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  • International Union of Crystallography (IUCr)
  • 2010-2014  (32)
  • 1965-1969  (2,736)
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  • 1
    Publication Date: 2014-04-08
    Description: Human carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the hydration and dehydration of CO2 and HCO3−, respectively. The reaction follows a ping-pong mechanism, in which the rate-limiting step is the transfer of a proton from the zinc-bound solvent (OH−/H2O) in/out of the active site via His64, which is widely believed to be the proton-shuttling residue. The decreased catalytic activity (∼20-fold lower with respect to the wild type) of a variant of CA II in which His64 is replaced with Ala (H64A CA II) can be enhanced by exogenous proton donors/acceptors, usually derivatives of imidazoles and pyridines, to almost the wild-type level. X-ray crystal structures of H64A CA II in complex with four imidazole derivatives (imidazole, 1-methylimidazole, 2-methylimidazole and 4-methylimidazole) have been determined and reveal multiple binding sites. Two of these imidazole binding sites have been identified that mimic the positions of the `in' and `out' rotamers of His64 in wild-type CA II, while another directly inhibits catalysis by displacing the zinc-bound solvent. The data presented here not only corroborate the importance of the imidazole side chain of His64 in proton transfer during CA catalysis, but also provide a complete structural understanding of the mechanism by which imidazoles enhance (and inhibit when used at higher concentrations) the activity of H64A CA II.
    Keywords: human carbonic anhydraseH64Aactivity enhancementrescueactivationimidazole
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 2
    Publication Date: 2014-04-08
    Description: Phosphatases function in the production, transport and recycling of inorganic phosphorus, which is crucial for cellular metabolism and bioenergetics, as well as in bacterial killing, since they are able to generate reactive oxygen species via Fenton chemistry. Diphosphonucleotide phosphatase/phosphodiesterase (PPD1), a glycoprotein plant purple acid phosphatase (PAP) from yellow lupin seeds, contains a bimetallic Fe–Mn catalytic site which is most active at acidic pH. Unlike other plant PAPs, PPD1 cleaves the pyrophosphate bond in diphosphonucleotides and the phosphodiester bond in various phosphodiesters. The homohexameric organization of PPD1, as revealed by a 1.65 Å resolution crystal structure and confirmed by solution X-ray scattering, is unique among plant PAPs, for which only homodimers have previously been reported. A phosphate anion is bound in a bidentate fashion at the active site, bridging the Fe and Mn atoms in a binding mode similar to that previously reported for sweet potato PAP, which suggests that common features occur in their catalytic mechanisms. The N-terminal domain of PPD1 has an unexpected and unique fibronectin type III-like fold that is absent in other plant PAPs. Here, the in vitro DNA-cleavage activity of PPD1 is demonstrated and it is proposed that the fibronectin III-like domain, which `overhangs' the active site, is involved in DNA selectivity, binding and activation. The degradation of DNA by PPD1 implies a role for PPD1 in plant growth and repair and in pathogen defence.
    Keywords: purple acid phosphatasediphosphonucleotide phosphatasephosphodiesterasePPD1bimetallic Fe–Mnfibronectin type III domaincrystal structureSAXS
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 3
    Publication Date: 2014-04-08
    Description: Acemetacin (ACM) is a non-steroidal anti-inflammatory drug (NSAID), which causes reduced gastric damage compared with indomethacin. However, acemetacin has a tendency to form a less soluble hydrate in the aqueous medium. We noted difficulties in the preparation of cocrystals and salts of acemetacin by mechanochemical methods, because this drug tends to form a hydrate during any kind of solution-based processing. With the objective to discover a solid form of acemetacin that is stable in the aqueous medium, binary adducts were prepared by the melt method to avoid hydration. The coformers/salt formers reported are pyridine carboxamides [nicotinamide (NAM), isonicotinamide (INA), and picolinamide (PAM)], caprolactam (CPR), p-aminobenzoic acid (PABA), and piperazine (PPZ). The structures of an ACM–INA cocrystal and a binary adduct ACM–PABA were solved using single-crystal X-ray diffraction. Other ACM cocrystals, ACM–PAM and ACM–CPR, and the piperazine salt ACM–PPZ were solved from high-resolution powder X-ray diffraction data. The ACM–INA cocrystal is sustained by the acid...pyridine heterosynthon and N—H...O catemer hydrogen bonds involving the amide group. The acid...amide heterosynthon is present in the ACM–PAM cocrystal, while ACM–CPR contains carboxamide dimers of caprolactam along with acid–carbonyl (ACM) hydrogen bonds. The cocrystals ACM–INA, ACM–PAM and ACM–CPR are three-dimensional isostructural. The carboxyl...carboxyl synthon in ACM–PABA posed difficulty in assigning the position of the H atom, which may indicate proton disorder. In terms of stability, the salts were found to be relatively stable in pH 7 buffer medium over 24 h, but the cocrystals dissociated to give ACM hydrate during the same time period. The ACM–PPZ salt and ACM–nicotinamide cocrystal dissolve five times faster than the stable hydrate form, whereas the ACM–PABA adduct has 2.5 times faster dissolution rate. The pharmaceutically acceptable piperazine salt of acemetacin exhibits superior stability, faster dissolution rate and is able to overcome the hydration tendency of the reference drug.
    Keywords: cocrystalhydratemelt crystallizationpiperazinepowder X-ray diffractionstructure determination from powder data (SDPD)
    Electronic ISSN: 2052-2525
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  • 4
    Publication Date: 2014-04-08
    Description: Crystal structure determinations of biological macromolecules are limited by the availability of sufficiently sized crystals and by the fact that crystal quality deteriorates during data collection owing to radiation damage. Exploiting a micrometre-sized X-ray beam, high-precision diffractometry and shutterless data acquisition with a pixel-array detector, a strategy for collecting data from many micrometre-sized crystals presented to an X-ray beam in a vitrified suspension is demonstrated. By combining diffraction data from 80 Trypanosoma brucei procathepsin B crystals with an average volume of 9 µm3, a complete data set to 3.0 Å resolution has been assembled. The data allowed the refinement of a structural model that is consistent with that previously obtained using free-electron laser radiation, providing mutual validation. Further improvements of the serial synchrotron crystallography technique and its combination with serial femtosecond crystallography are discussed that may allow the determination of high-resolution structures of micrometre-sized crystals.
    Keywords: protein microcrystallographyserial crystallographyin vivo grown microcrystals
    Electronic ISSN: 2052-2525
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  • 5
    Publication Date: 2014-04-08
    Description: X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.
    Keywords: two-dimensional protein crystalfemtosecond crystallographysingle layer X-ray diffractionmembrane protein
    Electronic ISSN: 2052-2525
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  • 6
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-04-08
    Keywords: biological crystallographyeditorialIUCrJ
    Electronic ISSN: 2052-2525
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  • 7
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-04-08
    Keywords: protein microcrystallographyserial crystallographyin vivo-grown microcrystals
    Electronic ISSN: 2052-2525
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  • 8
    Publication Date: 2014-04-08
    Description: The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals, such as 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole [Paul, Kubicki, Jelsch et al. (2011). Acta Cryst. B67, 365–378], it may not be sufficient for a correct description of the charge-density distribution. Multipole refinement using harmonic atom vibrations does not lead to the best electron density model in this case and the so-called `shashlik-like' pattern of positive and negative residual electron density peaks is observed in the vicinity of some atoms. This slight disorder, which cannot be modelled by split atoms, was solved using third-order anharmonic nuclear motion (ANM) parameters. Multipole refinement of the experimental high-resolution X-ray diffraction data of 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole at three different temperatures (10, 35 and 70 K) and a series of powder diffraction experiments (20 ≤ T ≤ 300 K) were performed to relate this anharmonicity observed for several light atoms (N atoms of amino and nitro groups, and O atoms of nitro groups) to an isomorphic phase transition reflected by a change in the b cell parameter around 65 K. The observed disorder may result from the coexistence of domains of two phases over a large temperature range, as shown by low-temperature powder diffraction.
