Journal of Applied Crystallography
http://journals.iucr.org/j/issues/2014/05/00/isscontsbdy.html
Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.enCopyright (c) 2014 International Union of Crystallography2014-09-09International Union of CrystallographyInternational Union of Crystallographyhttp://journals.iucr.orgurn:issn:1600-5767Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.text/htmlJournal of Applied Crystallography, Volume 47, Part 5, 2014textyearly62002-02-01T00:00+00:005472014-09-09Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallography1479urn:issn:1600-5767med@iucr.orgSeptember 20142014-09-09Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
http://journals.iucr.org/j/issues/2014/05/00/isscontsbdy.html
Still imageThe structure of casein micelles: a review of small-angle scattering data
http://scripts.iucr.org/cgi-bin/paper?pd5050
Casein micelles are association colloids found in mammalian milk. Small-angle scattering data on casein micelles have been collected and are reviewed, including contrast variation. The scattering spectra are quite consistent at medium and high scattering wavevectors [Q = 4πnsin(θ/2)/λ, where n is the refractive index, λ is the wavelength and θ is the scattering angle]. Differences are noted, especially at low Q, which may be attributed to sample preparation, particularly the presence of residual fat globules. Scattering spectra are calculated using a generalized scattering function and a composite particle model, and it is possible to give a self-consistent calculation of the spectra using one set of parameters for all contrasts in both small-angle X-ray scattering and small-angle neutron scattering. The data and calculations show that a casein micelle is a homogeneous particle. The polydispersity in size is about 35% and therefore experimental data on particle size depend very much on the method used. A `reference set' of numbers is proposed for casein micelles from pooled cows' milk, which may be given as follows: β = 0.35, R10 = 60 nm, Rg = 110 nm, Rhydr = 96 nm (at 90° scattering). Often, use is made of dynamic light scattering (DLS), which gives an Rhydr = 〈R6〉/〈R5〉 of 80–100 nm at 90° scattering. Values will be considerably higher at low(er) angles, and lower at backscattering angles, which are currently used in many DLS setups. Larger values are probably due to clusters of casein micelles or residual fat. The structure of a casein micelle can best be described as a protein matrix in which calcium phosphate clusters (2 nm radius) are dispersed. The protein matrix has density variations on a similar length scale. The casein micelle–submicelle model and models with large voids and channels are highly improbable.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767De Kruif, C.G.2014-08-16doi:10.1107/S1600576714014563International Union of CrystallographySmall-angle scattering spectra on casein micelles from milk are critically reviewed. Casein micelles from pooled milk can be described as spherical protein particles incorporating inhomogeneities, of a few nanometres, of protein and calcium phosphate clusters.ENcasein micellescolloidsmammalian milksmall-angle neutron scatteringsmall-angle X-ray scatteringCasein micelles are association colloids found in mammalian milk. Small-angle scattering data on casein micelles have been collected and are reviewed, including contrast variation. The scattering spectra are quite consistent at medium and high scattering wavevectors [Q = 4πnsin(θ/2)/λ, where n is the refractive index, λ is the wavelength and θ is the scattering angle]. Differences are noted, especially at low Q, which may be attributed to sample preparation, particularly the presence of residual fat globules. Scattering spectra are calculated using a generalized scattering function and a composite particle model, and it is possible to give a self-consistent calculation of the spectra using one set of parameters for all contrasts in both small-angle X-ray scattering and small-angle neutron scattering. The data and calculations show that a casein micelle is a homogeneous particle. The polydispersity in size is about 35% and therefore experimental data on particle size depend very much on the method used. A `reference set' of numbers is proposed for casein micelles from pooled cows' milk, which may be given as follows: β = 0.35, R10 = 60 nm, Rg = 110 nm, Rhydr = 96 nm (at 90° scattering). Often, use is made of dynamic light scattering (DLS), which gives an Rhydr = 〈R6〉/〈R5〉 of 80–100 nm at 90° scattering. Values will be considerably higher at low(er) angles, and lower at backscattering angles, which are currently used in many DLS setups. Larger values are probably due to clusters of casein micelles or residual fat. The structure of a casein micelle can best be described as a protein matrix in which calcium phosphate clusters (2 nm radius) are dispersed. The protein matrix has density variations on a similar length scale. The casein micelle–submicelle model and models with large voids and channels are highly improbable.text/htmlThe structure of casein micelles: a review of small-angle scattering datatext5472014-08-16Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Rhombohedral distortion analysis of ultra-thin Pt(111) films deposited under Ar–N2 atmosphere
http://scripts.iucr.org/cgi-bin/paper?nb5114
A rhombohedral analysis method for analysing the lattice distortion in a (111)-textured face-centred cubic film under rotationally symmetric stress is proposed. Because no material constants, such as diffraction elastic constants, are required, the expressions of the distortion, namely the angle and the lattice parameter, are universal and can be readily used to compare different films. Using this rhombohedral distortion analysis method, (111)-textured Pt films deposited under argon–nitrogen atmosphere are systematically investigated, and the thickness-dependent lattice deformation in as-deposited and annealed films is described by the two geometrical parameters of the rhombohedral cell.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Harumoto, T.Sannomiya, T.Muraishi, S.Shi, J.Nakamura, Y.2014-08-16doi:10.1107/S1600576714014484International Union of CrystallographyA rhombohedral analysis method for analysing the lattice distortion in a (111)-textured face-centred cubic film under rotationally symmetric stress is proposed and applied to ultra-thin Pt films deposited under argon–nitrogen atmosphere.ENstresstexturedistortionprimitive cellsrhombohedralultra-thin filmsA rhombohedral analysis method for analysing the lattice distortion in a (111)-textured face-centred cubic film under rotationally symmetric stress is proposed. Because no material constants, such as diffraction elastic constants, are required, the expressions of the distortion, namely the angle and the lattice parameter, are universal and can be readily used to compare different films. Using this rhombohedral distortion analysis method, (111)-textured Pt films deposited under argon–nitrogen atmosphere are systematically investigated, and the thickness-dependent lattice deformation in as-deposited and annealed films is described by the two geometrical parameters of the rhombohedral cell.text/htmlRhombohedral distortion analysis of ultra-thin Pt(111) films deposited under Ar–N2 atmospheretext5472014-08-16Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00A hybrid immune–evolutionary strategy algorithm for the analysis of the wide-angle X-ray diffraction curves of semicrystalline polymers
