bluuebunny/crossref_metadata_2025 huggingface dataset:
The Pseudo-Symmetric Structure of Pb(SPh)2
Authors: Rae A. D. , Craig D. C. , Dance I. G. , Scudder M. L. , Dean P. A. W. , Kmetic M. A. , Payne N. C. , Vittal J. J.
Published: July 2002

The crystal structure of Pb(SC6H5)2 is pseudo-C-centred orthorhombic, a = 54.06 (1), b = 11.468 (1), c = 7.4387 (8) Å, \alpha = \beta = \gamma = 90°, Z = 16, and may be described as a partial ordering of a 1:1 disordered parent structure of symmetry Pmcn, Z = 4 (a′ = a/2, b′ = b/2, c′ = c), in which the mirror imposes a 1:1 disorder on two-dimensionally polymeric layers perpendicular to a*. An ideally ordered structure has monoclinic space group C1121/d (P21/c using an alternative axis system b, c, [a + b]/2), but may also be described as two inversion-related substructures of Cmc21 pseudo- symmetry, where the b-glide planes of one substructure coincide with the mirror planes of the other and vice versa. Moving one substructure by b/2 relative to the other creates a different orientation of the structure. The crystal studied showed a partial disorder of each substructure relative to origins b/2 apart [0.964 (4):0.036 for one substructure and 0.584 (3):0.416 for the other]. This lowers the symmetry of the average structure to C1121 with intensities realistically described as K
2[(1−\delta)|F(hkl)|2 + \delta|F(hkl)|2], where K
2 for h odd, k odd reflections is 0.444 (7) of the value for h even, k even reflections, \delta is 0.325 (5) and F(hkl) is the structure factor for an ideally ordered structure. Final values for R of 0.046 and 0.090 were obtained for the 844 h even, k even and 687 h odd, k odd reflections with I(h) > 3\sigma(I(h)) used in refinement. A bond-valence interpretation of the bonding within the polymeric layer structure is given.
Structure Analysis of C60 Low-Temperature Phase by Electron Crystallography with Cryo-TEM
Authors: Ogawa T. , Isoda S. , Kobayashi T.
Published: July 2002

The crystal structure of C60 at liquid helium temperature was examined by the electron diffraction method using an imaging plate and cryo-TEM (transmission electron microscopy). The crystal of C60 was so thin that the electron scattering from this sample was able to be treated kinematically. However, the least-squares fitting among observed and kinematically calculated diffraction intensities resulted in an R-factor of 0.23 for a structure model with only one major orientation. Similar large R-factors are usually reported in the electron crystallography of thin crystals, in which a single perfect structure was assumed as a model structure. By considering structural disorders in the C60 crystal, however, the R-factor could be reduced to 0.12, when a minor crystal in a different orientation and also the f.c.c. (face-centered cubic) component were introduced to the model in addition to the major orientation crystal. Disorder in the crystal might be as important a factor as the dynamical scattering effect to be considered in electron crystallography for analyzing structures of thin crystals.
Neutron Diffraction Study of the Ambient-Pressure, Rutile-Type and the High-Pressure, CaCl2-Type Phases of Ruthenium Dioxide
Authors: Haines J. , Léger J. M. , Schulte O. , Hull S.
Published: July 2002

The structures of the ambient-pressure, rutile-type and the high-pressure, CaCl2-type phases of RuO2 were refined by time-of-flight neutron powder diffraction. Refinement of the data obtained from the ambient-pressure phase (P42/mnm, Z = 2) yielded cell constants a = 4.49307 (7) and c = 3.10639 (7) Å and an oxygen positional parameter x = 0.3056 (1). The principal axes of the displacement ellipsoids of the oxygen ions lie along the directions which correspond to the normal coordinate of the B
1g soft mode that drives the transition to the CaCl2-type structure. The CaCl2-type phase (Pnnm, Z = 2) was refined in situ at 5.3 (3) GPa and the following cell constants and oxygen positional parameters were obtained: a = 4.4865 (5), b = 4.4347 (5), c = 3.0934 (3) Å, x = 0.3101 (5) and y = 0.3005 (5). In the CaCl2-type phase at 5.3 (3) GPa the RuO6 octahedra are rotated by 1.1 (2)° with respect to their orientation in the ruffle-type phase. There is little change in the internal angles of the octahedron between 0.1 MPa and 5.3 GPa. Compression of the octahedron is anisotropic with a much greater reduction of the Ru—O contacts in the ab plane.
New Bond-Valence Sum Model
Authors: Naskar J. P. , Hati S. , Datta D.
Published: July 2002

A new expression is devised empirically to accommodate zero and some negative oxidation states in the bond-valence sum approach. The method is worked out in detail for a number of homoleptic copper and nickel complexes of various coordinating atoms in several oxidation states of the metals. An implication of the expression is a linear variation between 1/r
eq and 1/r
ax in octahedral MX
6 moieties, where r
eq and r
ax are, respectively, the average equatorial and axial bond lengths. This is verified in Cu2+
X
6 chromophores for X = F, O, N and S. The usefulness of the new expression in assessing the compatibility of a coordination sphere with an oxidation state of a metal ion is demonstrated by exemplary applications to some inorganic complexes, azurin and urease.
Multi-Solution Genetic Algorithm Approach to Surface Structure Determination Using Direct Methods
Authors: Landree E. , Collazo-Davila C. , Marks L. D.
Published: July 2002

We show that it is possible to use a multi-solution genetic algorithm search method utilizing direct methods to solve surface structures from surface diffraction data. We suggest that the method is generally applicable and able to replace random searches of the solution space.
Comparison of Experimental and Theoretical Structure Amplitudes and Valence Charge Densities of GaAs
Authors: Stahn J. , Möhle M. , Pietsch U.
Published: July 2002

