Acta Crystallographica Section A: Foundations and Advances最新文献

{"title":"Case study of using the single-atom R1 method to solve a small protein structure.","authors":"Xiaodong Zhang","doi":"10.1107/S2053273326005668","DOIUrl":"10.1107/S2053273326005668","url":null,"abstract":"<p><p>A small protein structure would not yield a solution via the single-atom R1 (sR1) method. A salient sign of trouble was that many atoms were dubiously accepted into the model because their introduction caused the sR1 value to increase. A plausible hypothesis is that this was very likely due to a hidden solvent diffraction effect. After accounting for this hidden solvent effect via padding additional C atoms, this small protein structure now has been successfully solved by the sR1 method. Further analysis of the protein crystal density indicated that the above successful padding of C atoms had over-accounted for the solvent content. However, empirical observations have indicated that, when an initial application of the sR1 method shows that many atoms are not welcomed into the model, padding numerous C atoms (even if over-accounting for the solvent content) benefits the sR1 calculation by making spotting plausible fragments more reliable and/or making the resulting model more complete.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"331-334"},"PeriodicalIF":2.1,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13325186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148315020","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":"A real rhombic dodecahedron: morphology and crystal shape variations.","authors":"D G Stepenshchikov, A D Pavlushin","doi":"10.1107/S2053273326003979","DOIUrl":"10.1107/S2053273326003979","url":null,"abstract":"<p><p>We propose a novel geometric characterization method for flat-faceted crystals bounded by a single simple crystallographic form - the rhombic dodecahedron. The approach utilizes distances between six pairs of parallel facets and the lengths of three false edges (out of six possible) resulting from anisotropic crystal growth. Our study has established the existence of exactly 34 combinatorially distinct, full-faceted real rhombic dodecahedra. For each type, we determined the range of crystal shape variations using the semi-axial lengths of the minimal-volume circumscribed ellipsoid. The results demonstrate that all real rhombic dodecahedra, except for eight special forms, can exhibit the complete spectrum of possible shape variations. These eight exceptional forms cannot develop tabular morphologies with bidirectional isometry. The obtained results provide valuable tools for precise analysis of rhombic dodecahedral crystal morphology and for establishing morphogenetic correlations between the degree of crystal distortions and the dissymmetry of the crystal-forming environment. This information is relevant for assessing the typomorphic features of natural diamonds, garnets, sodalites and magnetite crystals, as well as their synthetic analogs and other chemical compounds.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"335-339"},"PeriodicalIF":2.1,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147939508","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":"Beyond complementarity: a reverse-engineering framework for de novo crystal structure determination from EXAFS.","authors":"O Murat Ozkendir, Selen Gunaydin","doi":"10.1107/S2053273326004766","DOIUrl":"10.1107/S2053273326004766","url":null,"abstract":"<p><p>This work introduces reverse EXAFS analysis (REA), a novel, ab initio framework that transforms extended X-ray absorption fine structure (EXAFS) spectroscopy from a complementary local probe into a primary tool for de novo crystal structure determination. By integrating iterative FEFF simulations with a reverse-fitting algorithm, REA directly extracts full crystallographic parameters, lattice constants, space group and atomic positions, from EXAFS oscillations, without requiring the user to supply an initial structural model from X-ray diffraction; instead, candidate models are retrieved from crystallographic databases and evaluated against EXAFS data. Validated on LiCrO₂ and CuFeO₂, REA uncovered unexpected phase complexities in CuFeO₂, identifying secondary CuFe₂O₄ and CuFe₅O₈ phases undetected by conventional methods. This paradigm shift enables accurate structure solving in disordered, nanostructured and novel materials where diffraction fails, establishing EXAFS as a stand-alone crystallographic technique.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"321-330"},"PeriodicalIF":2.1,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148256621","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":"MIDAS: a quantitative framework for high-energy diffraction microscopy. Part II: accuracy, robustness and best practices.","authors":"Hemant Sharma, Jun Sang Park, Sarvjit Shastri, Peter Kenesei","doi":"10.1107/S2053273326004018","DOIUrl":"10.1107/S2053273326004018","url":null,"abstract":"<p><p>The increasing complexity of in situ high-energy diffraction microscopy (HEDM) experiments demands a quantitative understanding of the data analysis pipeline to ensure reproducible science. However, the influence of key analysis parameters on the accuracy and precision of microstructural reconstructions is often not well quantified, creating a barrier to progress. This paper addresses this critical gap by presenting