Open-access and free articles in Acta Crystallographica Section A: Foundations of Crystallography
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Acta Crystallographica Section A: Foundations and Advances covers theoretical and fundamental aspects of the structure of matter. The journal is the prime forum for research in diffraction physics and the theory of crystallographic structure determination by diffraction methods using X-rays, neutrons and electrons. The structures include periodic and aperiodic crystals, and non-periodic disordered materials, and the corresponding Bragg, satellite and diffuse scattering, thermal motion and symmetry aspects. Spatial resolutions range from the subatomic domain in charge-density studies to nanodimensional imperfections such as dislocations and twin walls. The chemistry encompasses metals, alloys, and inorganic, organic and biological materials. Structure prediction and properties such as the theory of phase transformations are also covered.en-gbCopyright (c) 2018 International Union of CrystallographyInternational Union of CrystallographyInternational Union of Crystallographyhttps://journals.iucr.orgurn:issn:0108-7673Acta Crystallographica Section A: Foundations and Advances covers theoretical and fundamental aspects of the structure of matter. The journal is the prime forum for research in diffraction physics and the theory of crystallographic structure determination by diffraction methods using X-rays, neutrons and electrons. The structures include periodic and aperiodic crystals, and non-periodic disordered materials, and the corresponding Bragg, satellite and diffuse scattering, thermal motion and symmetry aspects. Spatial resolutions range from the subatomic domain in charge-density studies to nanodimensional imperfections such as dislocations and twin walls. The chemistry encompasses metals, alloys, and inorganic, organic and biological materials. Structure prediction and properties such as the theory of phase transformations are also covered.text/htmlOpen-access and free articles in Acta Crystallographica Section A Foundations and Advancestextyearly62002-01-01T00:00+00:00med@iucr.orgActa Crystallographica Section A Foundations and AdvancesCopyright (c) 2018 International Union of Crystallographyurn:issn:0108-7673Open-access and free articles in Acta Crystallographica Section A: Foundations of Crystallographyhttp://journals.iucr.org/logos/rss10a.gif
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Still imageRigid units revisited
http://scripts.iucr.org/cgi-bin/paper?me6016
Copyright (c) 2018 International Union of Crystallographyurn:issn:2053-2733Phillips, A.E.2018-09-01doi:10.1107/S2053273318012007International Union of CrystallographyRigid-unit modes, which allow coordination polyhedra to remain undistorted and hence cost little energy, provide a way of understanding many important physical properties. Campbell et al. [Acta Cryst. (2018). A74, 408–424] have developed an elegant new algebraic approach to finding these distortion modes.enRIGID-UNIT MODES; SILICATES; PEROVSKITES; TUNGSTEN BRONZEStext/htmlRigid units revisitedtext745Copyright (c) 2018 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2018-09-01406scientific commentaries2053-2733September 2018med@iucr.org4072053-2733Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?td9026
Corrections are made to Table 1 in the article by van Genderen et al. [Acta Cryst. (2016), A72, 236–242].https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733van Genderen, E.Clabbers, M.T.B.Das, P.P.Stewart, A.Nederlof, I.Barentsen, K.C.Portillo, Q.Pannu, N.S.Nicolopoulos, S.Gruene, T.Abrahams, J.P.2018-10-30doi:10.1107/S2053273318014079International Union of CrystallographyA correction is made to the article by van Genderen et al. [Acta Cryst. (2016), A72, 236–242].enELECTRON NANOCRYSTALLOGRAPHY; TIMEPIX QUANTUM AREA DETECTOR; CARBAMAZEPINE; NICOTINIC ACID; ELECTRON DIFFRACTION STRUCTURE DETERMINATIONCorrections are made to Table 1 in the article by van Genderen et al. [Acta Cryst. (2016), A72, 236–242].text/htmlAb initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector. Corrigendumtext6742018-10-30Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733addenda and errata709med@iucr.orgNovember 20187092053-2733Atomic scale analyses of {\bb Z}-module defects in an NiZr alloy
http://scripts.iucr.org/cgi-bin/paper?td5054
Some specific structures of intermetallic alloys, like approximants of quasicrystals, have their unit cells and most of their atoms located on a periodic fraction of the nodes of a unique {\bb Z}-module [a set of the irrational projections of the nodes of a (N > 3-dimensional) lattice]. Those hidden internal symmetries generate possible new kinds of defects like coherent twins, translation defects and so-called module dislocations that have already been discussed elsewhere [Quiquandon et al. (2016). Acta Cryst. A72, 55–61; Sirindil et al. (2017). Acta Cryst. A73, 427–437]. Presented here are electron microscopy observations of the orthorhombic phase NiZr – and its low-temperature monoclinic variant – which reveal the existence of such defects based on the underlying {\bb Z}-module generated by the five vertices of the regular pentagon. New high-resolution electron microscopy (HREM) and scanning transmission electron microscopy high-angle annular dark-field (STEM-HAADF) observations demonstrate the agreement between the geometrical description of the structure in five dimensions and the experimental observations of fivefold twins and translation defects.