bluuebunny/crossref_metadata_2025 huggingface dataset:
Solving the problem of SANS instrument optimization
Authors: Margaça F. M. A. , Falcão A. N. , Salgado J. F. , Carvalho F. G.
Published: July 2002

The problem of the optimization of small-angle neutron scattering instruments installed at steady neutron sources is discussed. The optimum solution is shown to be that in which full use is made of either the available luminous area of the source or the available hall space and not necessarily that corresponding to the equal-flight-paths design. Design criteria and their implementation are discussed taking into account space constraints on the instrument's layout. It is shown that the performance of currently operating SANS facilities can be substantially improved by following the optimization procedure proposed by the authors.
The X-ray diffraction station at the ADONE wiggler facility: preliminary results (including crystal perfection)
Authors: Colapietro M. , Cappuccio G. , Marciante C. , Pifferi A. , Spagna R. , Helliwell J. R.
Published: July 2002

The single-crystal X-ray diffractometer installed at the PWA Laboratory in Frascati is described. The Huber four-circle goniometer is controlled by an IBM-compatible personal computer by means of a plug-in board interface based on the LSI chip Am9513. The program CS running under MS-DOS performs a wide variety of operations from random search to data collection. The angular resolution of the diffractometer is 0.0025°, while the instrumental resolution at 8 keV, with an Si(lll) monochromator, is 0.0026°. After preliminary tests, 2Zn insulin crystals were mounted on the diffractometer and reflections were measured using synchrotron radiation. The rocking curves show full widths at half-maxima (FWHM) in the range 0.013–0.031° mainly due to the mosaicity.
Texture in Rietveld refinement
Authors: Popa N. C.
Published: July 2002

A texture model suitable for use in Rietveld-refinement programs is proposed. It is based on the series expansion of the pole distribution function in symmetrized harmonics. The model was tested on a textured plate sample of Al2O3.
Crystal structure determination of lithium diborate hydrate, LiB2O3(OH).H2O, from X-ray powder diffraction data collected with a curved position-sensitive detector
Authors: Louër D. , Louër M. , Touboul M.
Published: July 2002

The crystal structure of lithium diborate hydrate, LiB2O3(OH).H2O, has been solved ab initio and refined by the Rietveld method from powder diffraction data collected with a curved position-sensitive detector (INEL CPS120) using Debye–Scherrer diffraction geometry with monochromatic X-rays. In the first stage the indexing of the powder pattern was performed by the successive dichotomy method from data collected with a diffractometer using Bragg–Brentano geometry. The lattice parameters are a = 9.7984 (10), b = 8.2759 (7) and c = 9.6138 (8) Å and the space group is Pnna. The structural model was obtained from direct methods and two difference Fourier maps. The Rietveld refinement converged to final crystal structure and profile indicators RF
= 0.05, RB
= 0.05, Rp
= 0.03 and Rwp
= 0.04. The structure consists of BO4 tetrahedra (T) and BO2(OH) triangles (Δ) sharing corners in order to form infinite chains along [010], with the shorthand notation 3:∞1(Δ + 2T). The particular linkage of the B3O3 rings leads to a new diborate anion {[B2O3(OH)]
n−

n
}, in which two tetrahedral B atoms have an occupation factor of 0.5. Li atoms, tetrahedrally surrounded by four O atoms, three belonging to separate chains and one to a water molecule maintain the cohesion of the structure.
Characterization of an image-plate detector used for quantitative small-angle-scattering studies
Authors: Né F. , Gazeau D. , Lambard J. , Lesieur P. , Zemb T. , Gabriel A.
Published: July 2002

This paper describes the characterization of an image-plate readout system used to calculate small-angle-scattering intensities as cross sections per unit volume. The raw data are the latent phosphorescent excitations stored on an image plate. Self-decay, self exposure, resolution, smearing, dynamic range and sensitivity are measured. Preliminary experiments show that an inexpensive neutron-imaging system can be obtained when the plates are placed behind a suitable neutron-to-X-ray converter.
Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants
Authors: Kabsch W.
Published: July 2002

An algorithm has been developed for the automatic interpretation of a given set of observed reciprocal-lattice points. It extracts a reduced cell and assigns indices to each reflection by a graph-theoretical implementation of the local indexing method. All possible symmetries of the observed lattice compatible with the metric of the reduced cell are recognized and reported, together with the unit-cell constants and the linear index transformation relating the conventional to the reduced cell. This algorithm has been incorporated into the program XDS [Kabsch (1988). J. Appl. Cryst.
21, 916–924], which is now able to process single-crystal area-detector data without prior knowledge of the symmetry and the unit-cell constants.
Time-of-Flight Texture Analysis of Limestone Standard: Dubna Results
Authors: Walther K. , Heinitz J. , Ullemeyer K. , Betzl M. , Wenk H.-R.
Published: July 2002

The pulsed reactor at the Joint Institute of Nuclear Research in Dubna, Russia, has been used to measure six pole figures of an experimentally deformed limestone sample that served as a round robin for neutron texture analysis. The time-of-flight data compare favourably with published results, both in resolution and texture information, and establish the technique as a viable alternative to more conventional methods of texture analysis.
Quantitative Analysis of Synchrotron Laue Diffraction Patterns in Macromolecular Crystallography
Authors: Ren Z. , Moffat K.
Published: July 2002