a rigorous, systematic validation of the HEDM data reduction methodology as implemented in the MIDAS software suite. Using a new, dedicated Ti-7 Al dataset, we investigate both far-field (FF) and near-field (NF) HEDM. Our results reveal critical sensitivities, demonstrating that grain position accuracy in FF-HEDM is highly dependent on the diversity of sampled diffraction vectors, while orientation precision in NF-HEDM improves dramatically with increased detector separation. We demonstrate the methodology's robustness against common experimental challenges, such as severe diffraction peak overlap, which is effectively filtered by requiring crystallographic consistency. Based on these quantitative findings, we establish a framework of best practices for HEDM data acquisition and analysis to guide the community towards more accurate and reliable results.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"305-320"},"PeriodicalIF":2.1,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13325190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148040258","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":"Renormalization techniques for inflation systems and some of their applications.","authors":"Michael Baake, Franz Gähler, Anna Klick, Neil Mañibo, Jan Mazáč","doi":"10.1107/S2053273326003918","DOIUrl":"10.1107/S2053273326003918","url":null,"abstract":"<p><p>Exact renormalization techniques are important and powerful, particularly for inflation-generated systems. We review recent results in this direction. We recall the necessary notions for inflation systems and show the renormalization principle, which allows us to obtain exact values of highly erratic functions, such as window covariograms. We apply these techniques to compute the diffraction pattern of the new monotile tilings with arbitrary precision. We also recall a recent invariant for a system with pure-point spectrum, the orbit separation dimension, and its relation to renormalization. Lastly, we recall results beyond the pure-point spectrum setting and show how renormalization and Lyapunov exponents can be used to exclude the presence of absolutely continuous parts of the spectra.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"294-304"},"PeriodicalIF":2.1,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13325193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148012755","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":"Crystallography in Open Science and its open educational resources.","authors":"John R Helliwell","doi":"10.1107/S2053273326004146","DOIUrl":"10.1107/S2053273326004146","url":null,"abstract":"<p><p>This article presents a review of the landscape of Open Science development and its relevance to crystallography. As open as possible as closed as necessary is the model for Open Science as commended by the UK and China. Mainland Europe requires compulsory release after 3 years since measurement of raw data. The USA policy situation has fluctuated considerably in recent years. Altogether, this article addresses the International Union of Crystallography's (IUCr) input into these activities. It considers its participation in international scientific and societal organizations, as well as its compliance with the policy recommendations. It considers the practical landscape in which crystallographers work, including their funding agencies, governments, central facilities and universities. This article sets the wider scene before describing how crystallography benchmarks against those under development. The IUCr's Teaching Pamphlets and the Online Dictionary of Crystallography are educational resources fully open to Global South and Global North readers and authors. Crystallography provides a mature, practice-based model of responsible openness that predates and can inform contemporary Open Science policy.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"229-241"},"PeriodicalIF":2.1,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13325185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148256590","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":"New algorithm for generating all coincidence-site lattices of the cubic crystal system.","authors":"Kazuaki Kawahara, Kazutoshi Inoue, Mitsuhiro Saito, Qian Chen, Yuichi Ikuhara","doi":"10.1107/S2053273326003645","DOIUrl":"10.1107/S2053273326003645","url":null,"abstract":"<p><p>Coincidence-site lattice (CSL) theory provides a fundamental framework for classifying commensurate crystal orientations and plays a central role in describing grain boundaries. In particular, Ranganathan's formula determines all CSL orientation relationships. However, it is not possible to avoid duplication and also to determine the equivalence of the duplicates, and number theoretical analysis can be required to address these issues. In this study, we provide a simple necessary condition to find all CSL orientation relationships in the cubic system by only using linear algebra. The necessary condition is given by calculating whether the (hkl) plane is commensurate to the (001) plane. We also found that the number of orientation relationships without symmetric tilt grain boundaries (GBs) increases as the Σ value increases by comparing the number of solutions of the equation for constructing symmetric tilt GBs with that of the necessary condition.