bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystallite size distribution and dislocation structure determined by diffraction profile analysis: principles and practical application to cubic and hexagonal crystals
Authors: Ungár T. , Gubicza J. , Ribárik G. , Borbély A.
Published: July 2002

Two different methods of diffraction profile analysis are presented. In the first, the breadths and the first few Fourier coefficients of diffraction profiles are analysed by modified Williamson–Hall and Warren–Averbach procedures. A simple and pragmatic method is suggested to determine the crystallite size distribution in the presence of strain. In the second, the Fourier coefficients of the measured physical profiles are fitted by Fourier coefficients of well establishedab initiofunctions of size and strain profiles. In both procedures, strain anisotropy is rationalized by the dislocation model of the mean square strain. The procedures are applied and tested on a nanocrystalline powder of silicon nitride and a severely plastically deformed bulk copper specimen. The X-ray crystallite size distributions are compared with size distributions obtained from transmission electron microscopy (TEM) micrographs. There is good agreement between X-ray and TEM data for nanocrystalline loose powders. In bulk materials, a deeper insight into the microstructure is needed to correlate the X-ray and TEM results.
Neural network application to the inverse scattering problem in high-resolution X-ray diffraction
Authors: Glorieux Christ , Zolotoyabko Emil
Published: July 2002

The complicated inverse scattering problem of reconstructing depth-dependent lattice parameters from high-resolution X-ray diffraction spectra is analysed by using neural networks. Attention is paid to the practically important case of structural modifications in the near-surface layers of ion-implanted single crystals. The feasibility of a neural network algorithm is assessed on the basis of the performance statistics on a large number of simulated examples. The performance of the method on experimental data is tested using high-resolution X-ray diffraction spectra taken from He-implanted lithium niobate crystals.
Réalisation de canevas stéréographiques pour l'interprétation de figures de pôles
Authors: Ruer D. , Baro R.
Published: July 2002

The stereographic nets presented in this article are the stereographic projections of the net of meridians and parallels of a sphere when it turns by steps of 5° round an axis located in the plane of projection. These nets provide a means to avoid the many constructions necessary to interpret a pole figure when only the Wulff net is used. They also make the determination of the fibre axes of a texture easier, and give, by simple reading, the angles between one pole and any other pole of a given pole figure.
A rigid-body least-squares program with angular and translation scan facilities
Authors: Kutschabsky L. , Krause C.
Published: July 2002

The described computer program, written in CERN Fortran, is designed to enlarge the convergence radius of the rigid-body least-squares method by allowing a stepwise change of the angular and/or translational parameters within a chosen range.
An X-ray camera for single-crystal studies at high temperatures under controlled atmosphere
Authors: Aldhart W. , Tzafaras N. , Sueno S. , Jagodzinski H. , Huber H.
Published: July 2002

A vacuum heating camera has been developed for extremely low background X-ray film work between room temperature and 2000 K. It can be used with modified conventional Weissenberg goniometers and with a specially designed focusing goniometer. The temperature control is maintained by a Pt/Pt–10% Rh thermocouple, a three-term proportional, integral and derivative (PID) controller and a programmable power supply. The accuracy in the absolute temperature setting is 10 K, the stability better than 1 K and the maximum thermal gradient over the crystal 7 K mm−1 at 1330 K. A small oxygen pressure can be applied, depending on the temperature, to control oxidation or reduction reactions of the sample.
Asymmetrically grooved monolithic crystal monochromators for suppression of harmonics in synchrotron X-radiation: erratum
Authors: Hashizume H.
Published: July 2002

A typographical error has occurred in Hashizume [J. Appl. Cryst. (1983). 16, 420–427]. The first two complete sentences on page 425 should read: A attains a minimum value of 0.024 at b
II = 0.27, where about half of the initial fundamental intensity is preserved. The initial rise of the fundamental intensity, which occurs in the range 1.0 > b
II ≥ 0.64, is accounted for by a close examination of the overlap pattern of R
(1)

HI and, R
(1)
0II at the relevant b
II values: the shifted and extended peak profile of R
(1)
0II admits the high-angle tail of R
(1)

HI and rejects the low-angle flank of R
(1)

HI
, and the gain due to the former more than compensates for the loss caused by the latter.
Diagrammes de poudres de l'iminostilbene, C14H11N, de l'iminodibenzyle, C14H13N, et de son derivé: le chloro-3 iminodibenzyle, C14H12ClN
Authors: Caranoni C. , Reboul J. P.
Published: July 2002

X-ray powder data have been obtained for the three title compounds, fundamental members of a group of psychotropic drugs. For the first two compounds, the crystal structures of which have previously been solved [Reboul, Cristau, Soyfer & Estienne (1980). Acta Cryst. B36, 2683–2688; Reboul, Cristau, Estienne & Astier, (1980). Acta Cryst. B36, 2108–2112], the powder patterns were indexed on the basis of an orthorhombic unit cell with the lattice constants a = 8.22 (1), b = 20.40 (1), c = 6.03 (1) Å, space group Pnma for C14H11N; C14H13N is monoclinic, space group P21/c with a = 11.60 (1), b = 11.27 (1), c = 20.05 (1) Å, and β = 126.5 (1)°. C14H12ClN is also monoclinic, P21 or P21/m, with Z = 2, a = 11.68 (1), b = 8.08 (1), c = 12.13 (1) Å and β = 95.6 (1)°. The JCPDS Diffraction File Nos. for these compounds are: C14H11N 34-1995; C14H13N 34-1996, C14H12ClN 34-1994.
A computer program for the deconvolution of X-ray diffraction profiles with the composite of Pearson type VII functions
Authors: Toraya H. , Yoshimura M. , Sōmiya S.
Published: July 2002