    Keywords: anharmonicityisomorphic phase transitionexperimental charge densityX-ray closed-circuit helium cryostatHansen–Coppens modelmultiple-temperature powder diffraction
    Electronic ISSN: 2052-2525
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  • 9
    Publication Date: 2014-04-08
    Description: The partitioning of space with Hirshfeld surfaces enables the analysis of fingerprint molecular interactions in crystalline environments. This study uses the decomposition of the crystal contact surface between pairs of interacting chemical species to derive an enrichment ratio. This quantity enables the analysis of the propensity of chemical species to form intermolecular interactions with themselves and other species. The enrichment ratio is obtained by comparing the actual contacts in the crystal with those computed as if all types of contacts had the same probability to form. The enrichments and contact tendencies were analyzed in several families of compounds, based on chemical composition and aromatic character. As expected, the polar contacts of the type H...N, H...O and H...S, which are generally hydrogen bonds, show enrichment values larger than unity. O...O and N...N contacts are impoverished while H...H interactions display enrichment ratios which are generally close to unity or slightly lower. In aromatic compounds, C...C contacts can display large enrichment ratios due to extensive π...π stacking in the crystal packings of heterocyclic compounds. C...C contacts are, however, less enriched in pure (C,H) hydrocarbons as π...π stacking is not so favourable from the electrostatic point of view compared with heterocycles. C...H contacts are favoured in (C,H) aromatics, but these interactions occur less in compounds containing O, N or S as some H atoms are then involved in hydrogen bonds. The study also highlights the fact that hydrogen is a prefered interaction partner for fluorine.
    Keywords: enrichment ratioHirshfeld surface analysiscrystal packingfingerprint plots
    Electronic ISSN: 2052-2525
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  • 10
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Keywords: Editorialchemical crystallographycrystal engineering
    Electronic ISSN: 2052-2525
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  • 11
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: The crystallographic structure solution of nucleotides and nucleotide complexes is now commonplace. The resulting electron-density maps are often poorer than for proteins, and as a result interpretation in terms of an atomic model can require significant effort, particularly in the case of large structures. While model building can be performed automatically, as with proteins, the process is time-consuming, taking minutes to days depending on the software and the size of the structure. A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software, with extended chain fragments built around the current view position in a fraction of a second. The speed of the method arises from the determination of the `fingerprint' of the sugar and phosphate groups in terms of conserved high-density and low-density features, coupled with a highly efficient scoring algorithm. Use cases include the rapid evaluation of an initial electron-density map, addition of nucleotide fragments to prebuilt protein structures, and in favourable cases the completion of the structure while automated model-building software is still running. The method has been incorporated into the Coot software package.
    Keywords: nucleic acid chain tracingCoot
    Electronic ISSN: 2052-2525
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  • 12
    Publication Date: 2014-11-12
    Description: Accurate structural models of reaction centres in zeolite catalysts are a prerequisite for mechanistic studies and further improvements to the catalytic performance. The Rietveld/maximum entropy method is applied to synchrotron powder X-ray diffraction data on fully dehydrated CHA-type zeolites with and without loading of catalytically active Cu2+ for the selective catalytic reduction of NOx with NH3. The method identifies the known Cu2+ sites in the six-membered ring and a not previously observed site in the eight-membered ring. The sum of the refined Cu occupancies for these two sites matches the chemical analysis and thus all the Cu is accounted for. It is furthermore shown that approximately 80% of the Cu2+ is located in the new 8-ring site for an industrially relevant CHA zeolite with Si/Al = 15.5 and Cu/Al = 0.45. Density functional theory calculations are used to corroborate the positions and identity of the two Cu sites, leading to the most complete structural description of dehydrated silicoaluminate CHA loaded with catalytically active Cu2+ cations.
    Keywords: CHA zeolitescatalytic activitylocation of Cu2+synchrotron powder X-ray diffractionRietveld/maximum entropy method
    Electronic ISSN: 2052-2525
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  • 13
    Publication Date: 2014-11-12
    Description: Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in diffraction patterns. However, if the Bravais symmetry is higher than the space-group symmetry, there will be multiple indexing options that are geometrically equivalent, and hence many ways to merge diffraction intensities from protein nanocrystals. Structure factor magnitudes from full reflections are required to resolve this ambiguity but only partial reflections are available from each XFEL shot, which must be merged to obtain full reflections from these `stills'. To resolve this chicken-and-egg problem, an expectation maximization algorithm is described that iteratively constructs a model from the intensities recorded in the diffraction patterns as the indexing ambiguity is being resolved. The reconstructed model is then used to guide the resolution of the indexing ambiguity as feedback for the next iteration. Using both simulated and experimental data collected at an X-ray laser for photosystem I in the P63 space group (which supports a merohedral twinning indexing ambiguity), the method is validated.
    Keywords: indexing ambiguityserial femtosecond crystallography (SFX)XFELsprotein crystallographyexpectation maximization algorithm
    Electronic ISSN: 2052-2525
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  • 14
    Publication Date: 2014-11-12
    Description: The time evolution of the electron density and the resulting time dependence of Fourier components of the X-ray polarizability of a crystal irradiated by highly intense femtosecond pulses of an X-ray free-electron laser (XFEL) is investigated theoretically on the basis of rate equations for bound electrons and the Boltzmann equation for the kinetics of the unbound electron gas. The photoionization, Auger process, electron-impact ionization, electron–electron scattering and three-body recombination have been implemented in the system of rate equations. An algorithm for the numerical solution of the rate equations was simplified by incorporating analytical expressions for the cross sections of all the electron configurations in ions within the framework of the effective charge model. Using this approach, the time dependence of the inner shell populations during the time of XFEL pulse propagation through the crystal was evaluated for photon energies between 4 and 12 keV and a pulse width of 40 fs considering a flux of 1012 photons pulse−1 (focusing on a spot size of ∼1 µm). This flux corresponds to a fluence ranging between 0.8 and 2.4 mJ µm−2. The time evolution of the X-ray polarizability caused by the change of the atomic scattering factor during the pulse propagation is numerically analyzed for the case of a silicon crystal. The time-integrated polarizability drops dramatically if the fluence of the X-ray pulse exceeds 1.6 mJ µm−2.
    Keywords: femtosecond pulseX-ray diffractionpolarizabilityelectron densityrate equations
    Electronic ISSN: 2052-2525
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  • 15
    Publication Date: 2014-11-12
    Description: Melting of native tapioca starch granules in aqueous pastes upon heating is observed in situ using simultaneous small- and wide-angle X-ray scattering (SAXS/WAXS) and solution viscometry. Correlated structure and viscosity changes suggest closely associated amylose and amylopectin chains in the semicrystalline layers, and the release of amylose chains for enhanced solution viscosity occurs largely after melting of the semicrystalline structure. Before melting, WAXS results reveal mixed crystals of A- and B-types (∼4:1 by weight), whereas SAXS results indicate that the semicrystalline layers are composed of lamellar blocklets of ca 43 nm domain size, with polydisperse crystalline (≃7.5 nm) and amorphous (≃1.1 nm) layers alternatively assembled into a lamellar spacing of ≃8.6 nm with 20% polydispersity. Upon melting, the semicrystalline lamellae disintegrate into disperse and molten amylopectin nanoclusters with dissolved and partially untangled amylose chains in the aqueous matrix which leads to increased solution viscosity. During subsequent cooling, gelation starts at around 347 K; successively increased solution viscosity coincides with the development of nanocluster aggregation to a fractal dimension ≃2.3 at 303 K, signifying increasing intercluster association through collapsed amylose chains owing to decreased solvency of the aqueous medium with decreasing temperature.
