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

{"title":"The incommensurate composite Y_xOs₄B₄ (x = 1.161).","authors":"Berthold Stöger, Oksana Sologub, Leonid Salamakha","doi":"10.1107/S205252062400982X","DOIUrl":"10.1107/S205252062400982X","url":null,"abstract":"<p><p>Y_xOs₄B₄ (x = 1.161) crystallizes as a tetragonal incommensurate composite of columns of Y atoms extending along [001] in an Os₄B₄ framework. The structure was refined using the superspace approach. The basic structure of the Y subsystem can be idealized as having I4/mmm symmetry, with a crystallographically unique Y atom located on the 4/mmm position. The actual superspace symmetry is P4₂/nmc(00σ₃)s0s0. The Y atoms feature only subtle positional modulation in the [001] direction. The Os₄B₄ subsystem [P4₂/ncm(00σ₃)00ss superspace symmetry] is built of columns of edge-sharing Os₄ tetrahedra extending along [001] and B₂ dumbbells. The Os₄ tetrahedra feature pronounced positional modulation with a distinct variation of the Os-Os bond lengths. Modulation of the B₂ dumbbells is best described as a rotation about the [001] axis.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602588","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":"The seventh blind test highlights exciting developments in crystal structure prediction.","authors":"Mihails Arhangelskis","doi":"10.1107/S2052520624011570","DOIUrl":"https://doi.org/10.1107/S2052520624011570","url":null,"abstract":"<p><p>Two reports on the seventh blind test on crystal structure prediction extensively discuss the cutting-edge avant-garde methods of structure generation and energy ranking.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765425","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":"A contribution to the crystal chemistry and topology of organic thiosulfates: bis(1-methylpiperazinium)·S₂O₃·H₂O versus 1-methylpiperazinediium·S₂O₃·3H₂O.","authors":"Dmitri O Charkin, Alexandru M Banaru, Semen A Ivanov, Vadim E Kireev, Sergey M Aksenov","doi":"10.1107/S2052520624007443","DOIUrl":"https://doi.org/10.1107/S2052520624007443","url":null,"abstract":"<p><p>Single crystals of two new compounds, (C₅H₁₄N₂)S₂O₃·H₂O (1) and (C₅H₁₃N₂)₂S₂O₃·3H₂O (2), were isolated from the reaction products of 1-methylpiperazine, sulfuric acid, and barium thiosulfate in aqueous media. The crystal structures have been determined by single-crystal X-ray diffraction. In agreement to the previous observations, the organic template may contribute to the formation of thiosulfates both as mono- and diprotonated species, but this is the first case where both products are reported for the same organic compound. In both structures 1 and 2, complex nets of hydrogen bonds involve all cations, anions and water molecules. Comparisons are made to the structures of other thiosulfates containing mono- or diprotonated diamine species.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765263","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":"Conformational disorder in quercetin dihydrate revealed from ultrahigh-resolution synchrotron diffraction.","authors":"Yvon Bibila Mayaya Bisseyou, Jonathan Wright, Christian Jelsch","doi":"10.1107/S2052520624010011","DOIUrl":"https://doi.org/10.1107/S2052520624010011","url":null,"abstract":"<p><p>Quercetin, a bioflavonoid abundant in plants, boasts antioxidant properties and plays a crucial role in various biological systems. The diffraction data of a quercetin dihydrate crystal have been measured at 20 (2) K to ultrahigh resolution (0.30 Å) using a synchrotron X-ray source. After meticulous multipolar refinement of the charge density, Fourier residual electron density peaks were identified, particularly at the position of hydrogen atom H15 of the catechol ring. This observation revealed a subtle disorder in the molecule, prompting the modelling of the catechol ring in two positions with occupancy percentages of 98.4% and 1.6% in the anti and syn conformations, respectively. Intermolecular interactions are analysed using Hirshfeld fingerprint plots and enrichment ratios. With the presence of numerous O-H...O hydrogen bonds, the packing shows good electrostatic complementarity between the quercetin molecule and its surroundings. The parallel displaced stacking interaction between two anti-quercetin molecules related by a translation along the a axis is, however, not attractive for its electrostatic contribution. The syn conformation shows more attractive quercetin dimers than the anti one. On the other hand, electrostatic interactions between quercetin and the two water molecules are stronger in the anti conformation. The electrostatic interactions of quercetin with human inositol polyphosphate multikinase were analysed in the structure of the complex found in the Protein Data Bank and compared with those the take place in the quercetin crystal packing.