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Sirindil, A.Kobold, R.Mompiou, F.Lartigue-Korinek, S.Perriere, L.Patriarche, G.Quiquandon, M.Gratias, D.2018-10-04doi:10.1107/S2053273318011439International Union of CrystallographyThis article describes the observation and determination of {\bb Z}-module defects (twins, translation faults and module dislocations) in NiZr by high-resolution electron microscopy (HREM), and scanning transmission electron microscopy bright-field (STEM-BF) and high-angle annular dark-field (STEM-HAADF).en{\BB Z}-MODULE; DEFECTS; TWINS; DISLOCATIONS; HREM-HAADFSome specific structures of intermetallic alloys, like approximants of quasicrystals, have their unit cells and most of their atoms located on a periodic fraction of the nodes of a unique {\bb Z}-module [a set of the irrational projections of the nodes of a (N > 3-dimensional) lattice]. Those hidden internal symmetries generate possible new kinds of defects like coherent twins, translation defects and so-called module dislocations that have already been discussed elsewhere [Quiquandon et al. (2016). Acta Cryst. A72, 55–61; Sirindil et al. (2017). Acta Cryst. A73, 427–437]. Presented here are electron microscopy observations of the orthorhombic phase NiZr – and its low-temperature monoclinic variant – which reveal the existence of such defects based on the underlying {\bb Z}-module generated by the five vertices of the regular pentagon. New high-resolution electron microscopy (HREM) and scanning transmission electron microscopy high-angle annular dark-field (STEM-HAADF) observations demonstrate the agreement between the geometrical description of the structure in five dimensions and the experimental observations of fivefold twins and translation defects.text/htmlAtomic scale analyses of {\bb Z}-module defects in an NiZr alloytext746https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-10-04research papers2053-2733November 2018med@iucr.org2053-2733Calculation of absorption and secondary scattering of X-rays by spherical amorphous materials in an asymmetric transmission geometry. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?ib9014
A revised version of Table 2 of Bendert et al. [Acta Cryst. (2013). A69, 131–139] is provided.Copyright (c) 2018 International Union of Crystallographyurn:issn:2053-2733Bendert, J.C.Blodgett, M.E.Kelton, K.F.2018-09-01doi:10.1107/S205327331801166XInternational Union of CrystallographyCorrections to Table 2 in Bendert et al. [Acta Cryst. (2013). A69, 131–139] are reported.enX-RAY SCATTERING; ATTENUATION CORRECTION FACTORS; SECONDARY SCATTERINGA revised version of Table 2 of Bendert et al. [Acta Cryst. (2013). A69, 131–139] is provided.text/htmlCalculation of absorption and secondary scattering of X-rays by spherical amorphous materials in an asymmetric transmission geometry. Corrigendumtext745Copyright (c) 2018 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2018-09-01613addenda and errata2053-2733September 2018med@iucr.org6132053-2733A symmetry roadmap to new perovskite multiferroics
http://scripts.iucr.org/cgi-bin/paper?me6013
Copyright (c) 2018 International Union of Crystallographyurn:issn:2053-2733Woodward, P.M.2018-07-05doi:10.1107/S2053273318009294International Union of CrystallographyThe new approach to the design of technologically important perovskites described by Senn and Bristowe [Acta Cryst. (2018), A74, 303–321] is discussed.enPEROVSKITES; MULTIFERROICS; SYMMETRYtext/htmlA symmetry roadmap to new perovskite multiferroicstext4742018-07-05Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2018 International Union of Crystallography2053-2733scientific commentaries291med@iucr.orgJuly 20182922053-2733Specular reflection intensity modulated by grazing-incidence diffraction in a wide angular range
http://scripts.iucr.org/cgi-bin/paper?wo5025
Grazing-incidence X-ray diffraction (GID) is a well known technique for the characterization of crystal surfaces. A theoretical study has been performed of the sensitivity of GID to the structure of a crystal surface and distorted nanometre-thin surface layers. To simulate GID from crystals that have a complex subsurface structure, a matrix formalism of the dynamical diffraction theory has been applied. It has been found that the azimuthal rocking curves of a crystal that has a distorted subsurface, measured over a wide angular range, show asymmetric thickness oscillations with two distinguishable sets of frequencies: one corresponding to the diffraction in the single-crystal subsurface layer and the second corresponding to the diffraction in the single-crystal substrate. Therefore, azimuthal rocking curves allow characterization of the subsurface structure of a single crystal. Furthermore, thickness oscillations induced by evanescent diffraction modulate the specular reflection intensity, showing high-intensity modulations. This will potentially allow implementation of subsurface crystal characterization using, for instance, a laboratory-scale X-ray diffractometer.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Nikolaev, K.V.Makhotkin, I.A.Yakunin, S.N.Kruijs, R.W.E.Chuev, M.A.Bijkerk, F.2018-09-01doi:10.1107/S2053273318008963International Union of CrystallographyA theoretical description is given of the novel X-ray diffraction effect in single-crystal structures with a distorted crystal subsurface based on the dynamical theory of diffraction.enCRYSTAL SURFACE; GRAZING-INCIDENCE X-RAY DIFFRACTION; GID; SPECULAR REFLECTION; AZIMUTHAL ROCKING CURVESGrazing-incidence X-ray diffraction (GID) is a well known technique for the characterization of crystal surfaces. A theoretical study has been performed of the sensitivity of GID to the structure of a crystal surface and distorted nanometre-thin surface layers. To simulate GID from crystals that have a complex subsurface structure, a matrix formalism of the dynamical diffraction theory has been applied. It has been found that the azimuthal rocking curves of a crystal that has a distorted subsurface, measured over a wide angular range, show asymmetric thickness oscillations with two distinguishable sets of frequencies: one corresponding to the diffraction in the single-crystal subsurface layer and the second corresponding to the diffraction in the single-crystal substrate. Therefore, azimuthal rocking curves allow characterization of the subsurface structure of a single crystal. Furthermore, thickness oscillations induced by evanescent diffraction modulate the specular reflection intensity, showing high-intensity modulations. This will potentially allow implementation of subsurface crystal characterization using, for instance, a laboratory-scale X-ray diffractometer.text/htmlSpecular reflection intensity modulated by grazing-incidence diffraction in a wide angular rangetext745https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-09-01545research papers2053-2733September 2018med@iucr.org5522053-2733Estimating the structure factors in X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?vk5022
