bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystal and molecular structure of 1,25-dihydroxycholecalciferol
Authors: Suwińska K. , Kutner A.
Published: July 2002

The structure of 1,25-dihydroxycholecalciferol, 1,25-dihydroxy-9,10-secocholesta-5,7,10(19)-trien-3-ol, has been solved by direct methods and refined against F
2 to R
1 = 0.08 for 2637 reflections with F > 4σ(F) and 0.222 for all 3412 data. Crystal data: C27H44O3.3H2O, Mr
= 470.67, orthorhombic, P212121, a = 6.234 (2), b = 15.628 (3), c = 30.749 (10) Å, V = 2995.7 (15) Å3, Z= 4, Dx
= 1.044 Mg m−3, (Cu Kα) = 1.54178 Å, μ = 0.572 mm−1, F(000) = 1040, room temperature. Of the three water molecules present in the crystals of this compound, one is involved in a network of hydrogen bonds formed with the hydroxyl groups of the compound, the remaining two are disorderly arranged in channels formed along the crystallographic x axis with no hydrogen-bonding interactions with the compound molecules. The conformation of the cyclohexane-like ring A was found to be exclusively in the β form. Stabilization of the conformer in the solid state may be due to the formation of hydrogen bonds to water molecules, as well as to the symmetry-related 1,25-(OH)2-vitamin D3 molecules.
Ab initio Hartree–Fock study of the electronic charge density of the cubic boron nitride and its comparison with experiments
Authors: Lichanot A. , Azavant P. , Pietsch U.
Published: July 2002

The electronic charge density of cubic boron nitride is calculated within the ab initio Hartree–Fock approximation using the program CRYSTAL. Based on Debye hypothesis, the thermal motion of atoms is considered by disturbing the atomic orbitals by mean-square displacements given from experiment. The calculated difference charge density obtained by subtraction of the total density and that of an independent atomic model (IAM) is characterized by a charge-density accumulation between next neighbours slightly shifted towards the nitrogen. The calculated X-ray structure amplitudes are compared with two different data sets [Josten (1985). Thesis. University of Bonn, Germany; Eichhorn, Kirfel, Grochowski & Serda (1991). Acta Cryst. B47, 843–848]. In both cases, very good agreement is found beyond the 420 reflection. The first six structure amplitudes are generally lower or larger compared with Josten's and Eichhorn et al.'s data, respectively. Whereas our charge density can be interpreted by a balanced ratio between covalent overlap and electronic charge transfer between neighbouring valence shells, the density plots calculated from experimental data express either the charge transfer (Josten, 1985) or the covalency (Eichorn et al., 1991).
Methyl group conformation-determining intermolecular C–H...O hydrogen bonds: structure of N-methyl-2-pyrrolidone
Authors: Müller G. , Lutz M. , Harder S.
Published: July 2002

The structure of N-methyl-2-pyrrolidone (NMP; 1-methyl-2-pyrrolidinone) was determined at 168 K. Crystal data: m.p. 249 K, monoclinic P21/c, a = 6.221 (3), b = 12.076 (2), c = 7.529 (4) Å, β = 111.03 (2)°, V = 527.9 (4) Å3, Z = 4, Dx
= 1.247 Mg m−3, μ = 0.082 mm−1, R = 0.058 for 1190 unique reflections. It adopts a slightly puckered ring conformation in the solid state, which is intermediate between a twist and an envelope conformation. The N-methyl group takes part in two almost linear intermolecular C—H...O hydrogen bonds to neighbouring keto groups [d(H...O) = 2.57 (2)/ 2.65 (2) Å, d(C...O) = 3.552 (2)/3.482 (2) Å, angle (C—H...O) = 160 (1)/148 (2)°], which cause a notable deviation from its usually preferred conformation with one C—H bond being almost eclipsed to the adjacent N—C amide bond. These findings are substantiated by force-field and high-level ab initio calculations on isolated NMP molecules.
Effect of Habit Modification on Optical and X-ray Structures of Sodium Halate Mixed Crystals: The Etiology of Anomalous Double Refraction
Authors: Crundwell G. , Gopalan P. , Bakulin A. , Peterson M. L. , Kahr B.
Published: July 2002

Structures of mixed crystals of the isomorphous salts NaClO3 and NaBrO3 (sodium chlorate and sodium bromate, respectively) were reinvestigated by X-ray diffraction. Contrary to previous reports, NaCl
x
Br1−x
O3 is not cubic. Data from adjacent {100} growth sectors of crystals of varying composition were refined in the triclinic space group P1; halate ions occupy nominally symmetry-related sites nonstatistically. Optical measurements showed that six asymmetric sectors in cubes are disposed to give an object with approximate tetrahedral point symmetry. We address forgotten anomalies, first observed almost 150 years ago, which could have been a sufficient basis for earlier structural reinvestigations. The mixed-crystal structure speaks to the general non-applicability of the Law of Isomorphism to solid solutions. A link between optical anisotropy and nonstatistical guest site occupancy was achieved by annealing crystals between 523 and 533 K. Na2S2O3 and Na2S2O6 were used as habit-modifying impurities to produce NaCl
x
Brl−x
O3 crystals with {111} and {\overline 1\overline 1\overline 1} habits, respectively. Diffraction data from {111} and {\overline 1\overline 1\overline 1} growth sectors were refined in the trigonal space group R3. In each case the pyramidal halate ion that was located on the special position was depleted in BrO3
−. Conoscopic optical investigations nevertheless showed that the crystals are biaxial with a small 2V (10–15°), in marked contrast to the 90° angle in {100} crystals. We failed to reconcile the optical and X-ray structures by calculating the optical indicatrix with bond polarizability sum models. This led us to estimate the magnitude of other factors which contribute to the optical properties, including strain associated with dislocations which may exert its influence through combined piezoelectric and linear electro-optic effects.
The perils of Cc revisited
Authors: Marsh R. E.
Published: July 2002

