bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase Improvement by Multi-Start Simulated Annealing Refinement and Structure-Factor Averaging
Authors: Rice Luke M. , Shamoo Yousif , Brünger Axel T.
Published: July 2002

Macromolecular crystallography increasingly pushes the limits of the size and complexity of the molecules and assemblies under study. Conformational variability in these assemblies frequently results in limited diffraction or in poorer phase information than that typically obtained from smaller macromolecules. Current methods for solving and refining crystal structures often perform poorly under these adverse conditions and thus new methods must be developed. Atomic-model refinement is particularly sensitive to the low information content of limited diffraction data. Here a multi-start procedure is presented for simulated annealing refinement. After multi-start refinement, poorly fitted regions of the model often display increased variability compared with correctly fitted regions. Structure-factor averaging over the resulting models improves the quality of phases derived from atomic models and reduces model bias. Averaging can be performed even at a minimum Bragg spacing of 3.5 Å, taking into account variability of atomic positions due to errors or intrinsic flexibility even when individualBfactors cannot be refined. The average structure factor is thus closer to the true structure factor and should provide a better starting point for estimations of σAvalues for electron-density-map calculations. Test cases show increased phase quality of the average structure factor. The method is most useful when the initial model is poor or when only moderate-resolution diffraction data are available and may allow meaningful phase improvement through atomic-model refinement where it was not previously possible.
Topological analysis of experimental electron densities
Authors: Souhassou Mohamed , Blessing Robert H.
Published: July 2002

Practical computing algorithms are described for analysing the topology of experimental electron density distributions represented as either three-dimensional grid densities or multipolar pseudoatom superpositions. The algorithms are implemented in the programNEWPROP, results from which are illustrated with applications to twoN-acetyl,C-methylamide blocked amino acid crystal structures.
X-ray diffraction texture analysis of cylindrical samples
Authors: Guillén R. , Cossu C. , Jacquot T. , François M. , Bourniquel B.
Published: July 2002

The effect of the curvature of the sample surface on X-ray diffraction has been studied. A theoretical model, based on a ray-tracing method, has been developed to take into account the geometric effects which modify the collected intensities. The model enables alignment corrections for the sample and the incident beam, in relation to the goniometer centre. This can be achieved by comparing experimental normalized intensities for a zero tilt angle (ψ = 0°) to the normalized intensities calculated by the model. The texture analysis of a zircaloy-4 tube (with a 9.5 mm diameter and an incident-beam spot size of 1.2 mm diameter) confirms the validity of the results.
Exploring reciprocal space of a quasicrystal by means of an imaging plate
Authors: Kopecky Milos , Colella Roberto
Published: July 2002

A monochromatic Laue technique is used to extract information about the reciprocal lattice of a quasicrystal. A synchrotron beamline, normally available for protein crystallography, was used in this study. Each photograph is a planar projection of a spherical cap, a portion of the Ewald sphere, in reciprocal space. The algorithms needed to relate the images to reciprocal space are described in detail. It is found that many weak, but readily detectable, Bragg reflections are found in unexpected positions in reciprocal space, as predicted from theory. Some very weak Bragg reflections are clearly visible on the imaging plate, but could not be detected by photon counting using a four-circle diffractometer. Some images show characteristic `rings' or `arcs' of diffuse scattering, as previously observed in other icosahedral quasicrystals. In view of the `extreme perfection' of the quasicrystalline specimen used in this study, it is proposed to view these rings (or arcs) as intrinsic features of the icosahedral quasicrystalline structure.
Making the most of commercial sparse-matrix protein crystallization screening kits
Authors: Albert Armando , Martínez-Ripoll Martín
Published: July 2002

A rational strategy to discern the solubility properties of a macromolecular sample is presented. The method uses the most popular crystallization screening kits. A small computer program has been developed to facilitate the analysis. Charts are included that show the dependence of the solubility on pH and precipitant concentrations.
The application of evolution strategies to disordered structures
Authors: Knorr Karsten , Mädler Fritz
Published: July 2002

Evolution strategies are applied to refine structural fragments, like molecules or complex anions, of orientationally disordered crystals. Optimal geometric embedding of the fragments into electron density distributions, resulting from maximum-entropy (ME) reconstructions, are performed. The evolution paradigm is found to be also applicable for the refinement against structure factors, for which the structural model is carefully selected from the ME densities. Suitably modified, the method is used successfully to compute reorientation pathways and to predict disordered high-pressure configurations in a non-classical qualitative model.
Investigation of Bragg surface diffraction in semiconductors and epitaxic structures by reciprocal-space analysis
Authors: Morelhão S. L. , Abramof E.
Published: July 2002

Bragg surface diffraction (BSD) is a special case of three-beam diffraction, where the secondary beam is scattered in the surface-parallel direction. Under the BSD condition, the surface-detour reflection (secondary plus coupling reflections) transfers some of the secondary-beam intensity into the monitored primary beam. The extinction regime in which such transfer takes place depends on the crystalline perfection of the surface. Based on this fact, the mapping of the BSD profile, in an ω:φ scan technique, has been proposed [Morelhão & Cardoso (1996).J. Appl. Cryst.29, 446–456] as a method to obtain information on the in-plane crystalline quality of the surface. With the X-ray optics for BSD mapping, the diffracting surface thickness that defines the profile could not be measured or compared with those under conventional Bragg diffraction. In this report, the BSD using a triple-axis diffractometer is investigated. Reciprocal-space mapping of the Bragg reflection (primary reflection) was performedinandoutof the BSD condition. It reveals the diffracting surface thickness of BSD in GaAs and Si substrates. The triple axis was also used to investigate the BSD in the SiGe multiple quantum well, and it has demonstrated the existence of effective satellite peaks for such structures.
New developments of computer-aided crystallographic analysis in transmission electron microscopy
Authors: Zaefferer Stefan
Published: July 2002