This article takes the concepts of the `new diffraction theory' [Fewster (2014). Acta Cryst. A70, 257–282] and examines the implications for the interpretation of experimental results and the estimation of structure factors. Further experimental evidence is included to justify the conclusions in the theory, showing that the residual intensity at twice the Bragg angle is a diffraction effect and not associated with the crystal shape. This `enhancement' effect is independent of whether kinematical or dynamical theories are applied and can lead to a clearer understanding of how the dynamical effects are suppressed in imperfect crystals. By applying the idea that the higher-order peaks are due to path lengths of nλ, it is shown that `systematically absent' reflections in the conventional theory may not be absent. Because this new theory considers the intensity to be more distributed, it suggests that the entire structure factor can be difficult to capture by experiment. This article suggests some routes to achieve a good approximation of the structure factors for typical methods of data collection. Any measurement of intensity with background removal will exclude some of the distributed intensity, again leading to an underestimate of the structure factors, and therefore the missing intensity needs to be estimated.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Fewster, P.F.2018-08-08doi:10.1107/S2053273318007593International Union of CrystallographyThe meaning of the structure factor and how it impacts on the determination of structures are reassessed. A route to obtaining the structure factors is presented for several data collection methods and crystal qualities.enSTRUCTURE FACTORS; IMPERFECT CRYSTALS; DIFFRACTION THEORY; SERIAL CRYSTALLOGRAPHY; POWDER DIFFRACTIONThis article takes the concepts of the `new diffraction theory' [Fewster (2014). Acta Cryst. A70, 257–282] and examines the implications for the interpretation of experimental results and the estimation of structure factors. Further experimental evidence is included to justify the conclusions in the theory, showing that the residual intensity at twice the Bragg angle is a diffraction effect and not associated with the crystal shape. This `enhancement' effect is independent of whether kinematical or dynamical theories are applied and can lead to a clearer understanding of how the dynamical effects are suppressed in imperfect crystals. By applying the idea that the higher-order peaks are due to path lengths of nλ, it is shown that `systematically absent' reflections in the conventional theory may not be absent. Because this new theory considers the intensity to be more distributed, it suggests that the entire structure factor can be difficult to capture by experiment. This article suggests some routes to achieve a good approximation of the structure factors for typical methods of data collection. Any measurement of intensity with background removal will exclude some of the distributed intensity, again leading to an underestimate of the structure factors, and therefore the missing intensity needs to be estimated.text/htmlEstimating the structure factors in X-ray diffractiontext745https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-08-08481research papers2053-2733September 2018med@iucr.org4982053-2733Response to Fraser & Wark's comments on A new theory for X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?ae5046
The criticisms of my theory, as given by Fraser & Wark [(2018), Acta Cryst. A74, 447–456], are built on a misunderstanding of the concept and the methodology I have used. The assumption they have made rules out my description from which they conclude that my theory is proved to be wrong. They assume that I have misunderstood the diffraction associated with the shape of a crystal and my calculation is only relevant to a parallelepiped and even that I have got wrong. It only appears wrong to Fraser & Wark because the effect I predict has nothing to do with the crystal shape. The effect though can be measured as well as the crystal shape effects. This response describes my reasoning behind the theory, how it can be related to the Ewald sphere construction, and the build-up of the full diffraction pattern from all the scatterers in a stack of planes. It is the latter point that makes the Fraser & Wark analysis incomplete. The description given in this article describes my approach much more precisely with reference to the Ewald sphere construction. Several experiments are described that directly measure the predictions of the new theory, which are explained with reference to the Ewald sphere description. In its simplest terms the new theory can be considered as giving a thickness to the Ewald sphere surface, whereas in the conventional theory it has no thickness. Any thickness immediately informs us that the scattering from a peak at the Bragg angle does not have to be in the Bragg condition to be observed. I believe the conventional theory is a very good approximation, but as soon as it is tested with careful experiments it is shown to be incomplete. The new theory puts forward the idea that there is persistent intensity at the Bragg scattering angle outside the Bragg condition. This intensity is weak (∼10−5) but can be observed in careful laboratory experiments, despite being on the limit of observation, yet it has a profound impact on how we should interpret diffraction patterns.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Fewster, P.F.2018-07-18doi:10.1107/S2053273318007489International Union of CrystallographyIn response to the comments by Fraser & Wark [(2018), Acta Cryst. A74, 447–456], experimental evidence and an explanation of the new theory in the context of a modified Ewald sphere construction are presented.enDIFFRACTION THEORY; POWDER DIFFRACTION; SMALL CRYSTALSThe criticisms of my theory, as given by Fraser & Wark [(2018), Acta Cryst. A74, 447–456], are built on a misunderstanding of the concept and the methodology I have used. The assumption they have made rules out my description from which they conclude that my theory is proved to be wrong. They assume that I have misunderstood the diffraction associated with the shape of a crystal and my calculation is only relevant to a parallelepiped and even that I have got wrong. It only appears wrong to Fraser & Wark because the effect I predict has nothing to do with the crystal shape. The effect though can be measured as well as the crystal shape effects. This response describes my reasoning