The space groups of 98 structures originally reported in Cc are revised. In 75 cases the revised space group is C2/c and the revision entails adding a center of symmetry, usually leading to large changes in bond lengths and angles. In the remaining 23 cases, where the revised space group is Fdd2, R3c or (in one case) I\overline 4c2, the lattice type is changed but no center is added; in these cases the molecular dimensions are effectively unchanged.
Diethyl 2-Benzimidazol-1-ylsuccinate–Picric Acid (1/1) – An Inclusion Molecular Complex
Authors: Zaderenko P. , Gil M. S. , López P. , Ballesteros P. , Fonseca I. , Albert A.
Published: July 2002

The crystal structure of the diethyl 2-benzimidazol-1-ylsuccinate–picric acid (1/1) molecular complex has been determined by X-ray diffraction analysis. Diethyl 2-benzimidazol-l-ylsuccinate molecules form channels along the a axis, in which the picric acid molecules are located. The benzimidazole moiety and the phenol group are held together by hydrogen bonding between the hydrogen of the phenol and the N3 atom of benzimidazole. Additionally, this hydrogen forms an intramolecular hydrogen bond with one O atom of the ortho-nitro group, thus producing a bifurcated hydrogen bond. 1H NMR spectra in DMSO-d
6 solution and CP/MAS solid 13 C NMR studies of this 2-benzimidazol-1-ylsuccinate–picric acid (1/1) molecular complex, as well as those of dimethyl, diethyl, di-n-butyl and 1-n-butyl-4-ethyl 2-imidazol-1-ylsuccinates, diethyl 2-pyrazol-1-ylsuccinate, ethyl imidazol-1-ylacetate, ethyl pyrazol-1-ylacetate and ethyl pyrazol-l-ylsuccinate, suggest that the picric acid linkage depends on the nature of the azole. Actual proton transfer is deduced for the imidazole derivatives, but only weak hydrogen bonding could be inferred for pyrazole derivatives.
Recognizing the (False Symmetry) Triclinic (aP) to (True Symmetry) Centred Monoclinic (mC) Pathology
Authors: Herbstein F. H.
Published: July 2002

Some fifty-odd published examples of corrections from (false symmetry) triclinic to (true symmetry) centred monoclinic (aP to mC) are analysed to see whether the need for correction of symmetry should have been obvious to the original investigators. We conclude that about two-thirds of the examples were transparent in that special features of the dimensions of the reduced triclinic cell should have aroused the suspicions of the investigator. For the other third, calculation of the metric tensor would have indicated the possibility of symmetry higher than triclinic. However, it should always be remembered that the true symmetry of a crystal is revealed by intensity rather than by metric relationships, or by other techniques such as optical microscopy.
Classification and Distortion in Six-Coordinate Bis(salicylaldiminato)nickel(II) Complexes: Crystal Structure of Bis[2-[[(2-hydroxyphenyl)methylene]amino]-1-phenyl-1,3-propanediolato]nickel(II).2H2O
Authors: Główka M. L. , Olczak A. , Karolak-Wojciechowska J. , Ciechanowska-Urbańska E.
Published: July 2002

The crystal structure of a NiII complex with a tridentate chiral ligand has been determined with a final R of 0.042. The crystals were hexagonal, space group P61 with Z = 6, a = b = 18.498 (2), c = 16.328 (2) Å. The complex shows local tetrahedral (skewed) coordination of the metal by two salicyladimine ligands with a tetrahedrality angle of 89.4 (2)° and the Ni shifted by 0.13 Å from the geometric center of the coordination octahedron, both values being the largest ones observed so far in similar NiII six-coordinate complexes. Also a new, simple classification of six-coordinate bis(salicylaldiminato) complexes, based on the relative positions of coordinating atoms, has been proposed.
Structural, Thermodynamic and Kinetic (Hysteresis) Aspects of the Enantiotropic First-Order Phase Transformations of N-Anilinophthalimide and N-(N'-Methylanilino)phthalimide
Authors: Botoshansky M. , Ellern A. , Gasper N. , Henck J.-O. , Herbstein F. H.
Published: July 2002

The crystal structures of the orthorhombic and monoclinic polymorphs of N-anilinophthalimide (m.p. of monoclinic polymorph 457 K) have been determined by X-ray diffraction at 293 K and were found to have only small differences between the molecular conformations in the two phases, but quite different molecular arrangements. There is very weak N—H...O hydrogen bonding in the orthorhombic phase and weak N—H...O hydrogen bonding in the monoclinic phase. The thermal motion in the crystals of both phases has been analyzed and their thermal expansion determined. The enthalpies of solution in a number of solvents have been calculated from the solubility measurements of Chattaway & Lambert [(1915), J. Chem. Soc.
107, 1773–1781], which also give the temperature and enthalpy of the enantiotropic `orthorhombic to monoclinic' phase transformation (Tc
= 283 K; ΔH
transf = 1.54 kJ mol−1). The phase-transformation endotherm in a DSC (differential scanning calorimetry) trace from the orthorhombic polymorph occurs only at ∼310 K on heating and there is no corresponding exotherm on cooling; the DSC trace gives ΔH
transf = 1.62 kJ mol−1 and ΔH
fus = 26.9 kJ mol−1. This phase transformation is an example of the common type (occurrence ∼95%) where ΔV
transf = (V
monoclinic − V
orthorhombic) is positive. Analogous (but less complete) results have been obtained for the monoclinic and triclinic polymorphs of N-(N′-methylanilino)phthalimide (m.p. of triclinic polymorph 398 K). There were only minor differences between the molecular conformations in the two phases, but the molecular arrangements were quite different. This `monoclinic to triclinic' phase transformation also has ΔV
transf = (V
triclinic − V
monoclinic) positive. The solubility (and other) measurements of Chattaway & Lambert (1915) gave Tc
= 328.43 K and ΔH
transf = 4.17 kJ mol−1. A DSC trace for the monoclinic crystals shows a broad endotherm at ∼372–376 K on heating, but there is no corresponding exotherm on cooling; ΔH
transf = 3.6 kJ mol−1 and ΔH
fus = 21.7 kJ mol−1. These two compounds provide further examples of molecular crystals with a large hysteresis in their first-order enantiotropic solid-state phase transformations, the transformation to the high-temperature phase occurring well above Tc
and the low-temperature phase not being recovered on cooling below Tc
. Presumably the hysteresis must be ascribed to as-yet unknown features of the nucleation processes.
Structural Investigation of P4W24O80: A New Monophosphate Tungsten Bronze
Authors: Roussel P. , Mather G. , Domengès B. , Groult D. , Labbé P.
Published: July 2002

