Acta Crystallographica Section A
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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.enCopyright (c) 2019 International Union of Crystallography2019-03-01International Union of CrystallographyInternational Union of Crystallographyhttp://journals.iucr.orgurn:issn:2053-2733Acta 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/htmlActa Crystallographica Section A: Foundations and Advances, Volume 75, Part 2, 2019textweekly62002-01-01T00:00+00:002752019-03-01Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances212urn:issn:2053-2733med@iucr.orgMarch 20192019-03-01Acta Crystallographica Section Ahttp://journals.iucr.org/logos/rss10a.gif
//journals.iucr.org/a/issues/2019/02/00/isscontsbdy.html
Still imageAperiodic order coming of age: from inorganic materials to dynamic protein superstructures
http://scripts.iucr.org/cgi-bin/paper?me6028
Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Borgstahl, G.Goldman, A.I.Thiel, P.A.2019-02-28doi:10.1107/S2053273319001165International Union of CrystallographyA collection of articles from presentations at the Aperiodic 2018 conference is introduced.ENAperiodic 2018aperiodic crystalsquasicrystalsincommensurate compositesincommensurate modulated phasesintergrowthsproteinstext/htmlAperiodic order coming of age: from inorganic materials to dynamic protein superstructurestext2752019-02-28Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aeditorial212213CO2 adsorption in Y zeolite: a structural and dynamic view by a novel principal-component-analysis-assisted in situ single-crystal X-ray diffraction experiment
http://scripts.iucr.org/cgi-bin/paper?sc5122
The increasing efficiency of detectors and brightness of X-rays in both laboratory and large-scale facilities allow the collection of full single-crystal X-ray data sets within minutes. The analysis of these `crystallographic big data' requires new tools and approaches. To answer these needs, the use of principal component analysis (PCA) is proposed to improve the efficiency and speed of the analysis. Potentialities and limitations of PCA were investigated using single-crystal X-ray diffraction (XRD) data collected in situ on Y zeolite, in which CO2, acting as an active species, is thermally adsorbed while cooling from 300 to 200 K. For the first time, thanks to the high sensitivity of single-crystal XRD, it was possible to determine the sites where CO2 is adsorbed, the increase in their occupancy while the temperature is decreased, and the correlated motion of active species, i.e. CO2, H2O and Na+. PCA allowed identification and elimination of problematic data sets, and better understanding of the trends of the occupancies of CO2, Na+ and water. The quality of the data allowed for the first time calculation of the enthalpy (ΔH) and entropy (ΔS) of the CO2 adsorption by applying the van 't Hoff equation to in situ single-crystal data. The calculation of thermodynamic values was carried out by both traditional and PCA-based approaches, producing comparable results. The obtained ΔH value is significant and involves systems (CO2 and Y zeolite) with no toxicity, superb stability and chemical inertness. Such features, coupled with the absence of carbonate formation and framework inertness upon adsorption, were demonstrated for the bulk crystal by the single-crystal experiment, and suggest that the phenomenon can be easily reversed for a large number of cycles, with CO2 released on demand. The main advantages of PCA-assisted analysis reside in its speed and in the possibility of it being applied directly to raw data, possibly as an `online' data-quality test during data collection, without any a priori knowledge of the crystal structure.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Conterosito, E.Palin, L.Caliandro, R.van Beek, W.Chernyshov, D.Milanesio, M.2019-02-06doi:10.1107/S2053273318017618International Union of CrystallographyIn situ single-crystal X-ray diffraction data were used to unravel the structural dynamics and enthalpy and entropy of adsorption of CO2 into Y zeolite. A principal-component-analysis- (PCA) based approach is applied in an innovative way to single-crystal X-ray diffraction data analysis, allowing one to selectively detect the information from the subset of active atoms. The potential of and limitations of PCA in single-crystal diffraction are discussed.ENin situ studiesY zeoliteprincipal component analysisenthalpy of adsorptionentropy of adsorptionThe increasing efficiency of detectors and brightness of X-rays in both laboratory and large-scale facilities allow the collection of full single-crystal X-ray data sets within minutes. The analysis of these `crystallographic big data' requires new tools and approaches. To answer these needs, the use of principal component analysis (PCA) is proposed to improve the efficiency and speed of the analysis. Potentialities and limitations of PCA were investigated using single-crystal X-ray diffraction (XRD) data collected in situ on Y zeolite, in which CO2, acting as an active species, is thermally adsorbed while cooling from 300 to 200 K. For the first time, thanks to the high sensitivity of single-crystal XRD, it was possible to determine the sites where CO2 is adsorbed, the increase in their occupancy while the temperature is decreased, and the correlated motion of active species, i.e. CO2, H2O and Na+. PCA allowed identification and elimination of problematic data sets, and better understanding of the trends of the occupancies of CO2, Na+ and water. The quality of the data allowed for the first time calculation of the enthalpy (ΔH) and entropy (ΔS) of the CO2 adsorption by applying the van 't Hoff equation to in situ single-crystal data. The calculation of thermodynamic values was carried out by both traditional and PCA-based approaches, producing comparable results. The obtained ΔH value is significant and involves systems (CO2 and Y zeolite) with no toxicity, superb stability and chemical inertness. Such features, coupled with the absence of carbonate formation and framework inertness upon adsorption, were demonstrated for the bulk crystal by the single-crystal experiment, and suggest that the phenomenon can be easily reversed for a large number of cycles, with CO2 released on demand. The main advantages of PCA-assisted analysis reside in its speed and in the possibility of it being applied directly to raw data, possibly as an `online' data-quality test during data collection, without any a priori knowledge of the crystal structure.text/htmlCO2 adsorption in Y zeolite: a structural and dynamic view by a novel principal-component-analysis-assisted in situ single-crystal X-ray diffraction experimenttext2752019-02-06Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers2142221884781High-speed tensor tomography: iterative reconstruction tensor tomography (IRTT) algorithm
http://scripts.iucr.org/cgi-bin/paper?vk5029