The current best sets of X-ray structure amplitudes for GaAs, gallium arsenide, are completed by highly precise data recorded at 0.50 < sin θ/λ < 1.35 Å−1. For the strong reflections the required accuracy of ΔF/F ≤ 1% was realized by the use of Pendellösung measurements at λ = 0.30 Å, recording the integral intensities as a function of the effective thickness from ∼500 µm thick GaAs wafers. Additionally, several weak reflections were determined from their integral intensities within the kinematic limit at wavelengths λ = 0.3, 0.56 and 0.71 Å. From these data individual Debye–Waller factors for gallium and arsenic were determined using the model of independent spherical atoms [B
Ga = 0.666 (4) and B
As = 0.566 (4) Å2]. The extended set of experimental structure factors now available is compared with those obtained by ab initio solid-state Hartree–Fock (HF) and density functional (DF) calculations. Therefore, the theoretical data were adapted to room temperature using the experimentally evaluated Debye–Waller factors and the model mentioned above. The valence and difference charge densities obtained from experimental and theoretical data show the expected charge accumulation between nearest neighbours slightly shifted towards the arsenic site. The disagreement remaining between the experimental and theoretical data, on the one hand, and between those of both ab initio methods, on the other hand, are of the same order of magnitude.
Accurate charge densities in days — use of synchrotrons, image plates and very low temperatures
Authors: Iversen B. B. , Larsen F. K. , Pinkerton A. A. , Martin A. , Darovsky A. , Reynolds P. A.
Published: July 2002

Extensive synchrotron (28 K) and conventional sealed-tube (9 K) X-ray diffraction data have been collected on tetrakis(dimethylphosphinodithioato-S,S′)thorium(IV), [Th(S2PMe2)4]. The use of very low temperatures, well below those obtained with liquid-nitrogen cooling, is crucial for the accuracy of the data. This is due to minimization of temperature-dependent systematic errors such as TDS and anharmonicity, and extension and intensification of the data in reciprocal space. Comparison of structural parameters derived separately from the sealed-tube data and the synchrotron data shows good agreement. The synchrotron data are markedly superior when comparing refinement residuals, standard uncertainties (s.u.'s) of the data and s.u.'s of the derived parameters. However, the study suggests that there are still small uncorrected systematic errors in the data. The very large extent [(\sin\theta/\lambda)max = 1.77 Å−1] of the synchrotron data and the very low temperature at which they were collected makes it possible to separate anharmonic effects from electron-deformation effects even with only an X-ray data set at a single temperature. The electron density shows a large polarization of the outer Th core of d-type symmetry. This deformation is successfully modelled with contracted multipolar functions, which are only slightly correlated with anharmonic expansions in reciprocal space when using the full extent of the data. In the data collection more than a factor of 100 in speed is gained by use of image-plate area detectors at the synchrotron source compared with conventional sequential measurements. Thus accurate, very low temperature synchrotron-radiation diffraction data can now be measured within days, which makes electron-density studies of compounds beyond the first transition series more frequently within reach.
Identification of a new trace 114R SiC by HREM
Authors: Yang X. Y. , Shi G. Y. , Meng X. M. , Huang H. L. , Wu Y. K.
Published: July 2002

Using electron diffraction patterns and high-resolution electron microscopy (HREM), a trace 114R SiC in commercial α-SiC powder (mainly 6H SiC according to X-ray diffraction) has been discovered. In a hexagonal unit cell its stacking sequence is [(33)4(34)2]3, the periodicity along the c axis is 286.14 Å and a = b = 3.073 Å. 114R belongs to the structure series of (33)
n34(33)
m34 predicted theoretically by Pandey & Krishna [Mater. Sci. Eng. (1975), 20, 243–249] on the basis of the faulted matrix model.
Single-crystal structure analysis of a novel aryl phosphinate diglycidyl ether
Authors: Cho Ching-Sheng , Liau Wen-Bin , Chen Leo-Wang
Published: July 2002

The crystal structure of 10-[2,5-bis(2,3-epoxy-1-propoxy)phenyl]-9-oxa-10-phosphaphenanthren-10-one has been studied by single-crystal X-ray diffraction. The unit cell of C24H21O6P, M

r
= 436.4, is triclinic, P1¯, with a = 8.507 (3), b = 10.613 (4), c = 12.457 (3) Å, α = 80.05 (3), β = 71.38 (2), γ = 76.69 (3)°, V = 1031.1 (6) Å3, Z = 2, D

x
= 1.406 Mg m−3 and μ(Mo Kα) = 0.17 mm−1. The final R (wR) is 0.063 (0.057) {w = 1/[σ2(F) + 0.0004F
2]} for 3619 unique reflections measured at 295 K. The aryl phosphinate group bonded to the central phenyl ring comes close to one of the two glycidyl ether groups, the epoxide ring of which is ordered. The epoxide ring far from the aryl phosphinate group is disordered. The NMR chemical shifts of the protons of the glycidyl ether group close to the aryl phosphinate group are reduced by the `ring-current effect'.
Metal arrays in structural units based on anion-centered metal tetrahedra
Authors: Krivovichev S. V. , Filatov S. K.
Published: July 2002