behind the theory, how it can be related to the Ewald sphere construction, and the build-up of the full diffraction pattern from all the scatterers in a stack of planes. It is the latter point that makes the Fraser & Wark analysis incomplete. The description given in this article describes my approach much more precisely with reference to the Ewald sphere construction. Several experiments are described that directly measure the predictions of the new theory, which are explained with reference to the Ewald sphere description. In its simplest terms the new theory can be considered as giving a thickness to the Ewald sphere surface, whereas in the conventional theory it has no thickness. Any thickness immediately informs us that the scattering from a peak at the Bragg angle does not have to be in the Bragg condition to be observed. I believe the conventional theory is a very good approximation, but as soon as it is tested with careful experiments it is shown to be incomplete. The new theory puts forward the idea that there is persistent intensity at the Bragg scattering angle outside the Bragg condition. This intensity is weak (∼10−5) but can be observed in careful laboratory experiments, despite being on the limit of observation, yet it has a profound impact on how we should interpret diffraction patterns.text/htmlResponse to Fraser & Wark's comments on A new theory for X-ray diffractiontext745https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-07-18457research papers2053-2733September 2018med@iucr.org4652053-2733A group-theoretical approach to enumerating magnetoelectric and multiferroic couplings in perovskites
http://scripts.iucr.org/cgi-bin/paper?ou5003
A group-theoretical approach is used to enumerate the possible couplings between magnetism and ferroelectric polarization in the parent Pm{\overline 3}m perovskite structure. It is shown that third-order magnetoelectric coupling terms must always involve magnetic ordering at the A and B sites which either transforms both as R-point or both as X-point time-odd irreducible representations (irreps). For fourth-order couplings it is demonstrated that this criterion may be relaxed allowing couplings involving irreps at X-, M- and R-points which collectively conserve crystal momentum, producing a magnetoelectric effect arising from only B-site magnetic order. In this case, exactly two of the three irreps entering the order parameter must be time-odd irreps and either one or all must be odd with respect to inversion symmetry. It is possible to show that the time-even irreps in this triad must transform as one of: X1+, M3,5− or R5+, corresponding to A-site cation order, A-site antipolar displacements or anion rocksalt ordering, respectively. This greatly reduces the search space for type-II multiferroic perovskites. Similar arguments are used to demonstrate how weak ferromagnetism may be engineered and a variety of schemes are proposed for coupling this to ferroelectric polarization. The approach is illustrated with density functional theory calculations on magnetoelectric couplings and, by considering the literature, suggestions are given of which avenues of research are likely to be most promising in the design of novel magnetoelectric materials.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Senn, M.S.Bristowe, N.C.2018-07-05doi:10.1107/S2053273318007441International Union of CrystallographyA symmetry-motivated approach for designing perovskites with ferroic and magnetoelectric couplings is proposed. The results highlight which kinds of magnetic orderings and structural distortions need to coexist within the same structure to produce the desired couplings.enMAGNETOELECTRIC COUPLINGS; MULTIFERROIC COUPLINGS; PEROVSKITES; IMPROPER FERROELECTRICITY; GROUP THEORY; IRREP ANALYSIS; ANHARMONIC COUPLINGSA group-theoretical approach is used to enumerate the possible couplings between magnetism and ferroelectric polarization in the parent Pm{\overline 3}m perovskite structure. It is shown that third-order magnetoelectric coupling terms must always involve magnetic ordering at the A and B sites which either transforms both as R-point or both as X-point time-odd irreducible representations (irreps). For fourth-order couplings it is demonstrated that this criterion may be relaxed allowing couplings involving irreps at X-, M- and R-points which collectively conserve crystal momentum, producing a magnetoelectric effect arising from only B-site magnetic order. In this case, exactly two of the three irreps entering the order parameter must be time-odd irreps and either one or all must be odd with respect to inversion symmetry. It is possible to show that the time-even irreps in this triad must transform as one of: X1+, M3,5− or R5+, corresponding to A-site cation order, A-site antipolar displacements or anion rocksalt ordering, respectively. This greatly reduces the search space for type-II multiferroic perovskites. Similar arguments are used to demonstrate how weak ferromagnetism may be engineered and a variety of schemes are proposed for coupling this to ferroelectric polarization. The approach is illustrated with density functional theory calculations on magnetoelectric couplings and, by considering the literature, suggestions are given of which avenues of research are likely to be most promising in the design of novel magnetoelectric materials.text/htmlA group-theoretical approach to enumerating magnetoelectric and multiferroic couplings in perovskitestext744https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-07-05308research papers2053-2733July 2018med@iucr.org3212053-2733Ted Janssen (1936–2017)
http://scripts.iucr.org/cgi-bin/paper?es5003
urn:issn:2053-2733Souvignier, B.2018-06-06doi:10.1107/S2053273318007088International Union of CrystallographyObituary for Ted Janssen.enOBITUARY; N-DIMENSIONAL CRYSTALLOGRAPHY; APERIODIC STRUCTURES; SUPERSPACE APPROACHtext/htmlTed Janssen (1936–2017) text4742018-06-06Acta Crystallographica Section A: Foundations and Advances2053-2733obituaries403med@iucr.orgJuly 20184042053-2733Indexing of grazing-incidence X-ray diffraction patterns: the case of fibre-textured thin films
http://scripts.iucr.org/cgi-bin/paper?wo5026