A new computer program for on-line crystallographic analysis in transmission electron microscopy (TEM) is presented. The program is based on the fast on-line determination of single-crystal orientations from Kikuchi and spot patterns. Spot patterns, which are particularly useful in the case of highly deformed metals, are analyzed by a new digital image processing procedure. This procedure improves the precision and ease of the orientation measurement. The program permits the on-line measurement of glide systems characterized by the Burgers vector and the crystallographic line direction of dislocations and their glide planes. The determination of twin systems, based on the misorientation calculation for any crystal structure, is included as well. The possibility of determining the foil thickness permits the complete crystallographic characterization of interfaces. Finally, the program facilitates the discrimination of phases and includes the fit of the lattice parametersa,bandcfrom diffraction patterns. The new procedures are described in detail. Application examples are given for all functions.
Integration procedure for the quantitative analysis of dispersive anomalous diffraction
Authors: Favre-Nicolin V. , Bos S. , Lorenzo J. E. , Bordet P. , Shepard W. , Hodeau J.-L.
Published: July 2002

The development of the energy/angular dispersive diffraction setup, which can be used for anomalous diffraction, allows the collection of diffracted intensities around an absorption edge, either over a continuous energy range [for DAFS (diffraction anomalous fine structure) studies], or at discrete energies [for simultaneous MAD (multiwavelength anomalous diffraction) studies]. Used with a large two-dimensional detector and an oscillating single crystal, this setup allows simultaneous collection of many reflections for a given energy range. An integration procedure has been developed along with a program,DAD(dispersive anomalous diffraction), for the collection and analysis of the raw images, to yield finally data in the formI(h, k, l, λ) for all reflections. Wavelength calibration and intensity corrections are made during the integration process, and parameters that may be needed in later stages of the analysis are extracted and referenced within the integrated data. A general procedure to calculate the positions of diffracted reflections, for a monochromatic oscillation scan with a two-dimensional detector, when the incident beam is not perpendicular to the oscillation axis, is also described.
Temperature-induced micelle to vesicle transition: kinetic effects in the DMPC/NaC system
Authors: Lesieur P. , Kiselev M.A. , Barsukov L.I. , Lombardo D.
Published: July 2002

The formation of spherical and monodisperse small unilamellar vesicles is observed upon temperature jumps in a mixed system composed of a phospholipid (dimyristoylphosphatidylcholine) and a bile salt (sodium cholate) in an aqueous buffer. In order to enhance the X-ray contrast of the system a mixed water/sucrose buffer is used. The spontaneous formation of unilamellar structures from mixed micelles upon temperature increase and the reverse solubilisation of membranes upon cooling is studied by means of synchrotron radiation small-angle X-ray scattering. The variations of the vesicle size are presented when the temperature and the surfactant / lipid ratio are modified. The kinetic conditions leading to monodisperse vesicles as well as the reversibility of the micelle to vesicle transition are investigated.
Formation of homogeneous gel-like phases by mixed triblock copolymer micelles in aqueous solution: FCC to BCC phase transition
Authors: Liu T. , Chu B.
Published: July 2002

The phase behavior of mixed block copolymers E99P69E99 and E45B14E45 (with E, P and B being oxyethylene, oxypropylene and oxybutylene, respectively) in aqueous solution is reported for the first time. Homogeneous gel-like structures, formed by the ordered packing of mixed block copolymer micelles, were studied by small-angle X-ray scattering (SAXS). Four different single phases could be identified: mixed solution, body-centered cubic (bcc), face-centered cubic (fcc) and hexagonal. Two fcc to bcc transitions occurred by increasing 99P69E99 concentration or by adding a small amount of E45B14E45 chains to the 99P69E99/water system while keeping the total polymer concentration constant at around 30 wt%.
Temperature and pressure effects on structural formations in a ternary microemulsion
Authors: Nagao M. , Seto H. , Kawabata Y. , Takeda T.
Published: July 2002

Small angle neutron scattering experiments were conducted on a temperature-induced phase transition in a ternary microemulsion composed of AOT (dioctyl sulfosuccinate sodium salt), D2 O and n-decane and the results were compared with those of pressure-induced one. Although the static features of both the temperature- and the pressure-induced phase behaviour were similar, a temperature dependence of its characteristic repeat distance at high temperature was quite different from a pressure dependence of that at high pressure. Neutron spin echo experiments were also performed on both the phase transitions. The dynamics of the high temperature phase was different from that of the high pressure phase. These results indicated that the effect of pressure on the structural formation was different from that of temperature.
On integrating the techniques of direct methods with anomalous dispersion: the one-phase structure seminvariants in the monoclinic and orthorhombic systems. III. Primitive non-centrosymmetric space groups of type 1P220. Erratum.
Authors: Velmurugan D. , Hauptman H. A.
Published: July 2002

There are two errors in the short communication by Velmurugan & Hauptman [Acta Cryst. (1989). A45, 656]. On line 9 in the Abstract, Φ
2h′2k′0 should read Φ
2h2k0 and on line 3 in Summary of final results, Φ
2h′2k′0 should read Φ
2h,2k,0.
IUCr: its formation and early development. Erratum
Authors: Kamminga H.
Published: July 2002

There is an unfortunate error in the caption to the figure on page 585 of the article by Kamminga [Acta Cryst. (1989). A45, 581-601]. The photograph was taken at the University of Leeds during the symposium held on 18-19 July 1946 and not 1948 as stated in the article.
Retrieval of the projected potential by inversion from the scattering matrix in electron–crystal scattering
Authors: Allen L. J. , Leeb H. , Spargo A. E. C.
Published: July 2002

