bluuebunny/crossref_metadata_2025 huggingface dataset:
Fast rigid-body refinement for molecular-replacement techniques
Authors: Castellano E. E. , Oliva G. , Navaza J.
Published: July 2002

A method for the least-squares rigid-body refinement of a general electron density model is described. The present formulation is different from a previously reported one in the computation of the derivatives of the calculated Fourier coefficients, which are derived analytically here. This, together with a judicious choice of the Fourier transform search arrays, makes the procedure extremely fast and sufficiently accurate. Although originally designed simply to optimize the values of the positional parameters obtained by Patterson search techniques, the method proved to be extremely efficient as an aid for evaluation of the correctness of potential molecular-replacement solutions.
X-ray diffraction study of KTP (KTiOPO4) crystals under a static electric field
Authors: Sebastian M. T. , Klapper H. , Bolt R. J.
Published: July 2002

X-ray diffraction studies are made on ion-conducting potassium titanyl phosphate (KTP) crystals with in situ DC electric field along different crystallographic directions. The X-ray rocking curves recorded with an electric field along the polar b axis (which is the direction of ion conduction) show a strong enhancement of the 040 reflection intensity (reflecting planes normal to the b axis) whereas the h0l reflections (reflecting planes parallel to the polar axis) do not show any intensity change. For an electric field normal to the polar axis no intensity change, either in 040 or in h0l reflections, occurs. This observation is supplemented by X-ray topography. The 040 X-ray topographs recorded with in situ electric field along b exhibit strong extinction contrast in the form of striations parallel to the polar (ion-conduction) axis. The 040 intensity increase and the striation contrast are attributed to lattice deformation by the space-charge polarization due to the movement of the K+ ions under the influence of the electric field.
A flame-heated gas-flow furnace for single-crystal X-ray diffraction
Authors: Peterson R. C.
Published: July 2002

A furnace using an inert-gas stream heated by an acetylene torch has been designed to conduct high temperature X-ray diffraction experiments. The design makes use of the stability of electrically heated gas-flow devices and the high-temperature capability of flame heaters. The gas flow is coaxial with the crystal mounting fibre resulting in a thermally stable environment controlled by the composition of the heated gas stream. Temperatures from 373 up to 1573 K are maintained by computer-controlled flow regulation of the acetylene flame based on the signal from a thermocouple on which the crystal is mounted. The results of a high-temperature X-ray diffraction study of Mg0.54Fe2+
0.46Fe2O4, spinel are given as an example of the application of this furnace.
Projection matrices for Niggli-reduced cells
Authors: Paciorek W. A. , Bonin M.
Published: July 2002

Crystallographic unit cells can be characterized by vectors in Euclidean six-dimensional space, with components derived from the Niggli matrices. All non-triclinic Bravais-lattice types are represented by vectors from one-, two-, three- and four-dimensional specific linear subspaces. Projection matrices onto these subspaces were derived. The distance between an experimentally determined and reduced cell and the projection onto each subspace can be easily calculated and used to select the correct Bravais lattice. Presented results are numerically exact.
Determination of the Cation Distribution in NiFe2(PO4)2 using Resonant X-ray and Neutron Powder Diffraction
Authors: Warner J. K. , Cheetham A. K. , Cox D. E.
Published: July 2002

The distribution of divalent iron and nickel over two metal sites of differing coordination geometry in NiFe2(PO4)2, sarcopside, has been investigated by resonant X-ray and time-of-flight neutron powder diffraction. To assess the reproducibility of the X-ray technique, data have been collected from instruments X7A at Brookhaven National Laboratory and 8.3 at the Synchrotron Radiation Source, Daresbury Laboratory, England, using wavelengths λ

X1 = 1.7437 (3) Å and λ

X2 = 1.7434 (1) Å, respectively, close to the Fe2+
K edge determined by X-ray absorption near-edge structure. The real part of the anomalous-scattering correction for iron at each energy, f′(Fe)
X1 = −7.81 (9) and f′(Fe)
X2 = −10.16 (6), was determined experimentally by diffraction from Fe3(PO4)2 under identical conditions. Occupancies obtained for iron at the M(1) site were found to be M(1)
X1 = 0.366 (6) and M(1)
X2 = 0.376 (3), compared with M(1)
N
= 0.26 (15) from time-of-flight neutron powder diffraction.
Lattice Parameters of Boron Nitride Polymorphous Modifications as a Function of Their Crystal-Structure Perfection
Authors: Kurdyumov A. V. , Solozhenko V. L. , Zelyavski W. B.
Published: July 2002

The data available in the literature on the lattice parameters of boron nitride (BN) polymorphic modifications have been analysed. A precise measurement of interplanar spacing has been carried out for hexagonal BN of different degrees of crystalline perfection and rhombohedral BN. The possibilities for alteration of wurtzitic BN lattice parameters have been studied. The results obtained have been used to establish the fundamental reference values of lattice parameters for all crystalline modifications of BN.
Deconvolution of Energy Overlaps in Laue Diffraction
Authors: Ren Z. , Moffat K.
Published: July 2002

The energy-overlap problem in Laue diffraction often makes a Laue diffraction data set incomplete in a systematic way: low-resolution reflections more commonly overlap with other reflections than do reflections at higher resolution. We describe the development and testing of a harmonic deconvolution procedure that resolves energy overlaps accurately and is based on the wavelength-normalization curve obtained from single reflections. The conditions for satisfactory harmonic deconvolution are identified by examination of a series of data sets that differ in their redundancy. This procedure has been incorporated in the software system LaueView [Ren & Moffat (1995). J. Appl. Cryst.
28, 461–481]. Results on Laue data sets from crystals of lysozyme and α-haemolysin demonstrate that Laue data sets can be more than 90% complete even at 10 Å resolution and that structure amplitudes derived from these deconvoluted multiples can be as accurate as those derived from the best monochromatic data.
Restitution conditions of the parent cubic texture from the inherited hexagonal texture in the β–α phase transformation
Authors: Humbert Michel , Gey Nathalie
Published: July 2002

