovaleva V. S.
Published: July 2002

A new approach for the parametrization of valence states of atoms in molecules and solids, facilitating the deciphering of experimental XANES spectra, is proposed. It is shown that energies and half-widths of XANES maxima of the one-electron origin depend mainly on the arrangement of atoms and energies and mean radii of atomic valence states. Just these quantities having distinct physical meaning must be determined above all from experiment. A procedure for such a determination is developed. Values of energies and mean radii of the nitrogen and oxygen atoms in some molecules are obtained.