The retrieval of a unique crystal potential from the scattering matrix {\cal S} in high-energy transmission electron diffraction is discussed. It is shown that, in general, data taken at a single orientation are not sufficient to determine all the elements of {\cal S}. Additional measurements with tilted incident beam are required for the determination of the whole {\cal S} matrix. An algorithm for the extraction of the crystal potential from the {\cal S} matrix measured at a single energy and thickness is presented. The limiting case of thin crystals is discussed. Several examples with simulated data are considered.
Divergent-beam technique used in a SEM to measure the cell parameters of isotopically distinct samples of LiF over the temperature range ∼15–375 K
Authors: Mendelssohn Monica J. , Milledge H. Judith
Published: July 2002

The cell parameters for LiF containing 90.4% 6Li and 50.2% 6Li were determined from a series of divergent-beam photographs taken at approximately 25 K intervals in the ∼15 to 375 K range. The divergent-beam photographs were generated in a Stereoscan S4 scanning electron microscope fitted with a liquid-helium cold finger and a Dingley Kossel camera. Lattice parameters can be determined from the ratios of lines joining conic intersections, and such data, measured on films taken at known temperatures, were correlated with equivalent data from computer-generated divergent-beam patterns using appropriate cell parameters; our cell parameters at 298 K are 6Li90.4%  = 4.0272 (2) and 6Li50.2%.  = 4.0266 (2) Å. If it is assumed that the stated isotopic compositions are correct, linear extrapolation to end-member cell parameters gives 6Li100%  = 4.0273 (2) and 6Li0%  = 4.0259 (2) Å. Since for a cubic crystal only one lattice-parameter measurement is required from each photograph, the usefulness of the ratio approach was tested by comparing values of the lattice parameter deduced from many such ratios obtained from photographs with no symmetry and with mirror symmetry.
Periodic intensity distribution (PID) of mica polytypes: symbolism, structural model orientation and axial settings
Authors: Nespolo Massimo , Takeda Hiroshi , Kogure Toshihiro , Ferraris Giovanni
Published: July 2002

Following a preliminary revisitation of the nomenclatures in use for mica polytypes, the properties of the periodic intensity distribution (PID) function, which represents the Fourier transform of the stacking sequence, are analysed. On the basis of the relative rotations of neighbouring layers, mica polytypes are classified into three types; for each type, the PID exists in different subspaces of the reciprocal space. A revised procedure to compute the PID, in which further restrictions on the structural model orientation are introduced, is presented. A unifying terminology based upon the most common symbols used to describe mica polytypes (RTW, Z and TS) is derived; these symbols represent the geometrical basis for the computation of the PID. Results are presented for up to four layer polytypes and are compared with the reflection conditions derived by means of Zvyagin's functions. Both the PID values and the reflection conditions are expressed in suitable axial settings and compared with previous partial reports, revealing some errors in previous analyses. A computer program to compute PID from the stacking symbols is available.
A new type of constraint in the maximum-entropy method using ambiguous phase information from anomalous-scattering powder data
Authors: Burger K. , Prandl W.
Published: July 2002

Anomalous scattering of X-rays at a synchrotron source can be used for the ab
initio structure determination of unknown crystal structures using only powder diffraction data. For noncentrosymmetric crystals, the phases of structure factors can only be determined with a remaining ambiguity, when one chemical element is used as resonant scatterer. A corresponding additional constraint function has been built into an enhanced version of the program MEED, so that now all types of information gained from an anomalous-scattering powder diffraction experiment can be used in a maximum-entropy calculation of the electron-density distribution: phased reflections, unphased reflections, intensities of groups of overlapping reflections, and now also reflections with a remaining ambiguity in the phase. This is important for practical use, since a lot of information is already lost in the powder diagram compared with single-crystal datasets and it is essential to use all remaining information. The new constraint is demonstrated with the structure of Cu5Zn8.
Synthesis, structure and magnetic properties of tetrakis-μ-carboxylato-bis(dodecylnicotinato)dicopper(II) complexes; crystal and molecular structure of the decyl carboxylate derivative
Authors: Rusjan Marcia , Chaia Zulema , Piro Oscar E. , Guillon Daniel , Cukiernik Fabio D.
Published: July 2002

Dodecylnicotinate bis-adducts of binuclear copper carboxylates, of the general formula Cu2(O2CC
n − 1H2n − 1)4(C5H4NCOOC12H25)2, were synthesized for n = 10, 12, 14, 16, 18 and 20, and their crystal structure, thermal behavior and magnetic properties studied. The molecular structure of the decyl derivative has been determined from single-crystal X-ray diffraction data. The dimer is centrosymmetric with the CuII ions in a square-pyramidal coordination with four O-alkyl O atoms [average d(Cu—O) 1.960 (6) Å] in the basal plane and the nicotine N atom at apical positions [d(Cu—N) 2.183 (3)  Å]. The copper ions, 2.615 (1) Å apart, are bridged by four O-alkyl carboxylate groups. Both the n = 20 and n  =  18 homologues exhibit lamellar phases, which can be related to the supramolecular arrangement found in the n = 10 derivative. The magnetic behavior of the decyl and octadecyl dimers was studied in the 2–300 K temperature range. They exhibit a strong intramolecular antiferromagnetic interaction (Cu–Cu superexchange coupling constant J  = −347 cm−1 for the decyl derivative), which can be attributed to a large overlap of the metal 3d orbitals and the oxygen lone pair orbitals of the linking carboxylate groups.
Crystal-to-crystal photodimerization of trans-cinnamamides
Authors: Hosomi Hiroyuki , Ito Yoshikatsu , Ohba Shigeru
Published: July 2002