Structural units based on anion-centered metal tetrahedra (XA
4; X = O, N; A = metal) are described as eutactic metal fragments with anions in tetrahedral interstices. In this respect these units may be subdivided into fluorite derivatives and units based on stellae quadrangulae (tetrahedral stars). To describe the geometry of the metal arrays a set of tetrahedrally packed metal radii, r
tp, is derived for A = Cu, Pb, Bi, and some rare-earth metals from the systematic analysis of the A...A distances within (XA
4) tetrahedra. Analysis of these radii and of the structural geometry of the units shows that the insertion of anions into tetrahedral interstices of the metal fragment causes its expansion and distortions by nonbonded anion–anion repulsions. The main effect is owing to the linkage of (XA
4) tetrahedra via edges, which leads to compression of the shared A...A edges and stretching of the unshared edges. The geometry of this effect is described by some empirical expressions. It is suggested that the eutactic arrangement of metal atoms in structural units based on anion-centered metal tetrahedra is caused by the closed-shell metal–metal bonding interactions
Structure of [(CH3)2NH2]2CoCl4 at elevated temperatures
Authors: Mahmoudkhani Amir H. , Langer Vratislav
Published: July 2002

The crystal structure of the title compound, dimethylammonium tetrachlorocobaltate(II), has been determined at four temperatures between 297 and 366 K, in order to investigate possible phase transitions at 313 and 353 K [Kapustianik, Polovinko & Kaluza et al. (1996). Phys. Status Solidi A, 153, 117–122]. We found that there is no significant change either in the hydrogen-bonding network or in the cell parameters, apart from a linear dilatation with temperature. This study reveals that the anomalous variation in electric conductivity and some of the other physical properties of the compound cannot be explained by structural changes.
Correlation between structural parameters of garnet and garnet-like structures
Authors: Pawlak Dorota A. , Woźniak Krzysztof , Frukacz Zygmunt
Published: July 2002

Statistical analysis of structural parameters of garnet and garnet-like structures retrieved from the Inorganic Crystal Structure Database has revealed strong correlations between them. The degree of correlation depends on doping site and garnet type. Structural parameters are not equally sensitive to changes imposed by doping. The strongest correlation exists between the unit-cell parameter and the doping-ion radius. In the case of doping at the dodecahedral sites, the most sensitive parameter is the shortest dodecahedral distance. Principal component analysis (PCA) clearly shows that the first component explains most of the variation of structural data. It has a geometric basis and correlates with the effective radii of the doping ion. Partial correlation helps to identify the strongest relations between pairs of variables when the influence of other structural variables on them is controlled. It appears that in some cases partial correlation has a different sign when compared with the results of the standard correlation technique.
Molecular structures and conformations of three 3-azabicyclononanes
Authors: Kumaran D. , Ponnuswamy M. N. , Shanmugam G. , Ponnuswamy S. , Jeyaraman R. , Shivakumar K. , Fun H.-K.
Published: July 2002

The structure, conformation, molecular geometry and the mode of packing of 7-tert-butyl-N-methyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonane (C25H33N; MTABN), N-acetyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonane (C22H25NO; AABN) and N-methyl-2,4-bis(2-methylphenyl)-3-azabicyclo[3.3.1]nonan-9-ol (C23H29NO; MHABN) are presented. The compounds MTABN and MHABN crystallize in monoclinic space groups, whereas AABN is orthorhombic. In each of the three structures, the bicyclic ring system adopts a chair–chair conformation and the phenyl rings are in equatorial orientation with respect to the piperidine ring. In AABN, apart from the van der Waals forces, weak intermolecular C—H...O type interactions are involved in the packing.
Investigation of the structural phase transitions near 190 K in 4,4′-dichlorobenzophenone
Authors: Mitkevich V. V. , Lirtsman V. G. , Strzhemechny M. A. , Avdeenko A. A. , Eremenko V. V.
Published: July 2002

X-ray structure studies have been carried out on single crystals of 4,4′-dichlorobenzophenone at temperatures from 164 to 295 K. The structure determined at 164 K is monoclinic I2/c. Crystal data: T = 164 K; a = 24.527 (6), b = 6.064 (1), c = 7.457 (4) Å; β = 100.10 (2)°; V = 1091.9 (6) Å3; Z = 4; d_{c} = 1.528 g cm^{-3}; \lambda(Mo K{\alpha}) = 0.71073 \AA; \mu = 0.565 mm^{-1}; F(000) = 512; R = 0.04. The temperature dependence of the unit-cell parameters and of the intensities of some symmetry-sensitive reflections has been measured over the range 164–293 K, both in warm-up and cool-down experiments. It has been established that the phase transformation between the C2/c and I2/c structures occurs as a sequence of two closely spaced first-order phase transitions. In between these phase transitions the crystal is in an intermediate state whose structure is different from both C2/c and I2/c. The experimental data give us ground to suppose that the intermediate state is disordered, having a primitive cell half as large as in the two ordered phases. Within the temperature interval where the said intermediate state exists the thermal expansivity along axis c is negative.
Extracting charge density distributions from diffraction data: a model study on urea
Authors: de Vries R. Y. , Feil D. , Tsirelson V. G.
Published: July 2002

The quality of the extraction of electron density distributions by means of a multipole refinement method is investigated. Structure factors of the urea crystal have been obtained from an electron density distribution (EDD) resulting from a density function calculation with the CRYSTAL95 package. To account for the thermal motion of the atoms, the stockholder-partioned densities of the atoms have been convoluted with thermal smearing functions, which were obtained from a neutron diffraction experiment. A POP multipole refinement yielded a good fit, R = 0.6%. This disagreement factor is based on magnitudes only. Comparison with the original structure factors gave a disagreement of 0.8% owing to differences in magnitude and phase. The fitted EDD still showed all the characteristics of the interaction density. After random errors corresponding to the experimental situation were added to the structure factors, the refinement was repeated. The fit was R = 1.1%. This time the resulting interaction density was heavily deformed. Repetition with another set of random errors from the same distribution yielded a widely different interaction density distribution. The conclusion is that interaction densities cannot be obtained from X-ray diffraction data on non-centrosymmetric crystals.
Structure refinement of Cu8GeS6 using X-ray diffraction data from a multiple-twinned crystal. Erratum
Authors: Onoda Mitsuko , Chen Xue-An , Kato Katsuo , Sato Akira , Wada Hiroaki
Published: July 2002

