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

{"title":"Computation screening for incorrectly determined cocrystal structures.","authors":"Simona Chalupná, Michal Hušák, Jan Čejka, František Fňukal, Jiří Klimeš","doi":"10.1107/S205252062500068X","DOIUrl":"10.1107/S205252062500068X","url":null,"abstract":"<p><p>Pharmaceutical solid forms, like salts and cocrystals, play a crucial role in drug formulation. Despite differing mainly by a single hydrogen atom, the regulatory requirements set by the US Food and Drug Administration for these forms vary significantly. We previously developed a DFT-based computational method to distinguish salts from cocrystals. This method, validated on 95 structures, performed well for systems where hydrogen bonds were longer than 2.613 (16) Å. Here, benefits of the rSCAN functional over the PBE functional are discussed. We expand the dataset to 404 cocrystal models. Analysis confirms that 301 of these forms are indeed cocrystals. Additionally, 87 salt-cocrystal continuum forms are identified and 16 cocrystals are classified as possible salts. These 16 problematic structures are further investigated and for seven of them, single crystals were grown and their structure determined using single-crystal X-ray diffraction. Among the phases exhibiting salt-like behaviour, five of them are identified as salts. In some cases, rSCAN alone gives unreliable results for strong hydrogen bonds, but these discrepancies are often corrected using better-renormalized or hybrid functionals (i.e. r2SCAN, PBE0 and PBE50). For future calculations, we recommend using the r2SCAN functional for salt-cocrystal differentiation, as it provides reliable results for O-H...N bonds longer than 2.554 (5) Å. The r2SCAN functional offers a good balance between accuracy and computational efficiency for systems with longer O-H...N bonds.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514324","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":"Intrusion of quantum crystallography into classical lands.","authors":"Sizhuo Yu, Jean Michel Gillet","doi":"10.1107/S2052520625000782","DOIUrl":"10.1107/S2052520625000782","url":null,"abstract":"<p><p>This article, written on the occasion of the International Year of Quantum Science and Technology, explores the development of alternative approaches to pure-state N-electron wavefunctions in quantum physics. It focuses on Quantum Crystallography tools and explains how the combination of X-ray coherent-elastic and incoherent-inelastic scattering data has enabled the description of mean-electron's quantum behaviour in phase space. The article gives a numerical example using a urea crystal to demonstrate the attainability of recovering a one-electron reduced density matrix and its associated reduced Wigner function. It emphasizes the importance of momentum-space measurements in obtaining a more accurate phase-space picture of electron quantum physics in crystals.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623168","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 magnetic properties of β-Li₂IrO₃ after grazing-angle focused ion beam thinning.","authors":"Nelson Hua, Franziska Breitner, Anton Jesche, Shih Wen Huang, Christian Rüegg, Philipp Gegenwart","doi":"10.1107/S2052520625000587","DOIUrl":"10.1107/S2052520625000587","url":null,"abstract":"<p><p>Manipulating the size and orientation of quantum materials is often used to tune emergent phenomena, but precise control of these parameters is also necessary from an experimental point of view. Various synthesis techniques already exist, such as epitaxial thin film growth and chemical etching, that are capable of producing specific sample dimensions with high precision. However, certain materials exist as single crystals that are often difficult to manipulate, thereby limiting their studies to a certain subset of experimental techniques. One particular class of these materials includes lithium and sodium iridates, which are promising candidates for hosting a Kitaev quantum spin liquid state. Here a controlled method of using a focused ion beam at grazing incidence to reduce the size of a β-Li₂IrO₃ single crystal to a thickness of 1-2 µm is presented. Subsequent X-ray diffraction measurements show the lattice remains intact, albeit with a larger mosaic spread. The integrity of the magnetic order is also preserved as the temperature dependent magnetic diffraction peak follows the same trend as its bulk counterpart with a transition temperature at T_N = 37.5 K. Our study demonstrates a technique that opens up the possibility of nonequilibrium experiments where submicron thin samples are often essential.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143717778","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":"The chemical theory of valence.","authors":"Ian David Brown","doi":"10.1107/S2052520625000022","DOIUrl":"10.1107/S2052520625000022","url":null,"abstract":"<p><p>Relaxing the restriction that valence can only adopt integer values removes the distinction between ionic and covalent bonds, resulting in a simple and powerful valence theory using the concept of the bonding strength of an element, defined as the ratio of its atomic valence to its average coordination number. Bonding strength, closely related to electronegativity, determines which atoms form stable bonds and the chemical properties of the resulting compounds of both organic and inorganic compounds.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397753","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":"Electric charge and salting in/out effects on glucagon's dipole moments and polarizabilities using the GruPol database.","authors":"Raphael F Ligorio, Rasmus H M Gehle, Leonardo H R Dos Santos, Anna Krawczuk","doi":"10.1107/S2052520625001088","DOIUrl":"10.1107/S2052520625001088","url":null,"abstract":"<p><p>This work demonstrates the use of the GruPol database to predict the functional group dipole moments and polarizabilities of glucagon in the presence of NaCl, simulating an electric charge distribution on the protein's backbone. A new feature of the database allows for the inclusion of ions on the protein backbone, effectively simulating a protein salt and predicting the impact on electrical properties. Glucagon was selected as a proof-of-concept molecule due to its relatively small chain, which enabled benchmarking against quantum mechanical calculations. Firstly, we simulated 70 different ionic configurations, varying the number of Na⁺ and Cl^- ions from zero to four NaCl moieties. Additionally, we investigated the effects of solvation under two distinct conditions: one involving just the peptide and water, and the other also including NaCl at a concentration of approximately 4.2 mol L^-1. Regarding the ab initio results, GruPol showed good accuracy, with an angular direction error of around 10° and a 15% difference in the magnitude of the dipole moments. However, the error in polarizability values was higher, most likely due to the lack of an augmented basis set in the ab initio quantum calculations (M06-HF/cc-pVDZ). The database entries were generated using the same functional along with the aug-cc-pVDZ basis set. In solution, a high ionic concentration lowered the overall dipole moment, while the main components of polarizability increased.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490143","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":"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}