Acta Crystallographica Section A: Foundations and Advances最新文献

{"title":"Phase seeding may provide a gateway to structure solution by deep learning.","authors":"Anders Østergaard Madsen","doi":"10.1107/S2053273325004814","DOIUrl":"10.1107/S2053273325004814","url":null,"abstract":"<p><p>The phase-seeding method proposed by Carrozzini et al. [(2025), Acta Cryst. A81, 188-201] introduces a strategy for integrating artificial intelligence (AI) with established ab initio phasing techniques. Rather than presenting an AI-based phasing solution itself, the authors demonstrate how traditional crystallographic methods can be significantly enhanced if provided with a small subset of approximate phase values - a `phase seed' - that could, in principle, be generated by a machine learning model. By discretizing phase values into a few angular bins, the method transforms the continuous phase problem into a classification task, thereby reducing the computational burden on AI training. This hybrid approach shows promise for improving structure solution, particularly for large and complex non-centrosymmetric crystals, and opens a pathway for future AI-assisted crystallographic workflows.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"251-253"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Symmetries of all lines in monolayer crystals.","authors":"Bernard Field, Sinéad M Griffin","doi":"10.1107/S205327332500422X","DOIUrl":"10.1107/S205327332500422X","url":null,"abstract":"<p><p>As `2D' materials (i.e. materials just a few atoms thick) continue to gain prominence, understanding their symmetries is critical for unlocking their full potential. In this work, we present comprehensive tables that tabulate the rod group symmetries of all crystallographic lines in all 80 layer groups, which describe the symmetries of 2D materials. These tables are analogous to the scanning tables for space groups found in Volume E of the International Tables for Crystallography, but are specifically tailored for layer groups and their applications to 2D materials. This resource will aid in the analysis of line defects, such as domain walls, which play a crucial role in determining the properties and functionality of 2D materials.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"339-349"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Updating direct methods III. Reduction of structural complexity when first-rank semi-invariants are estimated via the Patterson map.","authors":"Carmelo Giacovazzo","doi":"10.1107/S2053273325003274","DOIUrl":"10.1107/S2053273325003274","url":null,"abstract":"<p><p>A new theory for the probabilistic estimation of first-rank one-phase semi-invariants is presented. In this approach, atomic positions are treated as primitive random variables but are constrained by the a priori knowledge of interatomic vectors. This information is always available, thus allowing the new technique to be considered an ab initio probabilistic method conditioned by the knowledge of the Patterson map. The theoretical foundation for the estimation of triplet invariants was outlined in the first paper of this series [Giacovazzo (2019). Acta Cryst. A75, 142-157]. Subsequent experimental tests, shown in the second paper of this series [Burla et al. (2024). J. Appl. Cryst. 57, 1011-1022], have demonstrated the significant superiority of this new approach over existing methods. The improvements were so notable that it has been suggested this technique could be valuable for the ab initio solution of macromolecular structures. This work expands the probabilistic approach to include the estimation of first-rank one-phase semi-invariants, The hope is that they can contribute to the ab initio solution of macromolecular structures. Only in this way can one-phase semi-invariants go from being a historical curiosity to an effective tool for solving macromolecular structures.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"269-278"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Band and Curie limit symmetry groups.","authors":"Yury L Voytekhovsky","doi":"10.1107/S2053273325003341","DOIUrl":"10.1107/S2053273325003341","url":null,"abstract":"<p><p>The paper discusses the contradiction between the 7 band (on a cylinder with infinite radius) symmetry groups and the 5 uniaxial Curie limit symmetry groups. Logical difficulties in understanding the symmetry axis ∞ as a true crystallographic one are shown. The formula n → ∞ is proposed to be understood as if the order n of the axis becomes as large as desired, but retains the properties of a natural number (even, odd etc.). In this way, the true inversion axes of symmetry and one-to-one correspondence of bands and limit groups are restored. Such an analysis may be useful in teaching a university course in crystallography.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"350-352"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Benchmarking 3D-ΔPDF analysis using in-house X-ray sources.","authors":"Karl O R Juul, Kristoffer A H Støckler, Bo B Iversen","doi":"10.1107/S2053273325003389","DOIUrl":"10.1107/S2053273325003389","url":null,"abstract":"<p><p>New detector technology has in recent years improved the data quality available from in-house X-ray diffractometers. A recent study compared high-resolution low-temperature X-ray diffraction data obtained from modern in-house diffractometers with synchrotron data in relation to extracting subtle electron-density details using the multipole model [Vosegaard et al. (2023). Acta Cryst. B79, 380-391]. It was concluded that for organic molecular crystals excellent agreement can be obtained, and only subtle electron-density details are better resolved at the synchrotron sources. This study aims to benchmark the quality of weak diffuse scattering