bluuebunny/crossref_metadata_2025 huggingface dataset:
Structures of three inclusion compounds of cholanamide with either (S)-enantiomer, (R)-enantiomer or an optically resolved mixture of butan-2-ol
Authors: Briozzo P. , Kondo T. , Sada K. , Miyata M. , Miki K.
Published: July 2002

The three types of inclusion compounds of cholanamide (CAM, 3α, 7α, 12α-trihydroxy-5β-cholan-24-amide) have been crystallized from the solutions of (S)-butan-2-ol (CAMSB), (R)-butan-2-ol (CAMRB) and racemic butan-2-ol (CAMSRB), respectively. The crystal structures have been determined. The three crystal structures are isomorphous to each other and revealed that the host CAM molecules form the same layered arrangements, providing channel spaces for the guest butan-2-ol molecules. As expected, the CAMSB and CAMRB crystals include the pure (S)- and (R)-enantiomers of butan-2-ol, whereas the (S)-enriched mixture of enantiomers is accommodated in CAMSRB with a molar ratio between the host CAM and guest butan-2-ol molecules of 1:1. The hydrogen-bond network is rigidly formed between the CAM molecules and also between CAM and butan-2-ol molecules. CAMSB and CAMRB have slightly different unit-cell dimensions: the channels in CAMRB have a larger section, resulting in a larger unit-cell volume. In CAMSRB, although both enantiomers of the guest alcohol are included, the (S)-enantiomer is more abundant, indicating that the optical resolution occurs during the crystallization step.
X-ray studies on crystalline complexes involving amino acids and peptides. XXX. Structural invariance and optical resolution through interactions with an achiral molecule in the histidine complexes of glycolic acid
Authors: Suresh S. , Vijayan M.
Published: July 2002

The crystals of DL-histidine glycolate and L-histidine glycolate were prepared and analysed as part of an ongoing programme aimed at studying biologically and evolutionarily important interaction and aggregation Patterns. Crystallization experiments involving DL-histidine and glycolic acid yielded, in addition to DL-histidine glycolate, a conglomerate containing crystals of L-histidine glycolate and D-histidine glycolate in an unusual process of chiral separation through interaction with an achiral molecule. The crystal structure of DL-histidine glycolate is made up of alternating layers of unlike molecules as in many other binary complexes involving amino acids. The structure of L-histidine glycolate involves packing of columns containing L-histidine molecules and glycolate ions tightly hydrogen bonded to one another. The arrangement is almost identical to that in the structure of L-histidine acetate, thus providing another example for the invariance of certain aggregation patterns with respect to changes in the molecules involved. The observed aggregation of molecules in the chiral complex also appears to provide a structural rationale for chiral separation of histidine in the presence of glycolic acid.
Temperature dependence of crystal structure of NaK0.72(NH4)0.28(+)-C4H4O6.4H2O in the paraelectric phase
Authors: Suzuki E. , Kabasawa H. , Honma T. , Nozaki R. , Shiozaki Y.
Published: July 2002

The crystal structures of the ferroelectric NaK0.72 (NH4)0.28(+)-C4H4O6.4H2O (RS0.72ARS0.28) have been studied in the paraelectric phase [Mr
= 276.32, orthorhombic, P21212,° Z = 4, F(000) = 575.04, λ(Mo Kα1) = 0.70926 Å]; T = 213 (1), 253 (1) and 293 (1) K. The crystal data are as follows: (I) at T = 213 (1) K: R = 0.0424, wR = 0.0399, number of reflections = 3414, a = 11.899 (2), b = 14.273 (2), c = 6.211 (1) Å, V = 1054.9 (2) Å3, Dx
= 1.740 g cm−3; (II) at T = 253 (1) K: R = 0.0498, wR = 0.0442, number of reflections = 3284, a = 11.929 (1), b = 14.297 (1), c = 6.221 (1) Å, V = 1061.0 (2) Å3, Dx
= 1.730 g cm−3; (III) at T = 293 (1) K: R = 0.0473, wR = 0.0392, number of reflections = 3179, a = 11.955 (1), b = 14.317 (1), c = 6.231 (1) Å, V = 1066.5 (1) Å3, Dx
= 1.721 g cm−3. X-ray investigations reveal details of structural change with temperature in the paraelectric phase. The carboxylate anion O(3)—C(4)—O(4) in the tartrate molecule is displaced along the a axis as the temperature decreases; moreover, the O(8) atom is displaced in the opposite direction against the shift of the carboxylate anion. The temperature dependence of the thermal motions of O(8) shows different behavior from the other O atoms of the water molecules. The amplitude of the thermal motion of O(8) does not tend to zero at T = 0 K, while the other O atoms of the water molecules tend to zero.
Structure of UMoO5 studied by single-crystal X-ray diffraction and high-resolution transmission electron microscopy
Authors: D'yachenko O. G. , Tabachenko V. V. , Tali R. , Kovba L. M. , Marinder B.-O. , Sundberg M.
Published: July 2002

A combination of X-ray diffraction and high-resolution transmission electron microscopy (HRTEM) has been used to study the crystal structure of molybdenum uranium pentoxide, UMoO5, obtained by hydrothermal and ceramic methods. Crystal data: Mr
= 414.0, orthorhombic, Pbaa (number 54), a = 12.746 (1), b = 7.3494 (7), c = 4.1252 (2) Å, V = 386.4 (1) Å3, Z = 4, Dx
= 7.116 Mg m−3, R = 0.037 for 723 reflections. The structure of UMoO5 is related to that of UVO5. Both are built up by slabs of pentagonal UO7 bipyramids with slabs of MO6 octahedra in-between. They differ in symmetry due to different types of displacement of the M atoms from the ab plane. The HRTEM study revealed a few defect regions in the UMoO5 crystals prepared by ceramic methods. Energy-dispersive spectroscopy (EDS) analyses indicate a slight excess of uranium in such crystals. Hypothetical models of defect regions are given.
Pressure-Induced Fm-3m
R-3 Phase Transition in NaSbF6
Authors: Sowa H.
Published: July 2002