Different factors calculated from theCcoefficients of the inherited orientation distribution function (ODF) allow us to check the importance of the variant selection. When no variant selection or a slight variant selection occurs by the cubic-to-hexagonal phase transformation, it is possible to calculate the ODF of the cubic parent phase present at high temperature from the ODF of the inherited hexagonal phase at room temperature. When a stronger variant selection occurs, qualitative information about the parent ODF can be obtained by using a specific correlation function, which we have named R(g).
Diffuse X-ray scattering by 2,3-dimethylnaphthalene
Authors: Schreier R. , Kalus J.
Published: July 2002

The diffuse intensity distribution of X-rays scattered from a dipolar disordered single crystal of 2,3-dimethylnaphthalene (2,3-DMN) has been measured and was found to be nearly independent of temperature in some restricted regions of the reciprocal space. This behaviour was related to a static disorder of the crystal. Lattice parameters were determined between room temperature and 9 K and phase transitions at 227 K and 112 K were observed. The results of the data analysis at 298 K are: the equivalent isotropic displacement parameterUeqfor the thermal Debye–Waller factor is (0.18 Å)2; the displacement parameters describing the static disorder are U\raise.15em{_{xx}}\kern-.65em^C\le(0.05 Å)2, U\raise.15em{_{yy}}\kern-.65em^C=[0.22\,(2) Å]2and U_{zz}^C= [0.35\,(3) Å]2. The molecules show an orientational Gaussian distribution around thexaxis with a width of 5.0 (8)°. All these results refer to the molecular inertia system. Correlation coefficients characterizing the mean mutual orientation of neighbouring molecules were determined. The highest correlation coefficient was found along [010]: C=-0.231\pm 0.004.
Deconvolution of the two-dimensional point-spread function of area detectors using the maximum-entropy algorithm
Authors: Graafsma H. , de Vries R. Y.
Published: July 2002

The maximum-entropy method (MEM) has been applied for the deconvolution of the point-spread function (PSF) of two-dimensional X-ray detectors. The method is robust, model and image independent, and only depends on the correct description of the two-dimensional point-spread function and gain factor of the detector. A significant enhancement of both the spatial resolution and the contrast ratio has been obtained for two phase-contrast images recorded with an ultra-high-resolution X-ray imaging detector. The method has also been applied to a Laue diffraction image of a protein crystal, showing an important improvement in both the peak separation of closely spaced diffraction peaks and the signal-to-noise ratio of medium and weak peaks. The principle of the method is explained and examples of its application are presented.
Pepinsky's Machine: an interactive graphics-based Fourier synthesis program with applications in teaching and research
Authors: Glykos Nicholas M.
Published: July 2002

A computer program has been developed which, given a set of structure-factor amplitudes for any centrosymmetric plane group, displays the amplitude-weighted reciprocal-lattice plane and allows the user interactively to assign and modify the phases of the structure factors, while observing the effect of these changes on the corresponding electron density function. The program has the added feature of being able to calculate and interactively display the electron density maps corresponding to all phase combinations of a user-defined subset of structure factors. Applications of the program in both crystallographic teaching and research are discussed.
A self-consistent method for X-ray diffraction analysis of multiaxial residual-stress fields in the near-surface region of polycrystalline materials. I. Theoretical concept
Authors: Genzel Christoph
Published: July 2002

In recent work, the scattering-vector method was shown to be well suited for the detection of residual stress fields, which vary significantly within the penetration depth τ of the X-rays. It allows the separate evaluation of individual components σij(τ) of the stress tensor directly from a series of measured ∊φψ(hkl, τ) depth profiles, which are obtained after stepwise rotation of the sample around the scattering vectorgφψfor fixed angle sets (φ, ψ). In this paper, a solution of improved stability for deriving the Laplace stress profiles σij(τ) is presented. It is based on the extreme sensitivity of the individual ∊φψ(hkl, τ) profiles with respect to the strain-free lattice spacingd0(hkl), which can be used as a criterion for a simultaneous determination ofd0(hkl) itself as well as of optimized σij(τ) profiles.
Facilitating preparation of gaskets for routine high-pressure diffraction studies
Authors: Katrusiak Andrzej
Published: July 2002

Preparation of gaskets for high-pressure diffraction studies can be considerably facilitated by modifying the procedure of loading single crystals or powders into diamond-anvil cells. An effective procedure of pre-indenting gaskets after drilling the holes and a simple spark eroder for preparing the gaskets in the laboratory are described.
Study of the influence of oxygen on structural perfection of silicon single crystals by high-resolution X-ray diffraction and infrared absorption measurements
Authors: Lal Krishan , Ramanan R. R. , Bhagavannarayana G.
Published: July 2002