The reduction of X-ray diffraction data obtained by the Laue method to accurate integrated intensities is more complicated and much less familiar than the reduction of monochromatic data. Problems of data accuracy and completeness have hindered the wide use of the Laue technique in macromolecular crystallography. Its unique advantage, data-collection speed, has been exploited only in situations such as fast time-resolved crystallography, to which monochromatic techniques are not as well suited. This paper reviews the major problems in data reduction in the Laue technique and provides a unified solution to the problems in integration of both streaky and spatially overlapping spots and data scaling. This solution has been incorporated into a new Laue diffraction data-reduction software package, LaueView. Laue data sets from crystals of lysozyme and α-haemolysin have been processed to test this solution, and demonstrate that Laue data sets can be reduced to yield structure amplitudes of at the very least the same quality as the best monochromatic data sets in terms of both accuracy and completeness.
A computer-simulation study of the `white-line effect' in diffraction patterns of mixed charge-transfer salts
Authors: Welberry T. R. , Fox N. J.
Published: July 2002

Computer simulations have been carried out to test the theory of the origin of the `white-line effect' in diffraction patterns of some mixed charge-transfer salts put forward by Ravy, Pouget & Comés (1992) [J. Phys. I France, 2, 1173–1190]. The diffraction patterns shown confirm that the pinning of charge-density waves to defects is responsible for the effect. The magnitudes of the atomic displacements, which were assumed to be small in development of the theory, are shown to be crucial for the effect to be observed. For displacements of ~0.008 Å, the phenomena are clearly visible, but for magnitudes of only ~0.08 Å they become masked by higher-order diffraction effects.
Determination of the Space Group of Ceramic BaO.Pr2O3.4TiO2 by Electron Diffraction
Authors: Azough F. , Champness P. E. , Freer R.
Published: July 2002

Ceramic specimens of BaO.Pr203
.4TiO2 (Ba4.5Pr9Ti18O54) were prepared by the mixed-oxide route. Electron diffraction indicated that the compound has orthorhombic symmetry with cell parameters a ≃ 22.2, b ≃ 12.2 and c ≃ 7.6 Å. The space group was identified as Pnam, one of the two possible space groups previously identified for Ba3.75Ln9.5Ti18O54, where Ln = Nd, La or Sm. The fact that Pnam is a subgroup of the 2c superlattice of Pbam and the existence of antiphase domains with a displacement vector c/2 in BaO.Pr2O3
.4TiO2 suggests that it underwent a phase transition during cooling from Pbam to Pnam in which the c axis doubled.
A quantitative measure for the goodness of fit in profile refinements with more than 20 degrees of freedom
Authors: Ihringer J.
Published: July 2002

A quality indicator Nσ
is defined that exhibits immediately the significance level of the result of a least-squares refinement. For a refinement with v degrees of freedom, Nσ
= (M − ν)/(2ν)1/2 expresses the deviation of the deviance M from its expected value v in terms of its standard deviation (2ν)1/2. The deviance M is the sum of weighted squared differences between observed and model data. For any ν > 20, |Nσ
| should be as small as possible; however, it should be < 3 for a sufficiently good refinement. Thus, Nσ
is a quantitative measure for the conformity of data, their weights and the model, independent of the number of the degrees of freedom.
Two computer programs for the automatic analysis of powder diffraction patterns
Authors: Clark S. M.
Published: July 2002

Two programs for the automatic analysis of large numbers of powder diffraction patterns have been developed. The first, PEAKFIT, fits functions describing the diffraction peaks and baseline to single or multiple peaks in a number of predefined regions of each powder pattern. The second, FULFIT, fits the entire powder pattern with a combination of functions describing the diffraction peaks and background. The use of these programs is illustrated with data analysed as part of kinetic studies of the I–II phase transition in ammonium chloride and the hydration of tricalcium silicate.
Determination of Deuterium Incorporation into RNA and Protein Components of the Escherichia Coli Ribosome at Biosynthetic Deuteration by Small-Angle Neutron Scattering
Authors: Fan L. , Zgurskaya E. I. , Shcherbakova I. , Serdyuk I. N.
Published: July 2002

A simple method for the determination of deuterium incorporation into nonexchangeable (C-bonded) positions of RNA and protein components of the Escherichia coli ribosome at biosynthetic deuteration has been proposed using small-angle neutron scattering. The theory of the method is based on the joint use of two measurements: one of them is the dependence of neutron scattering intensity at zero angle on the contrast; the second is the dependence of the radius of gyration on the contrast. The main advantage of the method over the standard procedure is that it requires neither separation of the ribosome into RNA and protein components nor a subsequent time-consuming analysis of the hydrolysis products by nuclear magnetic resonance or mass spectrometry.
Partial Reversion of Small GP Zones in an Al–Zn Binary Alloy
Authors: Okuda H. , Tanaka M. , Osamura K. , Amemiya Y.
Published: July 2002

The reversion process of very small Guinier-Preston (GP) zones in Al–Zn binary alloys has been studied by time-resolved synchrotron-radiation small-angle X-ray scattering (SR-SAXS) measurements. Al–15 at.% Zn alloys with GP zones of 1.0 to 1.3 nm in radius formed by aging at 274 K were up-quenched up to 463 K. During reversion, the Guinier radius increased rapidly while the integrated intensity decreased. This rapid increase of the radius was completely different from what was found during the reversion of larger GP zones above the miscibility gap. It is concluded that a process of simultaneous dissolution and coarsening has been observed.
Two-Dimensional Small-Angle X-ray Scattering Investigation of Stretched Borosilicate Glasses
Authors: Polizzi S. , Riello P. , Fagherazzi G. , Bark M. , Borrelli N. F.
Published: July 2002