Crystal structure solutions from thin films are often performed by grazing-incidence X-ray diffraction (GIXD) experiments. In particular, on isotropic substrates the thin film crystallites grow in a fibre texture showing a well defined crystallographic plane oriented parallel to the substrate surface with random in-plane order of the microcrystallites forming the film. In the present work, analytical mathematical expressions are derived for indexing experimental diffraction patterns, a highly challenging task which hitherto mainly relied on trial-and-error approaches. The six lattice constants a, b, c, α, β and γ of the crystallographic unit cell are thereby determined, as well as the rotation parameters due to the unknown preferred orientation of the crystals with respect to the substrate surface. The mathematical analysis exploits a combination of GIXD data and information acquired by the specular X-ray diffraction. The presence of a sole specular diffraction peak series reveals fibre-textured growth with a crystallographic plane parallel to the substrate, which allows establishment of the Miller indices u, v and w as the rotation parameters. Mathematical expressions are derived which reduce the system of unknown parameters from the three- to the two-dimensional space. Thus, in the first part of the indexing routine, the integers u and v as well as the Laue indices h and k of the experimentally observed diffraction peaks are assigned by systematically varying the integer variables, and by calculating the three lattice parameters a, b and γ. Because of the symmetry of the derived equations, determining the missing parameters then becomes feasible: (i) w of the surface parallel plane, (ii) the Laue indices l of the diffraction peak and (iii) analogously the lattice constants c, α and ß. In a subsequent step, the reduced unit-cell geometry can be identified. Finally, the methodology is demonstrated by application to an example, indexing the diffraction pattern of a thin film of the organic semiconductor pentacenequinone grown on the (0001) surface of highly oriented pyrolytic graphite. The preferred orientation of the crystallites, the lattice constants of the triclinic unit cell and finally, by molecular modelling, the full crystal structure solution of the as-yet-unknown polymorph of pentacenequinone are determined.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Simbrunner, J.Simbrunner, C.Schrode, B.Röthel, C.Bedoya-Martinez, N.Salzmann, I.Resel, R.2018-07-05doi:10.1107/S2053273318006629International Union of CrystallographyCrystal structure solutions from fibre-textured crystals within thin films are frequently achieved by grazing-incidence X-ray diffraction experiments. In the present work, analytical mathematical expressions are derived for the indexing of experimental diffraction patterns.enGRAZING-INCIDENCE X-RAY DIFFRACTION; THIN FILMS; INDEXING; SPECULAR SCAN; MATHEMATICAL CRYSTALLOGRAPHYCrystal structure solutions from thin films are often performed by grazing-incidence X-ray diffraction (GIXD) experiments. In particular, on isotropic substrates the thin film crystallites grow in a fibre texture showing a well defined crystallographic plane oriented parallel to the substrate surface with random in-plane order of the microcrystallites forming the film. In the present work, analytical mathematical expressions are derived for indexing experimental diffraction patterns, a highly challenging task which hitherto mainly relied on trial-and-error approaches. The six lattice constants a, b, c, α, β and γ of the crystallographic unit cell are thereby determined, as well as the rotation parameters due to the unknown preferred orientation of the crystals with respect to the substrate surface. The mathematical analysis exploits a combination of GIXD data and information acquired by the specular X-ray diffraction. The presence of a sole specular diffraction peak series reveals fibre-textured growth with a crystallographic plane parallel to the substrate, which allows establishment of the Miller indices u, v and w as the rotation parameters. Mathematical expressions are derived which reduce the system of unknown parameters from the three- to the two-dimensional space. Thus, in the first part of the indexing routine, the integers u and v as well as the Laue indices h and k of the experimentally observed diffraction peaks are assigned by systematically varying the integer variables, and by calculating the three lattice parameters a, b and γ. Because of the symmetry of the derived equations, determining the missing parameters then becomes feasible: (i) w of the surface parallel plane, (ii) the Laue indices l of the diffraction peak and (iii) analogously the lattice constants c, α and ß. In a subsequent step, the reduced unit-cell geometry can be identified. Finally, the methodology is demonstrated by application to an example, indexing the diffraction pattern of a thin film of the organic semiconductor pentacenequinone grown on the (0001) surface of highly oriented pyrolytic graphite. The preferred orientation of the crystallites, the lattice constants of the triclinic unit cell and finally, by molecular modelling, the full crystal structure solution of the as-yet-unknown polymorph of pentacenequinone are determined.text/htmlIndexing of grazing-incidence X-ray diffraction patterns: the case of fibre-textured thin filmstext4742018-07-05Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733research papers373med@iucr.orgJuly 20183872053-2733A method to estimate statistical errors of properties derived from charge-density modelling
http://scripts.iucr.org/cgi-bin/paper?ae5043
Estimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating charge-density models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variance–covariance matrix issued from the least-squares refinement. This `SSD methodology' procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure. The method is exemplified with the charge density of compound (E)-5-phenylpent-1-enylboronic acid, refined at 0.45 Å resolution. The procedure is implemented in the freely available MoPro program dedicated to charge-density refinement and modelling.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Fournier, B.Guillot, B.Lecomte, C.Escudero-Adán, E.C.Jelsch, C.2018-05-03doi:10.1107/S2053273318004308International Union of CrystallographyErrors on molecular properties including the topology of electron density and electrostatics are estimated from a sample of deviating models generated using the variance–covariance matrix issued at the end of the charge-density refinement.enMONTE CARLO METHODS; ELECTRON DENSITY; UNCERTAINTY; TOPOLOGY; INTERMOLECULAR INTERACTIONSEstimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating charge-density models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variance–covariance matrix issued from the least-squares refinement. This `SSD methodology' procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure. The method is exemplified with the charge density of compound (E)-5-phenylpent-1-enylboronic acid, refined at 0.45 Å resolution. The procedure is implemented in the freely available MoPro program dedicated to charge-density refinement and modelling.text/htmlA method to estimate statistical errors of properties derived from charge-density modellingtext3742018-05-03Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733research papers170med@iucr.orgMay 20181832053-2733Comments on A new theory for X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?ae5039
In an article entitled A new theory for X-ray diffraction [Fewster (2014). Acta Cryst. A70, 257–282], hereafter referred to as NTXRD, it is claimed that when X-rays are scattered from a small crystallite, whatever its size and shape, the diffraction pattern will contain enhanced scattering at angles of exactly 2θB, whatever the orientation of the crystal. It is claimed that in this way scattering from a powder, with randomly oriented crystals, gives rise to Bragg scattering even if the Bragg condition is never satisfied by an individual crystallite. The claims of the theory put forward in NTXRD are examined and they are found to be in error. Whilst for a certain restricted set of shapes of crystals it is possible to obtain some diffraction close to (but not exactly at) the Bragg angle as the crystallite is oriented away from the Bragg condition, this is generally not the case. Furthermore, contrary to the claims made within NTXRD, the recognition of the origin of the type of effects described is not new, and has been known since the earliest days of X-ray diffraction.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Fraser, J.T.Wark, J.S.2018-07-18doi:10.1107/S2053273318003959International Union of CrystallographyFewster [(2014), Acta Cryst. A70, 257–282] claimed that a new theory of X-ray diffraction is required, and that small crystallites will give rise to scattering at angles of exactly twice the Bragg angle, whatever their orientation. This article demonstrates that this theory is in error.enDIFFRACTION THEORY; POWDER DIFFRACTION; SMALL CRYSTALSIn an article entitled A new theory for X-ray diffraction [Fewster (2014). Acta Cryst. A70, 257–282], hereafter referred to as NTXRD, it is claimed that when X-rays are scattered from a small crystallite, whatever its size and shape, the diffraction pattern will contain enhanced scattering at angles of exactly 2θB, whatever the orientation of the crystal. It is claimed that in this way scattering from a powder, with randomly oriented crystals, gives rise to Bragg scattering even if the Bragg condition is never satisfied by an individual crystallite. The claims of the theory put forward in NTXRD are examined and they are found to be in error. Whilst for a certain restricted set of shapes of crystals it is possible to obtain some diffraction close to (but not exactly at) the Bragg angle as the crystallite is oriented away from the Bragg condition, this is generally not the case. Furthermore, contrary to the claims made within NTXRD, the recognition of the origin of the type of effects described is not new, and has been known since the earliest days of X-ray diffraction.text/htmlComments on A new theory for X-ray diffractiontext745https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-07-18447research papers2053-2733September 2018med@iucr.org4562053-2733Precise implications for real-space pair distribution function modeling of effects intrinsic to modern time-of-flight neutron diffractometers
http://scripts.iucr.org/cgi-bin/paper?ib5055
Total scattering and pair distribution function (PDF) methods allow for detailed study of local atomic order and disorder, including materials for which Rietveld refinements are not traditionally possible (amorphous materials, liquids, glasses and nanoparticles). With the advent of modern neutron time-of-flight (TOF) instrumentation, total scattering studies are capable of producing PDFs with ranges upwards of 100–200 Å, covering the correlation length scales of interest for many materials under study. Despite this, the refinement and subsequent analysis of data are often limited by confounding factors that are not rigorously accounted for in conventional analysis programs. While many of these artifacts are known and recognized by experts in the field, their effects and any associated mitigation strategies largely exist as passed-down `tribal' knowledge in the community, and have not been concisely demonstrated and compared in a unified presentation. This article aims to explicitly demonstrate, through reviews of previous literature, simulated analysis and real-world case studies, the effects of resolution, binning, bounds, peak shape, peak asymmetry, inconsistent conversion of TOF to d spacing and merging of multiple banks in neutron TOF data as they directly relate to real-space PDF analysis. Suggestions for best practice in analysis of data from modern neutron TOF total scattering instruments when using conventional analysis programs are made, as well as recommendations for improved analysis methods and future instrument design.urn:issn:2053-2733Olds, D.Saunders, C.N.Peters, M.Proffen, T.Neuefeind, J.Page, K.2018-06-06doi:10.1107/S2053273318003224International Union of CrystallographyA systematic overview of the effects of common aberrations in time-of-flight neutron powder diffraction data on real-space pair distribution functions is provided, and methods and best practices to mitigate these effects are discussed.enTOTAL SCATTERING; PAIR DISTRIBUTION FUNCTION; INSTRUMENT RESOLUTION FUNCTION; TIME-OF-FLIGHT PEAK SHAPESTotal scattering and pair distribution function (PDF) methods allow for detailed study of local atomic order and disorder, including materials for which Rietveld refinements are not traditionally possible (amorphous materials, liquids, glasses and nanoparticles). With