Acta crystallographica Section B, Structural science, crystal engineering and materials最新文献

{"title":"Crystallography of the litharge to massicot phase transformation from neutron powder diffraction data.","authors":"Roderick J Hill, Lachlan M D Cranswick","doi":"10.1107/S205252062401254X","DOIUrl":"10.1107/S205252062401254X","url":null,"abstract":"<p><p>The crystallographic phase change from tetragonal litharge (α-PbO; P4/nmm) to orthorhombic massicot (β-PbO; Pbcm) has been studied by full-matrix Rietveld analysis of high-temperature neutron powder diffraction data collected in equal steps from ambient temperature up to 925 K and back down to 350 K. The phase transformation takes place between 850 and 925 K, with the coexisting phases having equal abundance by weight at 885 K. The product massicot remains metastable on cooling to near ambient temperature. Both structures are layered networks of OPb₄ tetrahedra and PbO₄ square pyramids, with the space between alternate layers of Pb atoms (in approximate cubic close packing) occupied either by O atom layers or Pb atom lone pairs. In massicot, the symmetric Pb and O layers of litharge become deeply corrugated parallel to [001], with the O-atom layers splitting into two layers, although these are still sandwiched between the approximately cubic close-packed Pb atom layers. The crystallite size of the initial litharge component decreases from around 3500 Å to around 1100 Å at the midpoint of the phase change at 885 K, whereupon the size of the massicot crystallites increases from a similar value to around 2500 Å at 350 K during the cool-down stage. The unit-cell dimensions and atomic coordinates of litharge change smoothly throughout the phase change, but there is a rapid expansion of the c-axis immediately prior to the recrystallization to massicot, and the one free coordinate (Pb z) decreases significantly to producer a thinning of the layers. Increases in the O displacment parameters suggest that this atom is `on the move' as the transformation approaches. Changes in the massicot parameters as its crystallites emerge from the transformation are largely unremarkable. The formation of the heavily corrugated layers in massicot requires significant movements of the O atoms (∼1.2 Å) from their positions in litharge and thus for Pb-O bonds to be broken during the phase change. The requirement for these bonds to be re-broken in a conversion back to litharge is likely to be the reason why massicot is metastable at ambient temperature. Evidence of a temporary intermediate `amorphous' phase in the phase transformation from which the massicot grows is provided in the form of broad, very low amplitude `peaks' in the high-temperature diffraction patterns.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":"146-160"},"PeriodicalIF":1.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystallization induced by fungi and bacteria.","authors":"Olga Frank-Kamenetskaya, Dmitry Vlasov","doi":"10.1107/S2052520624011041","DOIUrl":"10.1107/S2052520624011041","url":null,"abstract":"<p><p>Crystallization induced by lithobiont microbial communities (fungi, bacteria, lichens) has received great attention in science and beyond. The studies discussed here focus on the mechanisms and factors of microbial biomineralization. The multilevel modelling approach, which made it possible to solve this interdisciplinary problem, is highlighted. The effect of chemical composition of biofilms, including acidity of the medium and cation oxidation degree, on oxalate formation is discussed. The variants of interaction between biofilm components and growing oxalate crystals are addressed. Particular attention is paid to the effect of metabolism of fungi, bacteria and their associations on carbonate and oxalate crystallization under various trophic conditions and the transitions between them. The possibility of applying the identified patterns to reveal the role of fungi and bacteria in the oxalate-carbonate pathway and in biotechnologies is considered.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":"1-10"},"PeriodicalIF":1.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electron density distribution in bis(guanidinium) disodium hypodiphosphate heptahydrate, (CH₆N₃)₂Na₂(P₂O₆)·7H₂O.","authors":"Przemysław Starynowicz, Katarzyna Anna Ślepokura, Paulina Kurowska, Vasyl Kinzhybalo","doi":"10.1107/S2052520624011120","DOIUrl":"10.1107/S2052520624011120","url":null,"abstract":"<p><p>X-ray structural analysis of bis(guanidinium) disodium hypodiphosphate heptahydrate, (CH₆N₃)₂Na₂(P₂O₆)·7H₂O revealed close Na⁺...guanidinium [Na...N 3.0366 (6) Å] and water...guanidinium O-H...N [H...N 2.07 Å, O...N 3.0401 (9) Å] contacts, the nature of which is explored with the use of electron density distribution and Hirshfeld surface analysis. The crystal structure is governed by coordination interactions to Na⁺ cations and an extensive network of hydrogen bonds, in which guanidinium cations, hypodiphosphate ions and water molecules are involved. Na⁺ cations are in tetragonal pyramidal or octahedral environment, which was proved by continuous shape measures. From ∇²ρ(r_c) and bond degree values, the character of P-P bonds are classified as shared shell or covalent bond types, whereas P-O bonds are of transit closed shell or polarized covalent types. Despite the lack of a lone electron pair on the N atom and positive charge of the guanidinium cation, the existence of an O-H...N hydrogen bond was confirmed by electron density studies.