In the crystals of trans-4-methylcinnamamide, C10H11NO (I), trans-4-chlorocinnamamide, C9H8ClNO (II), trans-3-(2-thienyl)acrylamide, C7H7NOS (III), and trans-cinnamamide, C9H9NO (IV), the shortest intermolecular C...C distances between the C=C double bonds are 3.670 (2), 3.632 (2), 3.762 (3) and 4.120 (2) Å, respectively, for the pair of molecules related by a center of symmetry. The structure analysis was also carried out for trans-2-(p-chlorophenyl)-cis-4-(p-chlorophenyl)-1-trans-3-diamidocyclobutane, C18H16Cl2N2O2 (V), which is the α-type photodimer of (II). The N—H...O hydrogen-bond networks in (I)–(III) are composed of two-dimensional pleated sheets, and those in (IV) and (V) of one-dimensional flat ribbons. The single crystals of (I), (II) and (IV) were photoirradiated with a 250 W ultra-high-pressure mercury lamp through a band-pass filter or a long-pass filter for 2–5 h. The photodimer was produced in each crystal with retention of the single-crystal form. The populations of the dimers were converged to 86.2 (4), 48.4 (6) and 4.5 (2)% in the refinement of the crystals after photoirradiation, (I^{\prime}), (II^{\prime}) and (IV^{\prime}), respectively. Although the intermolecular N—H...O hydrogen-bond network remained in (I^{\prime}) and (II^{\prime}), the network was partly broken in (IV^{\prime}) in the process of photoreaction.
Electron density and atomic displacements in KTaO3
Authors: Zhurova Elizabeth A. , Ivanov Yury , Zavodnik Valery , Tsirelson Vladimir
Published: July 2002

The atomic interactions and anharmonicity of atomic displacements in the virtual ferroelectric KTaO3, potassium tantalate, have been studied using accurate single-crystal X-ray diffraction at room temperature. The multipole analysis of electron density and Gram–Charlier series description of anharmonic atomic displacements allowed us to perform a quantitative analysis of the chemical bonding and atomic motion in this crystal. Closed-shell interactions between Ta—O and K—O pairs of atoms were found, while no interaction was observed for the Ta—K and O—O atomic pairs. The character of the anharmonic atomic displacements is discussed and compared with those in SrTiO3.
Electron density and electrostatic properties of two peptide molecules: tyrosyl-glycyl-glycine monohydrate and glycyl-aspartic acid dihydrate
Authors: Pichon-Pesme Virginie , Lachekar Hassane , Souhassou Mohamed , Lecomte Claude
Published: July 2002

The electron density and electrostatic properties of Tyr-Gly-Gly and Gly-Asp molecules have been determined from high-resolution X-ray diffraction data at 123 K. Topological properties of the charge distribution are discussed and compared with those derived from other experimental studies on peptide molecules, and the characteristics of the (3,−1) critical points of the C=O, C—N, C—C bonds are analysed. Crystal data for Tyr-Gly-Gly: C13H17N3O5·H2O, Mr
= 313, orthorhombic, P212121, Z = 4, T = 123 ± 2 K; lattice parameters: a = 7.984 (2), b = 9.535 (3), c = 18.352 (5) Å, V = 1397.1 (6) Å3, Dx
= 1.49 g cm−3, μ = 1.2 cm−1 for λMo = 0.7107 Å. Crystal data for Gly-Asp: C6H10N2O5·2H2O, Mr
= 212, orthorhombic, P212121, Z = 4, T = 123 ± 2 K; lattice parameters: a = 9.659 (1), b = 9.672 (1), c = 10.739 (1) Å, V = 1003.3 (4) Å3, Dx
= 1.40 g cm−3, μ = 1.3 cm−1 for λMo = 0.7107 Å.
Migration of the proton in the strong O—H...O hydrogen bond in urea–phosphoric acid (1/1)
Authors: Wilson Chick C.
Published: July 2002

The structure of urea–phosphoric acid is reported at a large number of temperatures in the range 150–335 K from neutron diffraction data collected using a novel multiple single-crystal data collection method. The work focuses on the behaviour of the H atom involved in the short strong O—H...O hydrogen bond in this material. The position of this atom is shown to vary significantly, by around 0.035  Å, as a function of temperature, becoming effectively centred at the highest temperatures studied. This result, only accessible due to the accurate determination of H-atom parameters by neutron diffraction, has implications for the potential governing the hydrogen bond.
Structures of copper(II) and manganese(II) di(hydrogen malonate) dihydrate; effects of intensity profile truncation and background modelling on structure models
Authors: Lenstra A. T. H. , Kataeva O. N.
Published: July 2002

The crystal structures of the title compounds were determined with net intensities I derived via the background–peak–background procedure. Least-squares optimizations reveal differences between the low-order (0 < s < 0.7 Å−1) and high-order (0.7 < s < 1.0 Å−1) structure models. The scale factors indicate discrepancies of up to 10% between the low-order and high-order reflection intensities. This observation is compound independent. It reflects the scan-angle-induced truncation error, because the applied scan angle (0.8 + 2.0 tan θ)° underestimates the wavelength dispersion in the monochromated X-ray beam. The observed crystal structures show pseudo-I-centred sublattices for three of its non-H atoms in the asymmetric unit. Our selection of observed intensities (I > 3σ) stresses that pseudo-symmetry. Model refinements on individual data sets with (h + k + l) = 2n and (h + k + l) = 2n + 1 illustrate the lack of model robustness caused by that pseudo-symmetry. To obtain a better balanced data set and thus a more robust structure we decided to exploit background modelling. We described the background intensities B(\displaystyle\mathrel{\mathop H^{\rightharpoonup}}) with an 11th degree polynomial in θ. This function predicts the local background b at each position \displaystyle\mathrel{\mathop H^{\rightharpoonup}} and defines the counting statistical distribution P(B), in which b serves as average and variance. The observation R defines P(R). This leads to P(I) = P(R)/P(B) and thus I = R − b and σ2(I) = I so that the error σ(I) is background independent. Within this framework we reanalysed the structure of the copper(II) derivative. Background modelling resulted in a structure model with an improved internal consistency. At the same time the unweighted R value based on all observations decreased from 10.6 to 8.4%. A redetermination of the structure at 120 K concluded the analysis.
Hydrogen-bonded hexagonal and pseudo-hexagonal grid motifs in supramolecular cobalt(II) and nickel(II) cupferronato complexes incorporating neutral N-donors with intermolecular NH2 connectors and solvent molecules
Authors: Deák Andrea , Kálmán Alajos , Párkányi László , Haiduc Ionel
Published: July 2002