High-pressure X-ray diffraction measurements on NaSbF6 powder were performed up to 5.63 (7) GPa. At ∼0.1 GPa the cubic low-pressure phase with ordered ReO3-type crystal structure undergoes a phase transition into a rhombohedral LiSbF6-type modification. The high-pressure behaviour of this phase is characterized by rotations and distortions of the coordination octahedra, but it also can be described with a sphere-packing deformation. The octahedral distortions are probably caused by cation–cation repulsions.
Transferability of Empirical Force Fields in Silicates: Lattice-Dynamical Evaluation of Atomic Displacement Parameters and Thermodynamic Properties for the Al2OSiO4 Polymorphs
Authors: Pilati T. , Demartin F. , Gramaccioli C. M.
Published: July 2002

A Born–von Karman rigid-ion lattice-dynamical model, using empirical atomic charges and valence force fields derived from the best fit to the vibrational frequencies of a group of silicates and oxides, has been applied to andalusite, kyanite and sillimanite, the three naturally occurring Al2OSiO4 polymorphs. For andalusite there is good agreement with the atomic anisotropic displacement parameters (ADP's) derived from accurate crystal structure refinement at different temperatures and with the values of thermodynamic functions, such as the specific heat and entropy. For kyanite, our calculations are successful in reproducing the values of thermodynamic functions, but not the ADP's, almost certainly due to the poor quality of the crystals used in the structure determination. For sillimanite, imaginary frequencies are obtained in a region of the Brillouin zone: such an inadequacy might be ascribed to the presence of fourfold coordinated Al, whose properties are considerably different from those of higher-coordinated Al present in andalusite and kyanite.
New Inclusion Compounds of Selenourea with Tetraethyl- and Tetra-n-propylammonium Halides
Authors: Li Q. , Mak T. C. W.
Published: July 2002

Air-sensitive selenourea inclusion complexes tetraethylammonium chloride–selenourea (1/2), (C2H5)4N+.C1−.2[(NH2)2CSe] (1), tetra-n-propyl-ammonium chloride–selenourea (1/3), (n-C3H7)4N+.C1−.3[(NH2)2CSe] (2), tetra-n-propylammonium bromide–selenourea (1/3), (n-C3H7)4N+.Br−.3[(NH2)2CSe] (3), and tetra-n-propylammonium iodide–selenourea (1/1), (n-C3H7)4N+.I−.(NH2)2CSe (4), have been prepared and characterized by X-ray crystallography. Crystal data, Mo Kα radiation: (1), space group P21/n, Z = 4, a = 8.768 (5), b = 11.036 (6), c = 19.79 (1) Å, β = 96.92 (1)°, R

F
= 0.055 for 1468 observed data; (2), space group Cc, Z = 4, a = 18.091 (4), b = 13.719 (3), c = 11.539 (2) Å, β = 111.93 (3)°, R

F
= 0.051 for 1187 observed data; (3), space group Cc, Z = 4, a = 18.309  (4), b = 13.807 (3), c = 11.577 (2) Å, β = 112.45 (3)°, R

F
= 0.049 for 1592 observed data; (4), space group P21/n, Z = 4, a = 8.976 (1), b = 14.455 (2), c = 15.377 (3) Å, β = 94.16(1)°, R

F
= 0.062 for 1984 observed data. In the crystal structure of (1) the parallel alternate arrangement of selenourea–chloride ribbons and selenourea chains generates a puckered layer and the cations are sandwiched between them. In the isomorphous complexes (2) and (3) wide selenourea–halide double ribbons are crosslinked by bridging selenourea molecules via N—H...Se and N—H...X hydrogen bonds [average N...Se = 3.521 (8) and 3.527 (7), N...Cl = 3.354 (8) and N...Br = 3.500 (7) Å in (2) and (3), respectively] to form a channel-like three-dimensional network and the cations are accommodated in a single column within each channel. In the crystal structure of (4) the selenourea molecules are joined in the shoulder-to-shoulder fashion via N—H...Se hydrogen bonds [N...Se = 3.529 (7) and 3.534 (7) Å] to generate a ribbon and each selenourea molecule also forms a pair of chelating N—H...I hydrogen bonds [N...I = 3.567 (7) and 3.652 (7) Å] to an adjacent iodide ion.
Phase Transition in K3Na(MoO4)2 and Determination of the Twinned Structures of K3Na(MoO4)2 and K2.5Na1.5(MoO4)2 at Room Temperature
Authors: Fábry J. , Petrícek V. , Vanek P. , Císarová I.
Published: July 2002

The room-temperature phases of sodium potassium molybdates K3Na(MoO4)2 and K2.5Na1.5(MoO4)2 are isostructural with the monoclinic low-temperature phases of KaNa(SeO4)2 and K3Na(CrO4)2, which are twinned distorted glaserite structures. In the molybdates there are two crystallographically independent potassiums and their environment slightly differs from those in K3Na(SeO4)2 and K3Na(CrO4)2. The excessive Na in K2.5Na1.5(MoO4)2 occupies the position of the more firmly bound potassium. A reversible phase transition at 513 K was discovered in KaNa(MoO4)2 by DSC (differential scanning calorimetry), but no such transition in K2.5Na1.5(MoO4)2 was detected. Both samples used in the diffractometer experiment were found to be composed of six domains being related by twinning operations of the point group 6. The twinning may be considered as a combination of a merohedral and a pseudo-merohedral twinning with two- and threefold rotations as twinning operations, respectively. However, a reversible domain switching, which is observable in the related ferroelastic crystals of KaNa(SeO4)2 and K3Na(CrO4)2, was not observed either in K3Na(MoO4)2 or in K2.5Na1.5(MoO4)2, either due to semitransparency of the samples or high ferroelastic distortion. This distortion is manifested by the values of the atomic displacement vectors which are about twice as large as those in the selenate or the chromate.
Nucleophile–Electrophile Interactions in 1,8-Disubstituted Naphthalenes: Structures of Three 1-Naphthaldehydes and a 1-Naphthyl Methyl Ketone
Authors: Gallucci J. C. , Hart D. J. , Young D. G. J.
Published: July 2002