The recent advent of tensor tomography techniques has enabled tomographic investigations of the 3D nanostructure organization of biological and material science samples. These techniques extended the concept of conventional X-ray tomography by reconstructing not only a scalar value such as the attenuation coefficient per voxel, but also a set of parameters that capture the local anisotropy of nanostructures within every voxel of the sample. Tensor tomography data sets are intrinsically large as each pixel of a conventional X-ray projection is substituted by a scattering pattern, and projections have to be recorded at different sample angular orientations with several tilts of the rotation axis with respect to the X-ray propagation direction. Currently available reconstruction approaches for such large data sets are computationally expensive. Here, a novel, fast reconstruction algorithm, named iterative reconstruction tensor tomography (IRTT), is presented to simplify and accelerate tensor tomography reconstructions. IRTT is based on a second-rank tensor model to describe the anisotropy of the nanostructure in every voxel and on an iterative error backpropagation reconstruction algorithm to achieve high convergence speed. The feasibility and accuracy of IRTT are demonstrated by reconstructing the nanostructure anisotropy of three samples: a carbon fiber knot, a human bone trabecula specimen and a fixed mouse brain. Results and reconstruction speed were compared with those obtained by the small-angle scattering tensor tomography (SASTT) reconstruction method introduced by Liebi et al. [Nature (2015), 527, 349–352]. The principal orientation of the nanostructure within each voxel revealed a high level of agreement between the two methods. Yet, for identical data sets and computer hardware used, IRTT was shown to be more than an order of magnitude faster. IRTT was found to yield robust results, it does not require prior knowledge of the sample for initializing parameters, and can be used in cases where simple anisotropy metrics are sufficient, i.e. the tensor approximation adequately captures the level of anisotropy and the dominant orientation within a voxel. In addition, by greatly accelerating the reconstruction, IRTT is particularly suitable for handling large tomographic data sets of samples with internal structure or as a real-time analysis tool during the experiment for online feedback during data acquisition. Alternatively, the IRTT results might be used as an initial guess for models capturing a higher complexity of structural anisotropy such as spherical harmonics based SASTT in Liebi et al. (2015), improving both overall convergence speed and robustness of the reconstruction.Copyright (c) 2019 Zirui Gao et al.urn:issn:2053-2733Gao, Z.Guizar-Sicairos, M.Lutz-Bueno, V.Schröter, A.Liebi, M.Rudin, M.Georgiadis, M.2019-02-06doi:10.1107/S2053273318017394International Union of CrystallographyA fast and robust reconstruction algorithm for small-angle scattering tensor tomography, named iterative reconstruction tensor tomography, is presented. It employs a second-rank tensor model and an iterative error backpropagation to simplify and accelerate tensor tomography reconstruction.ENsmall-angle X-ray scatteringtensor tomographyiterative reconstruction algorithmThe recent advent of tensor tomography techniques has enabled tomographic investigations of the 3D nanostructure organization of biological and material science samples. These techniques extended the concept of conventional X-ray tomography by reconstructing not only a scalar value such as the attenuation coefficient per voxel, but also a set of parameters that capture the local anisotropy of nanostructures within every voxel of the sample. Tensor tomography data sets are intrinsically large as each pixel of a conventional X-ray projection is substituted by a scattering pattern, and projections have to be recorded at different sample angular orientations with several tilts of the rotation axis with respect to the X-ray propagation direction. Currently available reconstruction approaches for such large data sets are computationally expensive. Here, a novel, fast reconstruction algorithm, named iterative reconstruction tensor tomography (IRTT), is presented to simplify and accelerate tensor tomography reconstructions. IRTT is based on a second-rank tensor model to describe the anisotropy of the nanostructure in every voxel and on an iterative error backpropagation reconstruction algorithm to achieve high convergence speed. The feasibility and accuracy of IRTT are demonstrated by reconstructing the nanostructure anisotropy of three samples: a carbon fiber knot, a human bone trabecula specimen and a fixed mouse brain. Results and reconstruction speed were compared with those obtained by the small-angle scattering tensor tomography (SASTT) reconstruction method introduced by Liebi et al. [Nature (2015), 527, 349–352]. The principal orientation of the nanostructure within each voxel revealed a high level of agreement between the two methods. Yet, for identical data sets and computer hardware used, IRTT was shown to be more than an order of magnitude faster. IRTT was found to yield robust results, it does not require prior knowledge of the sample for initializing parameters, and can be used in cases where simple anisotropy metrics are sufficient, i.e. the tensor approximation adequately captures the level of anisotropy and the dominant orientation within a voxel. In addition, by greatly accelerating the reconstruction, IRTT is particularly suitable for handling large tomographic data sets of samples with internal structure or as a real-time analysis tool during the experiment for online feedback during data acquisition. Alternatively, the IRTT results might be used as an initial guess for models capturing a higher complexity of structural anisotropy such as spherical harmonics based SASTT in Liebi et al. (2015), improving both overall convergence speed and robustness of the reconstruction.text/htmlHigh-speed tensor tomography: iterative reconstruction tensor tomography (IRTT) algorithmtext2752019-02-06Copyright (c) 2019 Zirui Gao et al.Acta Crystallographica Section Aresearch papers223238Shape transform phasing of edgy nanocrystals
http://scripts.iucr.org/cgi-bin/paper?ae5058
Diffraction patterns from small protein crystals illuminated by highly coherent X-rays often contain measurable interference signals between Bragg peaks. This coherent `shape transform' signal introduces enough additional information to allow the molecular densities to be determined from the diffracted intensities directly, without prior information or resolution restrictions. However, the various correlations amongst molecular occupancies/vacancies at the crystal surface result in a subtle yet critical problem in shape transform phasing whereby the sublattices of symmetry-related molecules exhibit a form of partial coherence amongst lattice sites when an average is taken over many crystal patterns. Here an iterative phase retrieval algorithm is developed which is capable of treating this problem; it is demonstrated on simulated data.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Chen, J.P.J.Donatelli, J.J.Schmidt, K.E.Kirian, R.A.2019-02-28doi:10.1107/S205327331900113XInternational Union of CrystallographyReconstruction of an object from the averaged coherent diffracted intensity of finite crystals of that object with arbitrary lattice occupancies is possible. An algorithm capable of reconstructing both the so-called averaged shape transform and the object density at the same time is demonstrated.ENiterative projection algorithmsshape transformsshape transform phasingphase retrievalnanocrystalsserial femtosecond crystallographyX-ray free-electron lasersDiffraction patterns from small protein crystals illuminated by highly coherent X-rays often contain measurable interference signals between Bragg peaks. This coherent `shape transform' signal introduces enough additional information to allow the molecular densities to be determined from the diffracted intensities directly, without prior information or resolution restrictions. However, the various correlations amongst molecular occupancies/vacancies at the crystal surface result in a subtle yet critical problem in shape transform phasing whereby the sublattices of symmetry-related molecules exhibit a form of partial coherence amongst lattice sites when an average is taken over many crystal patterns. Here an iterative phase retrieval algorithm is developed which is capable of treating this problem; it is demonstrated on simulated data.text/htmlShape transform phasing of edgy nanocrystalstext2752019-02-28Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers239259Characterizing modulated structures with first-principles calculations: a unified superspace scheme of ordering in mullite