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"276-284"},"PeriodicalIF":2.1,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147939469","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":"Relativistic Dirac-Hartree-Fock X-ray scattering factors. III. Chemically relevant atomic anions for Z = 1-85.","authors":"Hampton Copeland, Yoshihiro Watanabe, Anatoliy Volkov","doi":"10.1107/S2053273326003554","DOIUrl":"https://doi.org/10.1107/S2053273326003554","url":null,"abstract":"<p><p>Relativistic X-ray scattering factors are reported for a broad and systematically defined set of chemically relevant atomic anions, including mono- and multivalent species, for elements with atomic numbers Z = 1-85 [Greenwood & Earnshaw (1997). Chemistry of the Elements]. Dirac-Hartree-Fock wavefunctions were generated using the DFRATOM code [Matsuoka & Watanabe (2001). Comput. Phys. Commun. 139, 218-234], with soft radial confinement applied where necessary to stabilize diffuse anionic states. The influence of this confinement on the resulting X-ray scattering factors is explicitly and systematically analyzed to ensure that the reported data reflect physically meaningful electronic structure trends rather than artifacts of the stabilization procedure. The quality of the resulting wavefunctions was assessed using previously reported high-quality benchmark energies [Visscher & Dyall (1997). At. Data. Nucl. Tables 67, 207-224], radial metrics, and direct comparison of X-ray scattering factors with established reference data for neutral atoms and several monovalent anions [Rez et al. (1994). Acta Cryst. A50, 481-497; Su & Coppens (1997). Acta Cryst. A53, 749-762; Macchi & Coppens (2001). Acta Cryst. A57, 656-662]. To ensure physically meaningful results, an X-ray scattering based perturbation metric was introduced to quantify the impact of confinement on the calculated X-ray scattering factors, together with additional high-sin θ/λ consistency checks. The resulting X-ray scattering factors were computed and tabulated in a format consistent with that used in the International Tables for Crystallography [Maslen et al. (2006). Vol. C, Section 6.1.1, pp. 554-589], facilitating direct crystallographic use. Analysis of representative main-group, transition-metal and heavy p-block elements demonstrates that electron attachment leads to a systematic enhancement of the X-ray scattering factors at small momentum transfer, governed primarily by the expansion of the valence electron density, while the high-sin θ/λ region remains dominated by largely invariant core electron contributions. The data presented here provide the first broad, internally consistent reference set of fully relativistic X-ray scattering factors spanning a wide range of multivalent atomic anions of chemical and crystallographic interest, and represent a natural extension of the studies by Olukayode et al. [Acta Cryst. (2023), A79, 59-79; Acta Cryst. (2023), A79, 229-245].</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":"82 Pt 3","pages":"200-217"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147757885","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":"Octagonal tilings with three prototiles.","authors":"April Lynne Say-Awen, Sam Coates","doi":"10.1107/S2053273326002767","DOIUrl":"10.1107/S2053273326002767","url":null,"abstract":"<p><p>Motivated by theoretically and experimentally observed structural phases with octagonal symmetry, we introduce families of octagonal tilings composed of three prototiles. These tilings are defined by substitution rules with inflation factors δ^(m,n) = m + n(1 + √2), where m, n are nonnegative integers. We consider the cases (m, n) = (1, 1), (2, 2), (1, 2), (3, 2) and describe their basic properties. In addition, we discuss variants of the first three cases, and for (1, 1) we derive the relative frequencies of the vertex stars.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"179-190"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147643292","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":"Adsorption of C₆₀ on Al₁₃Fe₄(010): a theoretical study.","authors":"Dario Job, Franck Polewczyk, Julian Ledieu, Lucile Dezerald, Emilie Gaudry","doi":"10.1107/S2053273326002962","DOIUrl":"10.1107/S2053273326002962","url":null,"abstract":"<p><p>Despite significant research, the surface properties of quasicrystals and their approximants are not yet fully understood. In this paper, buckminsterfullerene (C₆₀ fullerene) is used as a probe to test the adsorption properties of the (010) surface of the quasicrystalline approximant Al₁₃Fe₄. Using first-principles calculations, we systematically explore 17 distinct adsorption sites and identify several energetically favorable configurations. Our analysis reveals that the symmetry matching between the C₆₀ molecule and the surface is a key parameter governing the interaction strength. Furthermore, surface aluminium atoms are shown to play a crucial role in stabilizing the adsorption. A comparative study with the Al₁₃Co₄(100) surface highlights similarities in the overall interaction trends, yet distinct differences arise due to variations in surface substructure. These findings underline the importance of both atomic composition and local geometric symmetry in molecule-intermetallic surface interactions.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"138-144"},"PeriodicalIF":1.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147687092","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}