4,8-Dimethoxy-5-(tosyloxy)-1-naphthaldehyde (1) and 8-methoxy-5-(tosyloxy)-1-naphthaldehyde (2) crystallize such that the formyl groups approach coplanarity with the naphthalene rings. 4′,8′-Dimethoxy-5′-(tosyloxy)-1′-acetonaphthone (4), however, crystallizes such that the acetyl group approaches orthogonality to the naphthalene ring. In all three compounds the methoxy group and carbonyl groups exhibit a leaning effect typical of nucleophile–electrophile interactions in 1,8-disubstituted naphthalenes. 8-(Benzoyloxy)-4-methoxy-1-naphthaldehyde (3) crystallizes with the formyl group nearly coplanar to the naphthalene ring and does not exhibit the leaning effect. It is suggested that these structural differences are largely due to differences in the steric requirements of formyl and acetyl groups.
The Yttrium Oxide Fluoride Solid Solution Described as a Composite Modulated System
Authors: Schmid S.
Published: July 2002

Single-crystal X-ray diffraction data (Mo Kα radiation) are used to determine the structure of the Δ = 0.174 member of a (YO1 − ΔFΔ)F1 + Δ, 0.12 ≤ Δ ≤ 0.22, wide-range non-stoichiometric solid solution in the yttrium oxide fluoride system. The structure is refined as a composite modulated structure composed of two mutually incommensurable Q and H substructures with overall superspace-group symmetry Acmm(0,0,1.174..)0s0. The Q substructure has lattice parameters a = 5.415 (2), bQ
= 5.534 (2) and cQ
= 5.525 (2) Å, and superspace-group symmetry Acmm(0,0,1.174..)0s0. The H substructure has lattice parameters a = 5.415 (2), bH
= 1/2bQ
= 2.767 (1) and cH
 = 4.696 (2) Å, and superspace-group symmetry Pmcm(0,1/2,0.8518...)s00. Refinement on 338 unique reflections converged to R = 0.025, while a previous conventional superstructure refinement led to R = 0.101. This lowering of the R factor goes hand-in-hand with a substantial reduction in the number of refined parameters.
Crystal and molecular structures of diazapyrenes and a study of π\cdotsπ interactions
Authors: Kiralj Rudolf , Kojić-Prodić Biserka , Piantanida Ivo , Žinić Mladen
Published: July 2002

Two diazapyrenes, 5,10-dimethyl-4,9-diazapyrene (1) and novel 2,7-dimethyl-4,9-diazapyrene (2) have been synthesized. Their crystal structures are reported here and are the first representatives of diazapyrenes. Crystal data: (1) monoclinic, P21/c, a = 4.0246 (5), b = 15.5147 (5), c = 9.1453 (9) Å, β = 101.23 (1)°, V = 560.1 (1) Å3, Z = 2, R = 0.043; (2) monoclinic, C2/m, a = 12.4968 (3), b = 11.4751 (4), c = 3.9615 (5) Å, β = 96.80 (1)°, V = 564.09 (5) Å3, Z = 2, R = 0.0405. The experimental bond lengths are compared with those calculated by molecular mechanics (MM3), semi-empirical methods (MOPAC6.0-PM3, AM1, MNDO) and values predicted by valence-bond and variable-electronegativity self-consistent field (VESCF) methods. π\cdotsπ interactions in (1), (2) and seventeen other pyrene and pyrene-like molecules selected from the Cambridge Structural Database [Allen & Kennard (1993). Chem. Des. Autom. News, 8, 131–137] have been studied. The following quantitative parameters of π\cdotsπ interactions have been calculated: the shortest crystallographic axis, the offset parameter, the interplanar angle, the interactive volume and the overlapping surfaces. They are used for the classification of crystal-packing motifs; a high predominance of β and a few cases of γ and sandwich-herringbone types are observed. In addition, electronegativity, the sum of partial atomic charges of the ring non-H atoms and the number of aromatic skeleton electrons are used as parameters for classification. MOPAC-PM3 was used to calculate the partial atomic charges in (1), (2) and pyrene analogues. Correlations between geometrical and electronic structure parameters reveal an analogy between the β-type structures and the crystal structure of graphite.
Structures of 2,6-disubstituted naphthalenes
Authors: Kaduk James A. , Golab Joseph T.
Published: July 2002

The crystal structures of 2,6-naphthalenedicarboxylic acid (NDA) and dimethyl 2,6-naphthalenedicarboxylate (NDC) have been solved ab initio using a combination of X-ray powder diffraction and computational chemistry techniques. These two crystal structures, and that of 2,6-dimethylnaphthalene (DMN), have been refined by the Rietveld technique. DMN crystallizes in the orthorhombic space group Pbca, with a = 7.4544 (4), b = 6.0826 (6), c = 20.0946 (12) Å, V = 911.1 (1) Å3 and Z = 4. The structure consists of a herringbone stacking parallel to a, resulting in loosely bound layers perpendicular to c. NDA crystallizes in the triclinic space group P1¯, with a = 3.7061 (8), b = 7.4688 (14), c = 8.5352 (22) Å, α = 86.62 (2), β = 85.49 (2), γ = 87.99 (2)°, V = 235.00 (6) Å3 and Z = 1. The structure consists of loosely packed hydrogen-bonded chains along [11¯1]. NDC crystallizes in the monoclinic space group P21/c, with a = 13.41931 (14), b = 6.14869 (5), c = 7.15257 (5) Å, β = 100.400 (1)°, V = 580.47 (1) Å3 at 300 K and Z = 2. The structure consists of layers of NDC molecules perpendicular to a. The ester group is twisted 20° out of the mean ring plane in NDC. The conformations of the carboxyl groups in NDA and NDC differ. MP2 calculations suggest that the observed twist in NDC corresponds to an increase in conformational energy of 9 kJ mol−1.
The application of phase relationships to complex structures. III. The optimum use of phase relationships
Authors: Germain G. , Main P. , Woolfson M. M.
Published: July 2002