    Keywords: tapioca starch granulesgelatinizationgelationSAXS/WAXSviscosity
    Electronic ISSN: 2052-2525
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  • 16
    Publication Date: 2014-11-12
    Description: Molecular self-assembly of nylon-12 rods in self-organized nanoporous alumina cylinders with two different diameters (65 and 300 nm) is studied with transmission electron microscopy (TEM) and wide-angle X-ray diffraction (WAXD) in symmetrical reflection mode. In a rod with a 300 nm diameter, the tendency of the hydrogen-bonding direction of a γ-form crystal parallel to the long axis of the rod is not clear because of weak two-dimensional confinement. In a rod with a diameter of 65 nm, the tendency of the hydrogen-bonding direction of a γ-form crystal parallel to the long axis of the rod is more distinct because of strong two-dimensional confinement. For the first time, selected-area electron diffraction (SAED) is applied in a transmission electron microscope to a polymer nanorod in order to determine the hydrogen-bond sheet and lamellar orientations. Results of TEM–SAED and WAXD showed that the crystals within the rod possess the γ-form of nylon-12 and that the b axis (stem axis) of the γ-form crystals is perpendicular to the long axis of the rod. These results revealed that only lamellae with 〈h0l〉 directions are able to grow inside the nanopores and the growth of lamellae with 〈hkl〉 (k ≠ 0) directions is stopped owing to impingements against the cylinder walls. The dominant crystal growth direction of the 65 nm rod in stronger two-dimensional confinement is in between the [−201] and [001] directions due to the development of a hydrogen-bonded sheet restricted along the long axis of the rod.
    Keywords: molecular self-assemblynanorodsselected-area electron diffractioncylindrical confinement
    Electronic ISSN: 2052-2525
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  • 17
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: For more than 30 years X-ray crystallography has been by far the most powerful approach for determining the structures of viruses and viral proteins at atomic resolution. The information provided by these structures, which covers many important aspects of the viral life cycle such as cell-receptor recognition, viral entry, nucleic acid transfer and genome replication, has extensively enriched our vision of the virus world. Many of the structures available correspond to potential targets for antiviral drugs against important human pathogens. This article provides an overview of the current knowledge of different structural aspects of the above-mentioned processes.
    Keywords: bacteriophagesgenome deliveryfusion proteinsRNA-dependent RNA polymerasesviral proteasesviral receptorsviruses
    Electronic ISSN: 2052-2525
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  • 18
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug–receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug–receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
    Keywords: charge-density researchmedicinal chemistrydrug designinvariomHansen–Coppens multipole modelquantum theory of atoms in molecules
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  • 19
    Publication Date: 2014-11-12
    Description: Metastable phases are often used to design materials with outstanding properties, which cannot be achieved with thermodynamically stable compounds. In many cases, the metastable phases are employed as precursors for controlled formation of nanocomposites. This contribution shows how the microstructure of crystalline metastable phases and the formation of nanocomposites can be concluded from X-ray diffraction experiments by taking advantage of the high sensitivity of X-ray diffraction to macroscopic and microscopic lattice deformations and to the dependence of the lattice deformations on the crystallographic direction. The lattice deformations were determined from the positions and from the widths of the diffraction lines, the dependence of the lattice deformations on the crystallographic direction from the anisotropy of the line shift and the line broadening. As an example of the metastable system, the supersaturated solid solution of titanium nitride and aluminium nitride was investigated, which was prepared in the form of thin films by using cathodic arc evaporation of titanium and aluminium in a nitrogen atmosphere. The microstructure of the (Ti,Al)N samples under study was tailored by modifying the [Al]/[Ti] ratio in the thin films and the surface mobility of the deposited species.
    Keywords: metastable thin filmsmicrostructureX-ray diffraction
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  • 20
    Publication Date: 2014-11-12
    Description: Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer–monomer interface is more extensive than that at the dimer–dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.
    Keywords: transthyretinamyloid assemblyneutron crystallographydeuteration
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  • 21
    Publication Date: 2014-11-12
    Description: The Mars Science Laboratory landed in Gale crater on Mars in August 2012, and the Curiosity rover then began field studies on its drive toward Mount Sharp, a central peak made of ancient sediments. CheMin is one of ten instruments on or inside the rover, all designed to provide detailed information on the rocks, soils and atmosphere in this region. CheMin is a miniaturized X-ray diffraction/X-ray fluorescence (XRD/XRF) instrument that uses transmission geometry with an energy-discriminating CCD detector. CheMin uses onboard standards for XRD and XRF calibration, and beryl:quartz mixtures constitute the primary XRD standards. Four samples have been analysed by CheMin, namely a soil sample, two samples drilled from mudstones and a sample drilled from a sandstone. Rietveld and full-pattern analysis of the XRD data reveal a complex mineralogy, with contributions from parent igneous rocks, amorphous components and several minerals relating to aqueous alteration. In particular, the mudstone samples all contain one or more phyllosilicates consistent with alteration in liquid water. In addition to quantitative mineralogy, Rietveld refinements also provide unit-cell parameters for the major phases, which can be used to infer the chemical compositions of individual minerals and, by difference, the composition of the amorphous component.
    Keywords: X-ray diffractionMarsextraterrestrial mineralogyCuriosity rover
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  • 22
    Publication Date: 2014-11-12
    Description: Small- and wide-angle X-ray scattering (SAXS, WAXS) are standard tools in materials research. The simultaneous measurement of SAXS and WAXS data in time-resolved studies has gained popularity due to the complementary information obtained. Furthermore, the combination of these data with non X-ray based techniques, via either simultaneous or independent measurements, has advanced understanding of the driving forces that lead to the structures and morphologies of materials, which in turn give rise to their properties. The simultaneous measurement of different data regimes and types, using either X-rays or neutrons, and the desire to control parameters that initiate and control structural changes have led to greater demands on sample environments. Examples of developments in technique combinations and sample environment design are discussed, together with a brief speculation about promising future developments.
    Keywords: SAXSWAXSSANScomplementary techniquessample environment
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  • 23
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: Membranes are amongst the most important biological structures; they maintain the fundamental integrity of cells, compartmentalize regions within them and play an active role in a wide range of cellular processes. Pressure can play a key role in probing the structure and dynamics of membrane assemblies, and is also critical to the biology and adaptation of deep-sea organisms. This article presents an overview of the effect of pressure on the mesostructure of lipid membranes, bilayer organization and lipid–protein assemblies. It also summarizes recent developments in high-pressure structural instrumentation suitable for experiments on membranes.
    Keywords: biological membraneslipidsbilayerslipid–protein assemblieshigh-pressure studies
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  • 24
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: Most properties of nanocrystalline materials are shape-dependent, providing their exquisite tunability in optical, mechanical, electronic and catalytic properties. An example of the former is localized surface plasmon resonance (LSPR), the coherent oscillation of conduction electrons in metals that can be excited by the electric field of light; this resonance frequency is highly dependent on both the size and shape of a nanocrystal. An example of the latter is the marked difference in catalytic activity observed for different Pd nanoparticles. Such examples highlight the importance of particle shape in nanocrystalline materials and their practical applications. However, one may ask `how are nanoshapes created?', `how does the shape relate to the atomic packing and crystallography of the material?', `how can we control and characterize the external shape and crystal structure of such small nanocrystals?'. This feature article aims to give the reader an overview of important techniques, concepts and recent advances related to these questions. Nucleation, growth and how seed crystallography influences the final synthesis product are discussed, followed by shape prediction models based on seed crystallography and thermodynamic or kinetic parameters. The crystallographic implications of epitaxy and orientation in multilayered, core-shell nanoparticles are overviewed, and, finally, the development and implications of novel, spatially resolved analysis tools are discussed.