A two-dimensional fit of a suitable model for interpreting small-angle X-ray scattering (SAXS) has been shown to be a valuable tool in obtaining quantitative microstructural information. The model is based on the hypothesis that dilute ellipsoidal particles are arranged parallel to each other. The method has been applied to two glasses containing oriented particles. The investigated materials are both alkali aluminoborosilicate glasses, thermally treated and redrawn at a temperature above their softening point. The Ag(Cl, Br) crystalline droplets, formed during the preliminary thermal treatment, assume, after drawing, a cigar-like shape, oriented in the stretching direction, and give the material birefringence properties. The volumetric particle distribution has an average of 22 × 70 nm and is skewed up to length values of about 1200 nm. The composition of the solid solution, determined by X-ray diffraction (XRD), is Ag(Cl0.35, Br0.65). When the Ag(Cl, Br) particles on the surface are chemically reduced to Ag, a material with polarizing properties is obtained (PolarcorTM). For this sample, two distributions of particles have been found: one with an average of 18 x 230 nm and skewed up to 600 nm, and one, very sharp, of much shorter particles (14 × 30 nm).
ASSA, a Program for Three-Dimensional Rendering in Solution Scattering from Biopolymers
Authors: Kozin M. B. , Volkov V. V. , Svergun D. I.
Published: July 2002

A program for three-dimensional rendering and interactive model refinement, ASSA, is presented. The program permits the simultaneous display and manipulation of low-resolution envelope models obtained from solution-scattering data and the crystallographic or electron microscopic models in the Brookhaven Protein Data Bank format. ASSA is coupled with the shape-determination program of Svergun, Volkov, Kozin, Stuhrmann, Barberato & Koch [J. Appl. Cryst. (1997). 30, 000–000], thus allowing one to monitor the shape determination process in real time. The program ASSA is written in C using the PHIGS+ standard for the three-dimensional solid rendering and the XView and XLib libraries for the menu-driven user interface. The system runs on a Sun SPARC ZX-20 workstation; a simplified IBM-PC version is also available.
Triple Isotopic Substitution Method in Small-Angle Neutron Scattering: Application to Some Problems of Structural Biology
Authors: Serdyuk I. N. , Zaccaï G.
Published: July 2002

The triple isotopic substitution (TIS) method is based on the analysis of a scattering curve which is the difference between the scattering of two solutions containing appropriately deuterium-labelled particles. A necessary condition for the application of the method is that the two solutions are identical in all respects except for the extent of the deuterium label. Such an experimental scheme has allowed a number of unique physical experiments to be performed, the main ones being: (1) elimination of the contribution of the interparticle interference; (2) addition of both small- and large-sized foreign particles to those studied without distortions of the structural data; (3) highlighting of individual (quite small) regions in the molecules; (4) suppression of the dimerization contribution to the scattering curve. The application of this method is of special interest for studying the mutual three-dimensional disposition of individual small regions of molecules (3D mapping) and for investigating the geometrical properties of the surfaces of globular proteins. It is evident that TIS has a wide range of experimental possibilities, demonstrating that small-angle neutron scattering is one of the most informative structural methods for low resolution.
Structural Evolution of Ag–Co and Ag–Ni Alloys Studied by Anomalous Small-Angle X-ray Scattering
Authors: Revenant-Brizard C. , Simon J. P. , Regnard J. R. , Manzini I. , Rodmacq B.
Published: July 2002

The structural evolution of co-sputtered Ag–20 (and 35) at.% Co and Ag–20 (and 35) at.% Ni was studied by anomalous small-angle X-ray scattering in the as-deposited state and after different anneals for 10 min at 573, 623 and 723 K. Anomalous scattering was used to separate the part of the scattering signal due to the transition metal particles from the signal of other heterogeneities. Strong segregation, involving about two-thirds of the Co (or Ni) atoms, already exists for the as-deposited state. After a 573 K anneal, the phases (Ag matrix and Co or Ni well defined particles) have almost reached equilibrium,i.e.complete immiscibility. Most of the magnetic particles are three dimensional with an average radius of 5–25 Å and the average distance between the particles varies from 17 to 110 Å, depending on the magnetic element and its concentration, and on the annealing conditions. The size distribution does not correspond to that of usual coarsening, but becomes broader after extended annealing. This is probably due to heterogeneous precipitation at grain boundaries of the Ag matrix.
EXPO: a program for full powder pattern decomposition and crystal structure solution
Authors: Altomare Angela , Burla Maria Cristina , Camalli Mercedes , Carrozzini Benedetta , Cascarano Giovanni Luca , Giacovazzo Carmelo , Guagliardi Antonietta , Moliterni Anna Grazia Giuseppina , Polidori Giampiero , Rizzi Rosanna
Published: July 2002

EXPOis the integration of two programs,EXTRAandSIRPOW.92, the first devoted to full powder pattern decomposition and the second to the solution and refinement of crystal structures. The program is able to exploit the prior information obtained during the crystal structure solution process for improving the classical decomposition.EXPOalso allows preliminary cycles of Rietveld refinement.
Use of cryoprotectants in combination with immiscible oils for flash cooling macromolecular crystals
Authors: Kwong Peter D. , Liu Yee
Published: July 2002

Two standard methods have generally been used to prevent destructive ice formation when flash cooling macromolecular crystals for cryocrystallography: (i) permeating the crystal lattice with a cryoprotectant, or (ii) replacing the external liquid around the crystal with an immiscible oil. In two cases where both of the standard methods failed, we obtained satisfactory results with a two-step procedure that combined the use of immiscible oil with diffusable cryoprotectant. The procedure enabled substantially lower concentrations of cryoprotectant to be used. Since many macromolecular crystals are susceptible to high concentrations of cryoprotectant and successful flash cooling is often a trade-off between damage from ice formation and damage from cryoprotectant, this combinatory procedure may find general application.
A self-consistent method for X-ray diffraction analysis of multiaxial residual-stress fields in the near-surface region of polycrystalline materials. II. Examples
Authors: Genzel Ch. , Broda M. , Dantz D. , Reimers W.
Published: July 2002