An improvement is described in the automatic procedure for solving crystal structures incorporated in the computer program LSAM. The development of signs from an initial set containing symbols is carried only as far as is necessary to establish strong relationships between the symbols. The information so gained is used in a fresh beginning of the symbolic-addition process. Some failure of relationships between symbols is allowed to give a multisolution method. A phase-permutation computer program for non-centrosymmetric structures, MULTAN, incorporates a weighted tangent formula. This is of the form {\rm tan}\varphi_{\bf h} = {{\sum_{\bf h'}w_{\bf h'},w_{\bf h-h'}|E_{\bf h'}E_{\bf h-h'}| \sin (\varphi_{\bf h'} + \varphi_{\bf h-h'})}\over{\sum_{\bf h'}w_{\bf h'},w_{\bf h-h'}|E_{\bf h'}E_{\bf h-h'}| \cos (\varphi_{\bf h'} + \varphi_{\bf h-h'})}} = {{T_{\bf h}}\over{B_{\bf h}}} and w_{\bf h} = {\rm tanh}\{ \sigma_3\sigma_2^{-3/2}|E_{\bf h}|(T_{\bf h}^2 + B_{\bf h}^2)^{1/2}\}.All phases are accepted as soon as they are found with the associated weight. This gives a fourfold increase in speed in development of the complete phase set. An absolute figure of merit is described to indicate probably correct phase sets for multisolution methods.
Debye–Waller factors of KBr at 4.2 and 295 K
Authors: Butt N. M. , Rouse K. D. , Thomas M. W. , Willis B. T. M.
Published: July 2002

The Debye-Waller factors of KBr have been determined both by X-ray and by neutron diffraction methods. Previous experiments have been carried out at or above room temperature. No such measurements have been reported at 4.2 K. Neutron diffraction experiments on a KBr powder at 295 and 4.2 K are reported here. The experimental results obtained were B
K = 2.55 ± 0.07, B
Br = 2.20 ± 0.04 Å2 at T = 295 K, and B
K = 0.43 ± 0.05, B
Br = 0.35 ± 0.02 Å2 at 4.2 K. These values differ from the theoretical estimates of Reid & Smith [J. Phys. Chem. Solids (1970), 31, 2689-2697], based on a quasiharmonic approximation using the shell model. The discrepancy may be attributed to the partial neglect of anharmonicity in the theoretical estimates.
1.72 Å Resolution Refinement of the Trigonal Form of Bovine Pancreatic Phospholipase A2
Authors: Sekar K. , Sekharudu C. , Tsai M.-D. , Sundaralingam M.
Published: July 2002

The trigonal crystal structure of the recombinant bovine pancreatic phospholipase A2 has been re-refined at a slightly higher resolution (1.72 Å). The crystals are trigonal, space group P3121, unit-cell parameters a = b = 46.78 and c = 102.89 Å and are isomorphous to the previous structure. The structure was refined to a final crystallographic R value of 19.5% (R
free = 28.4%) using 10 531 reflections. A total of 106 solvent molecules were included in the refinement compared with the earlier refinement which contains only 85 water molecules and 8 925 reflections at 1.8 Å resolution. The root-mean-square deviation from the ideal bond lengths and bond angles is considerably better in the present refinement. The active site is extended (\sim14 Å) from Ala1 to the calcium. The three catalytic residues (Asp99, His48 and the catalytic water) are connected by the conserved structural water and the N-terminal Ala1 on one side, and by the calcium through an equatorial water on the other. The water molecules play a role in the activity of the enzyme PLA2. The Ala1 end of the extended active site performs the activation of the phospholipid membranes while the opposite end performs the hydrolysis of the monomeric phospholipids.
Structural Parameters for Proteins Derived from the Atomic Resolution (1.09 Å) Structure of a Designed Variant of the ColE1 ROP Protein
Authors: Vlassi Metaxia , Dauter Zbigniew , Wilson Keith S. , Kokkinidis Michael
Published: July 2002

The crystal structure of a designed variant of the ColE1 repressor of primer (ROP) protein has been refined with SHELXL93 to a resolution of 1.09 Å. The final model with 510 non-H protein atoms, 576 H atoms in calculated positions and 114 water molecules converged to a standard R factor of 10% using unrestrained blocked full-matrix refinement. For all non-H atoms six-parameter anisotropic thermal parameters have been refined. The majority of atomic vibrations have a preferred orientation which is approximately perpendicular to the bundle axis; analysis with the TLS method [Schomaker & Trueblood (1968). Acta Cryst. B24, 63–77] showed a relatively good agreement between the individual atomic displacements and a rigid-body motion of the protein. Disordered residues with multiple conformations form clusters on the surface of the protein; six C-terminal residues have been omitted from the refined model due to disorder. Part of the solvent structure forms pentagonal or hexagonal clusters which bridge neighbouring protein molecules. Some water molecules are also conserved in wild-type ROP. The unrestrained blocked full-matrix least-squares refinement yielded reliable estimates of the standard deviations of the refined parameters. Comparison of these parameters with the stereochemical restraints used in various protein refinement programs showed statistically significant differences. These restraints should be adapted to the refinement of macromolecules by taking into account parameters determined from atomic resolution protein structures.
Crystallization and preliminary X-ray diffraction study of lactonohydrolase from Fusarium oxysporum
Authors: Kataoka Michihiko , Yamamoto Kazuhiko , Shimizu Sakayu , Ohta Mayumi , Kita Akiko , Higuchi Yoshiki , Miki Kunio
Published: July 2002