A computer program for the deconvolution of X-ray diffraction profiles has been written in Fortran IV. The deconvolution procedure is based on the minimization of the difference between the observed data function and a calculated function, where the latter is the convolution of the instrumental function and the true data function approximated with an analytical expression. The composite of two asymmetric Pearson type VII functions was assumed to represent the true data function, and the simplex method was used for the minimization. The stability of convergence and the influences of the truncation effect and the step width of intensity data on the deconvoluted profile were examined. The computer program can deconvolute the X-ray diffraction profile in moderate computation time without generating spurious oscillations due to the truncation effect.
The relation of wavelength dispersion and scan mode in X-ray diffractometry with a monochromator
Authors: Mathieson A. M.
Published: July 2002

The contribution to the size of a Bragg reflection due to the interaction of the wavelength dispersion of a monochromator crystal, M, and of a specimen crystal, c, is considered from the two-dimensional Δω, Δ2θ viewpoint. Its variation with change in scan mode is demonstrated. For the ω/θ scan mode, the contribution in respect of Δ2θ [i.e. (Δλ/λ)tan θc
] is independent of the monochromator used and is the same as for the non-monochromator case. For the ω/2θ scan mode, the corresponding contribution [(Δλ/λ)tan θM
] is constant and so, for the conventional one-dimensional measurement procedure, a receiving aperture of constant width may be used to collect intensities over the full range of θc
.
Reassessment of atomic radii for CN12 and CN8 obtained from elemental f.c. and b.c. cubic structures
Authors: Pearson W. B.
Published: July 2002

Differences of atomic radii R
CN12 and R
CN8 obtained from (i) elemental f.c. cubic (or c.p. hexagonal) and b.c. cubic structures, (ii) from calculation with Pauling's equation, R
(1) − R
(n) = 0.3 log n and (iii) by calculation for the condition of equal atomic volumes in the f.c. and b.c. cubic structures are compared as a function of R
CN8. Observations and recommendations are made.
The tensor of compositional deformation. A new crystallographic way to analyse syncrystallization
Authors: Chanh N. B. , Clastre J. , Gaultier J. , Haget Y. , Meresse A. , Lajzerowicz J. , Filhol A. , Thomas M.
Published: July 2002

Syncrystallization can be analysed through a new approach: the determination of the `tensor of compositional deformation'. It is a convenient way to take structural anisotropy into account and to point out the directions of strongest and weakest modifications of the intermolecular interactions due to the substitution process. The example of 2-chloronaphthalene-2-methylnaphthalene alloys is given in order to illustrate the interest of this new tool.
Simultaneous structure refinement of neutron, synchrotron and X-ray powder diffraction patterns
Authors: Maichle J. K. , Ihringer J. , Prandl W.
Published: July 2002

A technique has been developed for the simultaneous analysis of several powder diffraction data on the basis of the Rietveld method. Counting rates from one specimen at a given temperature taken at neutron, synchrotron or X-ray powder diffractometers are joined to one single data set with weights given by the counting statistics. The structure is refined from this data set with a parameter field containing one structural model and individual zero points, scale factors and FWHM parameters for each of the methods and data sets. A new definition of the residuals is given. The residuals and goodness-of-fit values are calculated for all as well as for the individual data sets.
A position-sensitive detector for neutron diffraction topography
Authors: Baruchel J. , Kuroda K. , Liaud P. , Michalowicz A. , Sillou D.
Published: July 2002

The first test of a position-sensitive photomultiplier in a thermal neutron diffraction topography experiment is reported: a spatial resolution was obtained of ≃200 μm in FWHM over a sensitive area of size ≃8 × 8 mm (≃1600 pixels) and a detection efficiency of the order of 15% when using a 0.25 mm thick ZnS–LiF (NE 426) scintillator. The advantages of this detector, its foreseeable improvements, and the scientific problems it could help to solve are discussed.
Background-filtered transmission diffraction with internal intensity calibration
Authors: Hiismäki P.
Published: July 2002

It is inferred that by frequency filtering the logarithm of the time-of-flight spectrum of neutrons that have passed through a powdered isotropic crystalline sample a diffractogram may be obtained with many desirable properties for achieving high-quality refinement of structural parameters. Apart from multiple scattering no wavelength-dependent effects or corrections need to be introduced, which implies automatic internal calibration of the Bragg intensities. For utilization of the inherent high resolution of the transmission geometry, a Fourier chopper in the pulsed beam from an intensity-optimized quasi-steady-state moderator is suggested. Results of model calculations are presented.
QUASI2D: a program written to demonstrate quasiperiodicity and phason fluctuation
Authors: Welberry T. R. , Lee A. , Owen K.
Published: July 2002

A program is described that demonstrates in two dimensions the concepts of quasiperiodic tiling and phason fluctuations. Tiling patterns having perfect fivefold or eightfold quasiperiodicity are displayed on the computer screen at any one of three chosen scales. These patterns are then progressively altered in real time by the application of phason flips to obtain disordered tiling patterns. Energy parameters may be specified to allow preference for different tile-pair combinations in the resulting distributions. In this way, with different combinations of the energies, distributions varying from pure random tiling to ones in which more ordered microdomains are to be seen may be obtained in real time via Monte Carlo simulation.
The π/2 Side-Reflection Laue Technique and the New Chart
Authors: Park Y.-H. , Yeom H.-Y. , Yoon H.-G. , Kim K.-W.
Published: July 2002