http://scripts.iucr.org/cgi-bin/paper?gv5003
The benefit of computational methods applying density functional theory for the description and understanding of modulated crystal structures is investigated. A method is presented which allows one to establish, improve and test superspace models including displacive and occupational modulation functions from first-principles calculations on commensurate structures. The total energies of different configurations allow one to distinguish stable and less stable structure models. The study is based on a series of geometrically optimized superstructures of mullite (Al4+2xSi2−2xO10−x) derived from the superspace group Pbam(α0½)0ss. Despite the disordered and structurally complex nature of mullite, the calculations on ordered superstructures are very useful for determining the ideal Al/Si ordering in mullite, extracting atomic modulation functions as well as understanding the SiO2–Al2O3 phase diagram. The results are compared with experimentally established models which confirm the validity and utility of the presented method.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Klar, P.B.Etxebarria, I.Madariaga, G.2019-02-12doi:10.1107/S2053273319000846International Union of CrystallographyQuantitative parameters of modulated crystal structures are determined from density functional theory calculations applied to superstructures obtained using the superspace formalism. The example of mullite is used to demonstrate that with this approach versatile aspects ranging from ordering phenomena to phase diagrams can be understood on a new level.ENdensity functional theory (DFT)superspacemodulation functionsAl/Si orderingsilicatesmulliteThe benefit of computational methods applying density functional theory for the description and understanding of modulated crystal structures is investigated. A method is presented which allows one to establish, improve and test superspace models including displacive and occupational modulation functions from first-principles calculations on commensurate structures. The total energies of different configurations allow one to distinguish stable and less stable structure models. The study is based on a series of geometrically optimized superstructures of mullite (Al4+2xSi2−2xO10−x) derived from the superspace group Pbam(α0½)0ss. Despite the disordered and structurally complex nature of mullite, the calculations on ordered superstructures are very useful for determining the ideal Al/Si ordering in mullite, extracting atomic modulation functions as well as understanding the SiO2–Al2O3 phase diagram. The results are compared with experimentally established models which confirm the validity and utility of the presented method.text/htmlCharacterizing modulated structures with first-principles calculations: a unified superspace scheme of ordering in mullitetext2752019-02-12Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers260272Ted Janssen and aperiodic crystals
http://scripts.iucr.org/cgi-bin/paper?gv5004
This article reviews some of Ted Janssen's (1936–2017) major contributions to the field of aperiodic crystals. Aperiodic crystals are long-range ordered structures without 3D lattice translations and encompass incommensurately modulated phases, incommensurate composites and quasicrystals. Together with Pim de Wolff and Aloysio Janner, Ted Janssen invented the very elegant theory of superspace crystallography that, by adding a supplementary dimension to the usual 3D space, allows for a deeper understanding of the atomic structure of aperiodic crystals. He also made important contributions to the understanding of the stability and dynamics of aperiodic crystals, exploring their fascinating physical properties. He constantly interacted and collaborated with experimentalists, always ready to share and explain his detailed understanding of aperiodic crystals.Copyright (c) 2019 Marc de Boissieuurn:issn:2053-2733de Boissieu, M.2019-02-06doi:10.1107/S2053273318016765International Union of CrystallographyTed Janssen's contributions to the field of aperiodic crystals are reviewed.ENaperiodic crystalssuperspace crystallographylattice dynamicsphasonsTed JanssenThis article reviews some of Ted Janssen's (1936–2017) major contributions to the field of aperiodic crystals. Aperiodic crystals are long-range ordered structures without 3D lattice translations and encompass incommensurately modulated phases, incommensurate composites and quasicrystals. Together with Pim de Wolff and Aloysio Janner, Ted Janssen invented the very elegant theory of superspace crystallography that, by adding a supplementary dimension to the usual 3D space, allows for a deeper understanding of the atomic structure of aperiodic crystals. He also made important contributions to the understanding of the stability and dynamics of aperiodic crystals, exploring their fascinating physical properties. He constantly interacted and collaborated with experimentalists, always ready to share and explain his detailed understanding of aperiodic crystals.text/htmlTed Janssen and aperiodic crystalstext2752019-02-06Copyright (c) 2019 Marc de BoissieuActa Crystallographica Section Aresearch papers273280A side-by-side comparison of the solidification dynamics of quasicrystalline and approximant phases in the Al–Co–Ni system
http://scripts.iucr.org/cgi-bin/paper?gv5001
Quasicrystals and their approximants have triggered widespread interest due to the challenge of solving their complex crystal structures as well as their possibly exceptional properties. The structural motifs of approximants are similar to those of the corresponding quasicrystals, but to what extent are their crystallization pathways the same? Unfortunately, there have been very few in situ experimental investigations to answer this question. Here, by leveraging the high penetrating power of hard X-rays, synchrotron-based X-ray tomography was conducted in order to capture the nucleation and growth of a decagonal quasicrystal and its related approximant. The combination of data-driven computational analysis with new thermodynamic databases allowed the characterization, with high precision, of the constitutional and kinetic driving forces for crystallization. The experimental results prove that the growth of both crystals from a liquid is dominated by first-order kinetics. Nevertheless, and somewhat surprisingly, significant differences were observed in their rates of nucleation and growth. The reasons for such divergent behaviours are discussed in light of contemporary theories of intermetallic crystallization.Copyright (c) 2019 Insung Han et al.urn:issn:2053-2733Han, I.Xiao, X.Sun, H.Shahani, A.J.2019-02-06doi:10.1107/S2053273318017114International Union of CrystallographyThe nucleation and growth dynamics of a decagonal quasicrystal and its approximant `X' phase are considered. Various similarities and differences are elucidated.ENquasicrystalsapproximant phasessynchrotron radiationnucleation and growthQuasicrystals and their approximants have triggered widespread interest due to the challenge of solving