The lactonohydrolase from the fungus Fusarium oxysporum AKU 3702 was crystallized by the vapour-diffusion procedure in the presence of polyethylene glycol 4000 as a precipitant. The crystals belong to the monoclinic space group P21 with unit-cell parameters a = 156, b = 100, c = 94.1 Å, β = 91.7°. Assuming that there are two lactonohydrolase-dimer molecules in the asymmetric unit, the crystal volume per unit molecular mass, Vm
, is calculated to be 2.94 Å3 Da−1.
Two crystal forms of ModE, the molybdate-dependent transcriptional regulator from Escherichia coli
Authors: Hall D. R. , Gourley D. G. , Duke E. M. H. , Leonard G. A. , Anderson L. A. , Pau R. N. , Boxer D. H. , Hunter W. N.
Published: July 2002

The molybdenum-responsive ModE regulatory protein from Escherichia coli has been purified and used in crystallization trials. Two crystal forms have been observed. Form I is tetragonal, P41212 (or enantiomorph), with a = b = 72.3, c = 246.2 Å and diffracts to medium resolution. Form II is orthorhombic, P21212, with a = 82.8, b = 127.9, c = 64.0 Å and diffraction has been observed beyond 2.8 Å resolution. Structural analysis, in combination with ongoing biochemical characterization, will assist the elucidation of the structure–activity relationship in regulating the uptake of molybdate in bacteria.
PBR: a heavy-atom refinement and phasing procedure to reduce phase bias when heavy-atom derivatives contain common sites
Authors: Chabrière E. , Charon M.-H. , Vellieux F. M. D.
Published: July 2002

A procedure, called PBR (phase-bias reduction), has been developed to properly refine heavy-atom derivatives and to generate less biased heavy-atom phases when these derivatives contain common heavy-atom sites. Two independent events are obtained by splitting the refinement and phasing calculations into two stages, the first in which one of the derivatives having common sites is used together with the native amplitudes and the second in which both derivatives with common sites are used simultaneously, with one of them being used as the native data set. Improved centroid phases and the corresponding figures of merit are obtained by phase combination. This procedure has been used in the structure determination of the iron-cluster-containing protein pyruvate–ferredoxin oxidoreductase. When the common heavy-atom sites are properly treated by the PBR procedure, the resulting calculated centroid phases are improved with respect to classical heavy-atom refinement centroid phases where all derivatives are refined together. This leads to improved electron-density distributions, since anomalous difference Fourier maps calculated with the PBR-refined centroid phases and corresponding figures of merit show more clearly the positions of the iron sites.
Crystallization and preliminary X-ray analysis of arabinanase A from Pseudomonas fluorescens subspecies cellulosa
Authors: Scott M. , Pickersgill R. W. , Hazlewood G. P. , Gilbert H. J. , Harris G. W.
Published: July 2002

Crystals of 1,5-α-arabinanase A from Pseudomonas fluorescens subspecies cellulosa have been obtained by vapour diffusion. The crystals belong to the space group P6122 with unit-cell parameters a = b = 91.6, c = 179.4 Å with one molecule in the asymmetric unit. The native crystals and, to a much greater extent, heavy-atom soaked crystals are sensitive to radiation which necessitates cryocooling. Suitable cryocooling conditions have been established, though a shrinkage of the unit cell is observed, with a = b = 88.8 and c = 176.9 Å.
Optimizing Shake-and-Bake for proteins
Authors: Weeks Charles M. , Miller Russ
Published: July 2002

Shake-and-Bake is a direct-methods procedure which has provided ab initio solutions for protein structures containing as many as 1000 independent non-H atoms. This algorithm extends the range of conventional direct methods by repetitively, unconditionally and automatically alternating reciprocal-space phase refinement with filtering in real space to impose constraints. The application of SnB to protein-sized molecules is significantly affected by the choice made for certain critical parameters, including the number of peaks used for density modification, the choice of phase-refinement method and the number of refinement cycles. The effects of parameter variation have been studied for six protein structures, all of which are solvable by Shake-and-Bake using data at 1.1 Å or higher resolution. Solvability in the resolution range 1.2–1.4 Å appears to be enhanced by the presence of heavier atoms (S, Cl). Furthermore, it appears that in this range the ratio of refinement cycles and triplet phase invariants to atoms in the structure must be increased. Large structures lacking atoms of any element heavier than oxygen also require non-traditional parameter values.
Ab initio structure determination of a small protein, rubredoxin, by direct methods
Authors: Mukherjee Monika
Published: July 2002

The direct-methods program SAYTAN has been applied successfully to a known protein, rubredoxin, which contains 52 amino-acid residues including an FeS4 unit, a sulfate ion and 102 solvent water molecules. Starting with initially random phases, useful sets can be obtained from multiple trials and selected by figures of merit at different resolutions. Phase extension followed by weighted Fourier recycling reveals a recognizable structure of rubredoxin. The model is refined against 1 Å resolution data to an R factor of 14.5% using the program SHELXL93.
Crystallographic analysis of the dsDNA bacteriophage HK97 mature empty capsid
Authors: Wikoff William R. , Duda Robert L. , Hendrix Roger W. , Johnson John E.
Published: July 2002

HK97 is a member of the Siphovirus family of dsDNA bacteriophages. It is similar in architecture to bacteriophage λ, the type member of this family, with an icosahedral capsid of triangulation number T = 7. No high-resolution structural information is available for the dsDNA phages, and HK97 is the only dsDNA bacteriophage capsid to produce crystals which diffract X-rays. At 650 Å in diameter, the large size of the particle and resultant large unit cell create crystallographic challenges. The empty Head II (mature) particles were expressed in Escherichia coli and assembled in vitro, but they have the same morphology as the mature HK97 capsid. Previously reported Head II crystals diffracting to 3.5 Å resolution are examined here in detail. Although the cell dimensions suggest an orthorhombic lattice, further analysis demonstrated that the space group was monoclinic. This has been confirmed by the present study. Images were recorded on the F1 beamline at CHESS and they were processed and scaled, resulting in a data set with a cumulative completeness of 65% and a scaling R factor of 7.7% to 7 Å. The cell dimensions after post-refinement were a = 580, b = 626, c = 788 Å, β = 90.0°. From the particle dimensions determined by cryo-electron microscopy (cryo-EM), there were determined to be two particles per unit cell. Systematic absences of even reflections along the 0k0 lattice line indicate that the space group is P21. The rotation function was used to determine the orientation of the particles in the unit cell and to confirm the space group. An icosahedral twofold axis is approximately, but not exactly, aligned with the crystallographic screw (b) axis. An icosahedral twofold axis orthogonal to the one approximately parallel to the b axis, is rotated 18° away from the a axis. The centers of the two particles must be positioned close to the minimum-energy packing arrangement for spheres, which places one particle at (1\over4, 0, 1\over4) and the other particle at (3\over4, 1\over2, 3\over4). The particle position and orientation were confirmed by calculating a Patterson function. The particles interact closely along icosahedral threefold axes, which occurs both along the crystallographic a axis and along the b axis. The particle dimensions derived from this packing arrangement agree well with those determined by cryo-EM and image reconstruction. The cryo-EM reconstruction will be used as a model to initiate phase determination; structure determination at 7 Å is under way.
The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina
Authors: Ladner Jane E. , Abdulaev Najmoutin G. , Kakuev Dmitri L. , Tordová Mária , Ridge Kevin D. , Gilliland Gary L.
Published: July 2002