An error in the figures is reported. In the paper by Onoda et al. [Acta Cryst. (1999), B55, 721–725] the figures are given in the wrong order. Fig. 1 on p. 723 should in fact be Fig. 2 on p. 724 and vice versa. The figure captions are given correctly.
Molecular analysis of the β-polymorphic form of trielaidin: crystal structure at low temperature
Authors: Culot Christine , Norberg Bernadette , Evrard Guy , Durant Francois
Published: July 2002

This work reports on the structure of trielaidin [EEE, 1,2,3-tri(trans-9-octadecenoyl)glycerol], a trans unsaturated triglyceride present in many refined fatty materials (margarines, chocolate products etc.). Firstly, the polymorphism, i.e. the existence of different crystalline forms at various temperature ranges, was defined. Secondly, the crystal growth was examined. By developing a particular growing system, monocrystals of the most stable polymorphic form, i.e. the β-form, were obtained. To reduce thermal vibrations the X-ray data were collected at low temperature (173 K) and the structure was solved using direct methods. The structure was then analyzed in terms of conformation and crystal packing and compared with those of the other known triglycerides.
Terephthalate salts: salts of monopositive cations
Authors: Kaduk James A.
Published: July 2002

The crystal structures of dilithium, disodium and diammonium terephthalate (1,4-benzenedicarboxylate) have been solved ab initio using Monte Carlo simulated annealing techniques, and refined using synchrotron powder data. The structures of dipotassium terephthalate, potassium hydrogen terephthalate and ammonium hydrogen terephthalate have been refined using single-crystal techniques. Li2C8H4O4 crystallizes in P2
1/c, with a = 8.35921 (5), b = 5.13208 (2), c = 8.48490 (5) Å, β = 93.1552 (4)°, V = 363.451 (3) Å3, Z = 2. The Li anions are tetrahedrally coordinated and the packing of the terephthalate anions resembles the γ-packing of aromatic hydrocarbons. Na2C8H4O4 crystallizes in Pbc2
1, with a = 3.54804 (5), b = 10.81604 (16), c = 18.99430 (20) Å, V = 728.92 (2) Å3, Z = 4. The coordination of the two independent Na is trigonal prismatic and the terephthalate packing resembles the β packing of hydrocarbons. (NH4)2C8H4O4 also crystallizes in Pbc21, with a = 4.0053 (5), b = 11.8136 (21), c = 20.1857 (24) Å, V = 955.1 (2) Å3, Z = 4. The cations and planar anions are linked by hydrogen bonds and the packing is a looser version of the β packing. K2C8H4O2 crystallizes in P21/c, with a = 10.561 (4), b = 3.9440 (12), c = 11.535 (5) Å, β = 113.08 (3)°, V = 442.0 (3) Å3, Z = 2. The K is trigonal prismatic and the packing is also β. Both KHC8H4O4 and (NH4)HC8H4O4 crystallize in C2/c, with a = 18.825 (4) and 18.924 (4), b = 3.770 (2) and 3.7967 (9), c = 11.179 (2) and 11.481 (2) Å, β = 98.04 (3) and 94.56 (5)°, V = 816.8 (3) and 790.9 (3) Å3, respectively, and Z = 4. The packing in the hydrogen-bonded acid salts is also β. Electrostatic interactions among the terephthalate anions appear to be important in determining the crystal packing.
Structure, phase transitions and ionic conductivity of K3NdSi6O15·xH2O. I. α-K3NdSi6O15·2H2O and its polymorphs
Authors: Haile S. M. , Wuensch B. J.
Published: July 2002

Hydrothermally grown crystals of α-K3NdSi6O15·2H2O, potassium neodymium silicate, have been studied by single-crystal X-ray methods. The compound crystallizes in space group Pbam, contains four formula units per unit cell and has lattice constants a = 16.008 (2), b = 15.004 (2) and c = 7.2794 (7) Å, giving a calculated density of 2.683 Mg m−3. Refinement was carried out with 2161 independent structure factors to a residual, R(F), of 0.0528 [wR(F
2) = 0.1562] using anisotropic temperature factors for all atoms other than those associated with water molecules. The structure is based on highly corrugated (Si2O5
2−)∞ layers which can be generated by the condensation of xonotlite-like ribbons, which can, in turn, be generated by the condensation of wollastonite-like chains. The silicate layers are connected by Nd octahedra to form a three-dimensional framework. Potassium ions and water molecules are located in interstitial sites within this framework, in particular, within channels that extend along [001]. Aging of as-grown crystals at room temperature for periods of six months or more results in an ordering phenomenon that causes the length of the c axis to double. In addition, two phase transitions were found to occur upon heating. The high-temperature transformations, investigated by differential scanning calorimetry, thermal gravimetric analysis and high-temperature X-ray diffraction, are reversible, suggesting displacive transformations in which the layers remain intact. Conductivity measurements along all three crystallographic axes showed the conductivity to be greatest along [001] and further suggest that the channels present in the room-temperature structure are preserved at high temperatures so as to serve as pathways for easy ion transport. Ion-exchange experiments revealed that silver can readily be incorporated into the structure.
The temperature factor of an atom in a rigid vibrating molecule. II. Anisotropic thermal motion
Authors: Pawley G. S. , Willis B. T. M.
Published: July 2002