their complex crystal structures as well as their possibly exceptional properties. The structural motifs of approximants are similar to those of the corresponding quasicrystals, but to what extent are their crystallization pathways the same? Unfortunately, there have been very few in situ experimental investigations to answer this question. Here, by leveraging the high penetrating power of hard X-rays, synchrotron-based X-ray tomography was conducted in order to capture the nucleation and growth of a decagonal quasicrystal and its related approximant. The combination of data-driven computational analysis with new thermodynamic databases allowed the characterization, with high precision, of the constitutional and kinetic driving forces for crystallization. The experimental results prove that the growth of both crystals from a liquid is dominated by first-order kinetics. Nevertheless, and somewhat surprisingly, significant differences were observed in their rates of nucleation and growth. The reasons for such divergent behaviours are discussed in light of contemporary theories of intermetallic crystallization.text/htmlA side-by-side comparison of the solidification dynamics of quasicrystalline and approximant phases in the Al–Co–Ni systemtext2752019-02-06Copyright (c) 2019 Insung Han et al.Acta Crystallographica Section Aresearch papers281296Principles of weakly ordered domains in intermetallics: the cooperative effects of atomic packing and electronics in Fe2Al5
http://scripts.iucr.org/cgi-bin/paper?gv5002
Many complex intermetallic structures feature a curious juxtaposition of domains with strict 3D periodicity and regions of much weaker order or incommensurability. This article explores the basic principles leading to such arrangements through an investigation of the weakly ordered channels of Fe2Al5. It starts by experimentally confirming the earlier crystallographic model of the high-temperature form, in which nearly continuous columns of electron density corresponding to disordered Al atoms emerge. Then electronic structure calculations on ordered models are used to determine the factors leading to the formation of these columns. These calculations reveal electronic pseudogaps near 16 electrons/Fe atom, an electron concentration close to the Al-rich side of the phase's homogeneity range. Through a reversed approximation Molecular Orbital (raMO) analysis, these pseudogaps are correlated with the filling of 18-electron configurations on the Fe atoms with the support of isolobal σ Fe–Fe bonds. The resulting preference for 16 electrons/Fe requires a fractional number of Al atoms in the Fe2Al5 unit cell. Density functional theory–chemical pressure (DFT-CP) analysis is then applied to investigate how this nonstoichiometry is accommodated. The CP schemes reveal strong quadrupolar distributions on the Al atoms of the channels, suggestive of soft atomic motions along the undulating electron density observed in the Fourier map that allow the Al positions to shift easily in response to compositional changes. Such a combination of preferred electron counts tied to stoichiometry and continuous paths of CP quadrupoles could provide predictive indicators for the emergence of channels of disordered or incommensurately spaced atoms in intermetallic structures.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Vinokur, A.I.Hilleke, K.P.Fredrickson, D.C.2019-02-21doi:10.1107/S2053273318017461International Union of CrystallographyThe Fe2Al5 structure is remarkable among intermetallic phases for its channels of weakly ordered Al atoms. This article traces the origins of these channels to the cooperative effects of soft atomic motions dictated by chemical pressure quadrupoles and preferred electron concentrations.ENintermetallic phaseschannel structureschemical bonding theorydisorderincommensurabilityMany complex intermetallic structures feature a curious juxtaposition of domains with strict 3D periodicity and regions of much weaker order or incommensurability. This article explores the basic principles leading to such arrangements through an investigation of the weakly ordered channels of Fe2Al5. It starts by experimentally confirming the earlier crystallographic model of the high-temperature form, in which nearly continuous columns of electron density corresponding to disordered Al atoms emerge. Then electronic structure calculations on ordered models are used to determine the factors leading to the formation of these columns. These calculations reveal electronic pseudogaps near 16 electrons/Fe atom, an electron concentration close to the Al-rich side of the phase's homogeneity range. Through a reversed approximation Molecular Orbital (raMO) analysis, these pseudogaps are correlated with the filling of 18-electron configurations on the Fe atoms with the support of isolobal σ Fe–Fe bonds. The resulting preference for 16 electrons/Fe requires a fractional number of Al atoms in the Fe2Al5 unit cell. Density functional theory–chemical pressure (DFT-CP) analysis is then applied to investigate how this nonstoichiometry is accommodated. The CP schemes reveal strong quadrupolar distributions on the Al atoms of the channels, suggestive of soft atomic motions along the undulating electron density observed in the Fourier map that allow the Al positions to shift easily in response to compositional changes. Such a combination of preferred electron counts tied to stoichiometry and continuous paths of CP quadrupoles could provide predictive indicators for the emergence of channels of disordered or incommensurately spaced atoms in intermetallic structures.text/htmlPrinciples of weakly ordered domains in intermetallics: the cooperative effects of atomic packing and electronics in Fe2Al5text2752019-02-21Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers2973061880449188044818804471880452Full real-space analysis of a dodecagonal quasicrystal
http://scripts.iucr.org/cgi-bin/paper?vf5004
The atomically resolved real-space structure of a long-range-ordered dodecagonal quasicrystal is determined based on scanning tunnelling microscopy. For the BaTiO3-derived oxide quasicrystal which spontaneously forms on a Pt(111) surface, 8100 atomic positions have been determined and are compared with an ideal Niizeki–Gähler tiling. Although the Niizeki–Gähler tiling has a complex three-element structure, the abundance of the triangle, square and rhomb tiling elements in the experimental data closely resembles the ideal frequencies. Similarly, the frequencies of all possible next-neighbour tiling combinations are, within the experimental uncertainty, identical to the ideal tiling. The angular and orientational distributions of all individual tiling elements show the characteristics of the dodecagonal quasicrystal. In contrast, the analysis of the orientation of characteristic and more complex tiling combinations indicates the partial decomposition of the quasicrystal into small patches with locally reduced symmetry. These, however, preserve the long-range quasicrystal coherence. The symmetry reduction from dodecagonal to sixfold is assigned to local interaction with the threefold substrate. It leads to atomic flips which preserve the number of quasicrystal tiling elements.