The crystal structures of two isoforms of nucleoside diphosphate kinase from bovine retina overexpressed in Escherischia coli have been determined to 2.4 Å resolution. Both the isoforms, NBR-A and NBR-B, are hexameric and the fold of the monomer is in agreement with NDP-kinase structures from other biological sources. Although the polypeptide chains of the two isoforms differ by only two residues, they crystallize in different space groups. NBR-A crystallizes in space group P212121 with an entire hexamer in the asymmetric unit, while NBR-B crystallizes in space group P43212 with a trimer in the asymmetric unit. The highly conserved nucleotide-binding site observed in other nucleoside diphosphate kinase structures is also observed here. Both NBR-A and NBR-B were crystallized in the presence of cGMP. The nucleotide is bound with the base in the anti conformation. The NBR-A active site contained both cGMP and GDP each bound at half occupancy. Presumably, NBR-A had retained GDP (or GTP) from the purification process. The NBR-B active site contained only cGMP.
Crystallization and preliminary X-ray analysis of Saccharomyces cerevisiae Ypd1p, a key intermediate in phosphorelay signal transduction
Authors: Lee Myong Gyong , Lee Jae Young , Song Hyun Kyu , Suh Se Won
Published: July 2002

Ypd1p, a 167-residue protein from Saccharomyces cerevisiae, plays a key role in osmosensing phosphorelay signal transduction. It forms part of a multistep phosphorelay system which also includes Sln1p hybrid histidine kinase and two response regulators, Ssk1p and Skn7p. It has been overexpressed in soluble form in Escherichia coli with a His6-tag at its C-terminus. The recombinant protein has been crystallized at room temperature using ammonium sulfate and lithium sulfate as precipitants. Native diffraction data have been collected to 2.3 Å using synchrotron radiation. The crystals are triclinic, belonging to the space group P1, with unit-cell parameters a = 65.78, b = 66.74, c  =  65.75 Å, α = 106.60, β = 106.48, γ = 115.53°. The asymmetric unit contains four molecules of the monomeric recombinant Ypd1p, with a corresponding Vm
of 2.75 Å3 Da−1 and a solvent content of 55.3%.
Crystallization and preliminary X-ray diffraction studies of guanidinoacetate methyltransferase from rat liver
Authors: Komoto Junichi , Huang Yafei , Hu Yongbo , Takata Yoshimi , Konishi Kiyoshi , Ogawa Hirofumi , Gomi Tomoharu , Fujioka Motoji , Takusagawa Fusao
Published: July 2002

Guanidinoacetate methyltransferase is the enzyme which catalyzes the last step of creatine biosynthesis. The enzyme is found ubiquitously and in abundance in the livers of all vertebrates. Recombinant rat-liver guanidinoacetate methyltransferase has been crystallized with guanidinoacetate and S-adenosylhomocysteine. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 54.8, b = 162.5, c = 56.1 Å, β = 96.8 (1)° at 93 K, and typically diffract beyond 2.8 Å.
Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance-B (NusB) from Mycobacterium tuberculosis
Authors: Gopal B. , Cox R. A. , Colston M. J. , Dodson G. G. , Smerdon S. J. , Haire L. F.
Published: July 2002

N-utilizing substance B (NusB) is a protein which forms part of a complex assembly in transcriptional antitermination in Mycobacterium tuberculosis. It forms a heterodimer with the product of the NusE gene (identical to the ribosomal protein S10) and mediates the process of transcriptional antitermination by forming the core complex with the nut site of the ribosomal RNA along with other protein factors. NusB has been cloned and overexpressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method. The space group is P212121, with unit-cell parameters a = 46.6, b = 64.2, c = 90.1 Å. A native data set complete to 1.6 Å resolution has been collected from a single crystal.
High-resolution X-ray spectroscopy of rare events: a different look at local structure and chemistry
Authors: Bergmann Uwe , Glatzel Pieter , Robblee John H. , Messinger Johannes , Fernandez Carmen , Cinco Roehl , Visser Henk , McFarlane Karen , Bellacchio Emanuele , Pizarro Shelly , Sauer Kenneth , Yachandra Vittal K. , Klein Melvin P. , Cox Billie L. , Nealson Kenneth H. , Cramer Stephen P.
Published: July 2002