High-resolution X-ray diffractometry, absolute integrated intensity (ρ) measurements, diffuse X-ray scattering (DXS) and infrared (IR) absorption techniques were used to investigate the influence of oxygen on the structural perfection of high purity (resistivity of the order of 4 kΩ cm) float zone (FZ) grown (111) silicon single crystals. A multicrystal diffractometer set in (+,-,-,+) geometry, with Mo Kα1radiation, was employed. From the infrared measurements, the oxygen concentration in the sample was determined to be 1.3 × 1017 atoms cm^{-3}. High-resolution X-ray diffraction curves of the as-grown crystal had half-widths of ∼11 arcsec; the ρ value was 3.5 × 10^{-5} rad. To incorporate oxygen in a controlled manner into the specimens, they were annealed under dry oxygen ambient for 8 h in the temperature range 573–1373 K (in eight steps). Up to 723 K there was no appreciable change in oxygen content or in the degree of perfection. Annealing at temperatures (AT) > 873 K resulted in considerable increases in the oxygen content, as well as significant improvements in the degree of perfection. For example, as the level of oxygen increased from 1.3 × 1017to 3.6 × 1017 atoms cm^{-3} for A_T=873 K, the values of half-widths and ρ decreased to ∼7 arcsec and 2.4 × 10^{-5} rad, respectively. However, annealing above 1273 K produced deterioration in lattice perfection. DXS measurements showed remarkable changes in the nature of point defects and their clusters with change inAT. Up to A_T=973 K, the defects were predominantly vacancy clusters. However, withATin the range 1073–1273 K, the predominent defects were isolated interstitials. Further increase inATled to interstitial cluster formation, which deteriorated the lattice perfection. This study clearly demonstrates that oxygen concentration in the range ∼3 × 1017to 13 × 1017atoms cm^{-3} leads to significant improvement in structural perfection of silicon single crystals.
Imaging of the helical arrangement of cellulose fibrils in wood by synchrotron X-ray microdiffraction
Authors: Lichtenegger H. , Müller M. , Paris O. , Riekel Ch. , Fratzl P.
Published: July 2002

A complete image of the helical arrangement of cellulose fibrils in the S2 layer of adjacent wood cells ofPicea abies(Norwegian spruce) was obtained by applying position-resolved synchrotron X-ray microdiffraction on cells in cross section. In contrast to conventional fiber diffraction studies, the incident beam was parallel to the longitudinal cell axis, resulting in a glancing angle μ far from 90° with respect to the cellulose fibrils. This special choice of diffraction geometry allowed us to take advantage of an asymmetry effect in the two-dimensional diffraction patterns arising from the curvature of the Ewald sphere to obtain information on the local orientation of the cellulose fibrils. The small size of the beam, smaller than the thickness of a single cell wall, allowed mesh scans over intact transverse sections of adjacent wood cells with a microscopic position resolution. The scan yielded a map of diffraction patterns that could readily serve as a microscopic image. Each of the diffraction patterns was then used to evaluate the local orientation of the cellulose fibrils at the actual beam position. The combination of these results gave an image of cellulose fibrils forming (Z) helices in several adjacent wood cells.
Three-beam interference measurements with a six-circle κ diffractometer
Authors: Thorkildsen G. , Larsen H. B. , Mathiesen R. H. , Mo F.
Published: July 2002

A procedure for calculating the correct angle setting for a specific three-beam situation on a six-circle κ diffractometer is outlined. It is experimentally shown that interference profiles can be recorded using this approach. Limitations owing to mechanical constraints, with particular emphasis on the ability to measure Friedel-related triplets, are discussed.
Sol phase and sol–gel transition in SnO2 colloidal suspensions
Authors: dos Santos L. R. B. , Craievich A.F. , Santilli C.V. , Pulcinelli S.H.
Published: July 2002

The effect of concentration on the structure of SnO2 colloids in aqueous suspension, on their spatial correlation and on the gelation process was studied by small angle x-ray scattering (SAXS). The shape of the experimental SAXS curves varies with suspension concentration. For diluted suspensions ([SnO2] ≤ 0.13 mol L−1), SAXS results indicate the presence of colloidal fractal aggregates with an internal correlation length ξ ≃ 20 Å, without any noticeable spatial correlation between them. This suggests that the aggregates are spatially arranged without any significant interaction like in ideal gas structures. For higher concentrations ([SnO2] = 0.16, 0.32, and 0.64 mol L−1), the colloidal aggregates are larger (ξ = 24 Å) and exhibit a certain degree of spatial correlation between them. The pair correlation function corresponding to the sol with the highest concentration (0.92 mol L−1) reveals a rather strong short range order between aggregates, characteristic of a fluid-like structure, with an average nearest-neighbor distance between aggregates d
1 = 125 Å and an average second-neighbor distance d
2 = 283 Å. The pair distribution function remains essentially invariant during the sol-gel transition, suggesting that gelation involves the formation of a few points of connection between the aggregates resulting in a gel network constituted by essentially linear chains of clusters.
Comparison of intensity profile analysis and correlation function methods for studying the lamellar structures of semi-crystalline polymers using small-angle X-ray scattering
Authors: Wang Z.-G. , Hsiao B.S. , Murthy N.S.
Published: July 2002

Changes in the lamellar structure during heating and cooling of a nylon 6,6 polymer were characterized using synchrotron small-angle x-ray scattering (SAXS). The SAXS data were analyzed using two different methods and the derived structural parameters were compared with each other. The first met hod was the conventional correlation function analysis in real space, and the second method was a direct intensity profile fitting in reciprocal space. Both methods yielded similar values of long period, lamellar thickness and amorphous layer thickness. The thickness of the inter-lamellar amorphous layer was smaller in the intensity analysis than by the correlation analysis. It could be that the crystal-amorphous boundary layer is a part of the crystal thickness in the intensity profile analysis. The linear crystallinity obtained by the two methods was similar, and was higher than the bulk crystallinity indicating the presence of significant amorphous material outside the lamellar stacks. However, coherence length of the lamellar stacks and the integrated intensity can be obtained in the intensity profile analysis and not in the correlation function method.
A small-angle scattering study of the ceramization process from organic polymer precursors
Authors: Kamiyama T. , Sasaki M. , Suzuki K.
Published: July 2002