The analysis in part I is generalized to any crystal containing rigid molecules which undergo anisotropic translational and librational motion about a site fixed by symmetry. The treatment is correct to terms in (ui

2)2 and (ωi

2)2, where (ui

2) is the mean-square translational displacement of the molecule along the ith axis and (ωi

2) is the mean-square angular libration about the same axis. The first-order treatment to terms in (ui

2) and (ωi

2) is shown to be equivalent to the rigid-body theory in current use.
A least-squares method for the determination of the orientation matrix in single-crystal diffractometry
Authors: Tichý K.
Published: July 2002

An appropriate choice of the function minimized permits linearization of the least-squares determination of the matrix which transforms the diffraction indices into the components of the reciprocal vector in the diffractometer φ-axis system of coordinates. The coefficients of the least-squares equations are based on diffraction indices and measured diffractometer angles of three or more non-coplanar setting reflexions.
Determination of the polarization vectors of lattice waves by anomalous neutron scattering
Authors: Ramesh T. G. , Ramaseshan S.
Published: July 2002

The Argand diagram representation of coherent inelastic scattering (one-phonon process) is presented. This is used to show that |F(H,q)| ≠ |F({\bar \bf H}, {\bar \bf q})| in a non-centrosymmetric two-atom structure when an anomalous scatterer is present and |F(H,q)| ≠ |F(H , {\bar \bf q})| even in a NaCl-type structure when both atoms are normal scatterers. This paper describes how the polarization vectors of lattice waves may be experimentally determined in a crystal containing a nuclide which scatters thermal neutrons anomalously. The procedures for the determination of the polarization vectors in centrosymmetric and non-centrosymmetric structures when they are, in general, complex and for a Bravais lattice when they are always linearly polarized have also been presented. It is shown that the `phase problem' associated with the determination of the initial phase of elliptic motion can, in principle, be solved by using anomalous neutron scattering.
X-ray studies of the NaCl:SrCl2 system
Authors: Laredo E. , Dartyge E.
Published: July 2002

High-temperature diffraction experiments have been carried out on the NaCl: SrCl2 system, both in its poly- and monocrystalline form. These experiments have led us to the determination of the dilution enthalpy of the SrCl2 precipitates in the NaCl matrix (hD
= 0.90 ± 0.05 eV). Brauer's method was used to calculate the distortion around one defect and Eshelby's model was used to evaluate the resulting change in the lattice parameter due to these perturbing centers. The concentrations of defects calculated from these models are in good agreement with those determined chemically. Small-angle X-ray scattering experiments were performed on the same crystals, with suitable thermal treatments, to follow the clustering of defects as a function of the annealing temperature. It is possible to maintain a large amount of nearly dispersed strontium in the lattice by quenching the crystals from high temperature. The point defects agglomerate by successive annealings from 100 to 300°C, forming clusters of increasing sizes. A discussion of the composition of those centers is included.
The orientational average of exp[2πi(h.x + k.y + l.z)]
Authors: Brosius J.
Published: July 2002

The unit vectors e
l, e
2, e
3 form a fixed orthogonal coordinate frame. The unit vectors e
l
', e
2
', e
3
' form a movable orthogonal frame with the same origin as the fixed frame. All orientations in space of the movable frame are assumed to be equally probable. Under these conditions the average of exp [2πi(Σ3
i,j = 1a
ij

e

i
.e
'

j
)] is calculated. As an application the average of exp [2πi(h.x + k.y + l.z)] is calculated where the vectors h,k,l are specified and where the magnitudes of the vectors x,y,z and the angles between them are specified. This integral is of importance in utilizing a priori knowledge of molecular structure as an aid in solving the phase problem.
X-ray Structure of the ZnII β-Lactamase from Bacteroides fragilis in an Orthorhombic Crystal Form
Authors: Carfi Andrea , Duée Emile , Paul-Soto Raquel , Galleni Moreno , Frère Jean-Marie , Dideberg Otto
Published: July 2002

β-Lactamases are extracellular or periplasmic bacterial enzymes which confer resistance to β-lactam antibiotics. On the basis of their catalytic mechanisms, they can be divided into two major groups: active-site serine enzymes (classes A, C and D) and the ZnII enzymes (class B). The first crystal structure of a class B enzyme, the metallo-β-lactamase from Bacillus cereus, has been solved at 2.5 Å resolution [Carfi, Pares, Duée, Galleni, Duez, Frère & Dideberg (1995). EMBO J. 14, 4914–4921]. Recently, the crystal structure of the metallo-β-lactamase from Bacteroides fragilis has been determined in a tetragonal space group [Concha, Rasmussen, Bush & Herzberg (1996). Structure, 4, 823–836]. The structure of the metallo-β-lactamase from B. fragilis in an orthorhombic crystal form at 2.0 Å resolution is reported here. The final crystallographic R is 0.196 for all the 32 501 observed reflections in the range 10–2.0 Å. The refined model includes 458 residues, 437 water molecules, four zinc and two sodium ions. These structures are discussed with reference to Zn binding and activity. A catalytic mechanism is proposed which is coherent with metallo-β-lactamases being active with either one Zn ion (as in Aeromonas hydrophila) or two Zn ions (as in B. fragilis) bound to the protein.
Accelerated X-ray Structure Elucidation of a 36 kDa Muramidase/Transglycosylase Using wARP
Authors: van Asselt Erik J. , Perrakis Anastassis , Kalk Kor H. , Lamzin Victor S. , Dijkstra Bauke W.
Published: July 2002