http://scripts.iucr.org/cgi-bin/paper?fs5076
Decomposition of wide-angle X-ray diffraction curves into crystalline peaks and amorphous components is one of the most difficult nonlinear optimization problems. For this reason, the elaboration of a reliable method that provides fast unambiguous solutions remains an important and topical task. This work presents a hybrid system dedicated to this aim, combining two methods of artificial intelligence – evolution strategies and an immune algorithm – with the classical method of Rosenbrock. A combination of the mechanisms of these three methods has given a very effective and convergent algorithm that performs very well a multicriterial optimization. Tests have shown that it is faster to converge and less ambiguous than the genetic algorithm.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Rabiej, M.2014-08-16doi:10.1107/S1600576714014782International Union of CrystallographyThis work presents a hybrid immune–evolution strategy algorithm which is a combination of two methods of artificial intelligence – evolution strategies and an immune algorithm – with the classical method of Rosenbrock. The system can be successfully used for decomposition of the wide-angle X-ray diffraction curves of semicrystalline polymers into crystalline peaks and amorphous halos.ENimmune algorithmsgenetic algorithmsevolution strategyhybrid immune–evolution strategy algorithmmulticriterial optimizationdecompositiondiffraction curvesDecomposition of wide-angle X-ray diffraction curves into crystalline peaks and amorphous components is one of the most difficult nonlinear optimization problems. For this reason, the elaboration of a reliable method that provides fast unambiguous solutions remains an important and topical task. This work presents a hybrid system dedicated to this aim, combining two methods of artificial intelligence – evolution strategies and an immune algorithm – with the classical method of Rosenbrock. A combination of the mechanisms of these three methods has given a very effective and convergent algorithm that performs very well a multicriterial optimization. Tests have shown that it is faster to converge and less ambiguous than the genetic algorithm.text/htmlA hybrid immune–evolutionary strategy algorithm for the analysis of the wide-angle X-ray diffraction curves of semicrystalline polymerstext5472014-08-16Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00X-ray absorption spectroscopy studies on the carbothermal reduction reaction products of 3 mol% yttria-stabilized zirconia
http://scripts.iucr.org/cgi-bin/paper?aj5231
Extended X-ray absorption spectroscopy (EXAFS) at the Zr K edge has been used to determine changes in various bond lengths in 3 mol% yttria-stabilized zirconia (YSZ) during zirconium carbide (ZrC) formation. The principal objective of this study was to determine if ZrC formation at the YSZ/carbon interface alters the zirconia structure. A mixed-phase sample (YSZ and graphite) was carbothermally reduced to form ZrC. X-ray diffraction phase quantification by Rietveld analysis confirmed the formation of ∼50% ZrC in the analyzed sample volume. EXAFS data of ZrC and YSZ powders and a sintered YSZ pellet (∼96.7% density) were used as standards to compare with the carbothermally reduced sample. Ab inito calculations using these spectra quantified various Zr—O, Zr—C and Zr—Zr bond distances in the system. Best fit results revealed Zr—OI (tetragonal), Zr—O (monoclinic), Zr—Zr (tetragonal) and Zr—Zr (monoclinic) bond length values of 2.10, 2.25, 3.65 and 3.52 Å, respectively, in the YSZ powder, Zr—OI (tetragonal) and Zr—Zr (tetragonal) bond length values of 2.12 and 3.62 Å, respectively, in the sintered pellet, and Zr—C and Zr—Zr bond lengths of 2.32 and 3.33 Å, respectively, in the ZrC powder. Similar fitting procedures were carried out on the carbothermally reduced pellet, with measured Zr—O, Zr—Zr (of YSZ), Zr—C and Zr—Zr (of ZrC) bond lengths of 2.13, 3.62, 2.36 and 3.33 Å, respectively. These bond lengths indicate that the formation of ZrC in the YSZ matrix does not influence the local structure when compared to pure standards. Therefore, carbothermal reduction does not induce any apparent strain or thermally induced effects on the first and second coordination shells of Zr as measured by the X-ray absorption spectra of the carbothermally reduced sample. Interestingly, the results indicated that sintering of the YSZ powder into pellets did not result in any significant change in the Zr—O and Zr—Zr distances for tetragonal YSZ.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Sondhi, A.Okobiah, O.Chattopadhyay, S.Shibata, T.Scharf, T.W.Reidy, R.F.2014-08-16doi:10.1107/S1600576714014642International Union of CrystallographyX-ray absorption spectroscopy (XAS) has been used to study the fine structure details of carbothermally reduced 3 mol% yttria-stabilized zirconia (YSZ) and understand the effect of sintering on various bond lengths in the starting powder and its sintered counterpart. The influence of ZrC formation on the YSZ matrix was determined with the help of X-ray diffraction and XAS. Bond lengths were deduced from the extended X-ray absorption spectroscopy pattern of the carbothermally reduced sample and compared with those of the pure standards.ENX-ray absorptionEXAFSzirconium carbideyttria-stabilized zirconiacarbothermal reductionsinteringExtended X-ray absorption spectroscopy (EXAFS) at the Zr K edge has been used to determine changes in various bond lengths in 3 mol% yttria-stabilized zirconia (YSZ) during zirconium carbide (ZrC) formation. The principal objective of this study was to determine if ZrC formation at the YSZ/carbon interface alters the zirconia structure. A mixed-phase sample (YSZ and graphite) was carbothermally reduced to form ZrC. X-ray diffraction phase quantification by Rietveld analysis confirmed the formation of ∼50% ZrC in the analyzed sample volume. EXAFS data of ZrC and YSZ powders and a sintered YSZ pellet (∼96.7% density) were used as standards to compare with the carbothermally reduced sample. Ab inito calculations using these spectra quantified various Zr—O, Zr—C and Zr—Zr bond distances in the system. Best fit results revealed Zr—OI (tetragonal), Zr—O (monoclinic), Zr—Zr (tetragonal) and Zr—Zr (monoclinic) bond length values of 2.10, 2.25, 3.65 and 3.52 Å, respectively, in the YSZ powder, Zr—OI (tetragonal) and Zr—Zr (tetragonal) bond length values of 2.12 and 3.62 Å, respectively, in the sintered pellet, and Zr—C and Zr—Zr bond lengths of 2.32 and 3.33 Å, respectively, in the ZrC powder. Similar fitting procedures were carried out on the