The combination of large-acceptance high-resolution X-ray optics with bright synchrotron sources permits quantitative analysis of rare events such as X-ray fluorescence from very dilute systems, weak fluorescence transitions or X-ray Raman scattering. Transition-metal Kβ fluorescence contains information about spin and oxidation state; examples of the characterization of the Mn oxidation states in the oxygen-evolving complex of photosystem II and Mn-consuming spores from the marine bacillus SG-1 are presented. Weaker features of the Kβ spectrum resulting from valence-level and `interatomic' ligand to metal transitions contain detailed information on the ligand-atom type, distance and orientation. Applications of this spectral region to characterize the local structure of model compounds are presented. X-ray Raman scattering (XRS) is an extremely rare event, but also represents a unique technique to obtain bulk-sensitive low-energy (<600 eV) X-ray absorption fine structure (XAFS) spectra using hard (∼10 keV) X-rays. A photon is inelastically scattered, losing part of its energy to promote an electron into an unoccupied level. In many cases, the cross section is proportional to that of the corresponding absorption process yielding the same X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) features. XRS finds application for systems that defy XAFS analysis at low energies, e.g. liquids or highly concentrated complex systems, reactive compounds and samples under extreme conditions (pressure, temperature). Recent results are discussed.
XMCD study of the Ruddlesden-Popper-phase La1.2Nd0.2Sr1.6Mn2O7
Authors: Weigand F. , Goering E. , Geissler J. , Justen M. , Dörr K. , Ruck K. , Schütz G.
Published: July 2002

X-ray magnetic circular dichroism (XMCD) measurements of the Ruddlesden-Popper Phase La1.2Nd0.2Sr1.6Mn2O7 are reported. The Mn K, La and Nd L2,L3 edges have been measured on a powder sample at two different magnetic fields at low temperature. The analysis of the spectra at B = 1T indicates a large orbital moment of the Nd 5d-states and a significant spin-polarization of the La 5d-band. Furthermore at the Mn K-edge a XMCD-signal is observed, showing a polarization of the Mn 4p-band. At lower field (0.2T) all XMCD-signals are about two times smaller corresponding to the lower total magnetization. The signal at the Nd L2 edge vanishes completely at 0.2T.
IFEFFIT : interactive XAFS analysis and FEFF fitting
Authors: Newville Matthew
Published: July 2002

IFEFFIT, an interactive program and scriptable library of XAFS algorithms is presented. The core algorithms of AUTOBK and FEFFIT have been combined with general data manipulation and interactive graphics into a single package. IFEFFIT comes with a command-line program that can be run either interactively or in batch-mode. It also provides a library of functions that can be used easily from C or Fortran, as well as high level scripting languages such as Tcl, Perl and Python. Using this library, a Graphical User Interface for rapid 'online' data analysis is demonstrated. IFEFFIT is freely available with an Open Source license. Outside use, development, and contributions are encouraged.
Local lattice distortion in high-T

c
cuprates
Authors: Sakai Toru
Published: July 2002

The dynamical local lattice distortion in the CuO2 plane of the cuprate high-temperature superconductors is investigated with the numerical diagonalization study for finite clusters of t-J model. It is found that the in-plane vibrations of the oxygens play an important role in the formation of some static orders like CDW and SDW through the polaronic self localization effect. The 1/8 problem is also discussed based on the present result.
Verification of NEXAFS assignments by a comparison of fragmentation between gaseous and condensed methyl formate
Authors: Ikeura-Sekiguchi Hiromi , Sekiguchi Tetsuhiro , Saito Norio , Suzuki Isao H.
Published: July 2002

According to the ion desorption from condensed methyl formate (DCOOCH3) by C 1s electron excitation, C+ yield was strongly enhanced at 289.1 eV, a higher energy side of C1s(DC) ⇒ π*(C=O) peak. This feature could not be clearly assigned. In this work, to clarify the feature, fragment-ion yield curves of gas-phase methyl formate were measured and compared with those of condensed one, since gas-phase and condensed systems are presumed to show more or less similar fragment-ion yield curves under similar excitations. The results demonstrate that fragment-ion yield curves are useful for the assignments of NEXAFS features in both gaseous and condensed polyatomic molecules.
In situ studies on the structure of copper oxide/zinc oxide catalysts
Authors: Günter Marco Maria , Bems Bettina , Schlögl Robert , Ressler Thorsten
Published: July 2002

Cu/ZnO supported on alumina is a well-known catalyst for steam reforming of methanol. In this work it is attempted to assess the influence of elemental composition on the resulting active copper phase. XAFS measurements of calcined precursors were carried out at the Cu K edge and the Zn K edge. Corresponding RDF show that both copper oxide and zinc oxide exhibit considerable deviations from a linear dependence of their structure on the composition coinciding with changes in phase composition of hydroxycarbonate precursor. From time-resolved in situ experiments at the Cu K edge the degree of reduction can be monitored using a combination of factor analysis (PCA) and least-squares XANES fitting with suitable reference spectra (e.g. Cu metal, Cu2O, and CuO). It is shown that Cu2O forms prior to Cu. The extent of reduction to Cu exhibited a typical nucleation growth behavior with an enhanced reaction rate for more diluted samples. Adding oxygen to the feed gas leads to the formation of mixed Cu2+ and Cu+ phases accompanied by a complete loss of activity in methanol steam reforming. After switching back to steam reforming conditions the activity is regained.
Annealed crystallization of ultrafine amorphous NiB alloy studied by XAFS
Authors: Wei Shiqiang , Li Zhongrui , Yin Shilong , Zhang Xinyi , Liu Wenhan , Wang Xiaoguang
Published: July 2002

XAFS has been used to investigate the local structure evolutions of ultrafine amorphous NiB alloy during the annealed crystal-lization process. A nanocrystalline Ni phase with the local structure of crystalline Ni-like and a crystalline Ni3B, have been produced for ultrafine amorphous NiB alloy under the annealed temperature of 573 K. The results rule out Rojo et al.'s devitrification mechanism of Ni80B20 amorphous alloy in which they considered that an amorphous pure Ni phase is formed in the first exothermic process. However, our results are almost identical with Riveiro et al.'s conclusion in which the intermediate state is interpreted as two metastable crystalline phases of Ni3B and Ni-rich NiB alloy. With the annealed temperature going onto 773 K, the ultrafine NiB sample is further decomposed and crystallized into crystalline Ni with long-range order.
Progress on inner-shell excitations of molecular van der Waals clusters
Authors: Rühl E. , Flesch R. , Tappe W. , Pavlychev A. A.
Published: July 2002