For the capability of dynamic studies of structural changes of crystals under the environment of heat, electric or magnetic field, the π/2 side-reflection Laue technique is performed in which the X-ray source, the specimen and the film are aligned along an L-shaped track. A new chart has also been designed for the analysis of π/2 side-reflection Laue patterns. This new chart is applied to the analysis of crystal orientation in the π/2 side-reflection Laue technique and to indexing the planes of simultaneous multiple-reflection images in Berg–Barrett topography. Also, the equation of zonal trace has been derived for depicting the zonal curves of configurations of π/2 side-reflection spots and confirming the results which are analyzed by the new chart.
Direct analysis of small-angle smeared intensity tails. I. General results
Authors: Ciccariello Salvino , Sobry Roger
Published: July 2002

The leading asymptotic terms of small-angle slit-smeared intensities, at large momentum transferh= (4π/λ)sin (θ/2), are obtained from the pinhole intensities by an integral transform whose kernel is the beam-height profile determined by the slits used in a Kratky camera. This profile, directly measurable, generally shows a trapezoidal shape characterized byQ0, the end point of its horizontal plateau, andQ1, the momentum-transfer value beyond which it vanishes. It results that any pinhole contribution, monotonically decreasing as 1/hα, after being smeared, decreases as 1/h(α−1)in the regionh<Q0, while the power exponent monotonically increases from (α − 1) to α in the outerhregion. The actual change explicitly depends on the slit length. On the contrary, the oscillatory damped contributions cos (hδ)/h4and sin (hδ)/h4, after being smeared, remain close, whatever the slit length, to those resulting from the smearing with an ideal slit.
Electron density in ammonium dihydrogen phosphate: non-uniqueness of the multipolar model in simple inorganic structures
Authors: Pérès N. , Boukhris A. , Souhassou M. , Gavoille G. , Lecomte C.
Published: July 2002

X-ray and neutron diffraction data of a single crystal of ammonium dihydrogen phosphate have been used for the determination of the electron density using multipolar expansion of the density around each nucleus. As the ammonium group was found to be nearly neutral from unconstrained multipole refinement, constrained refinements have been performed with the charge of the ammonium group ranging from zero to one. On the other hand, the expansion of the radial functions of the phosphorus atom was varied. All refinements led to almost the same agreement factors and residual densities. The consequences of such uncertainties on the topology of the electron density are discussed, namely the topology of the P—O bond critical point.
Seminvariant density decomposition and connectivity analysis and their application to very low resolution macromolecular phasing
Authors: Lunin V. Y. , Lunina N. L. , Urzhumtsev A. G.
Published: July 2002

A low-resolution Fourier synthesis is thought to show a molecule as a compact region of a high electron density. As a consequence, the number of such regions, chosen at a proper cut-off level, should be equal to the number of molecules in the unit cell. This hypothesis may be used as a basis for selection criteria in multisolution ab initio phasing procedures. However, when working with a small number of reflections, this hypothesis may break down. The suggested Fourier-synthesis decomposition explains some reasons for failure and provides a connectivity-based procedure for the determination of macromolecular position in the crystal unit cell and the phasing of several low-resolution reflections. The simplest decomposition consists in separating the reflections into two sets according to whether their phases do or do not depend on a permitted origin shift. It is shown that the partial Fourier syntheses corresponding to these subsets are simply a half-sum and a half-difference of the initial electron-density distribution with its shifted copy. Therefore, they display the true images overlapped with the shifted ones (or with shifted and additionally flipped copies for the latter synthesis). The paper generalizes the decomposition for the case of a finite subgroup of the group of permitted origin shifts and reveals the role of one-phase seminvariants.
Refinement of crystal structural parameters using two-dimensional energy-filtered CBED patterns
Authors: Tsuda Kenji , Tanaka Michiyoshi
Published: July 2002

A new method to refine crystal structural parameters using convergent-beam electron diffraction (CBED), which is applicable to nanometre-size crystal structure analysis, is proposed. This method is based on the fitting between theoretical calculations and experimental intensities of energy-filtered two-dimensional CBED patterns containing higher-order Laue-zone (HOLZ) reflections. The use of HOLZ reflections is essential for the method because small displacements of atoms can be sensitively detected using HOLZ reflections with large reciprocal vectors. For this purpose, a new Ω-filter transmission microscope (JEM-2010FEF), which can take energy-filtered CBED patterns up to a high angle with a small distortion, and a new analysis program to refine structural parameters, which is based on many-beam Bloch-wave calculations and nonlinear least-squares fitting, have been developed. As a test example, a positional parameter and isotropic and anisotropic Debye–Waller factors of CdS have been refined. Two-dimensional CBED patterns calculated with the refined parameters show very good agreement with the experimental ones, and the refined values of the parameters also agree well with the result of a single-crystal X-ray diffraction experiment. Important problems of the analysis procedure are discussed item by item.
X-ray intensity patterns from finite perfect crystals
Authors: Thorkildsen Gunnar , Larsen Helge B.
Published: July 2002