The X-ray structure of the 36 kDa soluble lytic transglycosylase from Escherichia coli has been determined starting with the multiple isomorphous replacement method with inclusion of anomalous scattering at 2.7 Å resolution. Subsequently, before any model building was carried out, phases were extended to 1.7 Å resolution with the weighted automated refinement procedure wARP, which gave a dramatic improvement in the phases. The electron-density maps from wARP were of outstanding quality for both the main chain and the side chains of the protein, which allowed the time spent on the tracing, interpretation and building of the X-ray structure to be substantially shortened. The structure of the soluble lytic transglycosylase was refined at 1.7 Å resolution with X-PLOR to a final crystallographic R factor of 18.9%. Analysis of the wARP procedure revealed that the use of the maximum-likelihood refinement in wARP gave much better phases than least-squares refinement, provided that the ratio of reflections to protein atom parameters was approximately 1.8 or higher. Furthermore, setting aside 5% of the data for an R_{\rm free} test set had a negative effect on the phase improvement. The mean W_{wARP}, a weight determined at the end of the wARP procedure and based on the variance of structure factors from six individually refined wARP models, proved to be a better indicator than the R_{\rm free} factor to judge different phase improvement protocols. The elongated Slt35 structure has three domains named the alpha, beta and core domains. The alpha domain contains mainly \alpha-helices, while the beta domain consists of a five-stranded antiparallel \beta-sheet flanked by a short \alpha-helix. Sandwiched between the alpha and beta domains is the core domain, which bears some resemblance to the fold of the catalytic domain of the previously elucidated 70 kDa soluble lytic transglycosylase from E. coli. The putative active site is at the bottom of a large deep groove in the core domain.
The Nucleic Acid Database: A Resource for Nucleic Acid Science
Authors: Berman Helen M. , Zardecki Christine , Westbrook John
Published: July 2002

The Nucleic Acid Database (NDB) distributes information about nucleic acid-containing structures. Here the information content of the database as well as the query capabilities are described. A summary of how the technology developed by this project has been used to develop other macromolecular databases is given.
Macromolecular Structure Databases: Past Progress and Future Challenges
Authors: Weissig Helge , Shindyalov Ilya N. , Bourne Philip E.
Published: July 2002

Databases containing macromolecular structure data provide a crystallographer with important tools for use in solving, refining and understanding the functional significance of their protein structures. Given this importance, this paper briefly summarizes past progress by outlining the features of the significant number of relevant databases developed to date. One recent database, PDB+, containing all current and obsolete structures deposited with the Protein Data Bank (PDB) is discussed in more detail. PDB+ has been used to analyze the self-consistency of the current (1 January 1998) corpus of over 7000 structures. A summary of those findings is presented (a full discussion will appear elsewhere) in the form of global and temporal trends within the data. These trends indicate that challenges exist if crystallographers are to provide the community with complete and consistent structural results in the future. It is argued that better information management practices are required to meet these challenges.
X-ray analysis of crystals of rat phosphatidylinositol-transfer protein with bound phosphatidylcholine
Authors: Oliver Randall L. , Tremblay Jacqueline M. , Helmkamp George M. , Yarbrough Lynwood R. , Breakfield Natalie W. , Yoder Marilyn D.
Published: July 2002

Phosphatidylinositol-transfer protein (PITP) is a soluble, ubiquitously expressed, highly conserved protein encoded by two genes in humans, rodents and other mammals. A cDNA encoding the alpha isoform of the rat gene was expressed to high levels in Escherichia coli, the protein purified and the homogeneous protein used for crystallization studies. Crystals of rat PITP-α were obtained by vapor-diffusion techniques using the sitting-drop method. Crystals grow within two weeks by vapor-diffusion techniques in the presence of polyethylene glycol 4000. Both crystal forms pack in the monoclinic space group P21. Crystal form I has unit-cell parameters a = 44.75, b = 74.25, c = 48.32 Å and β = 114.14°. Unit-cell parameters for crystal form II are a = 47.86, b = 73.59, c = 80.49 Å and β = 98.54°. Crystal form I has a Vm
of 2.295 Å3 Da−1 and an estimated solvent content of 46.4% with one molecule per asymmetric unit, while crystal form II has a Vm
of 2.196 Å3 Da−1 and an estimated solvent content of 44.0%, assuming two molecules per asymmetric unit.
Crystallization and preliminary crystallographic analysis of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E: a novel dioxygenase involved in the biodegradation of polychlorinated aromatic compounds
Authors: Benvenuti Manuela , Briganti Fabrizio , Scozzafava Andrea , Golovleva Ludmilla , Travkin Vasily M. , Mangani Stefano
Published: July 2002

Hydroxyquinol 1,2-dioxygenase (HQ1,2O) from Nocardioides simplex 3E, an enzyme involved in the aerobic biodegradation of a large class of chloroaromatic compounds such as 2,4-dichlorophenoxyacetate (2,4-D) and 2,4,5-trichlorophenoxyacetate (2,4,5-T), has been crystallized. HQ1,2O, which specifically catalyzes the intradiol cleavage of hydroxyquinol (1,2,4-trihydroxybenzene), an intermediate in the degradation of a variety of aromatic pollutants, to maleylacetate, has been recently purified to homogeneity. The enzyme is an homodimer composed of two identical subunits in a α2-type quaternary structure, has a molecular weight of about 65 kDa and contains a catalytically essential Fe(III) ion. Crystals of HQ1,2O obtained using 2% PEG 400 and 2 M ammonium sulfate at pH 7.5 as precipitants belong to the orthorhombic space group P212121, with unit-cell parameters a = 81.15 (6), b = 86.79 (7), c = 114.93 (8). Assuming one dimer per asymmetric unit, the Vm
value is 2.51 Å3 Da−1. A complete native data set to 1.8 Å resolution has been collected on a laboratory source. This is the first intradiol dioxygenase which specifically catalyzes the cleavage of hydroxyquinol to give diffraction-quality crystals.
Crystallization and preliminary X-ray diffraction analysis of hydroxynitrile lyase from cassava (Manihot esculenta)
Authors: Lauble Hanspeter , Decanniere Klaas , Wajant Harald , Förster Siegfried , Effenberger Franz
Published: July 2002