Amorphous polyborosil azane bulk ceramics are prepared by heat treatment above 1273 K from organometallic bulk precursors which are formed by sintering precursor powders using cold isostatic pressing. A structural change during the conversion process of the polyborosilazane bulk precursors causes a change of small-angle X-ray scattering (SAXS) profiles in the high q region. The analysis of the SAXS intensities indicates that the size of the precipitates increases monotically with increasing heat-treated temperature and that they develop to small particles with sharp interfaces distributed in the amorphous phase after heat treatments above 1173 K. All the scattering profiles of the polyborosil azane bulk specimens throughout the conversion process can be fitted using the PercusYevick model of particle scattering including the concept of adepleted zone. The SAXS measurements show that the structural inhomogeneities originating from organometallic polymers arechanged by the heat-treatment above about 973 K to structures where the nano-sized precipitates embedded in the amorphous matrix occupy smaller volume fractions compared with those heat treated below 873 K.
Combining USAXS with osmotic pressure measurements: a tool for investigating the equation of states of diluted charged colloids
Authors: Lyonnard S. , Belloni L. , Réus V. , Zemb Th.
Published: July 2002

We have developed a cell allowing in situ measurement of the osmotic pressure of solutions under Ultra Small-Angle X-ray Scattering (USAXS) examination. The coupled set-up made of a Bonse/Hart camera and a deionisation close circuit allows the combined determination of the structure factor and the equation of state of colloidal suspensions. A precise control of ions concentration inside the reservoir allows to vary the ionic strength of the suspensions from the very pure case of colloidal crystals to sols with tunable screening of electrostatic repulsive interactions. We describe in detail the experimental set-ups and the data treatment methodology that we have been developing in the last years to allow detailed measurements of interactions and correlations between spherical particles. A review of our recent results obtained on the model system of negatively charged parabromostyrene latex particles forming solutions, crystals and microcrystals, is given as an illustration.
Direct determination of triplet phases and enantiomorphs of non-centrosymmetric structures. II. Experimental results
Authors: Hümmer K. , Weckert E. , Bondza H.
Published: July 2002

Direct measurements of triplet phase relationships for non-centrosymmetric light-atom organic structures with medium-size unit cells are reported. The phase information can be extracted from the three- beam profiles of a Renningerψ-scan experiment. The measurements were carried out with a specialψ-circle diffractometer installed on a rotating Cu-anode generator. The incident-beam divergence is reduced to 0.02°. The experimental results confirm the theoretical considerations of paperIof this work [Hümmer & Billy (1986).Acta Cryst.A42, 127-133]. As triplet phases of +90° can be distinguished, the absolute structure can be determined unambiguously. The measurements show that the triplet-phase-dependent interference effects may be superposed on phase-independentUmweganregungorAufhellungeffects. By a comparison of theψ-scan profiles of two centrosymmetrically related three-beam cases, the triplet phases of which have opposite signs, it is possible to evaluate the phase-independent effects and to determine the value of the triplet phase with an accuracy of at least 90°.
Space groups rare for organic structures. Erratum
Authors: Wilson A. J. C.
Published: July 2002

There is an error in the Appendix of the paper by Wilson [Acta Cryst.(1988), A44, 715-724]. Equation (A3) should read (p) = I/(N+ 2) =N-1. (A3)
Si/SiO2 interface-depth determination in glancing-incidence X-ray diffraction experiments
Authors: Aleksandrov P. A. , Belova N. E. , Fanchenko S. S. , Polandova I. X.
Published: July 2002

The Si/SiO2 interface of a single crystal has been investigated by the double-crystal inclination method, the surface peak being measured. The distorted layer depth is shown to be of the order of 1 nm and the amorphous film depth of the order of 6 nm.
Application of the statistical dynamical theory to \boldgamma-ray diffraction experiments on low-dislocation quartz single crystals
Authors: Kurbakov Alexander , Sokolov Alexei
Published: July 2002

Highly monochromatic (\Delta\lambda/\lambda=10^{-6}) short-wavelength (\lambda=0.03 Å) γ radiation has been used in the study of the diffraction processes in real single crystals. Dislocation-free silicon crystals and quartz crystals with small concentrations of chaotically distributed dislocations were investigated. The experimental results were processed with use of statistical dynamical theories of diffraction, both fundamental and advanced. It is shown that the advanced version is more reliable in both cases. However, the values of the average lattice phase E, describing the long-range distortions of the lattice, can differ markedly from the value of 1 for quartz crystals, and parameter L=-{\rm ln(E) has a square dependence on the extinction length.
Enumeration of four-connected three-dimensional nets. III. Conversion of edges of three-connected two-dimensional nets into saw chains
Authors: Han Shaoxu , Smith Joseph V.
Published: July 2002

A three-repeat saw (s) chain has each vertical edge separated by a tooth composed of two tilted edges zig and zag. Some horizontal (h) edges from a parallel stack of three-connected two-dimensional (2D) nets can be converted into an s chain. Each resulting four-connected vertex in the three-dimensional (3D) net may be part of either one, two or three s chains. The first type of (h,s)* 3D net is related by a sigma-type mirror plane to a (h,z)* net listed in paper II [Han & Smith (1998). Acta Cryst. A55, 342–359]. The second type does not have an (h,z)* relative. Using the same three-connected 2D nets as in paper II, 174 four-connected 3D nets were selected from the first two types, including six in known structures: `nepheline hydrate' (International Zeolite Association Structure Commission code JBW), AlPO4-12-TAMU (ATT), offretite (OFF), Linde Type L (LTL), SUZ-4 (SZF) and ZSM-10 (ZST). The third type with three back-to-back s chains is represented by edingtonite (EDI), and systematic enumeration is in progress. The geometrical and topological properties of the 3D nets are given. Idealized unit-cell data and atomic coordinates for tetrahedral bonding were obtained for 40 selected 3D nets by distance-least-squares (DLS) refinement.
Algorithms for deriving crystallographic space-group information
Authors: Grosse-Kunstleve R. W.
Published: July 2002