The crystallographic study of the tungsten phosphate bronze P4W24O80 was performed from three-dimensional single-crystal X-ray diffraction data and electron microscopy. This compound crystallizes in the orthorhombic system with unit-cell dimensions a = 5.312 (1), b = 6.5557 (8), c = 42.196 (8) Å and space group P212121. The crystal structure was solved by direct methods and Fourier techniques, and refined to the reliability factor R = 0.0284 (wR = 0.0272). Its determination confirms that it belongs to the monophosphate tungsten bronze family of the general formula (PO2)4(WO3)2m
with the value m = 12. Large empty cages surrounded by 18 O atoms are built up of eight WO6 octahedra and four PO4 tetrahedra sharing corners. They are located between two WO3-type slabs forming pentagonal-shaped tunnels running in the a direction. Electron microscopy investigations confirm that the studied crystal does not imply modulation phenomena when other crystals of the same composition exhibit satellite reflections with a modulation vector q* involving a doubling of a. The observations also reveal the existence of a monoclinic form of the m = 12 compound, which is a regular intergrowth of m = 11 and m = 13 members in a similar way to the m = 5 member of the series where the same feature has already been observed. On each edge of a WO3-type slab, a large variation (from 1.73 to 2.09 Å) of the six W—O distances within the WO6 octahedron is noted, which yields an oxidation state of W near 6, whereas for the WO6 octahedra located in the middle part of the slab the six W—O distances are gathered about their mean value (1.92 Å), which involves a more important electronic delocalization. The thermal motion of the W atoms is described. The absolute structural configuration is tested on the basis of some calculated structure factors, which are more sensitive to the x, y, z → −x, −y, −z change of atomic positions.
Carbonyl–Carbonyl Interactions can be Competitive with Hydrogen Bonds
Authors: Allen F. H. , Baalham C. A. , Lommerse J. P. M. , Raithby P. R.
Published: July 2002

The geometries and attractive energies of carbonyl–carbonyl interactions have been investigated using crystallographic data and ab initio molecular-orbital calculations. Analysis of crystallographic data for 9049 carbon-substituted >C=O groups shows that 1328 (15%) form contacts with other >C=O groups, in which d(C...O) < 3.6 Å. Three common interaction motifs are observed in crystal structures: (a) a slightly sheared antiparallel motif (650 instances) involving a pair of short C...O interactions, together with (b) a perpendicular motif (116 instances) and (c) a highly sheared parallel motif (130 instances), which both involve a single short C...O interaction. Together, these motifs account for 945 (71%) of the observed interactions. Ab-initio-based molecular-orbital calculations (6-31G** basis sets), using intermolecular perturbation theory (IMPT) applied to a bis-propanone dimer model, yield an attractive interaction energy of −22.3 kJ mol−1 for a perfect rectangular antiparallel dimer having both d(C...O) = 3.02 Å and attractive energies < −20 kJ mol−1 over the d(C...O) range 2.92–3.32 Å. These energies are comparable to those of medium-strength hydrogen bonds. The IMPT calculations indicate a slight shearing of the antiparallel motif with increasing d(C...O). For the perpendicular motif, IMPT yields an attractive interaction energy of −7.6 kJ mol−1, comparable in strength to a C—H...O hydrogen bond and with the single d(C...O) again at 3.02 Å.
Crystal lattice and phase transitions in Na4TiP2O9 (NTP) and Na4.5FeP2O8(O,F) (NFP) superionic conductors as a function of high pressures and temperatures
Authors: Maximov B. , Sirota M. , Werner S. , Schulz H.
Published: July 2002

The lattice dynamics of Na4TiP2O9 (tetrasodium titanium diphosphorus nonaoxide, NTP) and Na4.5FeP2O8(O,F) (nonasodium diiron tetraphosphorus difluoride octadecaoxide, NFP) crystals, which are superionic conductors with Na+-ion conductivity, were studied under high pressures. Lattice constants as a function of hydrostatic pressure were measured on a four-circle diffractometer using a high-pressure cell with diamond anvils. At 1.78 \pm 0.15 GPa NTP undergoes a reversible phase transition from the modulated monoclinic (pseudo-orthorhombic) modification which is stable under atmospheric conditions. A similar phase transition in NTP is observed at 523 K. For NFP, it may be assumed that at least three phase transitions occur when the pressure increases from atmospheric to 12 GPa, at 1.39\pm0.08, 4.52 \pm0.32, and 6.02\pm0.02 GPa, as concluded from the change in the unit-cell parameters and in the color of the crystals: the color changes from ginger (dark orange) to pink at \sim1.5–2.0 GPa pressure and to violet at \sim6.0 GPa.
3(5),4-Dimethyl- and 3,4,5-trimethylpyrazole at 200 K. X-ray crystallography and quantum-chemical analysis
Authors: Infantes Lourdes , Foces-Foces Concepción , Elguero Jose
Published: July 2002