carbothermally reduced pellet, with measured Zr—O, Zr—Zr (of YSZ), Zr—C and Zr—Zr (of ZrC) bond lengths of 2.13, 3.62, 2.36 and 3.33 Å, respectively. These bond lengths indicate that the formation of ZrC in the YSZ matrix does not influence the local structure when compared to pure standards. Therefore, carbothermal reduction does not induce any apparent strain or thermally induced effects on the first and second coordination shells of Zr as measured by the X-ray absorption spectra of the carbothermally reduced sample. Interestingly, the results indicated that sintering of the YSZ powder into pellets did not result in any significant change in the Zr—O and Zr—Zr distances for tetragonal YSZ.text/htmlX-ray absorption spectroscopy studies on the carbothermal reduction reaction products of 3 mol% yttria-stabilized zirconiatext5472014-08-16Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Potential of full pattern fit methods for the texture analysis of geological materials: implications from texture measurements at the recently upgraded neutron time-of-flight diffractometer SKAT
http://scripts.iucr.org/cgi-bin/paper?po5001
The application of Rietveld texture analysis (RTA) to time-of-flight (TOF) neutron diffraction data allows complex materials with many diffraction peaks to be investigated, for example, rocks composed of different minerals. At the recently upgraded SKAT texture diffractometer at the JINR in Dubna (Russia), which provides three alternative multidetector systems, resolution and accessible range of lattice d spacings can be adapted to sample requirements. In order to infer the optimum experimental setup and the reliability of texture estimates from complicated TOF patterns, the influence of counting statistics and various spectral resolutions on texture deconvolution was investigated. Comparing the results obtained at different resolutions and from different sections of the d patterns indicates that the textures of a four-phase sample can be determined, but using a section at small d spacings with a larger number of peak overlaps leads to smoother textures. A complex seven-phase sample shows orientation differences in addition to the smoothing effect. Weak textures and textures of the minor rock constituents are inaccurate owing to multiple peak overlaps. Consequently, good resolution is essential for RTA on such samples. Grid thinning tests confirmed that no more than 150 diffraction spectra are needed to characterize the texture of a monomineralic sample, and approximately 350 spectra are sufficient for a four-phase sample. The irregular grid point arrangement caused by the SKAT geometry has no negative consequences.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Keppler, R.Ullemeyer, K.Behrmann, J.H.Stipp, M.2014-08-16doi:10.1107/S1600576714015830International Union of CrystallographyThe upgraded time-of-flight diffractometer SKAT the JINR in Dubna (Russia) is described. The reliability of texture analyses of polymineralic samples applying Rietveld texture analysis is evaluated.ENtexture analysisneutron time-of-flight diffractometersgeological materialsfull pattern fit methodsThe application of Rietveld texture analysis (RTA) to time-of-flight (TOF) neutron diffraction data allows complex materials with many diffraction peaks to be investigated, for example, rocks composed of different minerals. At the recently upgraded SKAT texture diffractometer at the JINR in Dubna (Russia), which provides three alternative multidetector systems, resolution and accessible range of lattice d spacings can be adapted to sample requirements. In order to infer the optimum experimental setup and the reliability of texture estimates from complicated TOF patterns, the influence of counting statistics and various spectral resolutions on texture deconvolution was investigated. Comparing the results obtained at different resolutions and from different sections of the d patterns indicates that the textures of a four-phase sample can be determined, but using a section at small d spacings with a larger number of peak overlaps leads to smoother textures. A complex seven-phase sample shows orientation differences in addition to the smoothing effect. Weak textures and textures of the minor rock constituents are inaccurate owing to multiple peak overlaps. Consequently, good resolution is essential for RTA on such samples. Grid thinning tests confirmed that no more than 150 diffraction spectra are needed to characterize the texture of a monomineralic sample, and approximately 350 spectra are sufficient for a four-phase sample. The irregular grid point arrangement caused by the SKAT geometry has no negative consequences.text/htmlPotential of full pattern fit methods for the texture analysis of geological materials: implications from texture measurements at the recently upgraded neutron time-of-flight diffractometer SKATtext5472014-08-16Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Peak broadening anisotropy in deformed face-centred cubic and hexagonal close-packed alloys
http://scripts.iucr.org/cgi-bin/paper?nb5104
The broadening of diffraction peaks representing different families of grain orientations has been measured for a number of deformed metals: austenitic stainless steel 316, nickel 200 and the titanium alloy Ti-6Al-4V. These measurements have been compared with predictions that explain differences in broadening in terms of the contrast factor of dislocations via two different approaches. This was done in order to understand the effect the contrast factor has on the results of diffraction peak profile analysis methods and the cause of broadening anisotropy. An approach that considers all grains and orientations to behave similarly was found to be unsuccessful in explaining the large variations of broadening in different peaks. These variations can be explained, and errors reduced, by adopting an approach that uses a polycrystal plasticity model. However, if the plasticity based approach is used to solely calculate changes in the contrast factor, it only partly explains changes in broadening. Instead, factors such as variations in the dislocation density and crystallite size in different orientations, the number of dislocations that are mobile, and the number of edge and screw dislocations need consideration. The way to incorporate these additional factors is difficult, but their contribution to broadening anisotropy can be as important as that of the contrast factor.