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":"135-145"},"PeriodicalIF":1.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SARAh - web representational analysis.","authors":"Andrew S Wills","doi":"10.1107/S2052520624010977","DOIUrl":"10.1107/S2052520624010977","url":null,"abstract":"<p><p>The online software server SARAh-webRepresentational Analysis is introduced. It replaces the previous Windows-versions of SARAh-Representational analysis and SARAh-Refine, and related theory. The new suite of web apps carries out a range representational analysis calculations, including those based on the works of Kovalev, Bertaut, Izyumov, Bradley, Cracknell, Birman and Landau, for magnetic structures and electronic properties within frameworks based on the crystallographic space groups and point groups. Irreducible representations are sourced from the works of Kovalev, tabulated and computations are carried out on a server using Mathematica.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":"28-36"},"PeriodicalIF":1.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural and theoretical studies of amantadinium fenamates.","authors":"Marta S Krawczyk, Monika K Krawczyk, Irena Majerz","doi":"10.1107/S2052520624011909","DOIUrl":"10.1107/S2052520624011909","url":null,"abstract":"<p><p>Two new crystals of amantadinium salts were obtained from fenamic and tolfenamic acid. The salt of fenamic acid is a model compound for interaction analysis, while amantadinium tolfenamate is a composition of a drug used in the treatment of symptoms of Parkinsonism and as a nonsteroidal anti-inflammatory drug. The crystal structures were studied and a theoretical analysis of the hydrogen bonds and weak interactions was carried out using quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) methods.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":"92-103"},"PeriodicalIF":1.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Review of honeycomb-based Kitaev materials with zigzag magnetic ordering.","authors":"V Ovidiu Garlea, Colin L Sarkis","doi":"10.1107/S2052520624009831","DOIUrl":"10.1107/S2052520624009831","url":null,"abstract":"<p><p>The search for a Kitaev quantum spin liquid in crystalline magnetic materials has fueled intense interest in the two-dimensional honeycomb systems. Many promising candidate Kitaev systems are characterized by a long-range-ordered magnetic structure with an antiferromagnetic zigzag-type order, where the static moments form alternating ferromagnetic chains. Recent experiments on high-quality single crystals uncovered the existence of intriguing multi-k magnetic structures, which evolved from zigzag structures. Those discoveries have sparked new theoretical developments and amplified interest in these materials. We present an overview of the honeycomb materials known to display this type of magnetic structure and provide detailed crystallographic information for the possible single- and multi-k variants.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":"11-27"},"PeriodicalIF":1.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modulation of the modulated magnetic structure of an Ho i-MAX phase described by a magnetic (3+2)-dimensional superspace group.","authors":"Claire V Colin, Quanzheng Tao, Christine Opagiste, Rafik Balou, Johanna Rosen, Thierry Ouisse, Václav Petříček","doi":"10.1107/S2052520624011053","DOIUrl":"10.1107/S2052520624011053","url":null,"abstract":"<p><p>The magnetic structures of the Ho-based i-MAX phase (Mo_2/3Ho_1/3)₂GaC were studied with neutron powder diffraction at low temperature. (Mo_2/3Ho_1/3)₂GaC crystallizes in the orthorhombic space group Cmcm. The material undergoes two successive antiferromagnetic transitions at T_N1 = 10 K and T_N2 = 7.2 K. The magnetic structure below T_N1 is incommensurate with the propagation vector k₁ = (0, k_y, 0) with k_y = 0.696 (1) at 9 K. For the analysis of the magnetic structure, a group-theoretical approach based on the space group of the nuclear structure and its subgroups was employed. A model in the (3+1)D superspace group Cmcm.1'(0β0)s0ss yielded the most accurate results in neutron powder diffraction refinements. The determined structure was found to be an incommensurate longitudinal amplitude-modulated magnetic structure. Below T_N2, additional magnetic satellites develop. They could be indexed by a propagation vector k₂ = (τ_x, 0, 0) with the τ_x value increasing below T_N2 until it stabilizes at approximately 3 K at 0.075. A magnetic structure determination considering two propagation vectors k₁ and k₂ was carried out using the superspace formalism by building the corresponding (3+2)D model. The determination was based on the observation that the additional magnetic peaks emerge exclusively in the vicinity of the incommensurate magnetic peaks with propagation vector k₁, and not in the vicinity of nuclear peaks. This indicates that only mixed-index reflections were observed, and not reflections purely related to k₂. The magnetic superspace group (MSSG) that was determined is Amma.1' (0,β,0)00s0 (0,0,γ)ss0s. The structure can be described as a longitudinal amplitude-modulated structure, which itself is amplitude-modulated in a perpendicular direction. This represents a very unusual case of a 2-k magnetic structure with no symmetry relation between the propagation vectors.