The cobalt(II) and nickel(II) cupferronato (N-nitroso-N-phenylhydroxylaminato) mixed-ligand complexes of 2-aminopyridine (2-NH2py) [Co(PhN2O2)2(2-NH2py)2] (1), [Ni(PhN2O2)2(2-NH2py)2] (2) and 2,6-diamino-4-phenyl-1,3,5-triazine (dpt) [Co(PhN2O2)2(dpt)2]·[Co(PhN2O2)2(EtOH)2] (3) have been synthesized and characterized by X-ray diffraction analysis. The cobalt (1) and nickel (2) complexes are isostructural. The crystal lattice of (3) contains different neutral cobalt(II) complexes [Co(PhN2O2)2(dpt)2] (3a) and [Co(PhN2O2)2(EtOH)2] (3b). Molecules of (1)–(3) contain octahedral metal centres with all-cis-(1) and -(2) and all-trans-(3) disposal of the ligands. Intramolecular N—H...O hydrogen bonding between the NH2 groups and the O atom of the cupferronato anion can be observed in (1)–(3). Intermolecular N—H...O and N—H...N interactions between symmetry-related molecules of (1) and (2) led to hexameric aggregates which connect through common edges into a two-dimensional supramolecular network of hexagonal-grid type. In complex (3) the self-complementary dpt units of the (3a) molecules are maintained by intermolecular N—H...N hydrogen bonds, generating infinite chains. These (3a) chains are crosslinked by the (3b) subunits via N—H...O and O—H...N hydrogen bonds, thus completing the parallel two-dimensional supramolecular network consisting of pseudo-hexagonal-grid sheets. In each crystal structure the two-dimensional supramolecular networks are controlled by both hydrogen bonds and π...π stacking interactions.
Hexagonal Frank–Kasper phases interpreted as modulated crystals
Authors: Uchida Masaya , Matsui Yoshio
Published: July 2002

The structures of the hexagonal Frank–Kasper phases F and K, which have been described in terms of the aggregation of clusters, are interpreted as modulated crystal structures. They are basically composed of two close-packed layers with ordered atomic vacancies rotated by 90° to each other about their normal.
Ferroelectricity and structure in the YMnO3 family
Authors: Abrahams S. C.
Published: July 2002

The 1963 discovery of ferroelectricity in YMnO3 was accompanied by an experimental Curie temperature (T

c
) reported as 913 K; this value was revised to 1270 K in the following decade. Subsequently, YInO3 was shown to be isostructural with YMnO3 and later demonstrated to satisfy the structural criteria for ferroelectricity; recent unpublished measurements give T

c
(YInO3) = 835 (15) K. The experimental T

c
value of 913 K for YMnO3 is in satisfactory agreement with the calculated 1220 (100) K value as derived from a very recent structural refinement, the experimental T

c
of 835 (15) K for YInO3 with the calculated 760 (120) K. The full YMnO3 family includes the AMnO3 subfamily with A = Y, Ho, Er, Tm, Yb, Lu, Sc, In; the AInO3 subfamily with A = Y, Gd, Dy, Ho, Tb; and the AGaO3 subfamily with A = Y, Ho, Er. The T

c
values of six family members with known structure, in addition to YMnO3 and YInO3, have been structurally derived as 1310 (110) K for ErMnO3, 1290 (165) K for LuMnO3, 1270 (110) K for YbMnO3, 1220 (105) K for ScMnO3, 540 (375) K for InMnO3 and 1020 (100) K for YGaO3. The agreement between predicted and experimental T

c
values for ErMnO3, LuMnO3 and YbMnO3, in addition to that for YMnO3 and YInO3, leads to the confident prediction that ScMnO3, InMnO3 and YGaO3 are new ferroelectrics. The remaining six members of the full YMnO3 family are also expected to be new ferroelectrics.
Prediction of the crystal structures of perovskites using the software program SPuDS
Authors: Lufaso Michael W. , Woodward Patrick M.
Published: July 2002

The software program SPuDS has been developed to predict the crystal structures of perovskites, including those distorted by tilting of the octahedra. The user inputs the composition and SPuDS calculates the optimal structure in ten different Glazer tilt systems. This is performed by distorting the structure to minimize the global instability index, while maintaining rigid octahedra. The location of the A-site cation is chosen so as to maximize the symmetry of its coordination environment. In its current form SPuDS can handle up to four different A-site cations in the same structure, but only one octahedral ion. Structures predicted by SPuDS are compared with a number of previously determined structures to illustrate the accuracy of this approach. SPuDS is also used to examine the prospects for synthesizing new compounds in tilt systems with multiple A-site coordination geometries (a
+
a
+
a
+, a
0
b
+
b
+, a
0
b
−
c
+).
Iodo-nitroarenesulfonamides: interplay of hard and soft hydrogen bonds, I...O interactions and aromatic π...π stacking interactions
Authors: Kelly Craig J. , Skakle Janet M. S. , Wardell James L. , Wardell Solange M. S. V. , Low John N. , Glidewell Christopher
Published: July 2002