the advent of modern neutron time-of-flight (TOF) instrumentation, total scattering studies are capable of producing PDFs with ranges upwards of 100–200 Å, covering the correlation length scales of interest for many materials under study. Despite this, the refinement and subsequent analysis of data are often limited by confounding factors that are not rigorously accounted for in conventional analysis programs. While many of these artifacts are known and recognized by experts in the field, their effects and any associated mitigation strategies largely exist as passed-down `tribal' knowledge in the community, and have not been concisely demonstrated and compared in a unified presentation. This article aims to explicitly demonstrate, through reviews of previous literature, simulated analysis and real-world case studies, the effects of resolution, binning, bounds, peak shape, peak asymmetry, inconsistent conversion of TOF to d spacing and merging of multiple banks in neutron TOF data as they directly relate to real-space PDF analysis. Suggestions for best practice in analysis of data from modern neutron TOF total scattering instruments when using conventional analysis programs are made, as well as recommendations for improved analysis methods and future instrument design.text/htmlPrecise implications for real-space pair distribution function modeling of effects intrinsic to modern time-of-flight neutron diffractometerstext4742018-06-06Acta Crystallographica Section A: Foundations and Advances2053-2733feature articles293med@iucr.orgJuly 20183072053-2733Spatial displacement of forward-diffracted X-ray beams by perfect crystals
http://scripts.iucr.org/cgi-bin/paper?sc5112
Time-delayed, narrow-band echoes generated by forward Bragg diffraction of an X-ray pulse by a perfect thin crystal are exploited for self-seeding at hard X-ray free-electron lasers. Theoretical predictions indicate that the retardation is strictly correlated to a transverse displacement of the echo pulses. This article reports the first experimental observation of the displaced echoes. The displacements are in good agreement with simulations relying on the dynamical diffraction theory. The echo signals are characteristic for a given Bragg reflection, the structure factor and the probed interplane distance. The reported results pave the way to exploiting the signals as an online diagnostic tool for hard X-ray free-electron laser seeding and for dynamical diffraction investigations of strain at the femtosecond timescale.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Rodriguez-Fernandez, A.Esposito, V.Sanchez, D.F.Finkelstein, K.D.Juranic, P.Staub, U.Grolimund, D.Reiche, S.Pedrini, B.2018-02-23doi:10.1107/S2053273318001419International Union of CrystallographyThe first experimental observation of transverse spatial echoes generated by forward Bragg diffraction of an X-ray beam propagating through a perfect thin crystal is reported.enX-RAY DYNAMICAL DIFFRACTION; PERFECT CRYSTALS; TRANSVERSE ECHO DISPLACEMENT; HARD X-RAY SELF-SEEDINGTime-delayed, narrow-band echoes generated by forward Bragg diffraction of an X-ray pulse by a perfect thin crystal are exploited for self-seeding at hard X-ray free-electron lasers. Theoretical predictions indicate that the retardation is strictly correlated to a transverse displacement of the echo pulses. This article reports the first experimental observation of the displaced echoes. The displacements are in good agreement with simulations relying on the dynamical diffraction theory. The echo signals are characteristic for a given Bragg reflection, the structure factor and the probed interplane distance. The reported results pave the way to exploiting the signals as an online diagnostic tool for hard X-ray free-electron laser seeding and for dynamical diffraction investigations of strain at the femtosecond timescale.text/htmlSpatial displacement of forward-diffracted X-ray beams by perfect crystalstext742https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-02-2375research papers2053-2733March 2018med@iucr.org872053-2733The development of powder profile refinement at the Reactor Centre Netherlands at Petten
http://scripts.iucr.org/cgi-bin/paper?ib5058
With thousands of references to `Rietveld refinement' it is forgotten that the method did not suddenly appear in a flash of inspiration of a single person, but was the result of the work of three individuals working in the 1960s at the Reactor Centre Netherlands at Petten, Loopstra, van Laar and Rietveld. This paper outlines the origins of `profile refinement', as it was called at Petten, and also looks at why it took so long for the scientific community to recognize its importance. With the recent passing of Hugo Rietveld, the death of Bert Loopstra in 1998 and before other pioneers also disappear, it is important to set down a first-hand account.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733van Laar, B.Schenk, H.2018-03-01doi:10.1107/S2053273317018435International Union of CrystallographyAround 1965 at the Reactor Centre Netherlands at Petten, Loopstra, van Laar and Rietveld developed `profile refinement'. Although Loopstra had the idea, van Laar worked it out mathematically and Rietveld wrote the computer program, the essential contributions of the first two are forgotten when using `Rietveld refinement'.enPOWDER PROFILE REFINEMENT; PROFILE REFINEMENT; RIETVELD REFINEMENTWith thousands of references to `Rietveld refinement' it is forgotten that the method did not suddenly appear in a flash of inspiration of a single person, but was the result of the work of three individuals working in the 1960s at the Reactor Centre Netherlands at Petten, Loopstra, van Laar and Rietveld. This paper outlines the origins of `profile refinement', as it was called at Petten, and also looks at why it took so long for the scientific community to recognize its importance. With the recent passing of Hugo Rietveld, the death of Bert Loopstra in 1998 and before other pioneers also disappear, it is important to set down a first-hand account.text/htmlThe development of powder profile refinement at the Reactor Centre Netherlands at Pettentext742https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-03-0188scientific comment2053-2733March 2018med@iucr.org922053-2733Quasicrystals: What do we know? What do we want to know? What can we know?