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Simm, T.H.Withers, P.J.Quinta da Fonseca, J.2014-08-16doi:10.1107/S1600576714015751International Union of CrystallographyThe broadening of diffraction peak profiles of plastically deformed face-centred cubic and hexagonal close-packed alloys, and results of the Warren–Averbach method, are shown to be dependent on the measurement direction. Polycrystal plasticity models are used to show that these changes could be due to the heterogeneity of deformation, which results in differences in the types of dislocations and dislocation structures in different orientations, highlighting how errors can result from the use of an unweighted contrast factor.ENdiffraction peak broadeninganisotropydeformed alloysgrain orientationThe broadening of diffraction peaks representing different families of grain orientations has been measured for a number of deformed metals: austenitic stainless steel 316, nickel 200 and the titanium alloy Ti-6Al-4V. These measurements have been compared with predictions that explain differences in broadening in terms of the contrast factor of dislocations via two different approaches. This was done in order to understand the effect the contrast factor has on the results of diffraction peak profile analysis methods and the cause of broadening anisotropy. An approach that considers all grains and orientations to behave similarly was found to be unsuccessful in explaining the large variations of broadening in different peaks. These variations can be explained, and errors reduced, by adopting an approach that uses a polycrystal plasticity model. However, if the plasticity based approach is used to solely calculate changes in the contrast factor, it only partly explains changes in broadening. Instead, factors such as variations in the dislocation density and crystallite size in different orientations, the number of dislocations that are mobile, and the number of edge and screw dislocations need consideration. The way to incorporate these additional factors is difficult, but their contribution to broadening anisotropy can be as important as that of the contrast factor.text/htmlPeak broadening anisotropy in deformed face-centred cubic and hexagonal close-packed alloystext5472014-08-16Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Collimation problem in small-angle X-ray scattering for anisotropic objects: statement and solution
http://scripts.iucr.org/cgi-bin/paper?fs5066
The problem of removal of collimation distortion due to employing a slit collimation system in small-angle X-ray scattering experiments is considered for anisotropic objects in general and for orientated macromolecules in particular. A mathematical statement of the problem is presented, and two approaches to `de-smear' the experimental scattering intensity are described. The first method seeks the theoretical scattering intensity as a linear combination of two-dimensional basis functions (B splines). The combination coefficients are found using the χ2 and two-dimensional curvature-minimization criteria. The second approach is based on the iterative Friedman method, which was generalized to be effective for the problem of interest. The described methods are applied to simulated and experimental data, and the results are discussed.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Zakharov, D.D.Smirnov, A.V.Fedorov, B.A.2014-09-04doi:10.1107/S1600576714017750International Union of CrystallographyThe problem of removal of collimation distortion due to employing a slit collimation system in small-angle X-ray scattering experiments is considered for anisotropic objects. A mathematical statement of the problem is presented, and two approaches to `de-smear' the experimental scattering intensity are described. The described methods are applied to simulated and experimental data, and the results are discussed.ENcollimation distortionsmall-angle X-ray scatteringThe problem of removal of collimation distortion due to employing a slit collimation system in small-angle X-ray scattering experiments is considered for anisotropic objects in general and for orientated macromolecules in particular. A mathematical statement of the problem is presented, and two approaches to `de-smear' the experimental scattering intensity are described. The first method seeks the theoretical scattering intensity as a linear combination of two-dimensional basis functions (B splines). The combination coefficients are found using the χ2 and two-dimensional curvature-minimization criteria. The second approach is based on the iterative Friedman method, which was generalized to be effective for the problem of interest. The described methods are applied to simulated and experimental data, and the results are discussed.text/htmlCollimation problem in small-angle X-ray scattering for anisotropic objects: statement and solutiontext5472014-09-04Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Crossing the boundary between face-centred cubic and hexagonal close packed: the structure of nanosized cobalt is unraveled by a model accounting for shape, size distribution and stacking faults, allowing simulation of XRD, XANES and EXAFS
http://scripts.iucr.org/cgi-bin/paper?po5012
The properties of nanostructured cobalt in the fields of magnetic, catalytic and biomaterials depend critically on Co close packing. This paper reports a structural analysis of nanosized cobalt based on the whole X-ray diffraction (XRD) pattern simulation allowed by the Debye equation. The underlying structural model involves statistical sequences of cobalt layers and produces simulated XRD powder patterns bearing the concurrent signatures of hexagonal and cubic close packing (h.c.p. and f.c.c.). Shape, size distribution and distance distribution between pairs of atoms are also modelled. The simulation algorithm allows straightforward fitting to experimental data and hence the quantitative assessment of the model parameters. Analysis of two samples having, respectively, h.c.p. and f.c.c. appearance is reported. Extended X-ray absorption fine-structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectra are simulated on the basis of the model, giving a tool for the interpretation of structural data complementary to XRD. The outlined structural analysis provides a rigorous structural basis for correlations with magnetic and catalytic properties and an experimental reference for ab initio modelling of these properties.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Longo, A.Sciortino, L.Giannici, F.Martorana, A.2014-09-04doi:10.1107/S1600576714015970International Union of CrystallographyA structural model of nanosized cobalt is fitted to X-ray diffraction (XRD) data using the Debye equation. The model allows for shape, size distribution, atom pair distance distribution and stacking faults. Extended X-ray absorption fine-structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectra are calculated on the basis of the fitted parameters.ENcobaltnanostructurestructure modelsface-centred cubichexagonal close packingThe properties of nanostructured cobalt in the fields of magnetic, catalytic and biomaterials depend critically on Co close packing. This paper reports a structural analysis of nanosized cobalt based on the whole X-ray diffraction (XRD) pattern simulation allowed by the Debye equation. The underlying structural model involves statistical sequences of cobalt layers and produces simulated XRD powder patterns bearing the concurrent signatures of hexagonal and cubic close packing (h.c.p. and f.c.c.). Shape, size distribution and distance distribution between pairs of atoms are also modelled. The simulation algorithm allows straightforward fitting to experimental data and hence the quantitative assessment of the model parameters. Analysis of two samples having, respectively, h.c.p. and f.c.c. appearance is reported. Extended X-ray absorption fine-structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectra are simulated on the basis of the model, giving a tool for the interpretation of structural data complementary to XRD. The outlined structural analysis provides a rigorous structural basis for correlations with magnetic and catalytic properties and an experimental reference for ab initio modelling of these properties.text/htmlCrossing the boundary between face-centred cubic and hexagonal close packed: the structure of nanosized cobalt is unraveled by a model accounting for shape, size distribution and stacking faults, allowing simulation of XRD, XANES and EXAFStext5472014-09-04Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Solving the structures of light-atom compounds with powder charge flipping