Molecules of N-(4′-iodophenylsulfonyl)-4-nitroaniline, 4-O2NC6H4NHSO2C6H4I-4′ (1), are linked by three-centre I...O2N interactions into chains and these chains are linked into a three-dimensional framework by C—H...O hydrogen bonds. In the isomeric N-(4′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4NHSO2C6H4NO2-4′ (2), the chains generated by the I...O2N interactions are again linked into a three-dimensional framework by C—H...O hydrogen bonds. Molecules of N,N-bis(3′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4N(SO2C6H4NO2-3′)2 (3), lie across twofold rotation axes in space group C2/c and they are linked into chains by paired I...O=S interactions: these chains are linked into sheets by a C—H...O hydrogen bond, and the sheets are linked into a three-dimensional framework by aromatic π...π stacking interactions. In N-(4′-iodophenylsulfonyl)-3-nitroaniline, 3-O2NC6H4NHSO2C6H4I-4′ (4), there are R^2_2(8) rings formed by hard N—H...O=S hydrogen bonds and R^2_2(24) rings formed by two-centre I...nitro interactions, which together generate a chain of fused rings: the combination of a C—H...O hydrogen bond and aromatic π...π stacking interactions links the chains into sheets. Molecules of N-(4′-iodophenylsulfonyl)-4-methyl-2-nitroaniline, 4-CH3-2-O2NC6H3NHSO2C6H4I-4′ (5), are linked by N—H...O=S and C—H...O(nitro) hydrogen bonds into a chain containing alternating R^2_2(8) and R^2_2(10) rings, but there are no I...O interactions of either type. There are two molecules in the asymmetric unit of N-(4′-iodophenylsulfonyl)-2-nitroaniline, 2-O2NC6H4NHSO2C6H4I-4′ (6), and the combination of an I...O=S interaction and a hard N—H...O(nitro) hydrogen bond links the two types of molecule to form a cyclic, centrosymmetric four-component aggregate. C—H...O hydrogen bonds link these four-molecule aggregates to form a molecular ladder. Comparisons are made with structures retrieved from the Cambridge Structural Database.
Single-crystal study of the m = 2 tubular cobalt oxide, Bi4Sr12Co8O30−δ
Authors: Perez O. , Masset A. C. , Leligny H. , Baldinozzi G. , Pelloquin D. , Dutheil M.
Published: July 2002

The structure of the m = 2 tubular compound Bi4Sr12Co8O30−δ, bismuth strontium cobalt oxide, was determined by single-crystal X-ray diffraction. This phase of orthorhombic symmetry exhibits a very strong tetragonal pseudosymmetry. The structure consists of 90°-oriented Bi2Sr2CoO6+δ slices, four Co atoms wide, forming [Sr4Co4O13]∞ pillars at their intersection. The Co atoms in these pillars form four corner-sharing CoO5 bipyramids. In the resulting [Co4O13] cluster, an anionic disorder is evidenced and discussed. Then, an accurate description of the particular structure of the pillars is given. Finally, a comparison with the Mn tubular compound Bi3.6Sr12.4Mn8O30−δ is carried out.
Crystal chemistry of zirconosilicates and their analogs: topological classification of MT frameworks and suprapolyhedral invariants
Authors: Ilyushin G. D. , Blatov V. A.
Published: July 2002

The first attempt is undertaken to consider systematically topological structures of zirconosilicates and their analogs (60 minerals and 34 synthetic phases), where the simplest structure units are MO6 octahedra and TO4 tetrahedra united by vertices ([TO4]:[MO6] = 1:1–6:1). A method of analysis and classification of mixed three-dimensional MT frameworks by topological types with coordination sequences {N

k
} is developed, which is based on the representation of crystal structure as a finite `reduced' graph. The method is optimized for the frameworks of any composition and complexity and implemented within the TOPOS3.2 program package. A procedure of hierarchical analysis of MT-framework structure organization is proposed, which is based on the concept of polyhedral microensemble (PME) being a geometrical interpretation of coordination sequences of M and T nodes. All 12 theoretically possible PMEs of MT
6 polyhedral composition are considered where T is a separate and/or connected tetrahedron. Using this methodology the MT frameworks in crystal structures of zirconosilicates and their analogs were analyzed within the first 12 coordination spheres of M and T nodes and related to 41 topological types. The structural correlations were revealed between rosenbuschite, lavenite, hiortdahlite, woehlerite, siedozerite and the minerals of the eudialyte family.
Anion packing density: a universal quantity for both dense and porous crystalline inorganic phases
Authors: Liebau F. , Küppers H.
Published: July 2002

To compare densities of inorganic high-pressure phases their molal volumes or specific gravities are usually employed, whereas for zeolites and other microporous materials the so-called framework density, FD, is applied. The definition of FD, which refers only to phases with three-dimensional tetrahedron frameworks, is extended to a `generalized framework density' d
f, which is independent of the dimensionality of the framework and the coordination number(s) of the framework cations. In this paper the anion packing density, d
ap, is introduced as a new quantity which is not only applicable to any inorganic phase but, in contrast to FD and d
f, also allows quantitative comparisons to be made for crystalline inorganic phases of any kind. The anion packing density can readily be calculated if the volume and content of the unit cell and the radii of the anions of a phase are known. From d
ap values calculated for high-pressure silica polymorphs studied under very high pressure, it is concluded that Shannon–Prewitt effective ionic radii do not sufficiently take into account the compressibility of the anions.
β Turns, water cage formation and hydrogen bonding in the structures of L-valyl-L-phenylalanine
Authors: Görbitz Carl Henrik
Published: July 2002