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Schenk, S.Zollner, E.M.Krahn, O.Schreck, B.Hammer, R.Förster, S.Widdra, W.2019-02-28doi:10.1107/S2053273319000056International Union of CrystallographyAnalysis of a dodecagonal quasicrystal based on 8100 vertices from atomically resolved scanning tunnelling microscopy has been carried out. A detailed frequency and orientational analysis is presented for the triangle–square–rhomb tiling of a BaTiO3-derived quasicrystal.EN2D oxide quasicrystalBaTiO3 on Pt(111)dodecagonal tilingstatistical analysisscanning tunnelling microscopyThe atomically resolved real-space structure of a long-range-ordered dodecagonal quasicrystal is determined based on scanning tunnelling microscopy. For the BaTiO3-derived oxide quasicrystal which spontaneously forms on a Pt(111) surface, 8100 atomic positions have been determined and are compared with an ideal Niizeki–Gähler tiling. Although the Niizeki–Gähler tiling has a complex three-element structure, the abundance of the triangle, square and rhomb tiling elements in the experimental data closely resembles the ideal frequencies. Similarly, the frequencies of all possible next-neighbour tiling combinations are, within the experimental uncertainty, identical to the ideal tiling. The angular and orientational distributions of all individual tiling elements show the characteristics of the dodecagonal quasicrystal. In contrast, the analysis of the orientation of characteristic and more complex tiling combinations indicates the partial decomposition of the quasicrystal into small patches with locally reduced symmetry. These, however, preserve the long-range quasicrystal coherence. The symmetry reduction from dodecagonal to sixfold is assigned to local interaction with the threefold substrate. It leads to atomic flips which preserve the number of quasicrystal tiling elements.text/htmlFull real-space analysis of a dodecagonal quasicrystaltext2752019-02-28Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers307313Bonding network and stability of clusters: the case study of Al13TM4 pseudo-tenfold surfaces
http://scripts.iucr.org/cgi-bin/paper?vf5005
Clusters, i.e. polyhedral geometric entities, are widely used to describe the structure of complex intermetallic compounds. However, little is generally known about their physical significance. The atomic and electronic structures of the Al13TM4 complex intermetallic compounds (TM = Fe, Co, Ru, Rh) have been investigated using a wide range of ab initio tools in order to examine the influence of the chemical composition on the pertinence of the bulk structure description based on 3D clusters. In addition, since surface studies were found to be a relevant approach to address the question of cluster stability in complex phases, the interplay of the cluster substructure with the 2D surface is addressed in the case of the Al13Co4(100) and Al13Fe4(010) surfaces.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Scheid, P.Chatelier, C.Ledieu, J.Fournée, V.Gaudry, É.2019-02-28doi:10.1107/S2053273319000202International Union of CrystallographyThe physical significance of clusters in Al13TM4 compounds is invesitgated through ab initio methods based on density functional theory.ENcomplex intermetallic compoundssurfacesbondingdensity functional theoryClusters, i.e. polyhedral geometric entities, are widely used to describe the structure of complex intermetallic compounds. However, little is generally known about their physical significance. The atomic and electronic structures of the Al13TM4 complex intermetallic compounds (TM = Fe, Co, Ru, Rh) have been investigated using a wide range of ab initio tools in order to examine the influence of the chemical composition on the pertinence of the bulk structure description based on 3D clusters. In addition, since surface studies were found to be a relevant approach to address the question of cluster stability in complex phases, the interplay of the cluster substructure with the 2D surface is addressed in the case of the Al13Co4(100) and Al13Fe4(010) surfaces.text/htmlBonding network and stability of clusters: the case study of Al13TM4 pseudo-tenfold surfacestext2752019-02-28Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers314324Monoclinic sphere packings. III. Trivariant lattice complexes of P2/c and P21/c
http://scripts.iucr.org/cgi-bin/paper?td5056
All homogeneous sphere packings were derived that refer to the trivariant lattice complexes of monoclinic space-group types P2/c and P21/c. In total, sphere packings of 55 types have been found. The maximal inherent symmetry is monoclinic for 17 types while the other types comprise at least one sphere packing with cubic (four cases), hexagonal (six cases), tetragonal (eight cases) or orthorhombic (20 cases) symmetry.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Sowa, H.2019-02-06doi:10.1107/S2053273318015814International Union of CrystallographyAll homogeneous sphere packings were derived that refer to the trivariant lattice complexes of monoclinic space groups of types P2/c and P21/c.ENsphere packingsmonoclinic crystal systemtrivariant lattice complexesAll homogeneous sphere packings were derived that refer to the trivariant lattice complexes of monoclinic space-group types P2/c and P21/c. In total, sphere packings of 55 types have been found. The maximal inherent symmetry is monoclinic for 17 types while the other types comprise at least one sphere packing with cubic (four cases), hexagonal (six cases), tetragonal (eight cases) or orthorhombic (20 cases) symmetry.text/htmlMonoclinic sphere packings. III. Trivariant lattice complexes of P2/c and P21/ctext2752019-02-06Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers325335Resolving 500 nm axial separation by multi-slice X-ray ptychography
http://scripts.iucr.org/cgi-bin/paper?wo5033
Multi-slice X-ray ptychography offers an approach to achieve images with a nanometre-scale resolution from samples with thicknesses larger than the depth of field of the imaging system by modeling a thick sample as a set of thin slices and accounting for the wavefront propagation effects within the specimen. Here, we present an experimental demonstration that resolves two layers of nanostructures separated by 500 nm along the axial direction, with sub-10 nm and sub-20 nm resolutions on two layers, respectively. Fluorescence maps are simultaneously measured in the multi-modality imaging scheme to assist in decoupling the mixture of low-spatial-frequency features across different slices. The enhanced axial sectioning capability using correlative signals obtained from multi-modality measurements demonstrates the great potential of the multi-slice ptychography method for investigating specimens with extended dimensions in 3D with high resolution.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Huang, X.Yan, H.He, Y.Ge, M.Öztürk, H.Fang, Y.-L.L.Ha, S.Lin, M.Lu, M.Nazaretski, E.Robinson, I.K.Chu, Y.S.2019-02-12doi:10.1107/S2053273318017229International Union of CrystallographyCombining multi-slice ptychography with multi-modality scanning probe microscopy reconstructs two planes of nanostructures separated by 500 nm with sub-20 nm lateral resolution, assisted by simultaneously measured fluorescence maps for decoupling low-spatial-frequency features.ENX-ray ptychographymulti-slice approachnanostructuresMulti-slice X-ray ptychography offers an approach to achieve images with a nanometre-scale resolution from samples with thicknesses larger than the depth of field of the imaging system by modeling a thick sample as a set of thin slices and accounting for the wavefront propagation effects within the specimen. Here, we present an experimental demonstration that resolves two layers of nanostructures separated by 500 nm along the axial direction, with sub-10 nm and sub-20 nm resolutions on two layers, respectively. Fluorescence maps are simultaneously measured in the multi-modality imaging scheme to assist in decoupling the mixture of low-spatial-frequency features across different slices. The enhanced axial sectioning capability using correlative signals obtained from multi-modality measurements demonstrates the great potential of the multi-slice ptychography method for investigating specimens with extended dimensions in 3D with high resolution.text/htmlResolving 500 nm axial separation by multi-slice X-ray ptychographytext2752019-02-12Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers336341Grazing-incidence small-angle X-ray scattering study of correlated lateral density fluctuations in W/Si multilayers