A theoretical study dealing with intensity interference patterns from the exit surfaces of finite perfect t\times l crystals has been undertaken using the Takagi–Taupin equations and the Riemann–Green technique. Numerical simulations have been performed for the 220 reflection in diamond allowing for different types of amplitude-modulated incoming plane waves. The effects caused by limiting the waves by a slit system are also discussed. The results show strong influence of the lateral crystal boundaries and are closely related to the geometrical region structures formed by the characteristic lines associated with the equations. In the limit of a semi-infinite crystal, the Borrmann–Lehmann interference patterns are retrieved.
P1 or P\bar 1? Corrigendum
Authors: Marsh Richard E.
Published: July 2002

The structure of bis((phenyl-O,N,N-azoxy)oxy)methane, C_{13}H_{12}N_4O_4, originally reported as triclinic, space group P1 [Zyuzin et al. (1997). Isz. Akad. Nauk SSSR Ser. Khim. pp. 1486–1492; CSD refcode NIXQAM] was recently revised to monoclinic, space group C2 [Marsh (1999). Acta Cryst. B55, 931–936]. It is properly described as orthorhombic, space group Fdd2.
Quantitative analysis of hydrogen bonding and atomic thermal motion in the organic non-linear optical material DCNP using X-ray and neutron diffraction
Authors: Cole Jacqueline M. , Wilson Chick C. , Howard Judith A. K. , Cruickshank Frank R.
Published: July 2002

A single-crystal neutron diffraction study of the organic non-linear optical material 3-(1,1-dicyanoethenyl)-1-phenyl-4,5-dihydro-1H-pyrazole (hereafter DCNP), space group Cc, is presented. The study was conducted in order to relate the structural characteristics of the compound to its physical properties. DCNP exhibits a very large second harmonic generation (SHG) output, an extremely large linear electro-optical effect and photoconductive and pyroelectric properties. The nature of the hydrogen-bonding revealed by the study, in part, accounts for the first two of these phenomena. The neutron study also shows that some rather atypical atomic thermal motion is present in part of the molecule. With the aid of a variable-temperature single-crystal X-ray diffraction study, in conjunction with the neutron study, this thermal motion is attributed to libration and is fully characterized. As a result, suitable corrections to the bond geometry and the anisotropic displacement parameters of DCNP are made. The libration is also shown to enhance the SHG effect. The cell parameters from the variable-temperature X-ray study are also used in order to evaluate the thermal expansivity coefficients of DCNP.
General method for the description, visualization and comparison of metal coordination spheres: geometrical preferences, deformations and interconversion pathways
Authors: Yao Jing Wen , Copley Royston C. B. , Howard Judith A. K. , Allen Frank H. , Motherwell W. D. Samuel
Published: July 2002

The coordination sphere geometry of metal atoms (M) in their complexes with organic and inorganic ligands (L) is often compared with the geometry of archetypal forms for the appropriate coordination number, n in MLn
species, by use of the k = n( n− 1)/2 L—M—L valence angles subtended at the metal centre. Here, a Euclidean dissimilarity metric, Rc
(x), is introduced as a one-dimensional comparator of these k-dimensional valence-angle spaces. The computational procedure for Rc
(x), where x is an appropriate archetypal form (e.g. an octahedron in ML
6 species), takes account of the atomic permutational symmetry inherent in MLn
systems when no distinction is made between the individual ligand atoms. It is this permutational symmetry, of order n!, that precludes the routine application of multivariate analytical techniques, such as principal component analysis (PCA), to valence angle data for all but the lowest metal coordination numbers. It is shown that histograms of Rc
(x) values and, particularly, scatterplots of Rc
(x) values computed with respect to two or more different appropriate archetypal forms (e.g. tetrahedral and square-planar four-coordinations), provide information-rich visualizations of the observed geometrical preferences of metal coordination spheres retrieved from, e.g. the Cambridge Structural Database. These mappings reveal the highly populated clusters of similar geometries, together with the pathways that map their geometrical interconversions. Application of Rc

(x) analysis to the geometry of four- and seven-coordination spheres provides information that is at least comparable to, and in some cases is more complete than, that obtained by PCA.
Charge distribution as a tool to investigate structural details. II. Extension to hydrogen bonds, distorted and hetero-ligand polyhedra
Authors: Nespolo Massimo , Ferraris Giovanni , Ivaldi Gabriella , Hoppe Rudolf
Published: July 2002

It is shown that one of the main reasons for most failures of the methods for calculating distance-dependent bond strengths is related to the distortion of the coordination polyhedra. The charge distribution (CD) method which depends on only one universal empirical parameter (contraction parameter) is modified to include: (i) an iterative calculation of the effective coordination number (ECoN), to deal with structures containing very distorted coordination polyhedra; (ii) a specific contraction parameter to treat structures containing any type of hydrogen bond; (iii) scale factors for coordination subshells, to treat structures with hetero-ligand polyhedra. The contraction parameter for the hydrogen bonds was obtained from 119 well refined structures based on neutron diffraction data. Examples of the application of the iterative charge distribution (CD-IT) are presented to show the efficiency of the new method in dealing with distorted (including hydrogen bonding) and hetero-ligand polyhedra. In particular, analysis of a series of 74 structures with pentacoordinated cations shows that deviations from overall trends are related to structure instability. The possible failure of the method with polyionic structures and `dynamic' structures is discussed.
Ag2Ti2P2S11: A New Layered Thiophosphate. Synthesis, Structure Determination and Temperature Dependence of the Silver Distribution
Authors: Gaudin E. , Fischer L. , Boucher F. , Evain M. , Petricek V.
Published: July 2002