The application of the formalism for residual-stress gradient evaluation based on the measuring principle of the scattering-vector method, which has been derived in the first paper of this series [Genzel (1999).J. Appl. Cryst.32, 770–778], is demonstrated by practical examples. Depending on the statistical scattering of the experimental data, either biaxial or even triaxial residual-stress states may be analysed; the latter case yields self-consistently the depth profiles of the in-plane stresses, σ11(τ) and σ22(τ), the normal stress component, σ33(τ), as well as the strain-free lattice spacing,d0(hkl). The results obtained by this new evaluation procedure are compared with those obtained by X-ray stress-gradient analysis performed on the basis of the sin2ψ method.
Derivation of infinite-slit-smeared small-angle scattering from porous surface and porous mass fractals
Authors: McMahon P. J. , Moss S. D.
Published: July 2002

Small-angle X-ray scattering (SAXS) is often used to study porous and aggregated fractal materials. Typically whenqis small or when large primary-beam intensities are required, the small-angle geometry employed introduces infinite-slit-height smearing into the experimental data. Herein, simple derivations for infinite-slit-height-smeared SAXS from porous surface and mass fractals are presented, including an approximation for aggregated mass fractals. The models allow rapid analysis of background-subtracted data without the need for deconvolution. An equation is derived that allows analysis of normalization from deconvolution routines applied to porous-fractal data. This model is tested using simulated and experimental SAXS data.
Comparison of the behaviour of polymers in supercritical fluids and organic solvents via small-angle neutron scattering
Authors: Melnichenko Y.B. , Kiran E. , Heath K.D. , Salaniwal S. , Cochran H.D. , Stamm M. , Van Hook W.A. , Wignall G.D.
Published: July 2002

Small-angle neutron scattering has been used to study the effect of temperature and pressure on the phase behaviour of semidilute solutions of polymers dissolved in organic and supercritical solvents. Above the theta temperature (TΘ), these systems exhibit a "good solvent" domain, where the molecules expand beyond the unperturbed dimensions in both organic solvents and in CO2. However, this transition can be made to occur at a critical "theta pressure" (PΘ) in CO2 and this represents a new concept in the physics of polymer-solvent systems. For T < TΘ, and P < PΘ, the system enters the "poor solvent" domain, where diverging concentration fluctuations prevent the chains from collapsing and allow them to maintain their unperturbed dimensions.
A tool for X-ray diffraction analysis of thin layers on substrates: substrate peak removal method
Authors: Kamminga J.-D. , Delhez R. , de Keijser Th. H. , Mittemeijer E. J.
Published: July 2002

A method is proposed that removes the substrate peaks from a diffraction pattern recorded from a substrate covered with a thin layer, using a separate measurement of the uncovered substrate. The obtained diffractogram without substrate peaks can then be used for the characterization of the microstructure of the thin layer. As an example, the method is shown to yield good results for a TiN layer deposited on a tool-steel substrate.
On the instrumental resolution in X-ray reflectivity experiments
Authors: Sentenac D. , Shalaginov A. N. , Fera A. , de Jeu W. H.
Published: July 2002

A general method to describe the instrumental resolution function for grazing-angle X-ray scattering experiments is presented. A resolution function {\scr R} is introduced as the Gaussian joint-distribution function of the (interdependent) random deviationq′ associated with the wavevector transferq. Useful expressions for the mean square values ofq′ are derived for some common scattering geometries, such as rocking scans, and scans out of the plane of incidence. The mean square values related to the incident beam dispersion and the detector acceptance angles are included in the treatment of {\scr R}. As an example, {\scr R} is incorporated in the calculation of the diffuse scattering from free-standing smectic films within the framework of the first Born approximation and the main resolution effects are discussed.
Time-resolved two-dimensional small-angle scattering of Guinier–Preston zones in Al–Ag alloys under weak shear
Authors: Okuda H. , Hiramatsu H. , Ito K. , Amemiya Y. , Osamura K.
Published: July 2002

Phase decomposition in Al-Ag single crystals under slow tensile deformation has been examined by means of in-situ synchrotron-radiation small-angle scattering. Al-1.5at%Ag single crystals were deformed at various aging temperatures, where time-resolved 2-dimensional small-angle scattering measurements were performed. In spite of a very small rate of about 10−5/s, the growth rate of Guinier-Preston zones were reduced by deformation process. During the process, no clear anisotropy of the zones related to the shear deformation was found.
Efficient evaluation of X-ray scattering integrals of Cartesian Gaussian-type functions
Authors: Barua M. , Weyrich W.
Published: July 2002

A general recurrence algorithm and explicit analytical results are given for scattering integrals with Cartesian Gaussian-type functions, in a form that is necessary for the evaluation of molecular form factors, Wigner distribution functions and Compton scattering cross sections. Overlap integrals are included as a special case.
The use of non-local constraints in maximum-entropy electron density reconstruction
Authors: Navaza J.
Published: July 2002

Different expressions of the maximum-entropy estimates of the electron density function, corresponding to different prior information are obtained. They show that no general-purpose configurational entropy of density maps exists. Some universal properties of the modellings are discussed. In particular, the meaning of super-resolution is clarified. The information of lower and upper bounds of the electron density is not in general strong enough to produce atomic maps. Atomicity is then introduced as non-local constraints and applied to the problem of phase extension using experimental data and low-resolution model phases. In all cases, the knowledge of phases up to 3.5-3 Å and observed moduli up to 1.5-1 Å allows an estimate of the electron density of roughly the same quality as the 1 Å map obtained from a Fourier summation to be produced.
New surface patches for minimal balance surfaces. II. Multiple catenoids
Authors: Koch E. , Fischer W.
Published: July 2002