    Keywords: nanocrystalline materialsplasmonicsshape prediction models
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  • 25
    Publication Date: 2014-11-12
    Description: Membrane fusion is essential for human health, playing a vital role in processes as diverse as neurotransmission and blood glucose control. Two protein families are key: (1) the Sec1p/Munc18 (SM) and (2) the soluble N-ethylmaleimide-sensitive attachment protein receptor (SNARE) proteins. Whilst the essential nature of these proteins is irrefutable, their exact regulatory roles in membrane fusion remain controversial. In particular, whether SM proteins promote and/or inhibit the SNARE-complex formation required for membrane fusion is not resolved. Crystal structures of SM proteins alone and in complex with their cognate SNARE proteins have provided some insight, however, these structures lack the transmembrane spanning regions of the SNARE proteins and may not accurately reflect the native state. Here, we review the literature surrounding the regulatory role of mammalian Munc18 SM proteins required for exocytosis in eukaryotes. Our analysis suggests that the conflicting roles reported for these SM proteins may reflect differences in experimental design. SNARE proteins appear to require C-terminal immobilization or anchoring, for example through a transmembrane domain, to form a functional fusion complex in the presence of Munc18 proteins.
    Keywords: SM proteinsSNARE proteinssyntaxinMunc18membrane trafficking
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 26
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: The biological solution small-angle X-ray scattering (BioSAXS) field has undergone tremendous development over recent decades. This means that increasingly complex biological questions can be addressed by the method. An intricate synergy between advances in hardware and software development, data collection and evaluation strategies and implementations that readily allow integration with complementary techniques result in significant results and a rapidly growing user community with ever increasing ambitions. Here, a review of these developments, by including a selection of novel BioSAXS methodologies and recent results, is given.
    Keywords: biological solution small-angle X-ray scattering (BioSAXS)synchrotron radiationbeamlinesstructural complexitybiostructural research
    Electronic ISSN: 2052-2525
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  • 27
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: The study of single-crystal diffuse scattering (SCDS) goes back almost to the beginnings of X-ray crystallography. Because SCDS arises from two-body correlations, it contains information about local (short-range) ordering in the sample, information which is often crucial in the attempt to relate structure to function. This review discusses the state of the field, including detectors and data collection and the modelling of SCDS using Monte Carlo and ab initio techniques. High-quality, three-dimensional volumes of SCDS data can now be collected at synchrotron light sources, allowing ever more detailed and quantitative analyses to be undertaken, and opening the way to approaches such as three-dimensional pair distribution function studies (3D-PDF) and automated refinement of a disorder model, powerful techniques that require large volumes of low-noise data.
    Keywords: single-crystal diffuse scatteringdisordersynchrotron light sources
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 28
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: The smart specialization declared in the European program Horizon 2020, and the increasing cooperation between research and development found in companies and researchers at universities and research institutions have created a new paradigm where many calls for proposals require participation and funding from public and private entities. This has created a unique opportunity for large-scale facilities, such as synchrotron research laboratories, to participate in and support applied research programs. Scientific staff at synchrotron facilities have developed many advanced tools that make optimal use of the characteristics of the light generated by the storage ring. These tools have been exceptionally valuable for materials characterization including X-ray absorption spectroscopy, diffraction, tomography and scattering, and have been key in solving many research and development issues. Progress in optics and detectors, as well as a large effort put into the improvement of data analysis codes, have resulted in the development of reliable and reproducible procedures for materials characterization. Research with photons has contributed to the development of a wide variety of products such as plastics, cosmetics, chemicals, building materials, packaging materials and pharma. In this review, a few examples are highlighted of successful cooperation leading to solutions of a variety of industrial technological problems which have been exploited by industry including lessons learned from the Science Link project, supported by the European Commission, as a new approach to increase the number of commercial users at large-scale research infrastructures.
    Keywords: X-ray techniquesindustryinnovation
    Electronic ISSN: 2052-2525
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  • 29
    Publication Date: 2014-11-12
    Description: Iron(II) and 2-oxoglutarate (2OG)-dependent dioxygenases involved in histone and DNA/RNA demethylation convert the cosubstrate 2OG and oxygen to succinate and carbon dioxide, resulting in hydroxylation of the methyl group of the substrates and subsequent demethylation. Recent evidence has shown that these 2OG dioxygenases play vital roles in a variety of biological processes, including transcriptional regulation and gene expression. In this review, the structure and function of these dioxygenases in histone and nucleic acid demethylation will be discussed. Given the important roles of these 2OG dioxygenases, detailed analysis and comparison of the 2OG dioxygenases will guide the design of target-specific small-molecule chemical probes and inhibitors.
    Keywords: dioxygenaseshistone demethylationDNA/RNA demethylationN6-methyladenosineALKBH5
    Electronic ISSN: 2052-2525
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  • 30
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: Worldwide research activity at the nanoscale is triggering the appearance of new, and frequently surprising, materials properties in which the increasing importance of surface and interface effects plays a fundamental role. This opens further possibilities in the development of new multifunctional materials with tuned physical properties that do not arise together at the bulk scale. Unfortunately, the standard methods currently available for solving the atomic structure of bulk crystals fail for nanomaterials due to nanoscale effects (very small crystallite sizes, large surface-to-volume ratio, near-surface relaxation, local lattice distortions etc.). As a consequence, a critical reexamination of the available local-structure characterization methods is needed. This work discusses the real possibilities and limits of X-ray absorption spectroscopy (XAS) analysis at the nanoscale. To this end, the present state of the art for the interpretation of extended X-ray absorption fine structure (EXAFS) is described, including an advanced approach based on the use of classical molecular dynamics and its application to nickel oxide nanoparticles. The limits and possibilities of X-ray absorption near-edge spectroscopy (XANES) to determine several effects associated with the nanocrystalline nature of materials are discussed in connection with the development of ZnO-based dilute magnetic semiconductors (DMSs) and iron oxide nanoparticles.
    Keywords: EXAFSXANESoxide nanomaterialsnanocrystalline materials
    Electronic ISSN: 2052-2525
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  • 31
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: The community of material scientists is strongly committed to the research area of multiferroic materials, both for the understanding of the complex mechanisms supporting the multiferroism and for the fabrication of new compounds, potentially suitable for technological applications. The use of high pressure is a powerful tool in synthesizing new multiferroic, in particular magneto-electric phases, where the pressure stabilization of otherwise unstable perovskite-based structural distortions may lead to promising novel metastable compounds. The in situ investigation of the high-pressure behavior of multiferroic materials has provided insight into the complex interplay between magnetic and electronic properties and the coupling to structural instabilities.
    Keywords: high pressuremultiferroicsmaterials science
    Electronic ISSN: 2052-2525
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  • 32
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: Metal–organic frameworks (MOFs) are one of the most intensely studied material types in recent times. Their networks, resulting from the formation of strong bonds between inorganic and organic building units, offer unparalled chemical diversity and pore environments of growing complexity. Therefore, advances in single-crystal X-ray diffraction equipment and techniques are required to characterize materials with increasingly larger surface areas, and more complex linkers. In addition, whilst structure solution from powder diffraction data is possible, the area is much less populated and we detail the current efforts going on here. We also review the growing number of reports on diffraction under non-ambient conditions, including the response of MOF structures to very high pressures. Such experiments are important due to the expected presence of stresses in proposed applications of MOFs – evidence suggesting rich and complex behaviour. Given the entwined and inseparable nature of their structure, properties and applications, it is essential that the field of structural elucidation is able to continue growing and advancing, so as not to provide a rate-limiting step on characterization of their properties and incorporation into devices and applications. This review has been prepared with this in mind.