The crystal and molecular structures of 3(5),4-dimethylpyrazole, C5H8N2, (I), and of 3,4,5-trimethylpyrazole, C6H10N2, (II), have been determined at 200 K. In (I) the 4,5-dimethylpyrazole tautomer is present in the solid state and the six independent molecules in the asymmetric unit form trimers via NH...N hydrogen bonds related by a pseudo centre of symmetry. The asymmetric unit of (II) contains one and a half molecules: these exhibit NH proton disorder and are hydrogen bonded to each other via their respective NH groups to form chains. Ab
initio calculations at HF and B3LYP/6-31G** levels indicate that the 3,4-dimethylpyrazole tautomer is more stable than the 4,5-dimethylpyrazole tautomer by only approximately 0.5  kcal  mol−1 (1 kcal mol−1 = 4.184 kJ mol−1).
Crystal structure, compressibility and possible phase transitions in \boldvarepsilon-FeSi studied by first-principles pseudopotential calculations
Authors: Vočadlo Lidunka , Price Geoffrey D. , Wood I. G.
Published: July 2002

An investigation of the relative stability of the FeSi structure and of some hypothetical polymorphs of FeSi has been made by first-principles pseudopotential calculations. It has been shown that the observed distortion from ideal sevenfold coordination is essential in stabilizing the FeSi structure relative to one of the CsCl type. Application of high pressure to FeSi is predicted to produce a structure having nearly perfect sevenfold coordination. However, it appears that FeSi having a CsCl-type structure will be the thermodynamically most stable phase for pressures greater than 13 GPa. Fitting of the calculated internal energy vs volume for the FeSi structure to a third-order Birch–Murnaghan equation of state led to values, at T = 0 K, for the bulk modulus, K
0, and for its first derivative with respect to pressure, K
0′, of 227 GPa and 3.9, respectively.
Octahedral deformations and cationic displacements in the ferroelectric PbHf0.8Ti0.2O3: a neutron powder diffraction study from 10 to 770 K
Authors: Muller Ch. , Baudour J.-L. , Bedoya C. , Bouree F. , Soubeyroux J.-L. , Roubin M.
Published: July 2002

Neutron powder diffraction data, collected over the temperature range 10–770 K, have been analysed in order to make a detailed characterization of the sequence of phase transitions occurring in the Hf-rich ferroelectric PbHf0.8Ti0.2O3, titanium hafnium lead oxide. Over the whole temperature range this compound undergoes two phase transitions, which involve cationic displacements and octahedral deformations (tilt and/or distortion) leading to strongly distorted perovskite-type structures. The first transition appears around 415 K between two ferroelectric rhombohedral phases: a low-temperature nonzero-tilt phase F
RL (space group R3c) and an intermediate zero-tilt phase F
RH (space group R3m). The second one, detected around 520 K, is associated with a ferroelectric to-paraelectric transition between the F
RH phase and the P

C
cubic phase (space group Pm3¯m). From high-resolution neutron powder diffraction data (diffractometer 3T2-LLB, Saclay, France, λ = 1.2251 Å), the crystallographic structure of the three successive phases has been accurately determined at the following temperatures: T = 10 K (F
RL): space group R3c, Z = 6, a
hex = 5.7827 (1), c
hex = 14.2702 (4) Å, V
hex = 413.26 (2) Å3; T = 150 K (F
RL): space group R3c, Z = 6, a
hex = 5.7871 (1), c
hex = 14.2735 (4) Å, V
hex = 413.98 (3) Å3; T = 290 K (F
RL): space group R3c, Z = 6, a
hex = 5.7943 (1), c
hex = 14.2742 (5) Å, V
hex = 415.04 (3) Å3; T = 440 K (F
RH): space group R3c, Z = 6, a
hex = 5.8025 (1), c
hex = 14.2648 (4) Å, V
hex = 415.94 (3) Å3; T = 520 K (P

C
): space group Pm3¯m, Z = 1, a
cub = 4.1072 (2) Å, V
cub = 69.29 (1) Å3. In addition, a neutron powder thermodiffractometry experiment, performed between 290 and 770 K (diffractometer D1B-ILL, Grenoble, France, λ = 2.533 Å), has been used to study in situ the temperature-induced phase transitions. From sequential Rietveld refinements, the temperature dependence of the cation displacements and the rotation and/or distortion of oxygen octahedra was derived.
Two phases of {[CsPH(η6-2,4,6-
t
Bu3C6H2)]2(η3-toluene)0.5}
x
: their structures and interconversions
Authors: Concolino Thomas E. , Lam Kin-Chung , Guzei Ilia A. , Rheingold Arnold L. , Rabe Gerd W.
Published: July 2002

The solvent-bridged caesium phosphide {[CsPH(η
6-2,4,6-
t
Bu3C6H2)]2(η
3-toluene)0.5}
x
, catena-[(μ-η3-toluene)-bis[caesium(2,4,6-tri-tert-butylphenylphosphide)]], undergoes a reversible solid-state, order–disorder phase transition characterized by the doubling of the unit-cell volume at low temperature achieved by doubling one unit-cell vector. The unit-cell parameters at 293 (2) K (form A) are: a = 11.147 (4), b = 14.615 (4), c = 14.806 (5) Å, α = 70.57 (3), β = 71.85 (3), γ = 72.93 (2)°, V = 2112.5 (12) Å3, Z = 2, ρcalc = 1.362 g cm−3, R
1 = 0.0513 for 5462 reflections, wR
2 = 0.0947 for all data. The unit-cell parameters at 173 (2) K (form B) are: a = 14.6241 (3), b = 14.7393 (3), c = 22.0720 (4) Å, α = 72.2117 (7), β = 73.3659 (8), γ = 70.2953 (7)°, V = 4174.8 (2) Å3, Z = 4, ρcalc = 1.379 g cm−3, R
1 = 0.0405 for 14 010 reflections, wR
2 = 0.1326 for all data. With a minor change, the key structural features discussed previously for form A [Rabe et al. (1998). Inorg. Chem.
37, 4235–4245] remain unchanged. The η
3-toluene ligand is observed to be disordered at 293 (2) K and ordered at 173 (2) K, with the order–disorder phase transition occurring at approximately 278 (2) K.
Analysis of diborane X-ray diffraction data utilizing structure factors calculated from molecular wave functions
Authors: Jones D. S. , Lipscomb W. N.
Published: July 2002