data and three-dimensional difference pair-distribution function (3D-ΔPDF) analysis for in-house X-ray sources against more accurate and better resolved synchrotron data using three examples (Cu_1.95Se, Nb_1-xCoSb and InTe). Since the 3D-ΔPDF method is still relatively new in crystallographic research, we also provide a general description of the pipeline of analysis. The three selected systems highlight important differences in correlated disorder and the corresponding analysis. In all three cases, the synchrotron data have better signal-to-noise ratios and extend to higher scattering vectors. Using the in-house 3D-ΔPDF on Cu_1.95Se, the same ordered 2D superstructure can be determined as for the synchrotron data, although additional arguments based on order within a 2D supercell or on ionic radii must be used to obtain an adequate model. For Nb_1-xCoSb, the preference for vacancies to avoid each other and the size effect associated with structural relaxation of the lattice near vacancies can also be observed and assigned in the in-house 3D-ΔPDF. For InTe, the weak diffuse scattering, radial broadening and higher temperature than the original study mean that, although most of the important features are visible in the in-house data, some features are obscured, and the full correlated disorder model cannot be constructed. Overall, it is found that many of the conclusions derived from synchrotron data can also be extracted from in-house data, but in some cases additional postulates are needed, and in general subtle details may be too noisy to be properly interpreted in the in-house data.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"254-268"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12207916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Refuting `a new theory for X-ray diffraction' - a reciprocal-space approach.","authors":"Elias Vlieg, Paul Tinnemans, René de Gelder","doi":"10.1107/S2053273325000762","DOIUrl":"10.1107/S2053273325000762","url":null,"abstract":"<p><p>Some ten years ago, Fewster proposed `a new theory for X-ray diffraction' in order to explain the completeness of powder diffraction patterns from samples with very few crystals, claiming to find extra intensity at Bragg scattering angles 2θ_B, even when a grain was not oriented in the Bragg condition, and claiming this to be a new approach to X-ray scattering [Fewster (2014). Acta Cryst. A70, 257-282]. Fraser & Wark [Acta Cryst. (2018), A74, 447-456] gave a detailed account of the errors and issues in the approach by Fewster, but the situation appears to be still undecided. To address this issue, we use a different perspective, based on conventional scattering theory and using a simpler description in reciprocal space, rather than the angular space used by Fewster and by Fraser & Wark. This allows us to focus on the crucial conceptual errors in the proposed theory. We show that Fewster is in fact not proposing a new theory, but finds effects that disagree with conventional theory because of errors in the path length calculation. We also discuss extensively the effect of residual intensity in reciprocal space, away from the Bragg peaks, and caused by the termination of crystals. We show that the residual intensity has no significant effect on the intensity of typical powder diffraction patterns. We hope that, with this account, we can put the discussion about the new theory to rest, along with the theory itself.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"306-316"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12207917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144148833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Double-slit X-ray dynamical diffraction in elastically deformed crystals.","authors":"Minas K Balyan","doi":"10.1107/S2053273325003481","DOIUrl":"10.1107/S2053273325003481","url":null,"abstract":"<p><p>Double-slit X-ray Laue symmetrical case dynamical diffraction in a crystal influenced by a constant temperature gradient perpendicular to the reflecting atomic planes is investigated. It is shown that on the exit surface of the crystal interference fringes similar to Young's fringes, known in optics, are formed. The contrast depends on the direction of the applied temperature gradient: it is better when the direction of the temperature gradient is parallel to the diffraction vector. For the period of the fringes an expression is obtained, which depends on the modulus of the temperature gradient and is polarization sensitive. The position of the fringes in the cross section of the beam depends on the deviation of the beam from the generalized exact Bragg angle in the deformed crystal. The deviation of the incident beam from the generalized exact Bragg direction on the order of one hundredth of an arc-second may cause a shift of the interference fringes from the centre of the beam on the order of 10 µm.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"294-305"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal tensor properties of magnetic materials with and without spin-orbit coupling. Application of spin point groups as approximate symmetries.","authors":"Jesus Etxebarria, J Manuel Perez-Mato, Emre S Tasci, Luis Elcoro","doi":"10.1107/S2053273325004127","DOIUrl":"10.1107/S2053273325004127","url":null,"abstract":"<p><p>Spin space groups, formed by operations where the rotation of the spins is independent of the accompanying operation acting on the crystal structure, are appropriate groups to describe the symmetry of magnetic structures with null spin-orbit coupling. Their corresponding spin point groups are the symmetry groups to be considered for deriving the symmetry constraints on the form of the crystal tensor properties of such idealized structures. These groups can also be