    Keywords: MOFsnon-ambient crystallographycrystal growth
    Electronic ISSN: 2052-2525
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  • 33
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 119-128 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The theoretical basis and the experimental procedures of the Pendellösung method are described. Structure factors |Fg| can be determined on the absolute scale by measuring the fringe spacing Λg on the diffraction topographs and the angles involved in a geometrical factor Φg. The experimental results so far obtained on Si, Ge and α-quartz are briefly reviewed in comparison with the results obtained by other methods. Effects of absorption and of lattice distortions are estimated to be of about 0.1%. The errors in measuring Λg are less than 0.1% in favourable cases. At present, the accuracy in |Fg| is limited by the difficulty in determining Φg accurately. It is about 1%. The ratio of structure factors can be determined with an accuracy of about 0.1% by taking the ratio of the fringe spacings. The following examples are described: (i) |Fhk, l|/|Fhk,_{{\bar l}}| of a α-quartz, (ii) the ratio of |Fg| of Si at low and room temperatures and (iii) |Fg|/|F0| of Si. Through the experiment (ii), the increase of the Debye temperature at low temperatures (∼ 40°K) was confirmed. In experiment (iii), the Pendellösung fringes and X-ray interferometry fringes are used, whose spacings are proportional to |Fg| and |F0|, respectively. Since |F0| is essentially the total charge Z in the unit cell, the |Fg| value determined by this method is the truly absolute value.
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  • 34
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 129-134 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In order to obtain accurate data on structure factors from electron diffraction data, it is necessary to take into account the inevitable n-beam dynamical diffraction effects. The comparison of intensity values from detailed computer calculations with observed intensities from perfect crystals is reviewed for the cases of convergent beam diffraction patterns from MgO crystals of uniform thickness and of dark-field images of wedge-shaped crystals of silicon. An analysis of the sources of error in each case suggests that it may be possible to derive structure factor values with an accuracy of better than one per cent. The method, recently proposed by Watanabe et al. [Acta Cryst. (1968). A24, 249] for deriving structure factors from the values of accelerating voltages for which some Kikuchi lines disappear, is reviewed and possible sources of error are examined.
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  • 35
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 140-142 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The problem of estimating the extinction factor by use of polarized X-rays has been re-examined in the light of the theory of X-ray diffraction in real crystals developed recently by Zachariasen. Expressions are given for deriving the extinction-free structure factors in terms of the observed integrated intensities for perpendicular and parallel polarizations. A simple attachment to a diffractometer for analysing the polarization of the diffracted beam is described. Measurements on quartz are presented; the extinction-free structure factors so obtained are in excellent agreement with Zachariasen's calculated values based on new f curves.
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  • 36
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 276-276 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 37
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 302-303 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A precise X-ray determination of the lattice constants of ruthenium dioxide, RuO2, has been made in the temperature range 30° to 702°C using a Unicam 19 cm high-temperature powder camera. It has been observed that the c parameter decreases with increasing temperature as in the case of FeF2 and CrO2 which also have a ruffle-type structure.
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  • 38
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 329-331 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: It is shown that the real one-dimensional irreducible representations of a crystallographic point group induce the magnetic symmetry groups associated with the point group and also give the number of independent non-vanishing constants required to describe any magnetic property for the induced magnetic symmetry groups.
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  • 39
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 335-338 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A new method of correction of X-ray powder diffraction line profiles by deconvolution is being developed. The convolution equation, representing the phenomenon of deformation of a true diffraction line profile, is approached with the help of a quadrature formula by a system of linear equations. The bad conditioning of this system has led to the use of a stabilization method enabling one to obtain a result converging to the true solution which satisfies the physical phenomenon. The quadrature formulae which are used are described. This method has been programmed in Fortran II for the IBM 1620.
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  • 40
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 484-486 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The contribution of the thermal diffuse scattering to the measured X-ray intensities of cubic powder patterns is calculated without making the approximation that T ≥ Θ. Correction curves are given which are valid at all temperatures.
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  • 41
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 493-493 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 42
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 400-400 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 43
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 407-411 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The X-ray a-axis Laue photographs of single crystals of cadmium iodide grown from solution sometimes show closed rings of various shapes, viz. hexagonal, trigonal, etc. and of various sizes, corresponding to each X-ray reflection. They have been satisfactory explained in terms of the formation of more than two tilt boundaries of dislocations during crystal growth. The boundaries result from a vertical alignment of triple nodes of dislocations created by simultaneous slip along close-packed directions. In most cases the slip is confined to the basal planes and occurs at regular intervals.
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  • 44
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 427-434 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Expressions which enable data to be `corrected' for twinning are examined. If the volume ratio of the twin individuals is known, structure factors may be calculated and used in the normal way. Particular care must, however, be taken with weighting. For least-squares refinement or for comparing observed and calculated intensities, overlapped data can be used directly in the normal Kennicott procedure which initially requires a knowledge of the volume ratio, but can refine it. Alternatively the data can be modified in such a way that calculations are independent of the volume ratio. All three methods have been successfully applied to overlapped data from Para Red (1-p-nitrobenzeneazo-2-naphthol).
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  • 45
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 455-459 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: It is argued that magnetic structures are likely to be found which will most fruitfully be explained with the aid of non-crystallographic magnetic point groups. The point groups are classified into families of `halving subgroups' and it is shown diagrammatically, with the aid of representation theory, how non-crystallographic Shubnikov groups can be constructed.
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  • 46
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 165-173 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Objective estimation of the error (σFmeas) in each structure factor (Fmeas), by a procedure such as that outlined in Acta Cryst. (1964). 17, 1327, allows the indicator \cal uα = [Σ (Δ2Fmeas/σ2Fmeas) ÷ χ2m − n,α]1/2 to be evaluated, where ΔFmeas = |Fmeas| − |Fcalc|, χ2m − n,α is given by the χ2 distribution at the α-significance level, and the model for which ΣΔ2Fmeas is minimized contains m independent Fmeas and n variables. The sensitivity of \cal uα to errors in Fmeas is examined under both real and hypothetical conditions. For the real case, the range in \cal u0.01 for eight recently measured inorganic crystals indicates the average minimum residual error in σFmeas to be about 1%, the maximum error to be about 21%. The hypothetical case is considered by propagating several types of error to a set of 772 independent Fmeas corresponding to a model consisting of 10 independent atoms undergoing isotropic thermal vibration. The indicator \cal u0.01 detects a systematic intensity error at a level in which the maximum intensity error in 97% of the data reaches 5%. Long term drift in the experiment is indicated with considerable sensitivity by \cal u0.01. Systematic error as a function of scattering angle is detectable only if the σFmeas contain a component due to the suspected error.
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  • 47
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 180-186 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The excellent agreement often obtained in least-squares refinement of X-ray data with the free-atom form factor model suggests that deviations from sphericity are small. However, the resulting parameters are affected by bonding effects to a small but significant extent. In the present paper, errors in Fcalc are defined as differences between the free-atom structure factors calculated with the true atomic parameters and those which would be obtained from an exact description of the electron density. An experimental measure of these errors can be obtained from the parameters determined independently by neutron diffraction. The structure factor errors for s-triazine and α-deutero-oxalic acid dideuterate are analysed and contrasted with errors in form factors resulting from neglect of overlap density, prepared state and orbital contraction. The theoretical curves indicate that deviations from the free-atom model persist at values of sin θ/λ larger than 0.6 Å−1. Improved models for molecular scattering based on valence bond and molecular orbital theories respectively, are discussed. The importance of errors in neutron scattering lengths is demonstrated by least-squares refinements of α-deutero-oxalic acid with various values of bD. Good agreement between Fobs and Fcalc is obtained at the expense of systematic deviations in the deuteron temperature factors. Finally a summary is given of the errors in X-ray parameters obtained by least-squares adjustment with the free-atom model.