http://scripts.iucr.org/cgi-bin/paper?po5010
While the powder charge flipping (pCF) algorithm has been applied successfully to a variety of inorganic compounds, reports on its application to organic structures, in particular those consisting of light atoms only, are rare. To investigate the reason for this apparent incongruity, a series of light-atom structures were tested using the pCF algorithm implemented in the program Superflip. The data sets, which covered varying degrees of reflection overlap, had resolutions of approximately 1 Å, and the structures ranged from 40 to 136 atoms per unit cell. Both centrosymmetric and noncentrosymmetric structures were investigated. A modified pCF approach, which was developed in a separate study, was tested on several compounds whose structures could not be solved by applying the basic pCF algorithm in Superflip. The results show that organic structures with no heavy atoms and low symmetry do indeed test the limits of the pCF algorithm in Superflip. The study has allowed a few guidelines for approaching such problems to be formulated.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Šišak Jung, D.Baerlocher, C.McCusker, L.B.Yoshinari, T.Seebach, D.2014-09-04doi:10.1107/S1600576714016732International Union of CrystallographyThe powder charge flipping algorithm has been applied to a variety of light-atom structures to test its limits, and a protocol for dealing with such structures is proposed.ENcharge flippingequal-atom structurespowder diffractionstructure solutionorganic compoundsWhile the powder charge flipping (pCF) algorithm has been applied successfully to a variety of inorganic compounds, reports on its application to organic structures, in particular those consisting of light atoms only, are rare. To investigate the reason for this apparent incongruity, a series of light-atom structures were tested using the pCF algorithm implemented in the program Superflip. The data sets, which covered varying degrees of reflection overlap, had resolutions of approximately 1 Å, and the structures ranged from 40 to 136 atoms per unit cell. Both centrosymmetric and noncentrosymmetric structures were investigated. A modified pCF approach, which was developed in a separate study, was tested on several compounds whose structures could not be solved by applying the basic pCF algorithm in Superflip. The results show that organic structures with no heavy atoms and low symmetry do indeed test the limits of the pCF algorithm in Superflip. The study has allowed a few guidelines for approaching such problems to be formulated.text/htmlSolving the structures of light-atom compounds with powder charge flippingtext5472014-09-04Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Structural analysis of lignin-derived carbon composite anodes
http://scripts.iucr.org/cgi-bin/paper?pd5045
The development of novel lignin-based carbon composite anodes consisting of nanocrystalline and amorphous domains motivates the understanding of the relationship of the structural properties characterizing these materials, such as crystallite size, intracrystallite d spacing, crystalline volume fraction and composite density, with their pair distribution functions (PDFs), obtained from both molecular dynamics simulation and neutron scattering. A model for these composite materials is developed as a function of experimentally measurable parameters and realized in 15 composite systems, three of which directly match all parameters of their experimental counterparts. The accurate reproduction of the experimental PDFs using the model systems validates the model. The decomposition of the simulated PDFs provides an understanding of each feature in the PDF and allows for the development of a mapping between the defining characteristics of the PDF and the material properties of interest.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767McNutt, N.W.Rios, O.Feygenson, M.Proffen, T.E.Keffer, D.J.2014-09-04doi:10.1107/S1600576714014666International Union of CrystallographyLignin-based carbon composite anodes consisting of nanocrystalline and amorphous domains are studied to develop a relationship of structural properties such as crystallite size, intracrystallite d spacing, crystalline volume fraction and composite density with their pair distribution functions, as obtained from both molecular dynamics simulation and neutron scattering.ENneutron scatteringmolecular dynamicsanodescarbon compositesnanocrystallitesThe development of novel lignin-based carbon composite anodes consisting of nanocrystalline and amorphous domains motivates the understanding of the relationship of the structural properties characterizing these materials, such as crystallite size, intracrystallite d spacing, crystalline volume fraction and composite density, with their pair distribution functions (PDFs), obtained from both molecular dynamics simulation and neutron scattering. A model for these composite materials is developed as a function of experimentally measurable parameters and realized in 15 composite systems, three of which directly match all parameters of their experimental counterparts. The accurate reproduction of the experimental PDFs using the model systems validates the model. The decomposition of the simulated PDFs provides an understanding of each feature in the PDF and allows for the development of a mapping between the defining characteristics of the PDF and the material properties of interest.text/htmlStructural analysis of lignin-derived carbon composite anodestext5472014-09-04Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00On the calibration of high-energy X-ray diffraction setups. II. Assessing the rotation axis and residual strains
http://scripts.iucr.org/cgi-bin/paper?to5080
