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) 2020 International Union of Crystallography2020-10-19International 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 76, Part 6, 2020textweekly62002-01-01T00:00+00:006762020-10-19Copyright (c) 2020 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances630urn:issn:2053-2733med@iucr.orgOctober 20202020-10-19Acta Crystallographica Section Ahttp://journals.iucr.org/logos/rss10a.gif
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Still imageFast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. III. Application to crystal structures via the Ewald and direct summation methods
http://scripts.iucr.org/cgi-bin/paper?lk5057
The previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170–175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536; Nguyen & Volkov (2019). Acta Cryst. A75, 448–464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, l-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283–4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10−5 kJ mol−1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28–64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.Copyright (c) 2020 International Union of Crystallographyurn:issn:2053-2733Nguyen, D.Macchi, P.Volkov, A.2020-09-18doi:10.1107/S2053273320009584International Union of CrystallographyThe exact potential and multipole moment method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom-based charge distributions is extended to the calculation of energies in molecular crystal structures. The proposed Ewald and direct summation techniques correctly account for the electron-density penetration effects that in the benchmark systems constitute 24–68% of the total electrostatic interaction energies, and thus cannot be ignored. In agreement with the literature, the Ewald summation method offers a higher precision of the evaluated energies (10−5 kJ mol−1) and a significantly better computational performance.ENelectrostatic interaction energycharge densitypseudoatom modelLöwdin α-functionmultipole expansionEwald summationlattice sumsThe previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170–175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536; Nguyen & Volkov (2019). Acta Cryst. A75, 448–464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, l-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283–4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10−5 kJ mol−1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28–64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.text/htmlFast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. III. Application to crystal structures via the Ewald and direct summation methodstext6762020-09-18Copyright (c) 2020 International Union of CrystallographyActa Crystallographica Section Aresearch papers00A flexible and standalone forward simulation model for laboratory X-ray diffraction contrast tomography
http://scripts.iucr.org/cgi-bin/paper?iv5008
Laboratory X-ray diffraction contrast tomography (LabDCT) has recently been developed as a powerful technique for non-destructive mapping of grain microstructures in bulk materials. As the grain reconstruction relies on segmentation of diffraction spots, it is essential to understand the physics of the diffraction process and resolve all the spot features in detail. To this aim, a flexible and standalone forward simulation model has been developed to compute the diffraction projections from polycrystalline samples with any crystal structure. The accuracy of the forward simulation model is demonstrated by good agreements in grain orientations, boundary positions and shapes between a virtual input structure and that reconstructed based on the forward simulated diffraction projections of the input structure. Further experimental verification is made by comparisons of diffraction spots between simulations and experiments for a partially recrystallized Al sample, where a satisfactory agreement is found for the spot positions, sizes and intensities. Finally, applications of this model to analyze specific spot features are presented.Copyright (c) 2020 International Union of Crystallographyurn:issn:2053-2733Fang, H.Juul Jensen, D.Zhang, Y.2020-09-18doi:10.1107/S2053273320010852International Union of CrystallographyA flexible and standalone forward simulation model has been developed to compute the diffraction projections for laboratory diffraction contrast tomography (LabDCT). The outputs are expected to be of great value for all present users of LabDCT as well as interested new users.EN3D grain mappingdiffraction contrast tomographyX-ray diffractionforward simulationgrain reconstructionLaboratory X-ray diffraction contrast tomography (LabDCT) has recently been developed as a powerful technique for non-destructive mapping of grain microstructures in bulk materials. As the grain reconstruction relies on segmentation of diffraction spots, it is essential to understand the physics of the diffraction process and resolve all the spot features in detail. To this aim, a flexible and standalone forward simulation model has been developed to compute the diffraction projections from polycrystalline samples with any crystal structure. The accuracy of the forward simulation model is demonstrated by good agreements in grain orientations, boundary positions and shapes between a virtual input structure and that reconstructed based on the forward simulated diffraction projections of the input structure. Further experimental verification is made by comparisons of diffraction spots between simulations and experiments for a partially recrystallized Al sample, where a satisfactory agreement is found for the spot positions, sizes and intensities. Finally, applications of this model to analyze specific spot features are presented.text/htmlA flexible and standalone forward simulation model for laboratory X-ray diffraction contrast tomographytext6762020-09-18Copyright (c) 2020 International Union of CrystallographyActa Crystallographica Section Aresearch papers00Effect of radiation damage and illumination variability on signal-to-noise ratio in X-ray free-electron laser single-particle imaging
http://scripts.iucr.org/cgi-bin/paper?ib5090