http://scripts.iucr.org/cgi-bin/paper?vk5033
A structural characterization of W/Si multilayers using X-ray reflectivity (XRR), scanning transmission electron microscopy (STEM) and grazing-incidence small-angle X-ray scattering (GISAXS) is presented. STEM images revealed lateral, periodic density fluctuations in the Si layers, which were further analysed using GISAXS. Characteristic parameters of the fluctuations such as average distance between neighbouring fluctuations, average size and lateral distribution of their position were obtained by fitting numerical simulations to the measured scattering images, and these parameters are in good agreement with the STEM observations. For the numerical simulations the density fluctuations were approximated as a set of spheroids distributed inside the Si layers as a 3D paracrystal (a lattice of spheroids with short-range ordering but lacking any long-range order). From GISAXS, the density of the material inside the density fluctuations is calculated to be 2.07 g cm−3 which is 89% of the bulk value of the deposited layer (2.33 g cm−3).Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Nikolaev, K.V.Yakunin, S.N.Makhotkin, I.A.Rie, J.Medvedev, R.V.Rogachev, A.V.Trunckin, I.N.Vasiliev, A.L.Hendrikx, C.P.Gateshki, M.Kruijs, R.W.E.Bijkerk, F.2019-02-12doi:10.1107/S2053273318017382International Union of CrystallographyAn inhomogeneity of material in W/Si multilayer structures was studied with grazing-incidence small-angle X-ray scattering. The experimental study revealed lateral density fluctuations in the Si spacer layers.ENdiffuse scatteringdensity fluctuationsmultilayer coatingsthin filmsA structural characterization of W/Si multilayers using X-ray reflectivity (XRR), scanning transmission electron microscopy (STEM) and grazing-incidence small-angle X-ray scattering (GISAXS) is presented. STEM images revealed lateral, periodic density fluctuations in the Si layers, which were further analysed using GISAXS. Characteristic parameters of the fluctuations such as average distance between neighbouring fluctuations, average size and lateral distribution of their position were obtained by fitting numerical simulations to the measured scattering images, and these parameters are in good agreement with the STEM observations. For the numerical simulations the density fluctuations were approximated as a set of spheroids distributed inside the Si layers as a 3D paracrystal (a lattice of spheroids with short-range ordering but lacking any long-range order). From GISAXS, the density of the material inside the density fluctuations is calculated to be 2.07 g cm−3 which is 89% of the bulk value of the deposited layer (2.33 g cm−3).text/htmlGrazing-incidence small-angle X-ray scattering study of correlated lateral density fluctuations in W/Si multilayerstext2752019-02-12Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers342351Phason-flips refinement of and multiple-scattering correction for the d-AlCuRh quasicrystal
http://scripts.iucr.org/cgi-bin/paper?ae5049
The origin of the characteristic bias observed in a logarithmic plot of the calculated and measured intensities of diffraction peaks for quasicrystals has not yet been established. Structure refinement requires the inclusion of weak reflections; however, no structural model can properly describe their intensities. For this reason, detailed information about the atomic structure is not available. In this article, a possible cause for the characteristic bias, namely the lattice phason flip, is investigated. The derivation of the structure factor for a tiling with inherent phason flips is given and is tested for the AlCuRh decagonal quasicrystal. Although an improvement of the model is reported, the bias remains. A simple correction term involving a redistribution of the intensities of the peaks was tested, and successfully removed the bias from the diffraction data. This new correction is purely empirical and only mimics the effect of multiple scattering. A comprehensive study of multiple scattering requires detailed knowledge of the diffraction experiment geometry.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Buganski, I.Strzalka, R.Wolny, J.2019-02-21doi:10.1107/S2053273318017254International Union of CrystallographyThe structure factor with lattice phason flips for a decagonal quasicrystal is derived. Bias in the calculated diffraction data is most likely to be a consequence of multiple scattering.ENphason flipsmultiple scatteringquasicrystalsstructure refinementThe origin of the characteristic bias observed in a logarithmic plot of the calculated and measured intensities of diffraction peaks for quasicrystals has not yet been established. Structure refinement requires the inclusion of weak reflections; however, no structural model can properly describe their intensities. For this reason, detailed information about the atomic structure is not available. In this article, a possible cause for the characteristic bias, namely the lattice phason flip, is investigated. The derivation of the structure factor for a tiling with inherent phason flips is given and is tested for the AlCuRh decagonal quasicrystal. Although an improvement of the model is reported, the bias remains. A simple correction term involving a redistribution of the intensities of the peaks was tested, and successfully removed the bias from the diffraction data. This new correction is purely empirical and only mimics the effect of multiple scattering. A comprehensive study of multiple scattering requires detailed knowledge of the diffraction experiment geometry.text/htmlPhason-flips refinement of and multiple-scattering correction for the d-AlCuRh quasicrystaltext2752019-02-21Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers352361Absorption and secondary scattering of X-rays with an off-axis small beam for a cylindrical sample geometry
http://scripts.iucr.org/cgi-bin/paper?wo5029
Expressions for X-ray absorption and secondary scattering are developed for cylindrical sample geometries. The incident-beam size is assumed to be smaller than the sample and in general directed off-axis onto the cylindrical sample. It is shown that an offset beam has a non-negligible effect on both the absorption and multiple scattering terms, resulting in an asymmetric correction that must be applied to the measured scattering intensities. The integral forms of the corrections are first presented. A small-beam limit is then developed for easier computation.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Van Hoesen, D.C.Bendert, J.C.Kelton, K.F.2019-02-21doi:10.1107/S2053273318017710International Union of CrystallographyAbsorption and secondary scattering corrections for a cylindrical sample geometry are developed for the case when the incident beam is smaller than the sample and, in general, off-center from the cylinder.ENX-ray scatteringcylindrical geometryabsorptionmultiple scatteringExpressions for X-ray absorption and secondary scattering are developed for cylindrical sample geometries. The incident-beam size is assumed to be smaller than the sample and in general directed off-axis onto the cylindrical sample. It is shown that an offset beam has a non-negligible effect on both the absorption and multiple scattering terms, resulting in an asymmetric correction that must be applied to the measured scattering intensities. The integral forms of the corrections are first presented. A small-beam limit is then developed for easier computation.text/htmlAbsorption and secondary scattering of X-rays with an off-axis small beam for a cylindrical sample geometrytext2752019-02-21Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers362369Aspects of the topology of actinide atom substructures in crystal structures and the concept of antiliquid