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  • 48
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 194-206 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A number of crystal structures have been precisely analyzed by both X-ray and neutron diffraction. Comparison between the results can lead to some understanding of the type and magnitude of error present in one or both methods. We discuss here the nature of systematic error in crystallographic experiments and in crystal structure refinement models. Statistical methods are presented for testing the significance of the difference between the parameters derived in two crystallographic experiments. These methods are applied to existing neutron and X-ray diffraction data on oxalic acid dihydrate, hydroxyapatite, s-triazine, potassium hydrogen diaspirinate and methylglyoxal bisguanylhydrazone. These tests show that there are strong systematic differences in thermal parameters for heavy atoms and in all parameters for hydrogen atoms. Differences in positional parameters for heavy atoms are marginal. The pattern of results strongly suggests that the differences between neutron and X-ray experiments have some physical bases rather than being due entirely to systematic error in one or both experiments. The results may also be interpreted as indicating that both position parameters and root-mean-square amplitudes of vibration may with care be determined to a precision of 0.001 Å in structures with a moderate number of atoms in the asymmetric unit.
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  • 49
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 640-640 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 50
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 642-642 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 51
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 304-305 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The measured structure factors for KCl at 300°K, including corrections due to the thermal diffuse scattering and dispersion, are given. The absolute scale of the structure factors has been obtained by a direct intensity measurement of the primary X-ray beam with use of both Cu Kα and Mo Kα radiation. The Debye–Waller factors and the ionic radii derived from the measured structure factors are 2.08 ± 0.05 Å2, 2.06 ± 0.05 Å2, 1.45 ± 0.07 Å and 1.70 ± 0.07 Å for K+ and Cl−, respectively. The calculations of the radial coefficients of the cubic harmonic expansion for K+ and Cl− indicate that these ions are almost exactly spherically symmetric.
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  • 52
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 319-329 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The first order thermal diffuse scattering contribution to integrated Bragg scattering intensities for monatomic, crystalline lattices has been analytically evaluated. Parallel arguments for evaluation of the integrated Bragg intensity and the integrated thermal diffuse scattering intensity are developed for a general diffractometer intensity scan. The resulting general expressions are reduced to a simplified form for several situations. In particular, the two standard integrated intensity scans, an ω-scan and an ω/2θ-scan, are considered. Comparison is made between the results of this calculation and previously published calculations, as well as with recently published experimental measurements of thermal diffuse scattering effects. The variation of the thermal diffuse scattering contributions to the measured intensity is discussed through consideration of a dimensionless parameter, which is independent of both temperature and the diffracting material. This parameter depends only on the experimental constants relating to the intensity measurement and is examined as a function of the detection window size, the scan width and type, and the diffraction angle. It is found, for the situations considered, that the ratio of the thermal diffuse scattering to the Bragg scattering tends to show a pronounced maximum in the intermediate-high angle region (60 ° ≲ 0 ≲ 80 °).
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  • 53
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 642-642 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 54
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 650-658 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Using Takagi's theory of X-ray diffraction by a perfect crystal and the general theory of differential equations, a solution of Takagi's equations is given in the form of a linear combination of two unit vectors of the vectorial space formed by the solutions of these equations. The amplitude distribution inside the crystal is then the sum of two terms, each term being the convolution of a function depending on the amplitude distribution on the incident surface and one of the two principal solutions of Takagi's equation which are Hankel functions of the first and second kind, H1o and H2o. This gives an extension of the notion of wavefields since this calculation can be done for any kind of incident wave on the entrance surface. It is shown that these two `generalized wavefields' present anomalous absorption. In the case of an incident plane wave or an incident spherical wave, these `generalized wavefields' become identical with the usual wavefields of the dynamical theory.
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  • 55
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 714-715 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An accurate neutron diffraction study of a nickel powder sample has been carried out at three different wavelengths. Excellent agreement was found between the data obtained at the various wavelengths and a least-squares refinement gave a value for the Debye–Waller temperature factor, BNi, of 0.426 (± 0.009) Å2 at room temperature (295°K).
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    Acta crystallographica 25 (1969), S. 718-718 
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    Acta crystallographica 25 (1969), S. 395-396 
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    Notes: An expression is obtained for the spherically averaged acoustic phonon polarization and velocity factor found in theories of 1-phonon thermal diffuse scattering that is valid for all real cubic crystals and easy to evaluate numerically. A comparison with the usual approximate form shows appreciable discrepancies for very anisotropic materials.
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    Acta crystallographica 25 (1969), S. 397-398 
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    Acta crystallographica 25 (1969), S. 399-399 
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    Acta crystallographica 25 (1969), S. 716-717 
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    Notes: Certain commonly used data-rejection procedures can cause specific patterns of prominent spurious peaks and holes in electron density maps.
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    Acta crystallographica 25 (1969), S. 719-731 
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    Acta crystallographica 25 (1969), S. 526-530 
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    Notes: An extension of Bertaut's macroscopic theory of magnetic and magnetoelectric couplings is presented. The components of electric and magnetic moments and the stress tensor are classified according to the irreducible representations of the crystal's magnetic group; couplings are possible only within a representation.
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    Acta crystallographica 25 (1969), S. 547-550 
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    Notes: A new method for obtaining the resolution function for a triple-axis neutron spectrometer is described, involving a combination of direct measurement and analytical calculation. All factors which contribute to the finite resolution of the instrument may be taken into account, and Gaussian or experimentally determined probability distributions may be used. The application to the study of the dispersion relation for excitations in a crystal is outlined.
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    Acta crystallographica 25 (1969), S. 551-552 
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    Notes: Probability trees and difference equations relating adjacent layers are given for C and CC faults in h.c.p. crystals and H faults in f.c.c. crystals.
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    Acta crystallographica 25 (1969), S. 588-588 
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    Acta crystallographica 25 (1969), S. 588-588 
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    Acta crystallographica 25 (1969), S. 595-602 
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    Notes: Transmission Kikuchi line patterns from wedge-shaped crystals of natural spinel have been studied. Especially near line intersections, extensive contrast anomalies attributable to multiple-beam interactions were observed, such as enhanced and diminished line segments, split lines and line segments which can not be indexed as ordinary Kikuchi lines. Several effects sometimes combine to form extensive patterns related to the Kikuchi envelope. The observed patterns are compared with calculated line contrast using several interacting beams. Most of the effects can be explained through three interacting beams; hence, three-beam effects in Kikuchi patterns are discussed in some detail. General rules for the dependence of contrast anomalies on signs and sizes of the Fourier potentials are derived. It is pointed out that, because of the wide range of diffraction conditions recorded in one exposure and the elimination of thickness-dependent oscillations, Kikuchi patterns give a very useful picture of the angular extent of the most important dynamic interactions. Applications of the results in connection with other diffraction techniques are discussed.
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    Acta crystallographica 25 (1969), S. 631-633 
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    Notes: Small single crystals of zinc of 99.99% purity were grown from the vapour at a temperature slightly less than the melting point. The dislocation structure of these crystallites was studied by thermal etching, which occurs when the crystals are cooled from the growth temperature to 10 to 15°C below the melting point in a few minutes. Various types of etch figures were observed and the mechanisms of their formation are discussed. It seems, on the basis of the available evidence, that the etch figures correspond to dislocations.