The calibration of high-energy X-ray diffraction setups using an area detector and a rotation axis is discussed. The characterization of the tilt and spatial distortions of an area detector was discussed in part one of this series [Borbély, Renversade, Kenesei & Wright (2014). J. Appl. Cryst. 47, 1042–1053]. Part II links the detector frame to the laboratory frame comprising an additional rotation axis and introduces a general diffractometer equation accounting for all sources of misalignment. Additionally, an independent high-accuracy method for the evaluation of the crystallographic orientation and cell parameters of the undeformed reference crystal is presented. Setup misalignments are mainly described in terms of a residual strain tensor, considered as a quality label of the diffractometer. The method is exemplified using data sets acquired at beamlines ID11 (European Synchrotron Radiation Facility) and 1-ID (Advanced Photon Source) on Al and W single crystals, respectively. The results show that the residual strain tensor is mainly determined by the detector spatial distortion, and values as small as 1–2 × 10−4 can be practically achieved.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Borbély, A.Renversade, L.Kenesei, P.2014-09-04doi:10.1107/S1600576714014290International Union of CrystallographyThe calibration of a high-energy diffractometer comprising a rotation axis and an area detector is assessed. An independent method for high-accuracy determination of the cell parameters of undeformed crystals is introduced.ENhigh-energy diffractionrotation axesreference lattice parametersstrain tensorsarea detectorsThe calibration of high-energy X-ray diffraction setups using an area detector and a rotation axis is discussed. The characterization of the tilt and spatial distortions of an area detector was discussed in part one of this series [Borbély, Renversade, Kenesei & Wright (2014). J. Appl. Cryst. 47, 1042–1053]. Part II links the detector frame to the laboratory frame comprising an additional rotation axis and introduces a general diffractometer equation accounting for all sources of misalignment. Additionally, an independent high-accuracy method for the evaluation of the crystallographic orientation and cell parameters of the undeformed reference crystal is presented. Setup misalignments are mainly described in terms of a residual strain tensor, considered as a quality label of the diffractometer. The method is exemplified using data sets acquired at beamlines ID11 (European Synchrotron Radiation Facility) and 1-ID (Advanced Photon Source) on Al and W single crystals, respectively. The results show that the residual strain tensor is mainly determined by the detector spatial distortion, and values as small as 1–2 × 10−4 can be practically achieved.text/htmlOn the calibration of high-energy X-ray diffraction setups. II. Assessing the rotation axis and residual strainstext5472014-09-04Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Time-resolved coherent X-ray diffraction imaging of surface acoustic waves
http://scripts.iucr.org/cgi-bin/paper?rg5067
Time-resolved coherent X-ray diffraction experiments of standing surface acoustic waves, illuminated under grazing incidence by a nanofocused synchrotron beam, are reported. The data have been recorded in stroboscopic mode at controlled and varied phase between the acoustic frequency generator and the synchrotron bunch train. At each time delay (phase angle), the coherent far-field diffraction pattern in the small-angle regime is inverted by an iterative algorithm to yield the local instantaneous surface height profile along the optical axis. The results show that periodic nanoscale dynamics can be imaged at high temporal resolution in the range of 50 ps (pulse length).Copyright (c) 2014 Jan-David Nicolas et al.urn:issn:1600-5767Nicolas, J.-D.Reusch, T.Osterhoff, M.Sprung, M.Schúlein, F.J.R.Krenner, H.J.Wixforth, A.Salditt, T.2014-09-04doi:10.1107/S1600576714016896International Union of CrystallographyThe time-dependent one-dimensional height profile of a standing surface acoustic wave on an LiNbO3 substrate has been reconstructed from stroboscopically recorded coherent grazing-incidence small-angle diffraction patterns.ENcoherent X-ray diffraction imagingsurface acoustic wavesnanostructureTime-resolved coherent X-ray diffraction experiments of standing surface acoustic waves, illuminated under grazing incidence by a nanofocused synchrotron beam, are reported. The data have been recorded in stroboscopic mode at controlled and varied phase between the acoustic frequency generator and the synchrotron bunch train. At each time delay (phase angle), the coherent far-field diffraction pattern in the small-angle regime is inverted by an iterative algorithm to yield the local instantaneous surface height profile along the optical axis. The results show that periodic nanoscale dynamics can be imaged at high temporal resolution in the range of 50 ps (pulse length).text/htmlTime-resolved coherent X-ray diffraction imaging of surface acoustic wavestext5472014-09-04Copyright (c) 2014 Jan-David Nicolas et al.Journal of Applied Crystallographyresearch papers00Mass-fractal growth in niobia/silsesquioxane mixtures: a small-angle X-ray scattering study
http://scripts.iucr.org/cgi-bin/paper?vh5007
The nucleation and growth of niobium pentaethoxide (NPE)-derived clusters in ethanol, through acid-catalyzed hydrolysis/condensation in the presence and absence of the silsesquioxane 1,2-bis(triethoxysilyl)ethane (BTESE), was monitored at 298–333 K by small-angle X-ray scattering. The data were analyzed with a newly derived model for polydisperse mass-fractal-like structures. At 298–313 K in the absence of BTESE the data indicated the development of relatively monodisperse NPE-derived structures with self-preserving polydispersity during growth. The growth exponent was consistent with irreversible diffusion-limited cluster agglomeration. At 333 K the growth exponent was characteristic for fast-gelling reaction-limited cluster agglomeration. The reaction yielded substantially higher degrees of polydispersity. In the presence of BTESE the growth exponents were substantially smaller. The smaller growth exponent in this case is not consistent with irreversible Smoluchowski-type agglomeration. Instead, reversible Lifshitz–Slyozov-type agglomeration seems to be more consistent with the experimental data.Copyright (c) 2014 Rogier Besselink et al.urn:issn:1600-5767Besselink, R.Elshof, J.E. ten2014-09-04doi:10.1107/S1600576714017105International Union of CrystallographyThe nucleation and growth of niobium pentaethoxide-derived clusters in ethanol was monitored at 298–333 K by small-angle X-ray scattering. The data were analyzed with a newly derived model for polydisperse mass-fractal-like structures.ENmass-fractal growthniobiasilsesquioxanesmall-angle X-ray scatteringThe nucleation and growth of niobium pentaethoxide (NPE)-derived clusters in ethanol, through acid-catalyzed hydrolysis/condensation in the presence and absence of the silsesquioxane 1,2-bis(triethoxysilyl)ethane (BTESE), was monitored at 298–333 K by small-angle X-ray scattering. The data were analyzed with a newly derived model for polydisperse mass-fractal-like structures. At 298–313 K in the absence of BTESE the data indicated the development of relatively monodisperse NPE-derived structures with self-preserving polydispersity during growth. The growth exponent was consistent with irreversible diffusion-limited cluster agglomeration. At 333 K the growth exponent was characteristic for fast-gelling reaction-limited cluster agglomeration. The reaction yielded substantially higher degrees of polydispersity. In the presence of BTESE the growth exponents were substantially smaller. The smaller growth exponent in this case is not consistent with irreversible Smoluchowski-type agglomeration. Instead, reversible Lifshitz–Slyozov-type agglomeration seems to be more consistent with the experimental data.text/htmlMass-fractal growth in niobia/silsesquioxane mixtures: a small-angle X-ray scattering studytext5472014-09-04Copyright (c) 2014 Rogier Besselink et al.Journal of Applied Crystallographyresearch papers00High-resolution synchrotron diffraction study of porous buffer InP(001) layers