L-Valyl-L-phenylalanine has been crystallized as an orthorhombic dihydrate (1) in the shape of needles and as a monoclinic trihydrate (2) with Z = 16 (P21, Z′ = 8) in the shape of thin plates. Peptide molecules in these two structures occur in three basic conformations, termed c
1, c
2A and c
2B. c
2B has not been observed previously for dipeptides. Together with c
1 it forms a model pair for Type I and Type II β-turns in protein structures. The crystal packing of (2) is remarkable in that some of the L-Val side chains are exposed to the solvent region of the crystal rather than being located in a hydrophobic layer. The crystal packing thus offers a unique and detailed view of hydrogen-bond cage formation around the hydrophobic groups by the 24 cocrystallized water molecules. The eight —NH_3^+...−OOC— contacts in the structure are unusually short and the minimum N...O distance of 2.649 (5) Å represents a new extreme limit for this type of hydrogen bond in peptide structures.
Four polymorphs of a cobaloxime complex with different solid-state photoisomerization rates
Authors: Sawada K. , Hashizume D. , Sekine A. , Uekusa H. , Kato K. , Ohashi Y. , Kakinuma K. , Ohgo Y.
Published: July 2002

The complex (2-cyanoethyl)bis(dimethylglyoximato)(triphenylphosphine)cobalt(III), [Co(C4H7N2O2)2(C3H4N){P(C6H5)3}], when it was crystallized rapidly from an aqueous methanol solution, has four crystal forms, three of which were obtained separately from different solvents in large amounts. The crystal structures of the four forms were determined by X-rays. The molecular structures in the four forms have different conformations around the Co—C and Co—P bonds. The packing energy calculation indicated that the four forms have approximately the same energy. The 2-cyanoethyl group of this complex was isomerized to the 1-cyanoethyl group when the powdered sample of the complex was irradiated with a xenon lamp. For three crystal forms prepared separately, the solid-state photoisomerization rates were measured from the change in the IR spectra, assuming first-order kinetics. A quantitative relationship between the rate constant and the size of the reaction cavity for the 2-cyanoethyl group has been obtained for the three crystal forms.
Temperature dependence of structure parameters in natural magnetite: single crystal X-ray studies from 126 to 773 K
Authors: Okudera H. , Kihara K. , Matsumoto T.
Published: July 2002

Structural parameters and their thermal changes in natural magnetite, Fe3O4, have been studied using the single-crystal X-ray diffraction method in the temperature range 126–773 K. The cell dimensions, oxygen coordinate and atomic mean square displacements (m.s.d.'s) reversibly change as a function of temperature. The coordinate of oxygen remains almost constant at x = 0.2549 (1) below ~600 K, but increases with increasing temperature above this temperature. This characteristic behavior of the oxygen coordinate with temperature indicates that the cation disordering over the tetrahedral (A) and octahedral (B) cation sites occurs above 600 K. All atomic m.s.d.'s increase monotonously with temperature rise. The m.s.d.'s of the B atom show a unique temperature dependence. At lower temperatures the B atom prefers to vibrate along [111], but this preference is reduced with a temperature rise up to 630 K, above which the m.s.d. normal to [111] becomes dominant.
Investigation into the Crystal Structure of the Perovskite Lead Hafnate, PbHfO3
Authors: Corker D. L. , Glazer A. M. , Kaminsky W. , Whatmore R. W. , Dec J. , Roleder K.
Published: July 2002

The room-temperature crystal structure of the perovskite lead hafnate PbHfO3 is investigated using both low-temperature single crystal X-ray diffraction (Mo Kα radiation, λ = 0.71069 Å) and polycrystalline neutron diffraction (D1A instrument, ILL, λ = 1.90788 Å). Single crystal X-ray data at 100 K: space group Pbam, a = 5.856 (1), b = 11.729 (3), c = 8.212 (2) Å, V = 564.04 Å3 with Z = 8, μ = 97.2 mm−1, F(000) = 1424, final R = 0.038, wR = 0.045 over 439 reflections with F >1.4σ(F). Polycrystalline neutron data at 383 K: a = 5.8582 (3), b = 11.7224 (5), c = 8.2246 (3) Å, V = 564.80 Å3 with χ2 = 1.62. Although lead hafnate has been thought to be isostructural with lead zirconate, no complete structure determination has been reported, as crystal structure analysis in both these materials is not straightforward. One of the main difficulties encountered is the determination of the oxygen positions, as necessary information lies in extremely weak l = 2n + 1 X-ray reflections. To maximize the intensity of these reflections the X-ray data are collected at 100 K with unusually long scans, a procedure which had previously been found successful with lead zirconate. In order to establish that no phase transitions exist between room temperature and 100 K, and hence that the collected X-ray data are relevant to the room-temperature structure, birefringence measurements for both PbZrO3 and PbHfO3 are also reported.
Pseudoacids. I. 4- and 5-Oxoacids
Authors: Valente E. J. , Fuller J. F. , Ball J. D.
Published: July 2002