taken as approximate symmetries (with some restrictions) of real magnetic structures, where spin-orbit coupling and magnetic anisotropy are however present. Here we formalize the invariance transformation properties that must satisfy the most important crystal tensors under a spin point group. This is done using modified Jahn symbols, which generalize those applicable to ordinary magnetic point groups [Gallego et al. (2019). Acta Cryst. A75, 438-447]. The analysis includes not only equilibrium tensors, but also transport, optical and non-linear optical susceptibility tensors. The constraints imposed by spin collinearity and coplanarity within the spin group formalism on a series of representative tensors are discussed and compiled. As illustrative examples, the defined tensor invariance equations have been applied to some known magnetic structures, showing the differences in the symmetry-adapted form of some relevant tensors, when considered under the constraints of its spin point group or its magnetic point group. This comparison, with the spin point group implying additional constraints in the tensor form, can allow one to distinguish those magnetic-related properties that can be solely attributed to spin-orbit coupling from those that are expected even when spin-orbit coupling is negligible.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"317-338"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12207915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Direct derivation of anisotropic atomic displacement parameters from molecular dynamics simulations in extended solids with substitutional disorder using a neural network potential.","authors":"Yoyo Hinuma","doi":"10.1107/S2053273325004620","DOIUrl":"10.1107/S2053273325004620","url":null,"abstract":"<p><p>Atomic displacement parameters (ADPs) are crystallographic information describing the statistical distribution of atoms around an atom site. Anisotropic ADPs by atom were directly derived from classical molecular dynamics (MD) simulations using a universal machine-learned potential. The (co)valences of atom positions were taken over recordings at different time steps in a single MD simulation. The procedure is demonstrated on extended solids, namely rocksalt structure MgO and three thermoelectric materials, Ag₈SnSe₆, Na₂In₂Sn₄ and BaCu_1.14In_0.86P₂. Unlike the very frequently used lattice dynamics approach, the MD approach can obtain ADPs in crystals with substitutional disorder and explicitly at finite temperature, but not under conditions where atoms migrate in the crystal. The calculated ADP approaches 0 when the temperature approaches 0, and the ADP is proportional to the temperature when the atom is in a harmonic potential and the sole contribution to the actual non-zero ADP is from the zero-point motion. The zero-point motion contribution can be estimated from the proportionality constant assuming this Einstein model. ADPs from MD simulations could act as a tool complementing experimental efforts to understand the crystal structure including the distribution of atoms around atom sites.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"279-293"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12207914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Topological coordination numbers and coordination reciprocity from electron-density distributions.","authors":"Frank R Wagner, Riccardo Freccero, Yuri Grin","doi":"10.1107/S2053273325002347","DOIUrl":"https://doi.org/10.1107/S2053273325002347","url":null,"abstract":"<p><p>Triangulated surface data sets of quantum theory of atoms in molecules (QTAIM) interatomic surfaces have been employed to calculate solid angles subtended at the nuclear positions by each diatomic contact surface. On this basis, topological effective coordination numbers were evaluated. This corresponds to a generalization of the established Voronoi-Dirichlet partitioning (VDP) based procedure. The topological coordination number (tCN) approach developed includes coordination reciprocity requirements necessary to extract coordination-consistent sub-coordination scenarios for identification of chemically meaningful coordination numbers. The ranking between different sub-coordination scenarios is accomplished by weighting functions derived from purely geometrical properties of square and semicircle areas. Exemplary cases analyzed using theoretical electron-density distributions span the range from the face centered cubic, body centered cubic, hexagonal close packed and diamond types of element structures, to rocksalt, CsCl and zincblende types of structures, to compounds of the TiNiSi structure type. An important difference compared with VDP-based coordination numbers arises from the natural inclusion of the effect of different atomic sizes in the tCN approach. Even in highly symmetrical element structures, differences between VDP and tCN results are obtained as an effect of atomic electron-density decay utilizing still available degrees of freedom in the crystal structure. Especially in the TiNiSi type of examples, the advantage of numerically ranking between different sub-coordination scenarios of similar importance emerges. Instead of being obliged to choose only one of them, a more precise characterization contains a listing of different scenarios with their relative weights and associated effective coordination numbers. This seems to be generally the more appropriate way to analyze atomic coordination, especially in more complex structures such as intermetallic phases, opening up its possible use as input for AI applications on structure-property relationships.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":"81 Pt 3","pages":"221-244"},"PeriodicalIF":1.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}