Eight new families of minimal balance surfaces are described. Their surface patches belong to a new kind, called multiple catenoids. The generating circuits of such a minimal surface are two congruent concave polygons with one point of self-contact each. The new minimal balance surfaces are complementary to other minimal balance surfaces which are built up from catenoid-like surface patches and have been known before.
Enumeration of four-connected three-dimensional nets. II. Conversion of edges of three-connected 2D nets into zigzag chains
Authors: Han Shaoxu , Smith Joseph V.
Published: July 2002

Four-connected three-dimensional (3D) nets were systematically enumerated by converting some horizontal edges of a vertical stack of three-connected two-dimensional (2D) nets into vertical zigzag chains. 77 out of 131 2D nets were selected for enumeration, and different arrangements of zigzag edges and horizontal edges were investigated. This yielded 138 3D nets of which 19 are represented by known structures: cristobalite; tridymite; MAPO-39 (International Zeolite Association Structure Commission code ATN); svyatoslavite; Li-A(BW) (ABW); cancrinite (CAN); AlPO-31 (ATO); MAPO-36 (ATS); BaFe2O4; `nepheline hydrate' (JBW); bikitaite (BIK); KBGe2O6; CsAlSi5O12 (CAS); UiO-6 (OSI); Theta-1 (TON); ZSM-12 (MTW); ZSM-23 (MTT); AlPO-53C; and CIT-5 (CFI).
Theory of moiré fringes on X-ray diffraction topographs of bicrystals
Authors: Ohler Michael , Härtwig Jürgen
Published: July 2002

The theory of moiré fringes on X-ray diffraction topographs of bicrystals is derived from the dynamical theory of X-ray diffraction for the reflection (Bragg) and the transmission (Laue) case. The influence on the moiré fringes of the diffraction geometry, of the geometry of the sample, of its optical properties and of the topographic method is investigated. The perfect-crystal theory is also expanded to weakly deformed bicrystals.
Diffraction of 100 to 200 keV X-rays from an Si1−x
Ge
x
gradient crystal: comparison with results from dynamical theory
Authors: Keitel Steffen , Malgrange Cécile , Niemöller Thomas , Schneider Jochen R.
Published: July 2002

In a large Czochralski-grown Si1−x
Ge
x
(0.02 \leq x \leq 0.07) gradient crystal, diffraction patterns have been measured in symmetrical Laue geometry using synchrotron radiation in the energy range 100–200 keV. The experimental data are in very good agreement with the results from geometrical optics theory for distorted crystals, if the creation of new wavefields for strain gradients larger than a critical value is taken into account. In this sense, the crystal behaves like an ideal gradient crystal. If the normal absorption is disregarded, for reflection 111 and 100 keV energy, the full width at half-maximum values and the peak reflectivities of the diffraction patterns range from 14.6′′ and 97%, respectively, to 70.9′′ and 74%, respectively, for a variation in the Ge concentration from 3.5 to 5.3 at.%.
Selective solvent inclusion as a tool for mapping molecular properties in crystal structures: a diethylstilbestrol example
Authors: Görbitz Carl Henrik , Hersleth Hans-Petter
Published: July 2002

Useful information about hydrogen bonding, the preferred modes of hydrophobic interaction and conformational preferences of a specific molecule can be obtained from cocrystallization of the solute with a selected series of solvent molecules. This method is used in a study of nine different crystal structures of diethylstilbestrol (DES) solvates. It is shown that solvent inclusion results not only in stronger hydrogen bonds, but usually also in a larger number of favorable C—H...π interactions between DES molecules. Furthermore, solvent molecules such as DMSO, DMF, acetonitrile and acetone demonstrate important hydrogen-bond donating properties in addition to their more familiar role as hydrogen-bond acceptors. Molecular conformations in the crystal structures compare favorably with results from molecular mechanics calculations.
Conformational transformation coupled with the order–disorder phase transition in 2-methyl-1,3-cyclohexanedione crystals. Erratum
Authors: Katrusiak Andrzej
Published: July 2002

In the recently published article by Katrusiak (2000) a misprint occurred in the name of one of the authors in a reference (Wąsicki et al., 1995) in the final printing stage. The correct spelling of the name is Wąsicki.
Structures of furanosides: geometrical analysis of low-temperature X-ray and neutron crystal structures of five crystalline methyl pentofuranosides
Authors: Evdokimov Artem , Gilboa A. Joseph , Koetzle Thomas F. , Klooster Wim T. , Schultz Arthur J. , Mason Sax A. , Albinati Alberto , Frolow Felix
Published: July 2002

Crystal structures of all five crystalline methyl D-pentofuranosides, methyl α-D-arabinofuranoside (1), methyl β-D-arabinofuranoside (2), methyl α-D-lyxofuranoside (3), methyl β-D-ribofuranoside (4) and methyl α-D-xylofuranoside (5) have been determined by means of cryogenic X-ray and neutron crystallography. The neutron diffraction experiments provide accurate, unbiased H-atom positions which are especially important because of the critical role of hydrogen bonding in these systems. This paper summarizes the geometrical and conformational parameters of the structures of all five crystalline methyl pentofuranosides, several of them reported here for the first time. The methyl pentofuranoside structures are compared with the structures of the five crystalline methyl hexopyranosides for which accurate X-ray and neutron structures have been determined. Unlike the methyl hexopyranosides, which crystallize exclusively in the C
1 chair conformation, the five crystalline methyl pentofuranosides represent a very wide range of ring conformations.
Salts of 3,5-dinitrobenzoic acid with organic diamines: hydrogen-bonded supramolecular structures in one, two and three dimensions
Authors: Burchell Colin J. , Glidewell Christopher , Lough Alan J. , Ferguson George
Published: July 2002