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    Acta crystallographica 25 (1969), S. 641-641 
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    Acta crystallographica 25 (1969), S. 643-650 
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    Notes: X-ray diffraction patterns from a polycrystalline material or a small distorted crystal do not always contain enough information for the determination of the (average) geometry and the degree of distortion of the crystal(s). To avoid the consequent difficulties in the interpretation of diffraction patterns from such small distorted crystals the author introduces for the material the average lattice function \cal P(x), that is, a repartition function. When the diffraction spots from the material can be measured separately, the \cal P(x) function belonging to that material has certain special properties. For that case the average coherently scattering region can be defined in terms of \cal P(x). It is shown that the intensity distribution in such a diffraction spot can be described with the aid of the product of C(x) and φ (x, Δx), where C(x) is the average form function of the coherently scattering regions, φ (xm, Δx), the special value of φ (x, Δx), is one peak of the quasiperiodic function \cal P(x) around the mth lattice point, xm, of the average lattice. The vector x represents the distance between two arbitrary unit cells in the structure; Δx = x−xm. Consequently the line profiles in a powder diffraction pattern can be described with the aid of C(t). φ(tm, L), the product of the projections of C(x) and φ (xm, Δx) on the perpendicular to the reflecting planes; L, t and tm are the projections of Δx, x and xm respectively. It is shown that the condition φ(tm, L) = 0 for |L| ≥ ½d (d is the interplanar spacing) holds when the diffraction lines can be measured separately. A criterion for the applicability of the Warren-Averbach method is given.
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    Acta crystallographica 25 (1969), S. 682-693 
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    Notes: The X-ray scattering amplitude of a crystal containing isolated imperfections is expressed in terms of the Fourier transform of the atomic displacement vectors. The amplitude contains only the local properties of the imperfections which are `seen' by the incident beam of a finite size. Disruption of the Borrmann transmitted (or diffracted) beam, narrowing of the dynamical diffraction range and `diffuse' scattering caused by dynamically diffracted X-rays are some of the results obtained from the calculated amplitude. Black, white and black-white images in topographs are explained by the present theory. Image contrast is also discussed in terms of the thickness of the crystal.
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    Acta crystallographica 25 (1969), S. 388-388 
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    Notes: Attention is drawn to phase relations of reflexions in tetragonal space groups missing from International Tables for X-ray Crystallography.
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    Acta crystallographica 25 (1969), S. 1-3 
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    Acta crystallographica 25 (1969), S. 12-29 
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    Notes: The practical significance of accurate structure factors F(S) is discussed and illustrated in terms of different sorts of detailed structural information that becomes accessible when accurate estimates of F(S) are available and analysed appropriately. The common and contrasting features of X-ray and neutron F(S) (of non-magnetic systems) are considered. Structure factor formalism is reviewed to show the simplifications that are implicit in the formalism normally adopted for operational data-treatment. Limitations in the normal formalism introduced by the `spherical atom' approximation and the Gaussian ellipsoid harmonic rectilinear vibration approximation are shown with reference to the generalized formalism which avoids these constraints. The use of the generalized formalism for studying electron distribution aspects of covalent bonding in diamond structures and anharmonic aspects of anionic motions in fluorite structures is considered in detail. The difficulties of making reliable judgements on the probable real accuracy of F(S)-estimates by referring them to `spherical atom' models are illustrated in terms of different sets of F(S) data reported for MgO. The results of applying a variety of such models to the various data sets are discussed. The limitations of conventional Gaussian vibration formalism for extended studies (by either X-rays or neutrons, or both) of organic systems possessing appreciable librational behaviour are illustrated in terms of the generalized (neutron) formalism of F(S) that is needed to take a proper account of libration in cubic hexamethylenetetramine (HMT). It is shown that limitations of the conventional formalism are such that no simple `libration correction' is strictly applicable to the atomic positional parameters of HMT as determined viathe normal structure factor formalism.
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    Acta crystallographica 25 (1969), S. 173-180 
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    Notes: Specimen-dependent properties of real crystals which influence the accuracy of intensity measurement are size, shape, homogeneity, stability and environment. Variations of any of these will affect the corrections necessary to allow for absorption and extinction in a given experimental measurement; these in turn will affect the evaluation of the absolute intensity, and the two principal tests for internal and external consistency, namely variation within any form {hkl}, and variation of mean values I{hkl} between different specimens. They may also affect the relative values of I{hkl} within one data set, leading for example to spurious anharmonicity in the temperature factors derived for an ellipsoidal crystal. Examples of practical solutions of actual problems involve waxes instead of glues for crystal mounting, miniature films or intensifying screens for use in unstable situations or with very small crystals, integrated oscillation photographs for intensity measurements from poor specimens, rotation photographs for high symmetry crystals, the use of Laue photographs for the detection of order-disorder phenomena, and the incorporation of an iron-55 source in an automated diffractometer to provide an internal standard for intensity measurements.
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    Acta crystallographica 25 (1969), S. 217-222 
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    Notes: The eventual objective of powder intensity measurements, in the present context, is to obtain absolute integrated Bragg intensities from specimens which are ideal with respect to all parameters such as extinction, preferred orientation, etc. At present, the Project has been limited to a comparison of X-ray techniques on a number of samples of carbonyl process nickel which are known to be non-ideal, but which were determined by actual measurement to yield identical integrated intensities using Cu Kα radiation. Eleven samples have been measured in ten laboratories and six of these have been standardized by measurement of the incident beam. The results show that integrated intensities may not be relied on to better than 5%, even on a relative basis. It appears that, at the present time, the techniques for making an accurate measurement of the incident beam may be more reliable than those for measuring relative intensities.
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    Acta crystallographica 25 (1969), S. 243-248 
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    Notes: A survey is made of X-ray powder work which has been done since 1960 to obtain information on electron states and electron charge distributions. The investigations are classified into three groups, depending upon there aims. Then the following three subjects are described: electron state of metallic nitrides, especially of Fe4N, deformation of charge cloud in ionic crystals and comparison of measurements on MgO.
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    Acta crystallographica 25 (1969), S. 363-367 
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    Notes: Space groups having the same translation subgroup and the same point group form an Abelian finite group. This property is used to simplify the construction of space groups. The case of magnetic groups is examined too, and the results are interpreted in Fourier space.
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    Acta crystallographica 25 (1969), S. 374-375 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A simple calculation shows that the experimentally determined electron density in the bifluoride ion is not incompatible with a theoretical model having a charge of + ½ on the hydrogen atom, as was previously believed.
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    Acta crystallographica 25 (1969), S. 387-388 
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    Notes: The triple fault in f.c.c. and the double fault in h.c.p. crystals are stacking faults of the type in which changes in sites of unit layers occur only at faults. The diffraction theory of the latter fault is dealt with on the basis of the matrix method.
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    Acta crystallographica 25 (1969), S. 393-394 
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    Notes: Strong minima in the rotation diagram about the 550 Bragg reflection from the (110) surface of tungsten are interpreted as being due to the excitation of forward diffracted Laue reflections having low index and large wave amplitude. The orientations of these minima correspond to the geometry for the excitation of the three beam case.
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    Acta crystallographica 25 (1969), S. 309-318 
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    Notes: A general theory is proposed for the diffraction line profiles of powders of close-packed crystals containing stacking faults. It covers two theories; one is the Gevers theory which combines the `growth fault' with s (Reichweite) = 2 and the `single deformation fault' in h.c.p., and the other the theory of the 'extended growth fault' with s = 2. The anomalies in the line profiles of nearly h.c.p. and nearly f.c.c. powders, i. e. peak displacement, broadening, and asymmetry, are expressed as functions of stacking fault probabilities. The conclusion is as follows. Although the Gevers–Warren theory, which is being widely used for interpreting experimental results, is useful from the practical point of view, the fault probabilities obtained by use of this theory should only be taken as very rough estimates.