Algorithms are presented for three-dimensional crystallographic space groups, handling tasks such as the generation of symmetry operations, the characterization of symmetry operations (determination of rotation-part type, axis direction, sense of rotation, screw or glide part and location part), the determination of space-group type [identified by the space-group number of the International Tables for Crystallography (Dordrecht: Kluwer Academic Publishers)] and the generation of structure-seminvariant vectors and moduli. The latter are an algebraic description of allowed origin shifts, which are important in crystal structure determination methods or for comparing crystal structures. The space-group type determination produces a change-of-basis matrix which transforms a given space-group representation to the standard one according to the International Tables for Crystallography. The algorithms were implemented and tested using the SgInfo library. The source code is free for non-commercial applications.
On the geometry of a modern imaging diffractometer
Authors: Paciorek W. A. , Meyer M. , Chapuis G.
Published: July 2002

The geometry of a modern imaging diffractometer is discussed in detail. A method to find all relevant instrument parameters from the control single-crystal measurement data is proposed and the limitations of such a procedure are indicated. Optimization of the instrument parameters by the least-squares method is presented.
Molecular packing groups and ab
initio crystal-structure prediction
Authors: Gao Daquan , Williams Donald E.
Published: July 2002

Ab
initio crystal structure prediction can proceed by minimization of the packing energy of Z independent molecules per cell, or alternatively by energy minimization taking one molecule as independent and Z-1 molecules as related by assumed space-group symmetry. In the former method, a large number of positional variables must be considered. In the latter method, a large number of space groups must be considered. An alternative, more efficient, procedure is proposed, where it is recognized that values of Z and the number of molecules in the asymmetric unit, Z′, impose restrictions on possible space groups. Examples of application of this method to crystal structure prediction are given.
SIR99, a program for the automatic solution of small and large crystal structures
Authors: Burla Maria Cristina , Camalli Mercedes , Carrozzini Benedetta , Cascarano Giovanni Luca , Giacovazzo Carmelo , Polidori Giampiero , Spagna Riccardo
Published: July 2002

The moduli and flow diagram of the program SIR99 are described. New phasing algorithms are proposed working both in direct and in reciprocal space. Their cooperative work is able to solve the structures of both small and large molecules. In particular, small proteins can be solved ab initio without any use of prior information and any user intervention. The efficiency of the various algorithms employed by SIR99 has been tested, and the role of the tangent formula clarified. The user is also provided with some practical information concerning the computer power needed.
Anisotropic dispersion of the band structure and formation of ring patterns in CBED
Authors: Peng L.-M. , Zuo J. M.
Published: July 2002

An off-axis ring pattern was observed in the \langle 1\bar{1}1 \rangle zone-axis CBED pattern of an NiO single crystal. The pattern was interpreted as resulting from anisotropic dispersion of the band structure of the two most strongly excited free Bloch waves and strong absorption of the most tightly bound 1s Bloch state. Comparison has also been made with the case of MgO which has the same structure as NiO but weaker scattering power. The tightly bound 1s Bloch state in MgO was found to play an important role together with a strongly excited free Bloch state and a more conventional zone-axis ring pattern similar to that observed in the \langle 001 \rangle zone-axis CBED pattern of silicon was observed.
Non-centrosymmetric racemates: space-group frequencies and conformational similarities between crystallographically independent molecules
Authors: Dalhus Bjørn , Görbitz Carl Henrik
Published: July 2002

DL-Allylglycine (DL-2-amino-4-pentenoic acid, C5H9NO2) yields crystals with Pca21 symmetry and two crystallographically independent yet pseudo-inversion-related enantiomers. The distribution among the common space groups of other crystalline racemates with more than one molecule in the asymmetric unit has been established. The conformational similarities between crystallographically independent enantiomers in 114 non-centrosymmetric racemates were quantified using the r.m.s. deviation for a molecular superposition. The analysis shows that in the majority of crystals the conformations of the crystallographically independent molecules are very similar with mean r.m.s. deviation = 0.190 Å. In almost 80% of the structures the mean r.m.s. deviations is in the interval 0–0.2 Å. It is estimated that racemates constitute 23% of the centrosymmetric organic structures in the Cambridge Structural Database.
Structural phase transitions of HfV2 at low temperatures
Authors: Zhao Yusheng , Chu Fuming , Von Dreele Robert B. , Zhu Qing
Published: July 2002

We report a high-resolution synchrotron X-ray powder diffraction study on HfV2, hafnium divanadium, at low temperatures. In this work we show, for the first time, a complete sequence of structural phase transitions of HfV2 from cubic (Fd3m) to tetragonal (I41/amd) to orthorhombic (Imma) in succession as temperature decreases. Peak splitting and extra diffraction peaks owing to lattice distortion can be clearly distinguished for the low-symmetry phases. The atomic positions and lattice parameters were obtained by Rietveld refinement. The bond lengths and angles of the HfV2 crystal structure at the low-symmetry phases were correctly determined from the structure refinement. The face-centered cubic (Fd3m) unit cell (Z = 24) transforms to a body-centered tetragonal (I41/amd) phase with a 45° rotation relative to the cubic cell and with a reduced number of atoms (Z = 12) in the unit cell at a temperature of T = 112 K. The orthorhombic phase occurs at T = 102 K and it keeps the body-centered symmetry (Imma) and Z = 12 in the unit cell. The refinement results indicate that there may be a small amount of untransformed cubic phase left over in the lower symmetry phases. The abnormal thermal contraction of both tetragonal phase and orthorhombic phase marks the significance of structural change in HfV2.
[Ni(cyclam)(OCOR)2], a finite molecular complex: hydrogen-bonded supramolecular aggregation in one, two and three dimensions, and coordination polymers in one and two dimensions
Authors: Zakaria Choudhury M. , Ferguson George , Lough Alan J. , Glidewell Christopher
Published: July 2002