The trigonally trisubstituted carboxylic acid 3,5-dinitrobenzoic acid, (O2N)2C6H3COOH, forms 2:1 salts with a range of organic diamines L, with the general composition [LH2]2+·[{(O2N)2C6H3COO}−]2. When L is a bis-tertiary amine the hard N—H...O hydrogen bonds generate finite three-component aggregates, anion...cation...anion, and these aggregates are further linked by soft C—H...O hydrogen bonds to form one-dimensional molecular ladders when L is N,N,N′,N′′-tetramethyl-1,2-diaminoethane and chains of rings when L is 4,4′-dipyridylethane or 4,4′-dipyridylethene; two-dimensional sheets are formed when L is 1,4-diazabicyclo[2.2.2]octane and a three-dimensional framework is formed when L is N,N′-dimethylpiperazine. When L is the bis-secondary amine piperazine, the hard N—H...O and soft C—H...O hydrogen bonds each generate continuous motifs in the form of distinct chains of rings, the combination of which generates sheets, while when L is the bis-primary amine 1,2-diaminoethane the hard N—H...O hydrogen bonds alone generate a three-dimensional framework.
Neutron diffraction study of φ-Bi8Pb5O17: structure refinement and analysis of cationic ordering
Authors: Righi Lara , Calestani Gianluca , Gemmi Mauro , Migliori Andrea , Bettinelli Marco
Published: July 2002

The triclinic crystal structure of the φ phase in the structure of the Bi2O3–PbO phase diagram has been recently solved by the synergetic use of electron and X-ray diffraction on a polycrystalline Bi8Pb5O17 sample. In the present work the problem is re-examined on the basis of powder neutron diffraction data: the structure has been confirmed and refined by the Rietveld method. The increased accuracy of the O-atom positions allowed the study of the cationic ordering in this structure by means of bond-valence calculations and charge distribution analysis. The results, confirmed by the refinement of the site occupancies, indicate that the structure is ordered to a large extent, with Bi and Pb atoms occupying preferentially different lattice sites. In this frame, the φ phase being the most ordered one in the considered region of the Bi2O3–PbO phase diagram, it should represent the thermodynamically stable low-temperature polymorph.
Dipyrimidine–copper(II) dinitrate complexes showing magnetic interactions
Authors: Yasui Masanori , Ishikawa Yoshimitsu , Akiyama Naoya , Ishida Takayuki , Nogami Takashi , Iwasaki Fujiko
Published: July 2002

Crystals of CuII(NO3)2(pm)3 (1), and two crystalline forms of CuII(NO3)2(H2O)2(pm)2, (2) and (3), showed ferromagnetic, antiferromagnetic and paramagnetic interactions at extremely low temperatures, respectively. Crystal structure analyses revealed that the complexes were catena-dinitrato[μ-pyrimidine-κN
1:κN
3]-(pyrimidine-N
1)copper(II), [Cu(NO3)2(pm)2]
n
, catena-diaquadinitrato[μ-pyrimidine-κN
1:κN
3]copper(II), [Cu(NO3)2(H2O)2(pm)]
n
, and diaquadinitratodipyrimidinecopper(II), Cu(NO3)2(H2O)2(pm)2 for (1), (2) and (3), respectively. In (1) the Cu atom is coordinated by the two nitrates and N atoms of the non-bridging pyrimidine and bridging pyrimidine to form a one-dimensional coordination polymer. The complex is a five-coordinated square pyramid and can be regarded as a pseudo-seven-coordinated complex, since other short non-bonding Cu...O contacts are observed. In the crystals of (2) the pyrimidine bridges the Cu atoms to form a one-dimensional coordination chain. On the other hand, complex (3) is not a coordination polymer. It is important to form a coordination polymer for the appearance of the magnetic interactions. Types of coordination of the bridging organic moieties should also play an important role in magnetic properties. Magnetic measurements of (1) and (2) show that they are good examples of uniform S = 1/2 ferro- and antiferromagnetic Heisenberg chains with exchange parameters 2J/kB = +1.8 and −36 K, respectively.
Basic forms of supramolecular self-assembly organized by parallel and antiparallel hydrogen bonds in the racemic crystal structures of six disubstituted and trisubstituted cyclopentane derivatives
Authors: Kálmán Alajos , Argay Gyula , Fábián László , Bernáth Gábor , Fülöp Ferenc
Published: July 2002