Crystal unit-cell structure factors for diborane, B2H6, have been calculated for four possible molecular geometries, using densities obtained from self-consistent field molecular wavefunctions. These structure factors were fitted for various B–H distances to the experimental X-ray data for B2H6 by varying the parameters of several thermal vibration models. B–H bond lengths so determined have values about 0.05 Å longer than those determined by the usual spherical atom analysis of the X-ray data. Consideration of additional factors, such as the X-ray B–H bond shortening due to rigid rotation of the molecule in the crystal, leads to the conclusion that the bond length correction given by this treatment accounts for about two-thirds of the observed discrepancy between X-ray and electron diffraction values for the B–H bond lengths in diborane.
Extinction in X-ray and neutron diffraction
Authors: Cooper M. J. , Rouse K. D.
Published: July 2002

Accurate neutron-diffraction measurements from crystals suffering from severe extinction have been used to test the recent general theory of extinction of Zachariasen (Acta Cryst. (1967). 23, 558). Analysis of these measurements indicates that certain of the approximations made in the theory are not generally valid and result in systematic deviations between theory and experiment, namely a marked angle-dependent effect and an inadequacy of the theory for strong extinction. The original theory is therefore extended to take these factors into account and to give agreement with the observed data.
Désordre linéaire dans les cristaux (cas du silicium, du quartz, et des pérovskites ferroélectriques)
Authors: Comès R. , Lambert M. , Guinier A.
Published: July 2002

Many crystals produce a diffuse scattering of X-rays which is localized in a series of relplanes. It is shown that the corresponding linear disorder in the crystal may have various origins. In silicon, the scattering is due to thermal vibrations and is well explained by the elastic properties of the crystal. In neutron irradiated quartz the radiation damage is responsible for the major part of the scattering. The case of BaTiO3 and KNbO3 is discussed in detail. A linear disorder is proposed which accounts better for the different distributions of the scattering in the 4 allotropic phases than the alternative explanation of the soft mode. In spite of some neutron inelastic scattering results it is not yet possible to distinguish between static and dynamic disorder.
Crystallization and preliminary structural studies of Scilla campanulata lectin complexed with α1–6 mannobiose
Authors: Wright Lisa M , Wood Stephen D. , Reynolds Colin D. , Rizkallah Pierre J. , Allen Anthony K.
Published: July 2002

Recent work has shown that Scilla campanulata agglutinin from bluebell bulbs has a strong affinity for α(1,3)- and α(1,6)-linked mannosyl residues and possesses moderate antiretroviral activity. This lectin has been crystallized by the hanging-drop method of vapour diffusion complexed with the disaccharide mannose-α1,6-D-mannose. The crystals are in the space group P21212 with unit-cell dimensions a = 70.63, b = 92.79 and c = 47.25 Å, and with a dimer in the asymmetric unit. The crystals diffract X-rays to beyond 1.5 Å resolution at 277 K and are stable in an X-ray beam. Data to 1.6 Å resolution have been collected using a MAR image-plate system at a synchrotron source and the structure of the complex has been solved by the molecular replacement method.
The FNR-like domain of the Escherichia coli sulfite reductase flavoprotein component: crystallization and preliminary X-ray analysis
Authors: Gruez Arnaud , Zeghouf Mahel , Bertrand Jay , Eschenbrenner Michel , Covès Jacques , Fontecave Marc , Pignol David , Fontecilla-Camps Juan-Carlos
Published: July 2002

The FNR-like domain of the Escherichia coli sulfite reductase flavoprotein subunit was crystallized using the hanging-drop technique, with PEG 4000 as precipitant. The crystals belong to space group P3112 or enantiomorph, with unit-cell parameters a = b = 171.0, c = 152.1 Å. A solvent content of 75% was determined by a calibrated tetrachloromethane/toluene gradient which corresponds to three monomers per asymmetric unit. A 3 Å resolution native data set was collected at beamline W32 of LURE, Orsay, France.
Crystallization and preliminary X-ray studies on the hyperstable 3-isopropylmalate dehydrogenase from the thermoacidophilic archaeon Sulfolobus sp. strain 7
Authors: Suzuki Toshiharu , Moriyama Hideaki , Hirose Raita , Sakurai Masahiro , Tanaka Nobuo , Oshima Tairo
Published: July 2002

3-Isopropylmalate dehydrogenase from the thermoacidophilic archaeon, Sulfolobus sp. strain 7, has been crystallized by the vapor-diffusion method. The crystals were grown from a solution containing ammonium sulfate, 2-methyl-2,4-pentanediol and magnesium chloride. The crystallization requires 2-methyl-2,4-pentanediol to avoid twinning of the crystals. The crystal belongs to the orthorhombic system with the space group P2221 and unit-cell dimensions a = 67.9, b = 93.3 and c = 134.1 Å.
Deposition of Macromolecular Structures
Authors: Keller Peter A. , Henrick Kim , McNeil Philip , Moodie Stuart , Barton Geoffrey J.
Published: July 2002

Macromolecular structures are being determined at an increasing rate, and are of interest to a wide diversity of researchers. Depositing a macromolecular structure with the Protein Data Bank makes it readily available to the community. Accuracy, consistency and machine-readability of the data are essential, as are clear indications of quality, and sufficient information to allow non-experimentalists to interpret the data. Good-quality depositions are necessary to allow this to be achieved. The PDB's AutoDep system allows deposition and some preliminary automatic checking to take place at multiple sites, prior to full processing and release of the structure by the PDB. However, depositing a structure currently requires the manual entry of a large amount of information at the time of deposition. The data-harvesting approach will allow much more information to be deposited, without placing an additional burden on the depositor. Deposition-ready files will be generated automatically during the course of a structure-determination experiment. The additional information will allow improved validation procedures to be applied to the structures, and the data to be made more useful to the wider scientific community.
Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules
Authors: Sussman Joel L. , Lin Dawei , Jiang Jiansheng , Manning Nancy O. , Prilusky Jaime , Ritter Otto , Abola Enrique E.
Published: July 2002