http://scripts.iucr.org/cgi-bin/paper?ib5056
More than 35 years and 11 000 publications after the discovery of quasicrystals by Dan Shechtman, quite a bit is known about their occurrence, formation, stability, structures and physical properties. It has also been discovered that quasiperiodic self-assembly is not restricted to intermetallics, but can take place in systems on the meso- and macroscales. However, there are some blank areas, even in the centre of the big picture. For instance, it has still not been fully clarified whether quasicrystals are just entropy-stabilized high-temperature phases or whether they can be thermodynamically stable at 0 K as well. More studies are needed for developing a generally accepted model of quasicrystal growth. The state of the art of quasicrystal research is briefly reviewed and the main as-yet unanswered questions are addressed, as well as the experimental limitations to finding answers to them. The focus of this discussion is on quasicrystal structure analysis as well as on quasicrystal stability and growth mechanisms.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Steurer, W.2018-01-01doi:10.1107/S2053273317016540International Union of CrystallographyThe state of the art of quasicrystal research is critically reviewed. Fundamental questions that are still unanswered are discussed and experimental limitations are considered.enQUASICRYSTALS; STRUCTURE ANALYSIS; HIGHER-DIMENSIONAL CRYSTALLOGRAPHY; STABILITY OF QUASICRYSTALS; QUASICRYSTAL GROWTHMore than 35 years and 11 000 publications after the discovery of quasicrystals by Dan Shechtman, quite a bit is known about their occurrence, formation, stability, structures and physical properties. It has also been discovered that quasiperiodic self-assembly is not restricted to intermetallics, but can take place in systems on the meso- and macroscales. However, there are some blank areas, even in the centre of the big picture. For instance, it has still not been fully clarified whether quasicrystals are just entropy-stabilized high-temperature phases or whether they can be thermodynamically stable at 0 K as well. More studies are needed for developing a generally accepted model of quasicrystal growth. The state of the art of quasicrystal research is briefly reviewed and the main as-yet unanswered questions are addressed, as well as the experimental limitations to finding answers to them. The focus of this discussion is on quasicrystal structure analysis as well as on quasicrystal stability and growth mechanisms.text/htmlQuasicrystals: What do we know? What do we want to know? What can we know?text741https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-01-011topical reviews2053-2733January 2018med@iucr.org112053-2733Small-angle X-ray scattering tensor tomography: model of the three-dimensional reciprocal-space map, reconstruction algorithm and angular sampling requirements
http://scripts.iucr.org/cgi-bin/paper?vk5021
Small-angle X-ray scattering tensor tomography, which allows reconstruction of the local three-dimensional reciprocal-space map within a three-dimensional sample as introduced by Liebi et al. [Nature (2015), 527, 349–352], is described in more detail with regard to the mathematical framework and the optimization algorithm. For the case of trabecular bone samples from vertebrae it is shown that the model of the three-dimensional reciprocal-space map using spherical harmonics can adequately describe the measured data. The method enables the determination of nanostructure orientation and degree of orientation as demonstrated previously in a single momentum transfer q range. This article presents a reconstruction of the complete reciprocal-space map for the case of bone over extended ranges of q. In addition, it is shown that uniform angular sampling and advanced regularization strategies help to reduce the amount of data required.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Liebi, M.Georgiadis, M.Kohlbrecher, J.Holler, M.Raabe, J.Usov, I.Menzel, A.Schneider, P.Bunk, O.Guizar-Sicairos, M.2018-01-01doi:10.1107/S205327331701614XInternational Union of CrystallographyThe mathematical framework and reconstruction algorithm for small-angle scattering tensor tomography are introduced in detail, as well as strategies which help to reduce the amount of data and therewith the measurement time required. Experimental validation is provided for the application to trabecular bone.enSMALL-ANGLE X-RAY SCATTERING; TENSOR TOMOGRAPHY; SPHERICAL HARMONICS; BONESmall-angle X-ray scattering tensor tomography, which allows reconstruction of the local three-dimensional reciprocal-space map within a three-dimensional sample as introduced by Liebi et al. [Nature (2015), 527, 349–352], is described in more detail with regard to the mathematical framework and the optimization algorithm. For the case of trabecular bone samples from vertebrae it is shown that the model of the three-dimensional reciprocal-space map using spherical harmonics can adequately describe the measured data. The method enables the determination of nanostructure orientation and degree of orientation as demonstrated previously in a single momentum transfer q range. This article presents a reconstruction of the complete reciprocal-space map for the case of bone over extended ranges of q. In addition, it is shown that uniform angular sampling and advanced regularization strategies help to reduce the amount of data required.text/htmlSmall-angle X-ray scattering tensor tomography: model of the three-dimensional reciprocal-space map, reconstruction algorithm and angular sampling requirementstext741https://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2018-01-0112research papers2053-2733January 2018med@iucr.org242053-2733