Recent progress on core-level excitation of molecular van der Waals clusters is reported. Resonant excitation near element K edges of isolated and clustered molecules gives rise to small spectral shifts that can only be detected with high spectral resolution. This requires the use of state-of-the-art storage-ring facilities along with insertion devices and high-resolution soft X-ray monochromators. Selected experimental results on carbon monoxide clusters are reported. For the vibrationally resolved C 1s → π* (v = 0) band of clustered CO, these indicate characteristic line broadening as well as a small red shift of 2 ± 1 meV compared with the isolated molecule. The results are discussed within the framework of the quasi-atomic approach with respect to intermolecular interactions, freezing of molecular rotations in clusters, and dynamic localization of resonant core-to-valence excitations.
Lattice disorder in strongly correlated lanthanide and actinide intermetallics
Authors: Booth C. H. , Bauer E. D. , Maple M. B. , Lawrence J. M. , Kwei G. H. , Sarrao J. L.
Published: July 2002

Lanthanide and actinide intermetallic compounds display a wide range of correlated-electron behavior, including ferromagnetism, antiferromagnetism, nonmagnetic (Kondo) ground states, and so-called `non-Fermi liquid' (NFL) behavior. The interaction between f electrons and the conduction band is a dominant factor in determining the ground state of a given system. However, lattice disorder can create a distribution of interactions, generating unusual physical properties. These properties may include NFL behavior in many materials. In addition, lattice disorder can cause deviations from standard Kondo behavior that is less severe than NFL behavior. A review of the lattice disorder mechanism within a tight-binding model is presented, along with measurements of the YbBCu4 and UPd
x
Cu5−x
systems, demonstrating the applicability of the model. These measurements indicate that while the YbBCu4 system appears to be well ordered, both site interchange and continuous bond-length disorder occur in the UPd
x
Cu5−x
series. Nevertheless, the measured bond-length disorder in UPdCu4 does not appear to be enough to explain the NFL properties simply with the Kondo disorder model.
EXAFS determination of the size of Co clusters on silica
Authors: Arčon Iztok , Tuel Alain , Kodre Alojz , Martin Guy , Barbier Arnaud
Published: July 2002

The metallic Co catalyst for the Fischer-Tropsch reaction is prepared by reduction of Co salts impregnating microporous silica. The average size of the metallic Co clusters is determined from the average number of neighbours deduced from Co K-edge EXAFS of catalyst samples. A model EXAFS signal constructed from the scattering paths of Co metal fcc lattice with lengths up to 5 Å is calibrated on a reference spectrum of Co metal foil. Catalyst spectra are interpreted with the same model expanded with variable neighbour fractions of the four nearest shells. Cluster size is obtained from comparison with the neighbour fractions of consecutive fcc magic-number clusters.
EXAFS study of PbS–SnS solid solution
Authors: Lebedev Alexander , Sluchinskaya Irina , Munro Ian
Published: July 2002

The local environment of the Pb atom in Pb
x
Sn1-x
S solid solution was studied by EXAFS technique. The shortest Pb—S bond length in orthorhombic samples was found to be by ≃0.2 Å shorter than in cubic PbS. This indicates that the 6s
2 lone pair of Pb is stereochemically active in the SnS host. Strong correlations found in the distribution of metal atoms in the second shell show that the orthorhombic samples can be considered as solid solutions with unexpectedly strong short-range order. One can expect that the short-range order in PbSnS2 may result in formation of superstructures with space groups C2v

7 or C2v

2.
Oxygen 1s ELNES study of perovskites (Ca,Sr,Ba)TiO3
Authors: Wu Ziyu , Langenhorst F. , Seifert F. , Paris E. , Marcelli A.
Published: July 2002

The O K-edge spectra of perovskites XTiO3 with X = Ca, Sr and Ba have been measured using electron energy-loss spectroscopy (EELS) and are analyzed using the ab initio full multiple-scattering (MS) calculations. The near-edge structures arise mainly from covalency by direct and/or indirect interaction between oxygen and metal. The coordination number of the cation and the site symmetry also influence the spectral shape and structures. Comparison of full MS simulations of different clusters around the excited atom allows to interpret and correlate the features present in the spectra of each compound to its specific atomic arrangement and electronic structure.
EXAFS study of Sb–Te alloy films
Authors: Tani Katsuhiko , Yiwata Noriyuki , Harigaya Makoto , Emura Shuichi , Nakata Yoshiyuki
Published: July 2002

The local structures of three phases; stable compound Sb2Te3, metastable crystalline c-SbTe and amorphous a-SbTe films having the atomic ratio Sb/Te=3; in Sb-Te system have been studied by EXAFS. The c-SbTe has a partly similar local structure to crystalline Sb2Te3. The a-SbTe film has a local structure of NaCl-type, which is topologically analogous to the crystalline form. The amorphous phase has shorter bond distances 2.86 Å (around Sb-site) and 2.83 Å (around Te-site) than the corresponding distances 2.89 Å and 2.87 Å in the crystalline phase. This unbalanced bond distances between the Sb-site and Te-site implies that site-disordering occurs. Shortening of bond distances in the amorphous phase is due to the relaxation of locally distorted crystalline structure.
EXAFS study of copper in waste incineration fly ashes
Authors: Hsiao M. C. , Wang H. Paul , Huang Y.-J. , Yang Y. W.
Published: July 2002

Copper species such as CuCO3, Cu(OH)2, CuS and CuO were found in the bag house and EP (electrostatic precipitator) fly ashes of waste incineration processes by X-ray absorption near edge structural (XANES) spectroscopy. A small amount of Cu(I) and metallic Cu was found in the bag house fly ash. The averaged Cu-O bond distance in the fly ashes determined by EXAFS (extended X-ray absorption fine structural) was 1.96 Å with coordination numbers of 2.4-3.9. However, the Cu-(O)-Cu (2nd shell) bond distance of the fly ashes in the incineration process was decreased by 0.19-0.21 Å if compared to that of the CuO standard. The coordination numbers of the 2nd shell contribution to the bag house fly ash were not very significant.