http://scripts.iucr.org/cgi-bin/paper?vh5009
X-ray reciprocal space mapping was used for quantitative investigation of porous layers in indium phosphide. A new theoretical model in the frame of the statistical dynamical theory for cylindrical pores was developed and applied for numerical data evaluation. The analysis of reciprocal space maps provided comprehensive information on a wide range of the porous layer parameters, for example, layer thickness and porosity, orientation, and correlation length of segmented pore structures. The results are in a good agreement with scanning electron microscopy data.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Lomov, A.A.Punegov, V.I.Nohavica, D.Chuev, M.A.Vasiliev, A.L.Novikov, D.V.2014-09-04doi:10.1107/S1600576714016392International Union of CrystallographyX-ray reciprocal space mapping was used for the investigation of porous InP layers. A new advanced statistical dynamical theory applied for numerical data evaluation provided quantitative values for the main structural parameters of the porous layers.ENX-ray reciprocal space mappingstatistical dynamical theoryporous layersindium phosphideX-ray reciprocal space mapping was used for quantitative investigation of porous layers in indium phosphide. A new theoretical model in the frame of the statistical dynamical theory for cylindrical pores was developed and applied for numerical data evaluation. The analysis of reciprocal space maps provided comprehensive information on a wide range of the porous layer parameters, for example, layer thickness and porosity, orientation, and correlation length of segmented pore structures. The results are in a good agreement with scanning electron microscopy data.text/htmlHigh-resolution synchrotron diffraction study of porous buffer InP(001) layerstext5472014-09-04Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00MolBridge: a program for identifying nonbonded interactions in small molecules and biomolecular structures
http://scripts.iucr.org/cgi-bin/paper?he5663
Identification and analysis of nonbonded interactions within a molecule and with the surrounding molecules are an essential part of structural studies, given the importance of these interactions in defining the structure and function of any supramolecular entity. MolBridge is an easy to use algorithm based purely on geometric criteria that can identify all possible nonbonded interactions, such as hydrogen bond, halogen bond, cation–π, π–π and van der Waals, in small molecules as well as biomolecules. The user can either upload three-dimensional coordinate files or enter the molecular ID corresponding to the relevant database. The program is available in a standalone form and as an interactive web server with Jmol and JME incorporated into it. The program is freely downloadable and the web server version is also available at http://nucleix.mbu.iisc.ernet.in/molbridge/index.php.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Kumar, P.Kailasam, S.Chakraborty, S.Bansal, M.2014-08-16doi:10.1107/S160057671401468XInternational Union of CrystallographyA freely available program dedicated to the identification of nonbonded interactions in small molecules as well as biomolecules is introduced. The standalone version of the program is currently available for download. The web server can be accessed at http://nucleix.mbu.iisc.ernet.in/molbridge/index.php.ENnonbonded interactionshydrogen bondscation–π interactionsπ–π interactionssmall moleculesbiomolecular structurescomputer programsIdentification and analysis of nonbonded interactions within a molecule and with the surrounding molecules are an essential part of structural studies, given the importance of these interactions in defining the structure and function of any supramolecular entity. MolBridge is an easy to use algorithm based purely on geometric criteria that can identify all possible nonbonded interactions, such as hydrogen bond, halogen bond, cation–π, π–π and van der Waals, in small molecules as well as biomolecules. The user can either upload three-dimensional coordinate files or enter the molecular ID corresponding to the relevant database. The program is available in a standalone form and as an interactive web server with Jmol and JME incorporated into it. The program is freely downloadable and the web server version is also available at http://nucleix.mbu.iisc.ernet.in/molbridge/index.php.text/htmlMolBridge: a program for identifying nonbonded interactions in small molecules and biomolecular structurestext5472014-08-16Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00processPIXEL: a program to generate energy-vector models from Gavezzotti's PIXEL calculations
http://scripts.iucr.org/cgi-bin/paper?kk5182
A command-line program is presented to convert the output from Gavezzotti's PIXEL calculations to Shishkin's energy-vector models representing the intermolecular interaction topology. The output models comprise sets of vectors joining the centres of the molecules in a crystal structure, scaled so that the vector representing the most stabilizing pairwise interaction has length equal to half of the corresponding intermolecular separation. When the energy-vector model is packed, the most stabilizing pairwise interaction is represented as a continuous line between interacting molecules, while the other intermolecular interactions are shown as discontinuous lines, with a smaller gap representing a more stabilizing interaction. The energy-vector models can be overlaid on the crystal structure using the Mercury visualizer to enable convenient visualization of structural motifs that contribute significantly to the overall crystal packing energy.