In the complexes [Ni(cyclam)(OCOR)2] (cyclam = 1,4,8,11-tetraazacyclotetradecane), where (RCOO)− is 2-naphtho-ate [bis-(2-naphthoato)-1,4,8,11-tetraazacyclotetradecanenickel(II), (I), monoclinic P21/c, Z′ = 0.5], 3,5-dinitrobenzoate [bis-(3,5-dinitrobenzoato)-1,4,8,11-tetraazacyclotetradecanenickel(II), (II), triclinic P\bar 1, Z′ = 0.5], 4-nitrobenzoate [bis-(4-nitrobenzoato)-1,4,8,11-tetraazacyclotetradecanenickel(II), (III), monoclinic P21/n, Z′ = 0.5], 3-hydroxybenzoate [bis-(3-hydroxybenzoato)-1,4,8,11-tetraazacyclotetradecanenickel(II), (IV), monoclinic P21/c, Z′ = 0.5] and 4-aminobenzo-ate [bis-(4-aminobenzoato)-1,4,8,11-tetraazacyclotetradecanenickel(II), (V), monoclinic C2/c, Z′ = 0.5], the Ni lies on a centre of inversion with monodentate carboxylato ligands occupying trans sites. Compound (I) consists of isolated molecules. In (II) and (III), N—H...O hydrogen bonds link the complexes into chains. Compounds (IV) and (III) form two- and three-dimensional structures generated entirely by hard hydrogen bonds. The 5-hydroxyisophthalate(2−) anion forms a hydrated complex, [Ni(cyclam)(5-hydroxyisophthalate)(H2O)]·4H2O {[aqua-(5-hydroxyisophthalato)-1,4,8,11-tetraazacyclotetradecanenickel(II)] tetrahydrate, (VI), monoclinic Cc, Z′ = 1}, in which the monodentate carboxylato ligand and a water molecule occupy trans sites at Ni: extensive hydrogen bonding links the molecular aggregates into a three-dimensional framework. The terephthalate(2−) anion forms a hydrated linear coordination polymer {catena-poly[terephthalato-1,4,8,11-tetraazacyclotetradecanenickel(II)] monohydrate, (VII), monoclinic C2/c, Z′ = 0.5}. In 1,2,4,5-benzenecarboxylate tris[1,4,8,11-tetraazacyclotetradecanenickel(II)] diperchlorate hydrate (VIII), [Ni(cyclam)]3·[1,2,4,5-benzenetetracarboxylate(4−)]·[ClO4]2·-[H2O]3, there are two distinct Ni sites: [Ni(cyclam)]2+ and centrosymmetric [C10H2O8]4− units form a two-dimensional coordination polymer, whose sheets are linked by centrosymmetric [Ni(cyclam)(H2O)2]2+ cations.
Inclusion compounds of a diol host with xylidines: controlled stoichiometries
Authors: Nassimbeni Luigi R. , Su Hong
Published: July 2002

The diol host, 1,1′-bis-(4-hydroxyphenyl)cyclohexane (DHPC) and a number of xylidine isomers as guests formed a series of inclusion compounds that gave rise to various host:guest ratios controlled by crystallization temperatures. For the host DHPC with a particular xylidine isomer, the number of guests included generally decreases as the crystallization temperature increases. The crystal structures of these host–guest compounds were elucidated using single-crystal X-ray diffraction. Their thermal stabilities were characterized by TG and DSC analysis. The selectivity of enclathration by the host was measured by carrying out a series of competition experiments. The kinetics of guest decomposition were studied using isothermal and non-isothermal methods and reconciled with the crystal structures.
Charge density study of hydrogen [(2,4-diaminopyrimidin-1-io)methyl]phosphonate monohydrate
Authors: Slouf Miroslav , Holy Antonin , Petříček Václav , Cisarova Ivana
Published: July 2002

The crystal structure and charge density of hydrogen (2,4-diaminopyrimidin-1-io)methyl]phosphonate monohydrate, C5H9N4O3P·H2O, have been determined by means of single-crystal X-ray diffraction. Diffraction data were collected at 105 K with Mo Kα radiation to a resolution of sin θ/λ = 1.08 Å−1. A four-circle diffractometer equipped with a CCD area detector was used to collect 50 161 reflections over 3 d. 6082 unique reflections with I > 3σ(I) were used in the multipole model to map the deformation electron density and gave the final statistical factors R(F) = 0.0329, wR(F) = 0.0235 and g.o.f. = 1.37. Structure determination revealed that two O atoms in the crystal structure of the title compound act as hydrogen-bond acceptors for more than one hydrogen bond. Examination of deformation electron density maps showed preferential polarization of the lone-pair electron density of the two O atoms into the shortest hydrogen bonds.
Interlayer interactions in M(OH)2: a neutron diffraction study of Mg(OH)2
Authors: Desgranges L. , Calvarin G. , Chevrier G.
Published: July 2002

Magnesium hydroxide, Mg(OH)2: Mr
= 58.3, trigonal, P{\bar 3}m1, a = 3.148 (1), c = 4.779 (2) Å, V = 41.015 Å3, Dx
= 2.36 g cm−3 at room temperature; a = 3.145 (1), c = 4.740 (2) Å, V = 40.602 Å3, Dx
= 2.39 g cm−3 at 70 K; Z = 1, λ = 0.8330 (5) Å, μ = 1.78 cm−1, F(000) = 9.503 fm; final R = 2.42, wR = 2.40, S = 3.22 for 82 unique reflections at room temperature; R = 1.84, wR = 1.82, S = 2.54 for 81 unique reflections at 70 K. Refinements have been carried out using anisotropic thermal coefficients for all atoms. To interpret the very large thermal motion of the H atom, subsequent refinements have been carried out with an anharmonic model and with a three-site split-atom model, and results are compared with those previously reported for Ca(OH)2. By comparing the interatomic distances O...O, H...H and H...O in the interlayer spacing of Mg(OH)2 and Ca(OH)2, as well as their temperature dependence, the nature and the strength of interlayer interactions in both compounds are discussed.
Structural studies on monohalogenated derivatives of the phytohormone indole-3-acetic acid (auxin)
Authors: Nigović B. , Kojić-Prodić B. , Antolić S. , Tomić S. , Puntarec V. , Cohen J. D.
Published: July 2002