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    Acta crystallographica 25 (1969), S. 373-374 
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    Notes: Two X-ray methods are given for studying crystals grown mainly in one direction. The first is based on Laue photographs; the second on the diffractometer. Twist of the crystals, small misorientations and axial screw dislocations can be detected.
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    Acta crystallographica 25 (1969), S. 385-386 
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    Notes: The Patterson method is applied to the determination of layer sequences in polytypes with close-packed structures and a Table is given which shows the relationship between the Zhdanov symbol and a set of quantities which are directly available from observed intensities.
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    Acta crystallographica 25 (1969), S. 389-391 
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    Notes: The Mössbauer spectrum of ilvaite has been measured at room temperature, and indicates the presence of both high-spin ferrous and ferric iron. Two distinguishable ferrous sites are detected, with the proportion of Fe2+ ions differing by about 20%. The ferric site is highly distorted.
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    Acta crystallographica 25 (1969), S. 396-397 
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    Notes: A method is suggested for obtaining a Patterson map which contains only vectors related to the atom giving rise to anomalous scattering. This map gives directly the position of the anomalous atom, and can be used in the first stage of the method suggested by Singh & Ramaseshan (1968) for the solution of the phase problem in neutron diffraction.
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    Acta crystallographica 25 (1969), S. 76-81 
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    Notes: Crystallographers have enjoyed a freedom of access to computers that cannot continue. In spite of widespread pressures to automate experiments, computers are not a substitute for proper experimental technique. As a group, crystallographers are remarkably naive not only regarding the evaluation or comparison of the experimental and computational techniques which they employ, but also regarding the actual cost and value of their efforts. Some concerted thought, effort and self-education must be undertaken soon lest extravagance endanger future support.
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    Acta crystallographica 25 (1969), S. 508-514 
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    Notes: The principles established for periodic objects in parts I and II are extended to non-periodic objects. The basis for the extension lies in the possibility of introducing a virtual lattice, which can be treated as in parts I and II when working with a primary wave field that has zero amplitude outside a given spatial region. Thus it becomes possible to form an image without the use of a lens in a manner similar to holography but based on different principles. A reference wave (as used in holography) is not required. The new principle can be applied in a number of variations, some of which are discussed.
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    Acta crystallographica 25 (1969), S. 471-475 
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    Notes: The diffraction pattern for a double hexagonal close-packed crystal containing deformation stacking faults is derived under the assumption that the crystal is infinite in size with faults covering entire basal planes and distributed at random. It is found that such faulting broadens only reflexions with H − K ≠ 0 mod. 3, L = 0 mod. 4, 1 mod. 4, 2 mod. 4, and 3 mod. 4. The broadening is equal and symmetrical without any shift in the position of the peaks.
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    Acta crystallographica 25 (1969), S. 584-585 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The covariance of a Fourier sine coefficient with a Fourier cosine coefficient takes three different forms, depending on whether the order of the sine coefficient is less than, equal to, or greater than that of the cosine coefficient. Explicit formulae are given.
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    Acta crystallographica 25 (1969), S. 584-584 
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    Notes: A single crystal of molybdenum trioxide bombarded by an intense beam of electrons in an electron microscope developed a new internal structure showing localized fringe patterns in different parts. The phenomenon is explained as being the result of recrystallization of MoO3 up to only a certain depth in the crystal. The fringe pattern is a rotation moiré fringe pattern resulting from a slight misorientation. This interpretation is confirmed by selected area diffraction patterns.
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    Acta crystallographica 25 (1969), S. 587-588 
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    Acta crystallographica 25 (1969), S. 543-547 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Fourier transform of a symmetric atom group that is sampled asymmetrically by the reciprocal lattice may be deduced by inspection of the weighted reciprocal lattice. The symmetry of the atom group impresses a pseudo-symmetry on the weighted reciprocal lattice. Superposition of the pseudo-symmetric parts of the lattice gives an increased sampling of the whole Fourier transform, permits recognition of maxima and nodes, and hence provides phase information.
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  • 94
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    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 564-568 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The X-ray (1.54 Å) scattering coefficient per unit solid angle, per unit thickness of sample has been measured for water in the forward direction. It is about eight per cent greater than the value given by density fluctuation theory. Double scattering is calculated and shown to contribute a six per cent excess flux in the forward direction in our geometry. In addition, short wavelength continuum X-rays slightly increase the measured scattering coefficient. After these corrections theory and experiment are in good agreement. The double scattered flux is sensitive to certain parameters of the diffractometer geometry. It is argued that water is not a desirable reference standard for absolute intensity calibrations.
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  • 95
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    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 615-621 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The correction of measured integrated Bragg intensities for first-order thermal diffuse scattering was considered in an earlier paper [Cooper & Rouse, Acta Cryst. (1968). A24, 405] using an approximate method, valid for pseudo-isotropic materials. A method is now derived for the evaluation of the correction for a crystal of any symmetry, allowing for the contributions from first- and second-order scattering for X-rays or neutrons. Allowance for the effects of experimental resolution is also considered.
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  • 96
    Electronic Resource
    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 589-594 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Diffuse X-ray scattering by silicon single crystals has been detected on the film by the use of a doubly bent crystal monochromator. The intensities of one diffuse streak were measured at 83 °K and 273 °K with a scintillation counter spectrometer. With rising temperature the intensity of the diffuse streaks was increased, confirming their thermal origin. In order to examine the scattering in detail, measurements of the absolute thermal scattering power were made through a large region of the (\bar 101) reciprocal lattice plane at 293 °K. These measurements were compared with the theoretical values of the thermal scattering power, given by the theory developed by Laval, in which temperature vibrations are expressed in terms of elastic waves. The first-order term only was calculated and higher-order terms were neglected. The measurements are in semi-quantitative agreement with this theory.
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  • 97
    Electronic Resource
    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 621-626 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of Sm(BrO3)3.9H2O has been solved by the neutron anomalous-dispersion method, with the use of data collected at two wavelengths. Five out of eight atoms in the asymmetric unit were located from the `anomalous difference Patterson' synthesis, and the remaining three from a Fourier synthesis. The structure is centrosymmetric, and the signs of 78% of the reflections were determined correctly from the differences in the Fobs values at the two wavelengths.
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  • 98
    Electronic Resource
    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 338-350 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The numerical method of deconvolution described in part I is applied to a study of a broadening factor of the diffractometer: the receiving slit. By considering this factor the validity of this direct method of deconvolution, which can also be applied to analytical profiles and to experimental profiles, is verified. These results are compared with those obtained with the Stokes method for the Fourier analysis of line profiles and with those obtained with the Ergun method. An experimental study shows the importance of the divergence of parallelism between the receiving slit and the beam of X-rays.
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  • 99
    Electronic Resource
    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 351-355 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Christian–Gevers theory of X-ray diffraction from homogeneous hexagonal close-packed (h.c.p.) crystals with deformation stacking faults is extended to include the effect of segregation of solute atoms at the faults. The results show that the breadths of reflexions remain unaffected by solute segregation. The ratios of integrated intensities of reflexions with H − K ≠ 0 mod 3, L = 1 mod 2 and L = 0 mod 2 respectively are affected, but only to a small extent, that is, within the limits of possible accuracy in experimental measurements of integrated intensity.
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  • 100
    Electronic Resource
    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 422-426 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of Para Red have been studied by photographic X-ray methods. Cooling the crystals produced reversible splitting of the diffraction spots. This was traced to the use of crystals twinned by pseudo-merohedry, in association with anisotropic thermal contraction. At room temperature the twin obliquity was only 0° 22′ and the diffraction spots of the two twin individuals were not resolved.
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