The Protein Data Bank (PDB) at Brookhaven National Laboratory, is a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules, with approximately 8000 entries. Data are easily submitted via PDB's WWW-based tool AutoDep, in either mmCIF or PDB format, and are most conveniently examined via PDB's WWW-based tool 3DB Browser.
Expression, crystallization and preliminary X-ray analysis of the E2 transactivation domain from papillomavirus type 16
Authors: Burns Julie E. , Moroz Olga V. , Antson Alfred A. , Sanders Cyril M. , Wilson Keith S. , Maitland Norman J.
Published: July 2002

The N-terminal transactivation domain of the E2 protein from human papillomavirus type 16 has been crystallized by vapour diffusion. Crystals belong to the space group P3121 (or P3221) with unit-cell dimensions a = b = 54.3, c = 155.5 Å. There is one molecule per asymmetric unit with a solvent content of 55%. Crystals diffract to at least 2.5 Å resolution and complete X-ray data to 3.4 Å have been collected on a conventional laboratory source. This 201- amino-acid domain of the E2 protein has been shown to interact functionally with both the HPV E1 protein and at least three cellular transcription factors, to fulfil its role in the control of viral transcription and replication. A knowledge of the structural basis of these multiple interactions should lead to a fuller understanding of the mechanism of action of this key regulator of the HPV life cycle.
Crystallization of L-aspartate oxidase, the first enzyme in the bacterial de novo biosynthesis of NAD
Authors: Bacchella Luca , Lina Claudio , Todone Flavia , Negri Armando , Tedeschi Gabriella , Ronchi Severino , Mattevi Andrea
Published: July 2002

The flavoenzyme L-aspartate oxidase from Escherichia coli was crystallized using the hanging-drop vapour-diffusion technique with PEG 4000 as precipitant. The crystals belong to space group P3121 (or P3221) with unit-cell parameters a = b = 84.9, c = 159.9 Å. A solvent content of 42% corresponds to a monomer (60 kDa) in the asymmetric unit. A complete 2.8 Å resolution data set was collected using a rotating-anode X-ray generator.
Bound-solvent structures for microgravity-, ground control-, gel- and microbatch-grown hen egg-white lysozyme crystals at 1.8 Å resolution
Authors: Dong Jun , Boggon Titus J. , Chayen Naomi E. , Raftery James , Bi Ru-Chang , Helliwell John R.
Published: July 2002

A number of methods can be used to improve the stability of the protein crystal-growth environment, including growth in microgravity without an air–liquid phase boundary, growth in gels and growth under oil (`microbatch'). In this study, X-ray data has been collected from and structures refined for crystals of hen egg-white lysozyme (HEWL) grown using four different methods, liquid–liquid dialysis on Earth and in microgravity using the European Space Agency's (ESA) Advanced Protein Crystallization Facility (APCF) on board the NASA Space Shuttle Life and Microgravity Spacelab (LMS) mission (STS-78), crystallization in agarose gel using a tube liquid–gel diffusion method and crystallization in microbatch under oil. A comparison of the overall quality of the X-ray data, the protein structures and especially the bound-water structures has been carried out at 1.8 Å. The lysozyme protein structures corresponding to these four different crystallization methods remain similar. A small improvement in the bound-solvent structure is seen in lysozyme crystals grown in microgravity by liquid–liquid dialysis, which has a more stable fluid physics state in microgravity, and is consistent with a better formed protein crystal in microgravity.
Solution of the structure of tetrameric human glucose 6-phosphate dehydrogenase by molecular replacement
Authors: Au Shannon W. N. , Naylor Claire E. , Gover Sheila , Vandeputte-Rutten Lucy , Scopes Deborah A. , Mason Philip J. , Luzzatto Lucio , Lam Veronica M. S. , Adams Margaret J.
Published: July 2002

Recombinant human glucose 6-phosphate dehydrogenase (G6PD) has been crystallized and its structure solved by molecular replacement. Crystals of the natural mutant R459L grow under similar conditions in space groups P212121 and C2221 with eight or four 515-residue molecules in the asymmetric unit, respectively. A non-crystallographic 222 tetramer was found in the C2221 crystal form using a 4 Å resolution data set and a dimer of the large β + α domains of the Leuconostoc mesenteroides enzyme as a search model. This tetramer was the only successful search model for the P212121 crystal form using data to 3 Å. Crystals of the deletion mutant ΔG6PD grow in space group F222 with a monomer in the asymmetric unit; 2.5 Å resolution data have been collected. Comparison of the packing of tetramers in the three space groups suggests that the N-terminal tail of the enzyme prevents crystallization with exact 222 molecular symmetry.
Purification, crystallization and preliminary crystallographic analysis of a natural complex of phospholipase A2 from Echis carinatus (saw-scaled viper)
Authors: Nagpal Akanksha , Chandra Vikas , Kaur Punit , Singh T. P.
Published: July 2002

A novel complex of phospholipase A2 complexed with another venom protein has been isolated and purified from saw-scaled viper (Echis carinatus) venom. The molecular weights of the two components are 16 and 14 kDa, respectively. The complex was purified using an Affigel blue column and an anion-exchange (DEAE Sephacel) column. Long diamond-shaped crystals were obtained by hanging-drop vapour diffusion. The protein complex was dissolved at a concentration of 10 mg ml−1 in 20 mM sodium cacodylate, 1 mM CaCl2 and 2% dioxane at pH 6.0. The reservoir contained the same buffer with 7%(w/v) PEG 4000. Crystals appeared within 2–3 weeks. Native data to 2.9 Å resolution have been obtained at 291 K. The crystals belong to the monoclinic space group P21 with unit-cell parameters a = 74.47, b = 47.87, c = 106.39 Å, β = 104.5° and contain two molecules per asymmetric unit. Structure determination by molecular replacement is in progress.
Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease–DNA complex
Authors: Horton Nancy C. , Dorner Lydia F. , Schildkraut Ira , Perona John J.
Published: July 2002