A selection of stereoisomeric 2-hydroxy-1-cyclopentanecarboxamides, a 4-tert-butyl derivative and three tert-butyl derivatives of the respective carboxylic acid were subjected to X-ray crystallography. The optically active molecules (I)–(VI) form racemic crystals. Each racemic structure is basically determined by two intermolecular hydrogen bonds of O—H...O=C—XH and O=C—X—H...OH types (X = O, NH). The partially similar patterns of close packing observed reflect five basic forms of supramolecular self-assembly. In the racemic crystals of chiral molecules, there are homo- and heterochiral chains of molecules formed by the principal (O—H...O=C) hydrogen bonds. These chains assemble either in a parallel or antiparallel mode. The parallel homochiral chains (hop) observed in structure (II), (1R*,2R*)-2-hydroxy-1-cyclopentanecarboxamide, demand the polar space group Pca21, while the parallel heterochiral chains (hep) are organized in antiparallel layers with space group P21/n in structure (VI), (1R*,2S*,5R*-5-tert-butyl-2-hydroxy-1-cyclopentanecarboxylic acid). Heterochiral chains in an antiparallel array (hea) are found in (I), (1R*,2S*)-2-hydroxy-1-cyclopentanecarboxamide, and (V) [(1R*,2S*4S*)-4-tert-butyl-2-hydroxy-1-cyclopentanecarboxylic acid, space group P21/c]. Structures (IV), (1R*,2S*,4R*)-4-tert-butyl-2-hydroxy-1-cyclopentanecarboxylic acid, and (III), (1R*,2R*,4S*)-4-tert-butyl-2-hydroxy-1-cyclopentanecarboxamide, reveal that homochiral chains in an antiparallel array (hoa; cross-linked by heterochiral dimers held together by the second hydrogen bonds) can be formed by either translation (space group P\bar 1) or a screw axis (space group P21/c). These alternatives are denoted hoa1 and hoa2. Similarly, within each pattern (hea, hep and hop) two slightly different alternatives can be expected. The partial similarities in the identified five patterns of hydrogen bonding are described by graph-set notations. Structures (I), (IV) and (V) can be characterized by a common supramolecular synthon, while the highest degree of similarity is shown by the isostructurality of (I) and (V).
Self-association and stereochemistry study of 2-methylthio-, 2-dimethylaminocyclohexanone oximes and the parent cyclohexanone oxime
Authors: Olivato Paulo R. , Ribeiro Douglas S. , Zukerman-Schpector J. , Bombieri Gabriella
Published: July 2002

X-ray diffraction analyses of 2-substituted cyclohexanone oximes C5H9(X)C=NOH [X = SMe (1), NMe2 (2)] and of the parent compound [X = H (3)] showed that their cyclohexyl rings are in a slightly distorted chair conformation. These compounds assume in the solid state the (E) configuration bearing the 2-substituents in the axial conformation. Compounds (1) and (2) exist as dimeric and polymeric hydrogen-bond associates, respectively. Low-temperature X-ray analysis of the cyclohexanone oxime (3) showed that the molecules are associated forming two independent trimers. The dimer in (1) and the trimer in (3) are built up via [O—H...N=C] hydrogen bonds, while the polymer of (2) is via the [OH...NMe2] hydrogen bond. The comparative IR νOH and νC=N analysis of the title compounds, in the solid state and in CCl4 solution, fully supports the nature of the associates for (1)–(3) obtained by X-ray diffraction. The IR azomethyne frequency shift analysis (ΔνC=N) also suggests the occurrence of the πC=N/σ*C—X
orbital interaction which stabilizes the axial conformations of (1) and (2).
Perchlorophenalenyl radical, C13Cl9: a modulated structure with nine threefold-symmetric molecules in the asymmetric unit
Authors: Koutentis P. A. , Haddon R. C. , Oakley R. T. , Cordes A. W. , Brock C. P.
Published: July 2002

The odd-alternant perchlorophenalenyl radical, C13Cl9, forms molecular stacks centered on crystallographic threefold rotation axes, but the spacing within the stacks (3.78 Å) is too large to allow good overlap of the orbitals in which the spin density is localized. The radical is ruffled because of the intramolecular repulsions between α Cl atoms (the Cl...Cl peri interactions); the average displacement of an α Cl atom from the molecular plane is ∼0.7 Å. The deviations from molecular planarity do not, however, determine the spacing within the stacks, which is determined instead by interactions between stacks. The modulations found in the P3c1 superstructure are a response to the short interstack contacts that would occur in the average pseudocell structure (R\bar 3m, c′ = c/6). The primary modulation is a pattern of enantiomeric alternation; a secondary modulation involves small rotations of the molecules around their threefold axes. The number (9) of independent molecules in the true cell is exceptionally large because of the conflict between the preference within the molecular stacks for threefold rotational symmetry and the preference in directions perpendicular to the stack axes for twofold alternation of enantiomers. The structural complexity reduces the precision of the distances and angles determined, but the average values found are in excellent agreement with those calculated by density functional theory.
Structural relationships between cations and alloys; an equivalence between oxidation and pressure
Authors: Vegas Angel , Jansen Martin
Published: July 2002

More than 100 examples are provided of the structural identity between the cation arrays in oxides and their corresponding alloys (binary compounds). Halides and halogenates, sulfides and sulfites and/or sulfates, selenides and selenates, phosphides and phosphates show this behaviour. In some cases, the structure of the cation subarray corresponds to the structure of the alloy at ambient conditions, but in other cases, cations stabilize structures which correspond to those of the high-pressure phases of the alloy, from which an analogy between the insertion of oxygen and the application of pressure can be established. In this last case, the oxides show polymorphism with temperature and when heated, the structure of the ambient pressure of the alloy is recovered as if heating would compensate the effect of pressure. From the results reported here, it is concluded that cations do not seem to be either the isolated entities, predicted by the ionic model, which occupy interstices of an oxygen matrix, or they arrange in a more or less arbitrary way, but they try to reproduce the structure of their corresponding alloy. Many of the phase transitions and the polymorphism exhibited by the oxides described here are better explained when they are considered as formed by previous entities which are the alloys. Oxides should be considered as `real stuffed alloys'. These features do not seem to be casual, but they obey a general principle: Cations recognize themselves in spite of being embedded in an oxygen bulk. The nature and the physical meaning of this recognition are problems which remain unsolved.
Two phases of C9H12O4: why is the structure at 295 K so complicated?
Authors: Duncan Laura L. , Patrick Brian O. , Brock Carolyn Pratt
Published: July 2002