Certain 4- and 5-oxoacids may exist in their cyclic lactol (or pseudoacid) forms. These commonly occur in compounds with proximate carboxylic acid and carbonyl (aldehyde or ketone) functions for the formation of five- or six-membered rings. Examples include trans-2,3-disubstituted aliphatic, (Z)-2,3-olefinic and o-disubstituted aromatic acids. Crystal structures of compounds in these categories are reported: trans-4-methyl-3-oxo-6-hydroxytetrahydropyran-3-carboxylic acid (6), monoclinic, C2/c, a = 25.412 (5), b = 6.291 (1), c = 10.757 (2) Å, β = 104.84 (3)°; penicillic acid (7), 4-methoxy-5-hydroxy-5-(2′-propenyl)dihydrofuran-2-one, tetragonal, P42/n, a = b = 15.83 (2), c = 7.016 (11) Å; mucochloric acid (8), (Z)-3,4-dichloro-5-hydroxydihydrofuran-2-one, triclinic, P1¯, a = 6.227 (5), b = 8.085 (5), c = 12.369 (9) Å, α = 99.50 (5), β = 102.38 (6), γ = 90.29 (6)°; 2-methanoylbenzoic acid (9), 3-hydroxy-1-(3H)-isobenzofuranone, monoclinic, P21, a = 4.006 (1), b = 11.489 (2), c = 7.347 (1) Å, β = 97.50 (3)°; 2-ethanoylbenzoic acid (10), 3-hydroxy-3-methyl-1-(3H)-isobenzofuranone, orthorhombic, P212121, a = 5.199 (6), b = 9.651 (14), c = 15.950 (17) Å; 2-(2′-oxoethyl)benzoic acid (11), 3-hydroxy-3,4-dihydroisobenzopyran-1-one, monoclinic, P21/n, a = 4.651 (3), b = 11.886 (7), c = 14.312 (11) Å, β = 90.86 (6)°. These compounds also exist in the cyclic forms in chloroform solution. A trimeric cyclic trioxane structure, analogous to paracetaldehyde, is confirmed as the solid form of 5-oxopentanoic acid (1), triclinic, P1¯, a = 5.640 (4), b = 8.571 (8), c = 18.962 (13) Å, α = 78.68 (6), β = 84.34 (5), γ = 80.38 (6)°. In solution (NMR), mixtures of the open aldoacid, trimeric acid and cyclic pseudoacid exist. In both furanoid and pyranoid pseudoacids, endocyclic lactol C—O bond lengths are lengthened (1.46–1.48 Å), while the exocyclic C—O(H) bonds are shortened (1.38 Å). Pseudoacids commonly form hydrogen-bonded chains linking the lactol hydroxy and carbonyl groups, but 3-hydroxy-3,4-dihydroisobenzopyran-1-one forms distinctive hydrogen-bonded dimers.
Structure, Charge and Spin Density in Na2Ni(CN)4.3H2O at 295 and 30 K
Authors: Ptasiewicz-Bak H. , Olovsson I. , McIntyre G. J.
Published: July 2002

The earlier reported structure of the title compound, disodium tetracyanonickelate(II) trihydrate, Na2Ni(CN)4.3H2O, has been found to be incorrect and has now been redetermined. The charge distribution has been determined by multipole refinements against single-crystal X-ray diffraction data. In the refinement based on 30 K data a comparison was made between the results obtained using hydrogen positions and displacement parameters from X-ray diffraction with those using the values determined by neutron diffraction. The spin density was investigated by polarized neutron diffraction at 1.6 K. Crystal data: at T = 30 K: a = 7.278 (4), b = 8.856 (5), c = 15.131 (8) Å, α = 89.32 (5), β = 87.39 (4), γ = 83.61 (4)°; at 295 K: a = 7.392 (4), b = 8.895 (4), c = 15.115 (8)  Å, α = 89.12 (2), β = 87.46 (2), γ = 84.54 (2)°. The structure contains practically square planar Ni(CN)_4^{2-} ions, which are stacked on top of each other in almost linear chains along the a direction. The separation between the Ni(CN)_4^{2-} planes is rather large, with Ni—Ni distances around 3.7 Å. The six crystallographically independent water molecules are each coordinated to two sodium ions, approximately in the tetrahedral (lone-pair) directions, and the polarizing influence of these sodium ions also appears to be reflected in the deformation density in the lone-pair plane. The charge density based on the deformation functions of all atoms in the structure is compared with the individual densities calculated from the deformation functions of only nickel or the separate water molecules. In this way the effects of simple superposition of the individual densities have been studied. In the planar Ni(CN)_4^{2-} ion the individual deformation density of nickel is in qualitative agreement with that expected from crystal-field theory. As the repulsion from the electrons is much weaker perpendicular to the Ni(CN)_4^{2-} plane than within this plane, the deformation density is considerably larger in the perpendicular direction. However, the largest maxima in the individual deformation density around nickel are not found precisely in the planes defined by nickel and the four cyanide ligands or in the perpendicular direction just mentioned, which illustrates that it is necessary to consider the crystal field due to the whole crystalline environment.
Carbides Ln10Ru10C19 (Ln = Y, Gd–Lu): Crystal Structure of their Subcells and the Superstructures of Er10Ru10C19
Authors: Hoffmann R.-D. , Jeitschko W.
Published: July 2002

The nine new rare earth ruthenium carbides (10/10/19) were prepared by arc-melting of the elemental components and subsequent annealing at 1173 K. Guinier powder patterns show these compounds to crystallize with a very pronounced subcell, which was solved from the single-crystal X-ray diffractometer data of Er10Ru10C19, erbium ruthenium carbide: Amm2, Z = 1, R = 0.031 for 1088 structure factors and 39 variable parameters. The single-crystal film data of Er10Ru10C19 reveal several superstructures. Two of these were refined from the single-crystal diffractometer data of multiple domain crystals; one of these in the space group Cm, Z = 2, R = 0.057 for 4848 F values and 147 variables; the other in Amm2, Z = 8, R = 0.078 for 2352 F values and 171 variables. In all of these structures most of the C atoms are paired with C—C distances corresponding to double bonds. Together with the Ru atoms, these C atoms form two-dimensionally infinite layers, which are separated from each other by the Er atoms. In the third dimension the ruthenium–carbon layers are linked by single C atoms and carbon pairs. The subcell shows the superposition of these isolated and paired C atoms, whereas in the idealized superstructures these C atoms are fully ordered and their atomic environments reflect this order. Lu10Ru10C19 is a metallic conductor and Pauli-paramagnetic. The carbides Ln10Ru10C19, with Ln = Gd–Tm, show Curie–Weiss behaviour with magnetic moments corresponding to the free Ln3+ ions. The magnetic ordering temperatures are all below 35 K. Chemical bonding in these compounds can be rationalized on the basis of simple concepts assuming the octet and the 18-electron rules to be valid for the C and Ru atoms, respectively.