The new Ag2Ti2P2S11 quaternary phosphosulfide disilver dititanium undecathiodiphosphate is obtained by heating the elements at ca 850 K in an evacuated silica tube. It crystallizes in orthorhombic symmetry, Pnma space group, with a = 8.5222 (11), b = 6.8359 (10), c = 24.142 (4) Å, V = 1406.4 (4) Å3 and Z = 4 at 293 K. The refinement of the room-temperature structure leads to a reliability factor of R = 0.0378 for 1556 independent reflections and 128 variables. Ag2Ti2P2S11 is composed of layers, separated by van der Waals gaps. The layers are composed of [Ti2S9] chains built from [TiS7] units (TiS6 octahedra in which a corner has been replaced by an S2 pair) and linked through regular [PS4] and highly distorted [AgS4] tetrahedra. The formula of the compound can be written as AgI
2TiIV
2PV
2(S2)−IIS−II
9. A Gram–Charlier anharmonic development of the atomic displacement factor for Ag atoms reveals a strong non-harmonic probability density deformation, especially in the direction of two empty neighbouring tetrahedra, away from the Ti and P cations. The temperature dependence of the effective one-particle potential shows that the Ag distribution is primarily static in nature. At high temperature the tetrahedrally coordinated site is the preferential site. At lower temperature the Ag atoms are redistributed over the tetrahedral site and the adjacent triangular site. The disorder could not be resolved due to a phase transition with splitting of spots just below room temperature.
Halogen...O(Nitro) Supramolecular Synthon in Crystal Engineering: A Combined Crystallographic Database and Ab Initio Molecular Orbital Study
Authors: Allen F. H. , Lommerse J. P. M. , Hoy V. J. , Howard J. A. K. , Desiraju G. R.
Published: July 2002

Crystallographic data for 309 C—X...O(nitro)—C, X = Cl, Br, I, interactions, involving 245 symmetry-independent X atoms, have been investigated out to 0.2 Å above van der Waals radii limits [\nu(O) + \nu(X)]. A total of 138 (45%) of these interactions are shorter than \nu(O) + \nu(X), with the degree of interpenetration of the X and O atoms increasing in the order Cl < Br < I. The analysis also shows that: (a) the C—X...O angle tends to linearity as the X...O distance shortens, (b) the angle of approach of X to the C—NO2 plane is preferentially less than 45° for Cl, with an increasing tendency to in-plane X approach in the order Cl < Br < I, and (c) the halogen (X) forms either (i) mono-coordinate interactions with one nitro O atom, with X...O in a cis relationship to the nitro C substituent about the N—O bond, or (ii) approaches both nitro O atoms in a bifurcated manner; the tendency to form such bifurcated motifs increases in the order Cl < Br < I. Only iodine consistently forms short interactions with both nitro O atoms. Ab-initio-based molecular orbital calculations, using intermolecular perturbation theory (IMPT) applied to a nitromethane–1-chloro-2-methylacetylene model dimer, agree with the analysis of experimental crystal structure geometries. The IMPT calculations yield an attractive interaction energy of ca −6 kJ mol−1 for Cl...O at the 6-31G* basis set level. Calculations for Br...O at the (only available) [6s4p1d] basis set level indicate that this interaction is more attractive than Cl...O.
Topological Description of Pseudosymmetries in trans-2,3,4,5,5a,6,7,8,9,9a-Decahydro-2-methyl-4-phenylaminocarbonylbenzo[f][1,4]oxazepin-3-one and Other Structures which Crystallize in Space Group P-1 with Z = 8
Authors: Kálmán A. , Argay Gy.
Published: July 2002

The pseudosymmetries of the title compound resemble a monoclinic unit cell with space group P1121/a. However, the structure of C17H22N2O3 was determined in a triclinic unit cell [a = 10.500 (4), b = 11.617 (3), c = 28.622 (3) Å, α = 83.15 (2), β = 83.41 (4), γ = 68.48 (2)°; V = 3215 (2) Å3, Z = 8: four molecules in the asymmetric unit] by direct methods and refined on F
2 values in space group P1¯ to final R[F
2 > 2σ(F
2)] = 0.0457 and wR(F
2) = 0.114. The conformation of molecule M1 basically agrees with that of M4, whereas molecules M2 and M3 form a second group of conformers. M1–M2 and M4–M3 dimers are related by a pseudoscrew axis along the c axis and complemented by a pseudoglide plane located at z ≃ 1\over 4 or 3\over 4, respectively. The analysis of pseudosymmetries in the title crystal was then extended to other structures selected from 66 Cambridge Structural Database entries with P1¯ and Z = 8. A topological survey of the pseudosymmetries reveals a rich variety of the *21/*c pair. In the unit cells of several crystals one or two coordinates of these types of pseudosymmetries are bound to (2n − 1)1\over 8 values or in their vicinity. Such operators (termed secondary pseudosymmetries) are accompanied by their respective complementary symmetries with translation(s) of ca (2n − 1)1\over 4. Their cooperation with primary pseudosymmetries (possessing standard position and translation) and with themselves seems to shed light on the origin of symmetries in crystals. These observations are also valid for a few monoclinic crystals.
Modelling the crystal structure of the 2-hydronitronylnitroxide radical (HNN): observed and computer-generated polymorphs
Authors: Filippini G. , Gavezzotti A. , Novoa J. J.
Published: July 2002