http://scripts.iucr.org/cgi-bin/paper?td5057
Using the parameters of Voronoi–Dirichlet (VD) polyhedra the authors have verified the maximum space-filling principle in substructures constructed of actinide atoms (from thorium to einsteinium) in all crystal structures from the Inorganic Crystal Structure Database (ICSD) and Cambridge Structural Database (CSD). It is shown that most of the actinide atoms in such substructures are surrounded by 14 or 12 neighboring atoms. It was discovered that U substructures with greater than or equal to 20 crystallographically independent U atoms in the unit cell feature 15-faceted VD polyhedra as the most common type. Analogous unimodal distributions of VD polyhedra with maxima at 15 faces are observed for F and H substructures and the model system `ideal gas', which has no order in the arrangement of atoms. This similarity allows one to assume that substructures of crystal structures with greater than or equal to 20 crystallographically independent atoms in the unit cell do not possess short-range (local) order in the mutual arrangement of atoms, but feature long-range order (translational symmetry). Thus, crystalline compounds with such substructures can formally be regarded as `antiliquid', that is the antipode of a liquid, whose structure possesses short-range order but lacks translational symmetry.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Serezhkin, V.N.Rogaleva, E.F.Savchenkov, A.V.Pushkin, D.V.Serezhkina, L.B.2019-02-21doi:10.1107/S2053273318018326International Union of CrystallographyConsideration of the maximum space-filling principle and the short-range (local) and long-range (translational) order using Voronoi–Dirichlet polyhedra reveals the most probable number of neighboring atoms and the concept of antiliquid.ENactinidessubstructuresantiliquidVoronoi–Dirichlet polyhedraUsing the parameters of Voronoi–Dirichlet (VD) polyhedra the authors have verified the maximum space-filling principle in substructures constructed of actinide atoms (from thorium to einsteinium) in all crystal structures from the Inorganic Crystal Structure Database (ICSD) and Cambridge Structural Database (CSD). It is shown that most of the actinide atoms in such substructures are surrounded by 14 or 12 neighboring atoms. It was discovered that U substructures with greater than or equal to 20 crystallographically independent U atoms in the unit cell feature 15-faceted VD polyhedra as the most common type. Analogous unimodal distributions of VD polyhedra with maxima at 15 faces are observed for F and H substructures and the model system `ideal gas', which has no order in the arrangement of atoms. This similarity allows one to assume that substructures of crystal structures with greater than or equal to 20 crystallographically independent atoms in the unit cell do not possess short-range (local) order in the mutual arrangement of atoms, but feature long-range order (translational symmetry). Thus, crystalline compounds with such substructures can formally be regarded as `antiliquid', that is the antipode of a liquid, whose structure possesses short-range order but lacks translational symmetry.text/htmlAspects of the topology of actinide atom substructures in crystal structures and the concept of antiliquidtext2752019-02-21Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers370378Group-theoretical analysis of 1:3 A-site-ordered perovskite formation
http://scripts.iucr.org/cgi-bin/paper?kx5068
The quadruple perovskites AA′3B4X12 are characterized by an extremely wide variety of intriguing physical properties, which makes them attractive candidates for various applications. Using group-theoretical analysis, possible 1:3 A-site-ordered low-symmetry phases have been found. They can be formed from a parent Pm{\bar 3}m perovskite structure (archetype) as a result of real or hypothetical (virtual) phase transitions due to different structural mechanisms (orderings and displacements of atoms, tilts of octahedra). For each type of low-symmetry phase, the full set of order parameters (proper and improper order parameters), the calculated structure, including the space group, the primitive cell multiplication, splitting of the Wyckoff positions and the structural formula were determined. All ordered phases were classified according to the irreducible representations of the space group of the parent phase (archetype) and systematized according to the types of structural mechanisms responsible for their formation. Special attention is paid to the structural mechanisms of formation of the low-symmetry phase of the compounds known from experimental data, such as: CaCu3Ti4O12, CaCu3Ga2Sn2O12, CaMn3Mn4O12, Ce1/2Cu3Ti4O12, LaMn3Mn4O12, BiMn3Mn4O12 and others. For the first time, the phenomenon of variability in the choice of the proper order parameters, which allows one to obtain the same structure by different group-theoretical paths, is established. This phenomenon emphasizes the fundamental importance of considering the full set of order parameters in describing phase transitions. Possible transition paths from the archetype with space group Pm{\bar 3}m to all 1:3 A-site-ordered perovskites are illustrated using the Bärnighausen tree formalism. These results may be used to identify new phases and interpret experimental results, determine the structural mechanisms responsible for the formation of low-symmetry phases as well as to understand the structural genesis of the perovskite-like phases. The obtained non-model group-theoretical results in combination with crystal chemical data and first-principles calculations may be a starting point for the design of new functional materials with a perovskite structure.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Talanov, M.V.2019-02-28doi:10.1107/S2053273318018338International Union of CrystallographyA group-theoretical analysis of 1:3 A-site-ordered perovskite structures is reported.ENquadruple 1:3 A-site-ordered perovskitesgroup-theoretical analysislow-symmetry phasesfull set of order parameterstilts of octahedraarchetype structureThe quadruple perovskites AA′3B4X12 are characterized by an extremely wide variety of intriguing physical properties, which makes them attractive candidates for various applications. Using group-theoretical analysis, possible 1:3 A-site-ordered low-symmetry phases have been found. They can be formed from a parent Pm{\bar 3}m perovskite structure (archetype) as a result of real or hypothetical (virtual) phase transitions due to different structural mechanisms (orderings and displacements of atoms, tilts of octahedra). For each type of low-symmetry phase, the full set of order parameters (proper and improper order parameters), the calculated structure, including the space group, the primitive cell multiplication, splitting of the Wyckoff positions and the structural formula were determined. All ordered phases were classified according