Crystals of the 60 kDa dimeric HincII restriction enzyme bound to a 12 base-pair dyad-symmetric duplex DNA carrying the specific 5′-GTCGAC recognition site have been obtained. Crystals grew by hanging-drop vapor diffusion from solutions containing polyethylene glycol 4000 as precipitating agent. The rod-shaped crystals belong to space group I222 (or I212121), with unit-cell dimensions a = 66.9, b = 176.7, c = 256.0 Å. There are most likely to be two dimeric complexes in the asymmetric unit. A complete native data set has been collected from a high-energy synchrotron source to a resolution of 2.5 Å at 100 K, with an R
merge of 4.8%.
Crystallization and preliminary X-ray analysis of the Escherichia coli UDP-MurNAc-tripeptide D-alanyl-D-alanine-adding enzyme (MurF)
Authors: Yan Youwei , Munshi Sanjeev , Li Ying , Pryor Kelly Ann D. , Marsilio Frank , Leiting Barbara
Published: July 2002

Crystals of the Escherichia coli UDP-MurNAc-tripeptide D-Ala-D-Ala-adding protein (MurF), which catalyzes the formation of the last metabolite of the bacterial cell-wall building block, have been grown in hanging-drop vapor-diffusion trials using PEG 8K as a precipitating agent. The crystals belong to hexagonal space group P61 or P65, with unit-cell dimensions a = b = 74, c = 425 Å. The asymmetric unit contains two molecules, with a crystal volume per protein mass (Vm
) of 3.4 Å3 Da−1 and a solvent content of about 64% by volume. A native data set to 2.8 Å resolution has been obtained from a frozen crystal using a synchrotron X-ray source.
Overexpression, purification, crystallization and preliminary structural study of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD), the fourth enzyme of the dTDP-L-rhamnose synthesis pathway, from Salmonella enterica serovar Typhimurium
Authors: Giraud Marie-France , McMiken Helen J. , Leonard Gordon A. , Messner Paul , Whitfield Chris , Naismith James H.
Published: July 2002

L-Rhamnose is an essential component of the cell wall of many pathogenic bacteria. Its precursor, dTDP-L-rhamnose, is synthesized from α-D-glucose-1-phosphate and dTTP via a pathway requiring four distinct enzymes: RmlA, RmlB, RmlC and RmlD. RmlD catalyses the terminal step of this pathway by converting dTDP-6-deoxy-L-lyxo-4-hexulose to dTDP-L-rhamnose. RmlD from Salmonella enterica serovar Typhimurium has been overexpressed in Escherichia coli. The recombinant protein was purified by a two-step protocol involving anion-exchange and hydrophobic chromatography. Dynamic light-scattering experiments indicated that the recombinant protein is monodisperse. Crystals of native and selenomethionine-enriched RmlD have been obtained using the sitting-drop vapour-diffusion method with polyethylene glycol as precipitant. Diffraction data have been collected from orthorhombic crystals of both native and selenomethionyl-derivatized protein, allowing tracing of the protein structure.
Use of differentially substituted selenomethionine proteins in X-ray structure determination
Authors: Gassner Nadine C. , Matthews Brian W.
Published: July 2002

Using heavily methionine-substituted T4 lysozyme as an example, it is shown how the addition or deletion of a small number of methionines can simplify the location of selenium sites for use in MAD phasing. By comparing the X-ray data for a large number of singly substituted lysozymes, it is shown that the optimal amino acid to be substituted by methionine is leucine, followed, in order of preference, by phenylalanine, isoleucine and valine. The identification of leucine as the first choice agrees with the ranking suggested by the Dayhoff mutation probability, i.e. by the frequency of amino-acid substitutions in the sequences of related proteins. The ranking of the second and subsequent choices, however, differ significantly.
X-ray natural circular dichroism and chiral-EXAFS in gyrotropic crystals
Authors: Goulon José , Goulon-Ginet Chantal , Rogalev Andrei , Benayoun Gisèle , Brouder Christian , Natoli Calogero R.
Published: July 2002

X-ray natural circular dichroism (XNCD) has been recently detected in the XANES region for uniaxial and biaxial gyrotropic crystals. Chiral-EXAFS (χ-EXAFS) spectra are reported for the first time over a wider energy range and are analysed in terms of multiple-scattering paths of relevant symmetry. For such heavily absorbing single crystals as lithium iodate, paratellurite or potassium titanyl phosphate, the differential absorption between left-handed and right-handed circularly polarized X-ray photons cannot be measured in transmission but gyrotropy effects can still be detected in fluorescence excitation spectra. Whereas XNCD and fluorescence-detected X-ray natural circular dichroism spectra are strictly identical for uniaxial crystals, it has been established that this was true only to the first order for biaxial crystals such as potassium titanyl phosphate.
Preparation of Ti–Si binary oxide thin film photocatalysts by the application of an ionized cluster beam method
Authors: Takeuchi Masato , Matsuoka Masaya , Yamashita Hiromi , Anpo Masakazu
Published: July 2002

No abstract
Synchronous scanning of undulator gap and monochromator for XAFS measurement in soft X-ray region
Authors: Tanaka Tomoaki , Matsubayashi Nobuyuki , Imamura Motoyasu , Shimada Hiromichi
Published: July 2002