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":"37-46"},"PeriodicalIF":1.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11801704/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. Part III: partitioning into torsional groups.","authors":"Isaac J Sugden, David H Bowskill, Benjamin I Tan, Yizu Zhang, Claire S Adjiman, Constantinos C Pantelides","doi":"10.1107/S2052520624010072","DOIUrl":"10.1107/S2052520624010072","url":null,"abstract":"<p><p>We present an approach to reduce this computational cost substantially, based on the partitioning of the molecule into geometrically separated torsional groups, with the dependence of the intramolecular energy and atomic point charges and dependent degrees of freedom on molecular conformation being computed as a linear combination of the contributions of these groups. This can lead to large savings in computational cost without a significant impact on accuracy, as demonstrated in the cases of N-acetyl-para-aminophenol (paracetamol) and methyl 4-hydroxybenzoate (methyl paraben). The approach is also applied successfully to two larger molecules, benzyl [4-(4-methyl-5-[(4-methylphenyl)sulfonyl]-1,3-thiazol-2-yl)phenyl]carbamate (molecule XX from the fifth CSP blind test) and (2S)-2-[4-(3-fluorobenzyloxy)benzylamino]propionamide (safinamide), for which we conduct the first reported CSP study. In both cases, the use of torsional groups results in over 99% reduction in computational cost, which enables the generation of an initial CSP landscape with high-quality structures found within the standard cutoff of 20 kJ mol^-1 for progression to refinement.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":"114-127"},"PeriodicalIF":1.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11801705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A rare case of Na/Zn isomorphism in the crystal structure of non-centrosymmetric zincophosphate Na₅Zn[Zn(PO₄)₃].","authors":"Olga V Yakubovich, Galina V Kiriukhina, Anatoly S Volkov, Olga V Dimitrova","doi":"10.1107/S2052520624011156","DOIUrl":"10.1107/S2052520624011156","url":null,"abstract":"<p><p>A microporous zincophosphate with the idealized formula Na₅Zn[Zn(PO₄)₃] was obtained through high-temperature hydrothermal synthesis and characterized by scanning electron microscopy, microprobe analysis and X-ray diffraction. The orthorhombic compound, which crystallizes in non-centrosymmetric space group Pna2₁ with unit-cell parameters a = 12.9901 (2), b = 16.2647 (3), c = 5.2158 (1) Å and Z = 4, is characterized by a new structure type. Each ZnO₄ tetrahedron shares all O atoms with four phosphate tetrahedra to form groups of five polyhedra, that are further linked via oxygen-bridging contacts of Zn- and P-centered tetrahedra in chains aligned in the c-axis direction. These one-periodic structural fragments [Zn(PO₄)₃]^7- define the prismatic habitus of the crystals. The negatively charged zincophosphate chains are balanced by Na⁺ cations, disposed in an open space between the chains, and somewhat `diluted' with Zn²⁺, Ca²⁺ and Mn²⁺ ions as impurities. A rare case of the Na/Zn occupation of one structural site was found in the structure. Theoretical calculations of possible pathways of alkali metal ion migration through the structure and activation energies revealed that the Li-substituted counterpart Li₅Zn[Zn(PO₄)₃] can be considered as a potential solid electrolyte.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":"62-68"},"PeriodicalIF":1.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural studies of hydrated rare earth nitrates within the stereoatomic model of crystal structures.","authors":"Anton V Savchenkov, Galina M Kuz'micheva","doi":"10.1107/S2052520624012071","DOIUrl":"10.1107/S2052520624012071","url":null,"abstract":"<p><p>All crystal structures containing nitrate ions, water molecules and one of the rare earth (RE) metal atoms (La-Lu, Y, Sc) were extracted from the Inorganic Crystal Structure Database. The composition of the identified compounds is analyzed in terms of the number of coordinated and uncoordinated water molecules and nitrate ions. Among the resulting compounds, several isotypic and morphotropic series are observed. The structures were analyzed within the stereoatomic model of crystal structures. Coordination numbers of RE metals are calculated using the method of intersecting spheres. The variation of RE-O distances is analyzed over the entire series of metal atoms. Coordination modes of both nitrate ions and water molecules are established. Combinatorial topological types of Voronoi-Dirichlet polyhedra of rare earth metal atoms as coordination centers in the studied compounds are calculated.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":"128-134"},"PeriodicalIF":1.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}