to the irreducible representations of the space group of the parent phase (archetype) and systematized according to the types of structural mechanisms responsible for their formation. Special attention is paid to the structural mechanisms of formation of the low-symmetry phase of the compounds known from experimental data, such as: CaCu3Ti4O12, CaCu3Ga2Sn2O12, CaMn3Mn4O12, Ce1/2Cu3Ti4O12, LaMn3Mn4O12, BiMn3Mn4O12 and others. For the first time, the phenomenon of variability in the choice of the proper order parameters, which allows one to obtain the same structure by different group-theoretical paths, is established. This phenomenon emphasizes the fundamental importance of considering the full set of order parameters in describing phase transitions. Possible transition paths from the archetype with space group Pm{\bar 3}m to all 1:3 A-site-ordered perovskites are illustrated using the Bärnighausen tree formalism. These results may be used to identify new phases and interpret experimental results, determine the structural mechanisms responsible for the formation of low-symmetry phases as well as to understand the structural genesis of the perovskite-like phases. The obtained non-model group-theoretical results in combination with crystal chemical data and first-principles calculations may be a starting point for the design of new functional materials with a perovskite structure.text/htmlGroup-theoretical analysis of 1:3 A-site-ordered perovskite formationtext2752019-02-28Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers379397Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies
http://scripts.iucr.org/cgi-bin/paper?ae5060
The transferable aspherical pseudoatom data bank, UBDB2018, is extended with over 130 new atom types present in small and biological molecules of great importance in biology and chemistry. UBDB2018 can be applied either as a source of aspherical atomic scattering factors in a standard X-ray experiment (dmin ≃ 0.8 Å) instead of the independent atom model (IAM), and can therefore enhance the final crystal structure geometry and refinement parameters; or as a tool to reconstruct the molecular charge-density distribution and derive the electrostatic properties of chemical systems for which 3D structural data are available. The extended data bank has been extensively tested, with the focus being on the accuracy of the molecular electrostatic potential computed for important drug-like molecules, namely the HIV-1 protease inhibitors. The UBDB allows the reconstruction of the reference B3LYP/6-31G** potentials, with a root-mean-squared error of 0.015 e bohr−1 computed for entire potential grids which span values from ca 200 e bohr−1 to ca −0.1 e bohr−1 and encompass both the inside and outside regions of a molecule. UBDB2018 is shown to be applicable to enhancing the physical meaning of the molecular electrostatic potential descriptors used to construct predictive quantitative structure–activity relationship/quantitative structure–property relationship (QSAR/QSPR) models for drug discovery studies. In addition, it is suggested that electron structure factors computed from UBDB2018 may significantly improve the interpretation of electrostatic potential maps measured experimentally by means of electron diffraction or single-particle cryo-EM methods.Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Kumar, P.Gruza, B.Bojarowski, S.A.Dominiak, P.M.2019-02-28doi:10.1107/S2053273319000482International Union of CrystallographyThe transferable aspherical pseudoatom data bank, UBDB2018, is extended with over 130 new atom types present in small and biological molecules of importance in biology and chemistry. UBDB2018 can be used to enhance the physical meaning of molecular electrostatic potentials which can be utilized in, amongst other fields, drug discovery studies.ENquantum crystallographypseudoatom data bankUBDB2018aspherical scattering factorselectrostatic potentialtransferable aspherical atom model (TAAM)structure refinementX-ray diffractionelectron diffractionelectron crystallographyThe transferable aspherical pseudoatom data bank, UBDB2018, is extended with over 130 new atom types present in small and biological molecules of great importance in biology and chemistry. UBDB2018 can be applied either as a source of aspherical atomic scattering factors in a standard X-ray experiment (dmin ≃ 0.8 Å) instead of the independent atom model (IAM), and can therefore enhance the final crystal structure geometry and refinement parameters; or as a tool to reconstruct the molecular charge-density distribution and derive the electrostatic properties of chemical systems for which 3D structural data are available. The extended data bank has been extensively tested, with the focus being on the accuracy of the molecular electrostatic potential computed for important drug-like molecules, namely the HIV-1 protease inhibitors. The UBDB allows the reconstruction of the reference B3LYP/6-31G** potentials, with a root-mean-squared error of 0.015 e bohr−1 computed for entire potential grids which span values from ca 200 e bohr−1 to ca −0.1 e bohr−1 and encompass both the inside and outside regions of a molecule. UBDB2018 is shown to be applicable to enhancing the physical meaning of the molecular electrostatic potential descriptors used to construct predictive quantitative structure–activity relationship/quantitative structure–property relationship (QSAR/QSPR) models for drug discovery studies. In addition, it is suggested that electron structure factors computed from UBDB2018 may significantly improve the interpretation of electrostatic potential maps measured experimentally by means of electron diffraction or single-particle cryo-EM methods.text/htmlExtension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studiestext2752019-02-28Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aresearch papers398408Thermoelectric transport properties in magnetically ordered crystals. Corrigendum and addenda
http://scripts.iucr.org/cgi-bin/paper?kx5070
A correction and additions concerning the limiting point groups are made to the article by Grimmer [Acta Cryst. (2017), A73, 333–345].Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733Grimmer, H.2019-02-06doi:10.1107/S2053273318016947International Union of CrystallographyA correction and additions concerning the limiting point groups are made to the article by Grimmer [Acta Cryst. (2017), A73, 333–345].ENthermoelectricitytransport propertiesmagnetic ordergalvanomagnetic effectsthermomagnetic effectsA correction and additions concerning the limiting point groups are made to the article by Grimmer [Acta Cryst. (2017), A73, 333–345].text/htmlThermoelectric transport properties in magnetically ordered crystals. Corrigendum and addendatext2752019-02-06Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Aaddenda and errata409409Aperiodic Order: Volume 2, Crystallography and Almost Periodicity. Edited by M. Baake and U. Grimm. Cambridge University Press, 2017. Pp. 404. Price GBP 110 (hardback). ISBN 9781139033862.
http://scripts.iucr.org/cgi-bin/paper?xo0110
Copyright (c) 2019 International Union of Crystallographyurn:issn:2053-2733de Boissieu, M.2019-02-28doi:10.1107/S2053273319000433International Union of CrystallographyENbook reviewaperiodic crystalsalmost periodicitytext/htmlAperiodic Order: Volume 2, Crystallography and Almost Periodicity. Edited by M. Baake and U. Grimm. Cambridge University Press, 2017. Pp. 404. Price GBP 110 (hardback). ISBN 9781139033862.text2752019-02-28Copyright (c) 2019 International Union of CrystallographyActa Crystallographica Section Abook reviews410410