The physiological properties of the phytohormone (auxin) indole-3-acetic acid (IAA) and its ring substituted derivatives have so far been rationalized by a number of contradictory hypotheses based on incomplete structural data deduced mainly by inspection of molecular models. In order to give more evidence for structure–activity relationships of monohalogenated IAA's, the molecular structures of the natural auxin 4-CI-IAA as well as 5-CI-IAA, 6-CI-IAA, 7-CI-IAA and 5-Br-IAA have been compared, as revealed by X-ray analysis, and molecular mechanics and dynamics. The influence of the substitution site and the size of the halogen atom and bioactivity is discussed. The typical structural feature of the molecules studied is the slight distortion of part of the indole nucleus around C7: bond length C6—C7 1.368 (6) Å and C6—C7—C71 117.6 (3)° (average values of five structures and seven molecules). The conformations of monohalogenated indole-3-acetic acid molecules, characteristic for auxins, are defined by rotations about two bonds only: one describes the relative orientation of a side chain towards the indole moiety and the second the orientation of the carboxylic group. The results of X-ray structure analysis, and molecular mechanics and dynamics revealed the folded shape of the molecules in all compounds studied. Ab initio calculations showed that the planar conformation can be adopted as well. Crystal data at 297 K for 4-CI-IAA, 6-CI-IAA, 7-CI-IAA and 5-Br-IAA, and at 220 K for 5-CI-IAA, using Mo Kα radiation (λ = 0.71073 Å), and CuKα (λ = 1.5418 Å) for 6-CI-IAA, are as follows: 4-CI-IAA, C10H8ClNO2, Mr
= 209.63, monoclinic, P21/c, a = 7.313 (4), b = 17.156 (4), c = 7.640 (4) Å, β = 92.71 (5)°, V = 957.5 (1) Å3, Z = 4, Dx
= 1.454 g cm−3, μ = 3.7 cm−1, F(000) = 432, R = 0.037, wR = 0.039 for 1040 symmetry-independent [I ≥ 3σ(I)] reflections; 5-CI-IAA, C10H8ClNO2, monoclinic, P21/c, a = 19.141 (4), b = 5.154 (2), c = 10.323 (3) Å, β = 116.23 (2)°, V = 913.5 (1) Å3, Z = 4, Dx
= 1.524  g cm−3, μ = 3.8 cm−1, F(000) = 432, R = 0.039, wR = 0.042 for 1184 symmetry-independent [I≥ 3σ(I)] reflections; 6-CI-IAA, C10H8ClNO2, orthorhombic, Pbca, a = 61.08 (1), b = 12.115 (7), c = 7.674 (5) Å, V = 5679 (5) Å3, Z = 24, Dx
= 1.471 g cm−3, μ = 33.9 cm−1, F(000) = 2592, R = 0.052, wR = 0.052 for 3030 symmetry-independent [I ≥ σ(I)] reflections; 7-CI-IAA, C10H8ClNO2, monoclinic, P21/c, a = 20.244 (5), b = 4.829 (2), c = 10.728 (4) Å, β = 116.30 (1)°, V = 940 (1) Å3, Z = 4, Dx
= 1.481 g cm−3, μ = 3.7 cm−1, F(000) = 432, R = 0.042, wR = 0.029 for 889 symmetry-independent [I ≥ 3σ(I)] reflections; 5-Br-IAA, C10H8BrNO2, Mr
= 254.08, triclinic, P{\bar 1}, a = 5.645 (3), b = 9.713 (4), c = 10.019 (4) Å, α = 116.02 (3), β = 92.67 (5), γ = 100.12 (4)°, V = 481.2 (5) Å3, Z = 2, Dx
= 1.754 g cm−3, μ = 42.0 cm−1, F(000) = 252, R = 0.029, wR = 0.020 for 1865 symmetry-independent [I ≥ 3σ(I)] reflections.
Structure and optical non-linearity of PbO.2B2O3
Authors: Corker D. L. , Glazer A. M.
Published: July 2002

The crystal structure of lead tetraborate, PbO.2B2O3, has been refined using single-crystal X-ray diffraction data (Mo Kα radiation, λ = 0.71069 Å). Crystal data at room temperature: Mr
= 362.43, orthorhombic, P21
nm (C
7
2v
), a = 4.251 (2), b = 4.463 (3), c = 10.860 (3) Å, V = 206.04 Å3 with Z = 2, μ = 402.6 cm−1, Dx
= 5.88 Mg m−3, F(000) = 316, final R = 0.022, wR = 0.025 over 655 reflections with I > 2.5σ(I). Atomic coordinates are in general agreement with those previously reported for the isostructural compound, SrO.2B2O3, by Perloff & Block [Acta Cryst. (1966), 20, 274–279]. All the borons are tetrahedrally coordinated with a three-dimensional network formed from O atoms that are common to either two or three tetrahedra. The tetrahedra show deformation because the B—O bonds involving the two-coordinated O atoms are much shorter than those involved with three-coordinated O atoms. The Pb atoms are situated in empty tunnels running along [010] left by the network of tetrahedra. The Pb atoms display a highly asymmetric distribution of Pb—O bonding, with the five shortest bonds covering the range 2.483 (5)–2.664 (5) Å, being all situated to one side of the Pb atom. Preliminary investigations of the non-linear optical behaviour of lead tetraborate are also discussed. The results indicate that doping with barium should lead to a new non-linear optical material that is both phase-matchable and has a high optical non-linearity.
Planarity of nitro-substituted phenothiazines
Authors: Brock C. P. , DeLaLuz P. J. , Golinski M. , Lloyd M. A. , Vanaman T. C. , Watt D. S.
Published: July 2002