The crystal structures of two polymorphs of 4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-1-oxyl 3-oxide (the 2-hydronitronylnitroxide radical, HNN) are analyzed by packing energy criteria. Other unobserved polymorphic crystal structures are generated using a polymorph predictor package and three different force fields, one of which is without explicit Coulomb-type terms. The relative importance of several structural motifs (hydrogen-bonded dimers, shape-interlocking dimers or extended hydrogen-bonded chains) is discussed. As usual, many crystal structures within a narrow energy range are generated by the polymorph predictor, confirming that ab initio crystal-structure prediction is still problematic. Comparisons of powder patterns generated from the atomic coordinates of the X-ray structure and from computational crystal structures confirm that although the energy ranking depends on the force field used, the X-ray structure of the \alpha polymorph was found to be among the most stable ones produced by the polymorph predictor, even using the chargeless force field.
A TEM study of long-period mica polytypes: determination of the stacking sequence of oxybiotite by means of atomic resolution images and Periodic Intensity Distribution (PID)
Authors: Kogure Toshihiro , Nespolo Massimo
Published: July 2002

In this study it is shown that the stacking sequences in long-period mica polytypes (including a rare example of a mixed-rotation polytype, with a 36-layer long periodicity) can be unambiguously determined using atomic resolution images recorded down two zone axes separated by 30° (e.g. [100] and [31¯0]) at the same area. Uniformity of these stacking sequences in a large area is further confirmed by the correspondence between computed and observed Periodic Intensity Distributions (PIDs) in electron diffraction patterns. The appearance of long-period polytypes containing layers with different orientation parity may be explained by the coalescence of two small crystals during crystal growth.
Hydrogen-bonding behaviour of benzene-1,2,4,5-tetracarboxylic acid: supramolecular structures of different dimensionality in the 2:1 adducts formed with 4,4′-bipyridyl and hexamethylenetetramine
Authors: Lough A. J. , Wheatley P. S. , Ferguson G. , Glidewell C.
Published: July 2002

Co-crystallization of benzene-1,2,4,5-tetracarboxylic acid, C10H6O8, with 4,4′-bipyridyl, C10H8N2, or with hexamethylenetetramine, C6H12N4, from methanol solutions yields in each case a 2:1 salt, [(C10H9N2)+]2·[(C10H4O8)2−] (1) and [(C6H13N4)+]2·[(C10H4O8)2−] (2). In (1) the carboxylate anions lie across centres of inversion, but they contain no intramolecular O—H...O hydrogen bonds: the cations and anions are linked by strong O—H...N and N—H...O hydrogen bonds into a chain-of-rings, and these chains are further linked into a three-dimensional framework structure by means of C—H...O hydrogen bonds and aromatic π...π stacking interactions. Compound (2) contains two independent three-molecule aggregates, comprising a central anion and two cations, linked to the anion by means of short N—H...O hydrogen bonds. One of these aggregates is centrosymmetric, but the other is not, and the two types of anion both form two intramolecular O—H...O hydrogen bonds. The two types of three-molecule aggregate, in which all the anions are virtually parallel, are linked by short C—H...O hydrogen bonds into a molecular staircase.
X-ray diffraction study of the phase transitions of (CH3)4NCdCl3 between 293 and 80 K: a quantitative analysis of the ferroelastic domains distribution below 118 K
Authors: Peral I. , Madariaga G. , Pérez-Etxebarria A. , Breczewski T.
Published: July 2002

X-ray diffraction patterns of [N(CH_{3})_{4}][CdCl_{3}], tetramethylammonium trichlorocadmate(II), have been investigated in the temperature range 80–293 K, which includes two phase transitions at 118 and 104 K, respectively. The main interest in this compound is to establish the mechanism of the structural phase transitions common to other members of the isostructural family [(CH_{3})_{4}N][MX_{3}]. It is supposed to be related to the ordering of the organic part together with some small distortion of the inorganic chains. The origin of the order–disorder mechanism would be the orientationally disordered distribution of the tetramethylammonium tetrahedra at room temperature. Maximum Entropy Methods suggest that the most probable distribution of the organic groups can be described through the so-called two-well model, in which one threefold axis of the tetramethylammonium tetrahedron coincides with the crystallographic threefold axis of the structure. Below 118 K the reflections are split. However, the splitting cannot be fully explained by the ferroelastic domains expected to appear after the phase transitions. Recent NMR results [Mulla-Osman et al. (1998). J. Phys. Condensed Matter, 10, 2465–2476] corroborate the existence of more domains than expected from symmetry considerations. A model of ferroelastic domains which is in agreement with both X-ray diffraction diagram and NMR measurements is proposed.
Structure of the inclusion complex of β-cyclodextrin with 1,12-dodecanedioic acid using synchrotron radiation data; a detailed dimeric β-cyclodextrin structure
Authors: Makedonopoulou Stella , Mavridis Irene M.
Published: July 2002