Hydroxynitrile lyase from M. esculenta (cassava) was crystallized in two different crystal forms by the hanging-drop vapour-diffusion method. Crystals of form I were obtained from a mixture of polyethylene glycol 8000 and 2-methyl-2,4-pentanediol, and belong to the tetragonal space group P41212 or its enantiomorph P43212, with unit-cell parameters a  =  b  =  105.9, c  =  188.9 Å and with two molecules in the asymmetric unit. These crystals diffract to 2.9 Å with conventional X-ray sources and beyond 2.1 Å resolution with synchrotron radiation. The crystals are relatively sensitive to radiation damage and conditions for flash-cooling the crystals have been established. A complete native data set has been collected up to 2.2 Å resolution. Crystal form II has been obtained at pH 5.6 using lithium sulfate as a precipitant. The crystals apparently belong to the orthorhombic space group P21212, with unit-cell parameters a = 117.52, b = 127.09 and c = 78.08 Å, have two molecules in the asymmetric unit and diffract to beyond 2.0 Å resolution. A complete native data set has been collected to 2.2 Å resolution.
Crystallization and preliminary X-ray study of two crystal forms of Klebsiella oxytoca diol dehydratase–cyanocobalamin complex
Authors: Masuda Jun , Yamaguchi Tetsuya , Tobimatsu Takamasa , Toraya Tetsuo , Suto Kyoko , Shibata Naoki , Morimoto Yukio , Higuchi Yoshiki , Yasuoka Noritake
Published: July 2002

Two crystal forms of Klebsiella oxytoca diol dehydratase complexed with cyanocobalamin have been obtained and preliminary crystallographic experiments have been performed. The crystals belong to two different space groups, depending on the crystallization conditions. One crystal (form I) belongs to space group P212121 with unit-cell parameters a = 76.2, b = 122.3, c = 209.6 Å, and diffracts to 2.2 Å resolution using an X-ray beam from a synchrotron radiation source. The other crystal (form II) belongs to space group P21 with unit-cell parameters a = 75.4, b = 132.7, c = 298.8 Å, β = 91.9°, and diffracts to 3.0 Å resolution. For the purpose of structure determination, a heavy-atom derivative search was carried out and some mercuric derivatives were found to be promising. Structure analysis by the multiple isomorphous replacement method is now under way.
Structure of ribosomal protein L30 from Thermus thermophilus at 1.9 Å resolution: conformational flexibility of the molecule
Authors: Fedorov Roman , Nevskaya Natalia , Khairullina Alphia , Tishchenko Svetlana , Mikhailov Albert , Garber Maria , Nikonov Stanislav
Published: July 2002

The crystal structure of ribosomal protein L30 from the extreme thermophilic bacterium Thermus thermophilus has been determined at 1.9 Å resolution. The crystals are trigonal and belong to space group P3221, with unit-cell parameters a = b = 63.5, c = 77.8 Å, α = β = 90, γ = 120° and two molecules per asymmetric unit. The structure was solved by the molecular-replacement method with AMoRe and refined with X-PLOR to an R value of 20.3% and an R
free of 25.3% in the resolution range 8–1.9 Å. Detailed analyses of the structures of the two molecules in the asymmetric unit and comparison of T. thermophilus L30 structure with the structure of homologous L30 from Bacillus stearothermophilus reveal two flexible regions at opposite ends of the rather elongated molecule. Such flexibility could be important for the protein fitting in the ribosome. A comparison with B. stearothermophilus L30 shows a higher number of salt bridges and unbound positively charged residues and an increased accessible hydrophobic area on the surface of T. thermophilus L30. This could contribute to the stability of both the extreme thermophile protein and the ribosome as a whole.
Structures of cellular retinoic acid binding proteins I and II in complex with synthetic retinoids
Authors: Chaudhuri Barnali Neel , Kleywegt Gerard J. , Broutin-L'Hermite Isabelle , Bergfors Terese , Senn Hans , Le Motte Peter , Partouche Olivier , Jones T. Alwyn
Published: July 2002

Retinoids play important roles in diverse cellular processes including growth, cell differentiation and vision. Many natural and synthetic retinoids are used as drugs in dermatology and oncology. A large amount of data has been accumulated on the cellular activity of different synthetic retinoids. They are stabilized and transported inside the cell cytoplasm by binding and transport proteins, such as cellular retinol-binding proteins and cellular retinoic acid binding proteins (CRABPs). The structures of human CRABP II in complex with two different synthetic retinoids, Ro13-6307 and Ro12-7310 (at 2.1 and 2.0 Å resolution, respectively) and of bovine CRABP I in complex with a retinobenzoic acid, Am80 (at 2.8 Å resolution) are described. The binding affinities of human CRABP I and II for the retinoids studied here have been determined. All these compounds have comparable binding affinities (nanomolar range) for both CRABPs. Apart from the particular interactions of the carboxylate group of the retinoids with specific protein groups, each structure reveals characteristic interactions. Studying the atomic details of the interaction of retinoids with retinoid-binding proteins facilitates the understanding of the kinetics of retinoid trafficking inside the cytoplasm.
EXAFS study on liquid gallium under high pressure and high temperature
Authors: Comez Lucia , Di Cicco Andrea , Minicucci Marco , Tossici Roberto , Itiè Jean Paul , Polian Alain
Published: July 2002