Synchronous scanning of the undulator gap and a monochromator was done to obtain smooth profiles of incident x-rays that are suitable for XAFS measurements. By changing the gap from 150 mm (B=0.12 T) to 140 mm (B=0.15 T) with the use of the 3rd to 11th harmonic peaks, soft x-rays with energy from 200 eV to1200 eV were obtained. The smooth profile of the incident x-rays provided high-quality measurement of XANES and EXAFS spectra in the soft x-ray region. Issues that would improve the synchronous scanning system are discussed.
A study of transferability of atomic background on EXAFS spectra of simple gaseous compounds of As
Authors: Kodre Alojz , Prešeren Rok , Arčon Iztok , Padežnik Gomilšek Jana , Borowski Michael
Published: July 2002

From EXAFS spectra of As and As2O3 vapors and arsine gas AsH3 the ab initio calculated structural signal is removed. The remainders comprise small absorption edges due to shake-up channels involving electrons from 3d or 3p subshell. With enhanced resolution, the edges reveal a fine splitting and a varying contribution of resonance channels, due to individual molecular energy-level structure of the samples. On the resolution level appropriate for routine EXAFS analysis the remainders coincide, representing a unique and transferable atomic absorption background for the range of As valence states spanned by the samples.
Orientation effects in elastic scattering of polarized X-rays by linear molecules
Authors: Yavna Victor , Hopersky Alexey , Nadolinsky Alexey , Yavna Svetlana
Published: July 2002

Strong orientation effect is discovered theoretically upon the change of the scheme of suggested experiment on anomalous elastic X-ray scattering of linearly polarized X-ray radiation by linear diatomics near the ionization thresholds of inner molecular orbitals. Studied are the effects on the shape of theoretical scattering spectra of additional excitations/ionizations of outer-shell electrons. Within the one-centre approximation for the molecular orbitals wavefunctions the analytical structure of the linear molecule's formfactor is obtained. The dipole transition matrix elements and photoabsorption cross sections are calculated by the methods of the theory of non-orthogonal orbitals.
Three-dimensional analysis of the local structure of Cu on TiO2(110) by in situ polarization-dependent total-reflection fluorescence XAFS
Authors: Tanizawa Yasuhiro , Chun Wang-Jae , Shido Takafumi , Asakura Kiyotaka , Iwasawa Yasuhiro
Published: July 2002

Cu K-edge XAFS of Cu/TiO2(110) was measured by polarization-dependent total-reflection fluorescence XAFS technique. XAFS of [001], [1\bar10] and [110] directions were measured to elucidate the three dimensional structure of Cu species on the TiO2(110) surface prepared by the deposition of Cu(DPM)2 followed by reduction with H2. Simulation of the EXAFS functions as well as conventional curve fitting analysis revealed that plane Cu3-4 small clusters with similar structure to Cu(111) plane were formed by the reduction at 363 K. The small clusters converted into spherical metallic Cu particles by the reduction at 473 K.
Yields of multiply charged ions in cascading decays of hollow argon and krypton with two initial vacancies in their K and/or L shells
Authors: Kochur Andrei
Published: July 2002

The yields of multiply charged ions produced by the cascading decay of doubly-inner-shell-ionized argon and krypton atoms are calculated via straightforward construction of de-excitation trees. The final-ion-charge spectra are found to be sensitive to the distribution of initial vacancies within K and L shells.
Liquid Rb micrometric droplets confined in paraffin wax: an X-ray absorption spectroscopy study
Authors: De Panfilis Simone , Di Cicco Andrea , Filipponi Adriano , Comez Lucia , Borowski Michael
Published: July 2002

We have performed high-quality X-ray absorption measurements on crystalline (c-Rb) and liquid (l-Rb) Rubidium in the range from 15 K to 320 K. Performing a consistent analysis that takes into account the contribution of the medium range structure, we observe that the l-Rb spectrum is compatible with pair correlation function g(r) previously determined by neutron diffraction experiments. Due to the micrometric size of the liquid droplets we were able to observe a slight undercooling down to 290 K. We were also able to study the details of the very strong multielectron excitations channels in terms of resonances, edges and shake-off features at proper theoretical energy values.
Studies of impurities in magnetic semiconductors: an example of important XAFS applications
Authors: Soo Y. L. , Kioseoglou G. , Huang S. , Kim S. , Kao Y. H. , Takatani Y. , Haneda S. , Munekata H.
Published: July 2002

The X-ray absorption fine structure (XAFS) technique has been employed to investigate the local structure and valency about Mn and Fe ions in the III-V diluted magnetic semiconductors In1-x
Mn
x
As and Ga1-x
Fe
x
As, prepared by molecular-beam-epitaxy under various growth conditions. These new systems are promising magnetic materials of considerable current interest and with important technical applications including photo-carrier induced magnetism and spin-polarized current devices. The local structure around the magnetic ions can play a pivotal role in affecting the magnetic properties of these semiconductors. Local structure information obtained from XAFS has provided the first direct evidence that the magnetic impurities can indeed substitute for the cation host atoms in samples prepared under appropriate conditions.
K- and L-edge XAFS determination of the local structure of aqueous Nd(III) and Eu(III)
Authors: D'Angelo Paola , Pavel Nicolae Viorel , Borowski Michael
Published: July 2002

The short-range coordination of Nd(III) and Eu(III) ions in aqueous solutions has been investigated by means of K-edge x-ray absorption spectroscopy. Experimental data are presented which demonstrate that an accurate determination of the Nd(III) and Eu(III) hydration structural parameters can be obtained from the analysis of the K-edge spectra. It is shown that the large widths of the core hole states do not appreciably reduce the potential structural information of the K-edge EXAFS data. In addition the available k-range of the K-edge spectra is much wider compared to that of the L3-edge which is affected by the presence of double-electron excitations in a more severe fashion.
New method of chemical state imaging by EPMA-EXEFS
Authors: Watanabe T. , Kawano A. , Ueda K. , Umesaki N. , Wakita H.
Published: July 2002

A novel two dimensional imaging technique of the chemical bonding state was developed by combining the extended X-ray emission fine structure method with an electron probe X-ray microanalyzer mapping technology. With this method, chemical state images of some aluminium standard samples were obtained. It was confirmed that the obtained images provide correct information of chemical states.