The deterioration of both the signal-to-noise ratio and the spatial resolution in the electron-density distribution reconstructed from diffraction intensities collected at different orientations of a sample is analysed theoretically with respect to the radiation damage to the sample and the variations in the X-ray intensities illuminating different copies of the sample. The simple analytical expressions and numerical estimates obtained for models of radiation damage and incident X-ray pulses may be helpful in planning X-ray free-electron laser (XFEL) imaging experiments and in analysis of experimental data. This approach to the analysis of partially coherent X-ray imaging configurations can potentially be used for analysis of other forms of imaging where the temporal behaviour of the sample and the incident intensity during exposure may affect the inverse problem of sample reconstruction.Copyright (c) 2020 International Union of Crystallographyurn:issn:2053-2733Gureyev, T.E.Kozlov, A.Morgan, A.J.Martin, A.V.Quiney, H.M.2020-10-12doi:10.1107/S2053273320012188International Union of CrystallographyThe signal-to-noise ratio and spatial resolution of 3D coherent diffractive imaging are investigated, taking into account the effects of radiation damage to the sample and variability of the incident X-ray intensity. The results are expected to be useful for the design and analysis of X-ray free-electron laser-based imaging experiments.ENXFEL imagingradiation damagesignal-to-noise ratioX-ray free-electron laser imagingspatial resolutionThe deterioration of both the signal-to-noise ratio and the spatial resolution in the electron-density distribution reconstructed from diffraction intensities collected at different orientations of a sample is analysed theoretically with respect to the radiation damage to the sample and the variations in the X-ray intensities illuminating different copies of the sample. The simple analytical expressions and numerical estimates obtained for models of radiation damage and incident X-ray pulses may be helpful in planning X-ray free-electron laser (XFEL) imaging experiments and in analysis of experimental data. This approach to the analysis of partially coherent X-ray imaging configurations can potentially be used for analysis of other forms of imaging where the temporal behaviour of the sample and the incident intensity during exposure may affect the inverse problem of sample reconstruction.text/htmlEffect of radiation damage and illumination variability on signal-to-noise ratio in X-ray free-electron laser single-particle imagingtext6762020-10-12Copyright (c) 2020 International Union of CrystallographyActa Crystallographica Section Aresearch papers00Similarity isometries of point packings
http://scripts.iucr.org/cgi-bin/paper?ug5009
A linear isometry R of {\bb R}^{d} is called a similarity isometry of a lattice \Gamma\subseteq{\bb R}^{d} if there exists a positive real number β such that βRΓ is a sublattice of (finite index in) Γ. The set βRΓ is referred to as a similar sublattice of Γ. A (crystallographic) point packing generated by a lattice Γ is a union of Γ with finitely many shifted copies of Γ. In this study, the notion of similarity isometries is extended to point packings. A characterization for the similarity isometries of point packings is provided and the corresponding similar subpackings are identified. Planar examples are discussed, namely the 1 × 2 rectangular lattice and the hexagonal packing (or honeycomb lattice). Finally, similarity isometries of point packings about points different from the origin are considered by studying similarity isometries of shifted point packings. In particular, similarity isometries of a certain shifted hexagonal packing are computed and compared with those of the hexagonal packing.Copyright (c) 2020 International Union of Crystallographyurn:issn:2053-2733Arias, J.C.H.Loquias, M.J.C.2020-10-19doi:10.1107/S2053273320011547International Union of CrystallographyThe notion of similarity isometries is extended to point packings. A characterization for the similarity isometries of point packings is provided and some planar examples are discusssed. Similarity isometries of point packings about points different from the origin are also examined by studying similarity isometries of shifted point packings.ENsimilarity isometriessimilar sublatticespoint packingshexagonal packingsA linear isometry R of {\bb R}^{d} is called a similarity isometry of a lattice \Gamma\subseteq{\bb R}^{d} if there exists a positive real number β such that βRΓ is a sublattice of (finite index in) Γ. The set βRΓ is referred to as a similar sublattice of Γ. A (crystallographic) point packing generated by a lattice Γ is a union of Γ with finitely many shifted copies of Γ. In this study, the notion of similarity isometries is extended to point packings. A characterization for the similarity isometries of point packings is provided and the corresponding similar subpackings are identified. Planar examples are discussed, namely the 1 × 2 rectangular lattice and the hexagonal packing (or honeycomb lattice). Finally, similarity isometries of point packings about points different from the origin are considered by studying similarity isometries of shifted point packings. In particular, similarity isometries of a certain shifted hexagonal packing are computed and compared with those of the hexagonal packing.text/htmlSimilarity isometries of point packingstext6762020-10-19Copyright (c) 2020 International Union of CrystallographyActa Crystallographica Section Aresearch papers00Prices of IUCr journals
http://scripts.iucr.org/cgi-bin/paper?es5026
Copyright (c) 2020 International Union of Crystallographyurn:issn:2053-2733Ashcroft, A.T.2020-10-12doi:10.1107/S2053273320013364International Union of CrystallographyENprices of journalstext/htmlPrices of IUCr journalstext6762020-10-12Copyright (c) 2020 International Union of CrystallographyActa Crystallographica Section Ainternational union of crystallography00A Journey into Reciprocal Space: A Crystallographer's Perspective. By A. M. Glazer. Morgan & Claypool, 2017. Paperback, pp. 190. Price USD 55.00. ISBN 9781681746203.
http://scripts.iucr.org/cgi-bin/paper?xo0123
Copyright (c) 2020 International Union of Crystallographyurn:issn:2053-2733Stöger,B.2020-10-19doi:10.1107/S2053273319006983International Union of CrystallographyENbook reviewreciprocal spacetext/htmlA Journey into Reciprocal Space: A Crystallographer's Perspective. By A. M. Glazer. Morgan & Claypool, 2017. Paperback, pp. 190. Price USD 55.00. ISBN 9781681746203.text6762020-10-19Copyright (c) 2020 International Union of CrystallographyActa Crystallographica Section Abook reviews00