A detailed crystal structure study of the dimeric inclusion complex of β-cyclodextrin (βCD) with 1,12-dodecanedioic acid is presented [IUPAC name: β-cyclodextrin–1,12-dodecanedioic acid (2/1)]. The structure was solved with synchrotron high-resolution data (0.65 Å) at 100 K [crystal data: P1, Z = 1, a = 18.153 (7), b = 15.456 (8), c = 15.251 (4) Å, α = 102.81 (2), β = 113.13 (2), γ = 99.90 (3)°, V = 3673 (3) Å3, R = 0.0474 for 25 134 unique reflections with I > 2σ(I)]. Moreover, the room-temperature structure is used for comparison [crystal data: P1, Z = 1, a = 18.220 (3), b = 15.488 (3), c = 15.409 (3) Å, α = 102.903 (6), β = 113.122 (5), γ = 99.708 (5)°, V = 3735.2 (12) Å3, R = 0.0828 for 8235 unique reflections with I > 2σ(I)]. Combining the high-resolution data and the low-temperature made possible the location of the disordered guest molecule, 1,12-dodecanedioic acid, inside the wide cavity of the macrocycle formed by two βCD monomers. Moreover, almost all the H atoms of the βCD macrocycle and many of the water molecules have been located in the low-temperature structure. Thus, for the first time, it has been possible to show in detail, up to now only given by neutron diffraction data, that two βCD monomers self-assemble through O3...O3 intermolecular hydrogen bonds to form the βCD dimer, as well as describe the hydrogen-bonding scheme between the dimer's hydroxyl groups among themselves and with water molecules in the lattice. The long guest threads through two host molecules forming a [3]pseudorotaxane. Its polar carboxyl groups, fully hydrated at the primary faces of the βCD dimers, influence their packing so that those faces are exposed to the solvent. This is in contrast to the packing of the β-cyclodextrin complexes of the corresponding aliphatic monoacids, where the dimeric complexes form channels in order to isolate the terminal methyl group from the water environment of the lattice.
Structure of the alums. I. On the sulfate group disorder in the α-alums
Authors: Nyburg Stanley C. , Steed Jon W. , Aleksovska Slobotka , Petruševski Vladimir M.
Published: July 2002

The crystal structures at room (296 K) and low (173 K) temperature of several α-alums have been refined by single-crystal X-ray structure analysis. Many α-alums of known structure are disordered, the sulfate anions occupying one of two possible sites. All those studied here exhibited such disorder and the relative occupancies of the two sites are in excellent agreement with those obtained by Raman spectroscopy, where the ν1(SO4) mode is seen as a doublet owing to the presence of two different types of sulfate ion. No phase transitions were noted on cooling but there is less disorder.
Electron density of KNiF3: analysis of the atomic interactions
Authors: Tsirelson Vladimir , Ivanov Yury , Zhurova Elizabeth , Zhurov Vladimir , Tanaka Kiyoaki
Published: July 2002

The topological analysis of the electron density in the perovskite KNiF3, potassium nickel trifluoride, based on the accurate X-ray diffraction data, has been performed. The topological picture of the atomic interactions differs from that resulting from the classic crystal chemistry consideration. The shapes of atoms in KNiF3 defined by zero-flux surfaces in the electron density are, in general, far from spherical. At the same time, their asphericity in the close-packed layer is very small. The topological coordination numbers of K and Ni are the same as the geometrical ones, whereas topological coordination for the F atom (6) differs from the geometrical value. The latter results from a specific shape of the Ni-atom basin preventing the bond-path formation between F atoms in the same atomic close-packed layer, in spite of the fact that the closest F—F distance is the same as K—F. Judging by the electron density value and curvature at the bond critical points, the K—F interaction in KNiF3 can be considered ionic, while the Ni—F bond belongs to the polar covalent type. No correlation of the topological ionic radii with crystal or ionic radii was found in KNiF3. Critical points in the electrostatic potential have also been studied.
Thermal vibrations and a lattice mode in calcite and sodium nitrate
Authors: Megaw H. D.
Published: July 2002

The observed direction of thermal motion of the oxygen atoms in calcite can be explained if the environment of the calcium atom is taken into consideration as well as the CO3 group. Rotation of Ca octahedra accompanied by an alternate steepening and flattening which retains the {\bar 3} point-symmetry and the Ca–O bond-length unchanged is associated with a screw-like movement of CO3 in which rotation in its own plane is geared to translation perpendicular to its plane. Concerted movements of all atoms in the structure satisfying these requirements can be described in terms of a single-oscillating parameter; they represent a single lattice mode. They are predictable using the assumption that small departures, in the `static' structure, of particular position parameters from ideal values indicate weaknesses of a kind that allow a large amplitude to vibrations in which the same parameters oscillate about their `static' value. Comparison of CaCo3 and the isomorphous NaNO3 with LaAlO3 and LiNbO3, which have very similar formal geometry but great differences in relative bond strength, helps to illustrate the principle involved.
Crystallization and preliminary X-ray diffraction studies of the catalytic core of acetyl xylan esterase from Trichoderma reesei
Authors: Hakulinen Nina , Tenkanen Maija , Rouvinen Juha
Published: July 2002

Acetyl xylan esterase is involved in the biodegradation of hemicellulose. It cleaves O-acetyl groups from xylan, which is the most abundant hemicellulose in nature. The catalytic core of acetyl xylan esterase from T. reesei has been crystallized and X-ray diffraction data at 2.3 Å collected. The crystal belongs to the triclinic space group P1 with unit-cell parameters a = 50.3, b = 62.1, c = 40.0 Å, α = 110.1, β = 113.6 and γ = 97.9°. The asymmetric unit contains two molecules.
Crystallization and preliminary X-ray crystallographic analysis of archaeal O
6-methylguanine–DNA methyltransferase
Authors: Hashimoto Hiroshi , Nishioka Motomu , Inoue Tsuyoshi , Fujiwara Shinsuke , Takagi Masahiro , Imanaka Tadayuki , Kai Yasushi
Published: July 2002