The structures of three nitro-substituted phenothiazines [1,3,4-trifluoro-2-nitrophenothiazine, 10-(4-chlorobutyl)-1,3,4-trifluoro-2-nitrophenothiazine and 10-(4-chlorobutyl)-3-nitrophenothiazine] have been determined. The first of these red compounds forms infinite stacks in the solid state, in which donor and acceptor regions of the approximately planar molecules alternate. The molecules of the other two compounds, which have folded, or `butterfly', conformations in the solid state, do not form stacks, presumably because the bulky chlorobutyl substituents cannot be accommodated. The very dark color of solid 3-nitrophenothiazine suggests the presence of extended molecular stacks, but crystals suitable for a structure determination could not be obtained.
Experimental charge density study of 7-dispiro[2.0.2.1]heptane carboxylic acid
Authors: Yufit D. S. , Mallinson P. R. , Muir K. W. , Kozhushkov S. I. , De Meijere A.
Published: July 2002

The experimental charge density distribution in 7-dispiro[2.0.2.1]heptane carboxylic acid has been determined using single-crystal X-ray diffraction data measured at 100 K. Multipole refinement converged at R = 0.023 for 5539 reflections with I ≥ 3σ(I) and sin θ/λ ≤ 1.08 Å−1. Inclusion of hexadecapole functions for C atoms in the refinement is shown to be necessary. Experimental maps of the deformation density and of the Laplacian of ρ are in good agreement with those from ab initio calculations and also have some features specific for polyspirocyclopropanes. Analysis of the bond critical-point properties reveals that the effect of the π-acceptor hydroxycarbonyl substituent is more pronounced on the endo-side of the molecule, which can be related to the chemical behaviour of the compound. The influence of small conformational changes on the bond length distribution in the skeleton is also discussed.
Kristallstruktur und zwillingsbildung der intermetallischen phase β-Bi2Rh
Authors: Ruck M.
Published: July 2002

β-Bi2Rh was prepared from the elements in the presence of iodine. At room temperature the lattice constants of the triclinic centrosymmetric structure are a = 6.743 (1), b = 7.030 (1), c = 7.067 (1) Å, α = 104.76 (1), β = 100.73 (1), γ = 105.79 (I)°. X-ray investigations on a single crystal revealed that each Rh atom is surrounded by seven Bi atoms in a monocapped trigonal prism. The prisms share common rectangular and trigonal faces to build infinite rows of double prisms, which are finally connected into parallel (100) layers. Twinning along [010] is commonly observed, indicating a pseudomonoclinic C-centered cell.
Structural relationship of various squarates
Authors: Lee C.-R. , Wang C.-C. , Wang Y.
Published: July 2002

This work illustrates the structural relationship between three types of metal squarates as well as the ligand in its acid form and in its monoanion salt. Squaric acid, H2C4O4, is known to have a polymeric layer structure with planar molecules connected through intermolecular hydrogen bonds. The interlayer distance is only 2.649 Å. The crystal of H2NMe2[H3(C4O4)2] is found to contain columns of [H3(C4O4)2
−] repeating units, again connected by intermolecular hydrogen bonds. Within the repeated unit, there is a symmetric hydrogen bond connected to two HC4O4 moieties. A new type of metal squarate with M(HC4O4)2(H2O)4
M = MnII, FeII both belong to space group P\bar 1, Z = 1, a = 5.194 (3), b = 7.454 (2), c = 8.901 (2) Å, α = 67.07 (2), β = 77.26 (3), γ = 74.46 (4)°, for MnII is shown to have a layer-type structure, where all [HC4O4] units are bonded into infinite chains via symmetric hydrogen bonds, each (HC4O4)2
2− ligand bridging two metal ions (μ-2) in a trans fashion. The structurally most well understood metal squarate M(C4O4)(H2O)4 (M = MnII, FeII, CoII, NiII and ZnII, space group C2/c, Z = 4) is again a polymeric chain with C4O4
2− serving as a bridging ligand between two metal ions (μ-2) in trans positions. A three-dimensional polymeric structure is found to have the formula M(C404)(H2O)2, where C4O4
2− is a bridging ligand between four metal ions (μ-4). Due to the slight difference in packing, there are two structure types in this category: one is in space group R{\bar 3} [M = FeII, a = 11.440 (2), c = 14.504 (3) Å, Z = 9], the other is in Pn{\bar 3}n [M = CoII, a = 16.255 (3) Å, Z = 24]. The structural relationship between all these structures relies heavily on the understanding of intra- and intermolecular hydrogen bonds. The interesting building blocks of each compound will be illustrated. There are tunnels of various sizes in all these structures.
The Elusive Crystal Structure of Uric Acid Dihydrate: Implication for Epitaxial Growth During Biomineralization
Authors: Artioli G. , Masciocchi N. , Galli E.
Published: July 2002

The crystal structure of the elusive uric acid dihydrate phase, a known component of human pathological biomineralizations, has been investigated by a combination of synchrotron and conventional X-ray diffraction experiments. C5H4N4O3.2H2O, orthorhombic, Pnab, a = 7.409 (1), b = 17.549 (3), c = 6.332 (1) Å, Z = 4, wR = 0.030 and 0.041 for two independently measured datasets. The molecular packing, encompassing hydrogen-bonded layers of water molecules and statistically disordered organic moieties, fully clarifies on a structural basis the observed epitaxic growth of uric acid dihydrate with associated phases in human stones, such as anhydrous uric acid and whewellite. Synchrotron data confirmed the existence of weak reflections violating the extinction conditions and are interpreted by the presence of short-range ordering of the uric acid molecules at distances of the order of a few adjacent cells.