Molecules of 4,4′-dimethyl-2-hydroxy-6-oxocyclohexene-1-carboxylic acid, C9H12O4, crystallize at 295 K in a modulated superstructure with five half-molecules in the asymmetric unit; each molecule is located on one of the mirror planes of the space group Cmc21. Reflections with k ≠ 5n are systematically weak; a satisfactory refinement can be obtained in a Cmcm pseudocell having b′ = b/5. The important modulation involves small rotations of the molecules around axes perpendicular to the mirror plane; there is also an up/down disorder of the CMe2 fragment in four of the five molecules (two molecules with occupancy factors ca 4:1; two with occupancy factors ca 3:2). The modulation is a response to packing problems that can be traced to the differences between the thin, electron- and oxygen-rich `head' of the molecule and the thicker, methyl-rich `tail'. At 130 K the length of b is reduced by 2/5 and the Pmnb structure is ordered. Both structures can be described as modulated variants of the Cmcm substructure; the wavevectors are 2b′*/5 for the room-temperature structure and b′*/2 for the low-temperature structure, where b′* is the reciprocal axis of the subcell. The structure at room temperature can also be understood as a hybrid of the fully disordered pseudocell structure and the ordered structure that is found at low temperature.
Chiral versus racemic building blocks in supramolecular chemistry: malate salts of organic diamines
Authors: Farrell Dorcas M. M. , Ferguson George , Lough Alan J. , Glidewell Christopher
Published: July 2002

(S)-Malic acid forms a salt with N,N′-dimethylpiperazine, [MeN(CH2CH2)2NMe]H2
2+·2C4H5O5
− (1) (triclinic, P1, Z′ = 1), in which the cations link pairs of hydrogen-bonded anion chains to form a molecular ladder. With 4,4′-bipyridyl, (S)-malic acid forms a 1:1 adduct which crystallizes from methanol to yield two polymorphs, (2) (triclinic, P1, Z′ = 1) and (3) (monoclinic, C2, Z′ = 1), while racemic malic acid with 4,4′-bipyridyl also forms a 1:1 adduct, (4) (monoclinic, P21/c, Z′ = 1). In each of (2), (3) and (4) the components are linked by O—H...N and N—H...O into chains of alternating bipyridyl and malate units, which are linked into sheets by O—H...O hydrogen bonds. In each of the 1:1 adducts (5) and (6), formed by, respectively, (S)-malic acid and racemic malic acid with 1,2-bis(4′-pyridyl)ethene, the diamine is disordered over two sets of sites, related by a 180° rotation about the N...N vector. In (5), (C12H10N2)H+·C4H5O5
− (triclinic, P1, Z′ = 1), the components are again linked by a combination of N—H...O and O—H...O hydrogen bonds into sheets, while in (6) (triclinic, P{\overline 1}, Z′ = 0.5) there is only partial transfer of the H atom from O to N and the malate component is disordered across a centre of inversion. With 1,4-diazabicyclo[2.2.2]octane, racemic malic acid forms a 1:2 salt, [(C6H12N2)H2]2+·2C4H5O5
− (7) (monoclinic, P21/c, Z′ = 2), while (S)-malic acid forms a 1:1 adduct, (8) (monoclinic, P21, Z′ = 3). There are thus six independent molecular components in each. In (7) the ions are linked by an extensive series of N—H...O and O—H...O hydrogen bonds into a three-dimensional framework, but in (8) there is extensive disorder involving all six components, and no refinement proved to be feasible.
Structural investigations of phosphorus–nitrogen compounds. 4. Steric and electronic effects in dibenzylamino derivatives of hexachlorocyclotriphosphazatriene and 4,4,6,6-tetrachloro-2,2-diphenylcyclotriphosphazatriene
Authors: Beşli Serap , Coles Simon J. , Davies David B. , Hursthouse Michael B. , Kılıç Adem , Mayer Thomas A. , Shaw Robert A. , Uslu Aylin
Published: July 2002

A systematic study is presented on the products of aminolysis of N3P3Cl6 (1) and N3P3Ph2Cl4 (4) with dibenzylamine. Two series of mono- and disubstituted derivatives of compounds (1) and (4), namely N3P3Cl5[N(CH2Ph)2] (2) and N3P3Cl4[N(CH2Ph)2]2 (3) and N3P3Ph2Cl3[N(CH2Ph)2] (5) and N3P3Ph2Cl2[N(CH2Ph)2]2 (6) [where (2), (3), (5) and (6) are new structures], are investigated in order to determine whether steric or electronic effects prevail in the formation of dibenzylamino-substituted cyclophosphazenes. The influence of an electron-releasing group (i.e. phenyl) on the stereochemistry and degree of substitution of the product is analysed by comparison of the above two series. The difference in unsymmetrically substituted endocyclic P—N bond lengths, Δ, is used as a measure of the degree of the electronic contribution, in combination with basicity constants, to quantify the degree of the electron-releasing capacity of the R group. In order to compare geminal versus non-geminal substitution, a difunctional secondary amine was used to form the compound N3P3Cl4[NMe(CH2)3NMe] (7) (a reinvestigation) for inclusion in this study. It is shown that electron-releasing groups have a greater effect on the lengthening of P—Cl bonds as opposed to endocyclic P—N bonds and that this effect is greater in the non-geminal PRCl case than for geminal PCl2. However, steric effects are shown to be dominant in the reactions of dibenzylamine with N3P3 derivatives, with a disposition to a trans stereochemistry in bisdibenzylamino derivatives.