EXAFS (Extended X-ray Absorption Fine Structure) spectra of liquid gallium near the Ga K-edge have been collected in wide pressure and temperature ranges. Reliable short-range pair distribution functions have been determined using advanced ab initio calculations (GNXAS) taking into account the medium and long-range structure obtained by previous neutron and X-ray-scattering studies.
X-ray absorption spectroscopy studies of Ba1-x
Ca
x
TiO3
Authors: Asokan K. , Jan J. C. , Chiou J. W. , Pong W. F. , Tseng P. K. , Lin I. N.
Published: July 2002

We report x-ray absorption near edge spectroscopy (XANES) of Ca and O K-edges of Ba1-xCaxTiO3 (x = 0, 0.01, 0.08, 1) and understand the spectral features related to the electronic structure of these perovskites. The XANES spectra of Ca K-edge possess a pre-edge peak similar to other 3d transition metals like Ti, Ni when present in perovskite structure and provides information about p-type or hole doping. Presence of considerable amount of 3d states justifies the reason to consider it as a light 3d transition metal. The O K-edge spectra display characteristic spectral features assigned as e

g
and t
2g
and show strong dependence on concentration.
A review of some characteristics of MIC caused by sulfate‐reducing bacteria: past, present and future
Authors: Javaherdashti Reza
Published: July 2002

Microbiologically‐influenced corrosion (MIC) is extremely harmful to both the industry and the environment. Sulfate‐reducing bacteria (SRB) are also important: we have to know what they really are and what they really do to us; this means we have to improve our understanding of SRB and their characteristics. MIC is the officially accepted terminology by NACE[1] to address this type of corrosion. It is a kind of corrosion in which effects of certain microorganisms are felt. MIC is still a matter open for discussion: we cannot explain what is really meant by “microbiological” component, i.e. does it express the possibility that some microbial activity observed at corroded sites on metal surfaces may not result from bacterial growth on metal, but rather that chemical or electrochemical attack on the metal may provide a favorable niche for bacteria to grow? Nor can we be sure about our understanding of the importance of working mechanisms and even the types of microorganisms involved in MIC. In order to have a deeper understanding about corrosion caused by sulfate‐reducing bacteria (SRB), we have to know more about SRB themselves. So, after discussing the importance of MIC, we will mainly focus on SRB and their characteristics that may be new and interesting to the reader.
Clarifying the use of competence and competency models in
recruitment, assessment and staff development
Authors: Rowe Christopher
Published: July 2002

Emphasizes the need for clear terminology; distinguishes between
“competence” and “competency”. Argues that
competence and competency models have been used in three different
areas: recruitment, skill assessment and development. Considers
competence models, such as the MCI standards in the area of skill
assessment, which focus on What people can do; require clear,
measurable standards; and exclude grading. Discusses behaviour
inventories – which focus on how people behave and can be
graded in relation to recruitment and staff development. Makes a
distinction between intellectually based and morally based behaviours
which allows a “dartboard” model to be created with
“hard” competences at the centre, phasing out through
intellectually based behaviours to “soft” morally based
behaviour at the periphery. Behaviours, capabilities and attributes are
added to the vocabulary, hopefully to provide greater clarification.
Creativity in assessment of library instruction
Authors: Williams Janet L.
Published: July 2002

The basic concepts of testing and item development, and the application of alternative assessments (non‐multiple choice) to information literacy content for library instruction are discussed. Alternative item types include selected response, constructed response, essay, and complex answers. The author relates the item types to the “Information Literacy Competency Standards for Higher Education”. Topic, content objectives, and behavioral objectives are included for each item.
Leadership and the company turnaround process
Authors: Harker Michael , Sharma Bishnu
Published: July 2002

Three firms engaged in the heavy engineering industry undergoing the transition from organisational decline to recovery were studied in‐depth in a period of significant change for the industry. The purpose of the study was to explore the way in which leaders manage the company turnaround process. The turnaround performance and processes of recovering firms were compared to those of a less successful rival. Effective turnaround management involved making a series of holistic changes to strategies, structures and practices throughout the organisation; changes which were orchestrated by leaders at different levels in the firms. This study of leaders at work presents a model linking leadership and the turnaround process which challenges conventional prescriptions for company revival in a mature industry and identifies three core dimensions which mediate the effectiveness of relationship between leadership and company turnarounds.
Development of partially‐automated disassembly plants for regaining reusable parts
Authors: Kiesgen Gerrit , Emenako Mike E. , Slawik Frank
Published: July 2002

Recycling of glass and paper found in household refuse is recognized as environmentally desirable but, as yet, little has been done to facilitate the recycling of hard‐wearing consumer goods, the majority of which are either dumped in land‐fill sites or incinerated. Complex consumer durables contain a wide variety of materials, all of which must be separated before efficient recycling can take place. Reports on the Eureka CLEANTECH project which aims to find new technological solutions for cost‐effective reuse of components and sub‐assemblies, as well as waste reduction for products with mainly electrical and electronic components.
Systematic layout planning: a study on semiconductor wafer fabrication facilities
Authors: Yang Taho , Su Chao‐Ton , Hsu Yuan‐Ru
Published: July 2002

This paper proposes to use Muther’s systematic layout planning procedure as the infrastructure to solve a fab layout design problem. A multiple objective decision making tool, analytic hierarchy process, is then proposed to evaluate the design alternatives. The proposed procedure is illustrated to be a viable approach for solving a fab layout design problem through a real‐world case study. It features both the simplicity of the design process and the objectivity of the multiple‐criteria evaluation process as opposed to existing solution methodologies.