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Bond, A.D.2014-09-04doi:10.1107/S1600576714016446International Union of CrystallographyA command-line program is presented to generate Shishkin's energy-vector models from the results of Gavezzotti's PIXEL calculations. The output models permit convenient visualization of the intermolecular interaction topology.ENintermolecular interaction topologyenergy-vector modelscomputer programsA command-line program is presented to convert the output from Gavezzotti's PIXEL calculations to Shishkin's energy-vector models representing the intermolecular interaction topology. The output models comprise sets of vectors joining the centres of the molecules in a crystal structure, scaled so that the vector representing the most stabilizing pairwise interaction has length equal to half of the corresponding intermolecular separation. When the energy-vector model is packed, the most stabilizing pairwise interaction is represented as a continuous line between interacting molecules, while the other intermolecular interactions are shown as discontinuous lines, with a smaller gap representing a more stabilizing interaction. The energy-vector models can be overlaid on the crystal structure using the Mercury visualizer to enable convenient visualization of structural motifs that contribute significantly to the overall crystal packing energy.text/htmlprocessPIXEL: a program to generate energy-vector models from Gavezzotti's PIXEL calculationstext5472014-09-04Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00SynchLink: an iOS app for ISPyB
http://scripts.iucr.org/cgi-bin/paper?he5667
The macromolecular crystallography (MX) user experience at synchrotron radiation facilities continues to evolve, with the impact of developments in X-ray detectors, computer hardware and automation methods making it possible for complete data sets to be collected on timescales of tens of seconds. Data can be reduced in a couple of minutes and in favourable cases structures solved and refined shortly after. The information-rich database ISPyB, automatically populated by data acquisition software, data processing and structure solution pipelines at the Diamond Light Source beamlines, allows users to automatically track MX experiments in real time. In order to improve the synchrotron users' experience, efficient access to the data contained in ISPyB is now provided via an iOS 6.0+ app for iPhones and iPads. This provides users, both local and remote, with a succinct summary of data collection, visualization of diffraction images and crystals, and key metrics for data quality in real time.Copyright (c) 2014 Helen Mary Ginn et al.urn:issn:1600-5767Ginn, H.M.Mostefaoui, G.K.Levik, K.E.Grimes, J.M.Walsh, M.A.Ashton, A.W.Stuart, D.I.2014-09-04doi:10.1107/S1600576714017531International Union of CrystallographyAn iOS app has been developed as a front end to ISPyB, a laboratory information system for macromolecular crystallography synchrotron beamlines.ENremote data collectionsynchrotron radiationmacromolecular crystallographylaboratory information management systems (LIMS)The macromolecular crystallography (MX) user experience at synchrotron radiation facilities continues to evolve, with the impact of developments in X-ray detectors, computer hardware and automation methods making it possible for complete data sets to be collected on timescales of tens of seconds. Data can be reduced in a couple of minutes and in favourable cases structures solved and refined shortly after. The information-rich database ISPyB, automatically populated by data acquisition software, data processing and structure solution pipelines at the Diamond Light Source beamlines, allows users to automatically track MX experiments in real time. In order to improve the synchrotron users' experience, efficient access to the data contained in ISPyB is now provided via an iOS 6.0+ app for iPhones and iPads. This provides users, both local and remote, with a succinct summary of data collection, visualization of diffraction images and crystals, and key metrics for data quality in real time.text/htmlSynchLink: an iOS app for ISPyBtext5472014-09-04Copyright (c) 2014 Helen Mary Ginn et al.Journal of Applied Crystallographycomputer programs00The lipid cubic phase or in meso method for crystallizing proteins. Bushings for better manual dispensing
http://scripts.iucr.org/cgi-bin/paper?gj5123
The lipid cubic phase or in meso method can be used to set up crystallization trials of soluble and membrane proteins. The cubic phase is noted for being a sticky and viscous mesophase. Dispensing the protein-laden mesophase by hand into wells on crystallization plates has been facilitated by the use of an inexpensive repeat dispenser. However, the assembled dispensing device is prone to damage. Specifically, the delicate plunger used to dispense the viscous mesophase by positive displacement can be bent and scarred when the locking nut that fixes the plunger to the ratchet-driven dispensing mechanism is inadvertently overtightened. A defective plunger can render the device useless as a dispensing tool. More importantly, it can lead to catastrophic loss of valuable protein and lipid due to leakage when the dispensing syringe is being recharged with fresh mesophase. This note describes two types of bushings designed to protect the plunger from mechanical damage, which provide facile and reliable dispenser performance. One is a split bushing in brass and is a highly durable solution. The other is a small sleeve made from readily available plastic tubing. While it lacks durability, the plastic sleeve is simple yet highly effective, and can be replaced as the need arises.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Caffrey, M.Eifert, R.Li, D.Howe, N.2014-08-16doi:10.1107/S1600576714015702International Union of CrystallographyBushings that protect the plunger in a repeat dispenser device for more effective setting up of lipid cubic phase crystallization trials are described.ENlipid cubic phasein meso crystallizationmembrane protein crystallizationdispensing devicesThe lipid cubic phase or in meso method can be used to set up crystallization trials of soluble and membrane proteins. The cubic phase is noted for being a sticky and viscous mesophase. Dispensing the protein-laden mesophase by hand into wells on crystallization plates has been facilitated by the use of an inexpensive repeat dispenser. However, the assembled dispensing device is prone to damage. Specifically, the delicate plunger used to dispense the viscous mesophase by positive displacement can be bent and scarred when the locking nut that fixes the plunger to the ratchet-driven dispensing mechanism is inadvertently overtightened. A defective plunger can render the device useless as a dispensing tool. More importantly, it can lead to catastrophic loss of valuable protein and lipid due to leakage when the dispensing syringe is being recharged with fresh mesophase. This note describes two types of bushings designed to protect the plunger from mechanical damage, which provide facile and reliable dispenser performance. One is a split bushing in brass and is a highly durable solution. The other is a small sleeve made from readily available plastic tubing. While it lacks durability, the plastic sleeve is simple yet highly effective, and can be replaced as the need arises.text/htmlThe lipid cubic phase or in meso method for crystallizing proteins. Bushings for better manual dispensingtext5472014-08-16Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallographylaboratory notes00