Crystals of archaeal O
6-methylguanine–DNA methyltransferase (MGMT) from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1 have been grown at room temperature using polyethylene glycol as a precipitant. The diffraction pattern of the crystal extends to 2.0 Å resolution at room temperature upon exposure to Cu K\alpha radiation. The crystal belongs to the space group P212121 with unit-cell dimensions of a = 52.8, b = 86.6 and c = 39.9 Å. The presence of one molecule per asymmetric unit gives a crystal volume per protein mass (Vm
) of 2.3 Å3 Da−1 and a solvent content of 48% by volume. A full set of X-ray diffraction data was collected to 2.0 Å Bragg spacings from the native crystal.
Crystallization and preliminary crystallographic analysis of winged bean acidic lectin
Authors: Manoj N. , Srinivas V. R. , Satish B. , Singha Netai C. , Suguna K.
Published: July 2002

The acidic lectin (WBAII) from the winged bean (Psophocarpus tetragonolobus) binds to the H-antigenic determinant on human erythrocytes and to the T-antigenic disaccharide Gal-β1,3-GalNAc. Two crystal forms of WBAII were obtained in the presence of methyl-α-D-galactose. Form I belongs to space group R3 with unit-cell dimensions a = b = 182.11, c = 44.99 Å and has one dimer in the asymmetric unit. Form II belongs to space group C2 with unit-cell dimensions a = 135.36, b = 127.25, c = 139.98 Å, β = 95.9° and has four dimers in the asymmetric unit. Intensity data were collected to 3.0 Å and to 3.5 Å from crystals of form I and II, respectively. The structures were solved by the molecular-replacement method using the coordinates of the basic form of winged bean lectin.
Conformational attractors on the Ramachandran map
Authors: Walther Dirk , Cohen Fred E.
Published: July 2002

Frequency distributions of protein backbone dihedral angles φ and ψ have been analyzed systematically for their apparent correlation with various crystallographic parameters, including the resolution at which the protein structures had been determined, the R factor and the free R factor, and the results have been displayed in novel differential Ramachandran maps. With improved sensitivity compared with conventionally derived heuristic Ramachandran maps, such differential maps automatically reveal conformational `attractors' to which φ/ψ distributions converge as the crystallographic resolution improves, as well as conformations tied specifically to low-resolution structures. In particular, backbone angular combinations associated with residues in α-helical conformation show a pronounced consolidation with substantially narrowed φ/ψ distributions at higher (better) resolution. Convergence to distinct conformational attractors was also observed for all other secondary-structural types and random-coil conformations. Similar resolution-dependent φ/ψ evolutions were obtained for different crystallographic refinement packages, documenting the absence of any significant artificial biases in the refinement programs investigated here. A comparison of differential Ramachandran maps derived for the R factor and the free R factor as independent parameters proved the better suitability of the free R factor for structure-quality assessment. The resolution-based differential Ramachandran map is available as a reference for comparison with actual protein structural data under WebMol, a Java-based structure viewing and analysis program (http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl).
Use of super-water-repellent fractal surfaces in the crystallization of macromolecules
Authors: Fujii Isao , Hirayama Noriaki
Published: July 2002

The effect of fractal surfaces on protein crystallization has been investigated. A super-water-repellent fractal surface consisting of alkylketene dimers was formed on microscope cover slips. Crystallization experiments with hen egg-white lysozyme using the sitting-drop vapour-diffusion method have been undertaken on the fractal and conventionally siliconized surfaces. The size of the crystals obtained on the fractal surface is significantly larger than on the conventionally siliconized surface. The number of crystals on the fractal surface is markedly smaller than on the conventionally siliconized surface. The results clearly indicate that the fractal surface is very effective and promising in the crystallization of macromolecules using the sitting-drop vapour-diffusion method.
Crystallization and preliminary X-ray studies on the molbindin ModG from Azotobacter vinelandii
Authors: Williams Clare E. M. , White Daniel J. , Delarbre Laure , Mitchenall Lesley A. , Pau Richard N. , Lawson David M.
Published: July 2002

Crystals of the molbindin ModG (subunit Mr
= 14359 Da), a cytoplasmic molybdate-binding protein from Azotobacter vinelandii, were grown by vapour diffusion. Both apo and tungstate-bound forms were crystallized and X-ray data were collected at 100 K. Apo-ModG crystallizes in space group P6322, with unit-cell dimensions a = b = 90.62, c = 79.46 Å. Native data to a resolution of 2.5 Å were collected from a single crystal, which showed a marked improvement in diffraction quality after annealing. Data from a single-site gold derivative were also collected at 2.7 Å resolution. Crystals of the ligand-bound form of ModG belong to space group P321, with unit-cell parameters a = b = 50.57, c = 79.29 Å. X-ray data to a resolution of 2.0 Å were collected.
Purification, crystallization and preliminary crystallographic studies on the N-terminal fragment of human protein disulfide isomerase
Authors: Wang Xin-Quan , Gui Lu-Lu , Dai Yong , Wang Chih-Chen , Chang Wen-Rui , Liang Dong-Cai
Published: July 2002

A fragment of human protein disulfide isomerase composed of the thioredoxin-like a and b domains (ab) has been expressed in Escherichia coli as a fusion protein with glutathione-S-transferase and purified after thrombin cleavage. Two forms of ab crystal were obtained with polyethylene glycol as precipitant and different additives at pH 7.5. The space group of form I is P41212 or P43212, with unit-cell dimensions a = 81.5, c = 259.7 Å. The space group of form II is P4122 or P4322, with unit-cell dimensions a = 82.7, c = 86.5 Å.