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765268","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":"Structures of hexamethyl-[1,1'-biphenyl]-4,4'-diammonium salts.","authors":"Rajakumar Kanthapazham, Artyom A Osipov, Dmitry A Zherebtsov, Andrey N Efremov, Sergey A Nayfert, Sergey A Adonin, Dar'ya V Spiridonova, Sergey V Atapin","doi":"10.1107/S2052520624009818","DOIUrl":"https://doi.org/10.1107/S2052520624009818","url":null,"abstract":"<p><p>The crystal structures of nine hexamethyl-[1,1'-biphenyl]-4,4'-diammonium (HMB) salts are described: the iodide (2), triiodide (3), succinate (4), fumarate (5), tetravanadate (6), hydroterephthalate (7) and perylenetetracarboxylate (8), as well as pentamethyl-[1,1'-biphenyl]-4,4'-diammonium iodide (1) and the metal-organic framework sodium diacetylenedisalicylate-HMB (9). HMB carbonate (10) has been synthesized as an important intermediate for a promising anti-metal-organic framework (`anti-MOF'). All the described compounds are characterized by high solubility in water. The results suggest that, during crystallization, crystallohydrates are formed from water. Compounds 6 and 9 are characterized by the presence of a rigid framework; compound 6 has an open framework structure filled with water molecules. Synchronous thermal analyses of compounds 2, 4, 6, 7, 8 and 10 allowed the identification of similarities in the mechanisms of thermolysis. At about 80-180°C, the loss of crystallization water molecules occurs. Between 180 and 250°C, a methyl group (methyl cation) is split off from the quaternary ammonium salt to form tetramethylbenzidinium. In the case of the iodides and salts of organic acids, the second thermolysis product is the methyl ester of this acid (methyliodide, dimethyl carbonate), which easily evaporates. In the range 240-355°C, tetramethylbenzidinium evaporates without decomposition.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765419","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":"Predicting co-crystal structures of N-halide phthalimides with 3,5-dimethylpyridine.","authors":"Zahrasadat Momenzadeh Abardeh, Faezeh Bahrami, Artem R Oganov","doi":"10.1107/S205252062401000X","DOIUrl":"https://doi.org/10.1107/S205252062401000X","url":null,"abstract":"<p><p>Crystal structure prediction (CSP) calculations were carried out to examine potential formation of co-crystals between N-halide phthalimides (Cl, Br or I) and 3,5-dimethylpyridine (35DMP). The co-crystal structure of N-bromophthalimide (nbp) with 35DMP (nbp-35DMP) is known, and the generated co-crystal structure of rank 1 is identical to experimental structure (VELXES). For the unknown crystal structure of N-iodophthalimide (nip), structure of rank 1 is suggested as a likely co-crystal structure. On the other hand, our calculations suggest the improbability of co-crystal formation between ncp and 35DMP. The CSP findings indicate that strong N-X...N interactions consistent with similar experimental structures in the Cambridge Structural Database play a major role in crystal structures of the studied compounds.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765411","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":"Coordination geometry flexibility driving supramolecular isomerism of Cu/Mo pillared-layer hybrid networks.","authors":"Marielsys Moya, Gustavo R Liendo-Polanco, Reinaldo Atencio, Pedro Silva, Jose A Henao, Julia Bruno-Colmenares","doi":"10.1107/S2052520624009934","DOIUrl":"https://doi.org/10.1107/S2052520624009934","url":null,"abstract":"<p><p>Hydrothermal synthesis led to four novel 3D pillared-layer metal-organic frameworks: [Cu₄(4,4'-bipy)₄(MoO₄)₄·0.3H₂O]_n (1), [Cu(4,4'-bipy)_0.5(MoO₄)·0.25H₂O]_n (2), [Cu(4,4'-bipy)(MoO₄)·0.1H₂O]_n (3), and [{Cu(4,4'-bipy)}₂(Mo₈O₂₆)_0.5]_n (4). These compounds exhibit diverse supramolecular isomerism within their 3D coordination networks, each incorporating bimetallic {CuMoO} layers linked by 4,4'-bipyridine, demonstrating a remarkable structural diversity. Compound 1 features a 3D network derived from conformational supramolecular isomerism. Its bimetallic layer comprises fused 16-membered {Cu₄Mo₄O₈} and eight-membered {Cu₂Mo₂O₄} rings, with varying O-Cu-O bond angles affecting the network puckering and Cu-Cu distances. In contrast, the coordination networks observed in 2, 3, and 4 correspond to structural supramolecular isomers from the earlier stated networks. In 2, centrosymmetric Cu²⁺ dimers with distorted square-pyramidal geometry are linked along the c axis by 4,4'-bipyridine, forming 1D {Cu₂(4,4'-bipy)}_n chains with a Cu-Cu distance of 2.95 Å. Its oxide substructure comprises bilayers of fused 12-membered {Cu₃Mo₃O₆} rings. Crystal structures 3 and 4 are particularly notable for their construction at the Cu⁺ centers. In compound 4, this isomerism is further influenced by the interplay between the distortion of the coordination geometry of both the Cu and Mo ions. The propensity to form these supramolecular isomers primarily stems from the flexible coordination environment of copper ions. Electron paramagnetic resonance measurements corroborated the structural descriptions of the paramagnetic compounds 1 and 2.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765289","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":"Variable stoichiometry and a salt-cocrystal intermediate in multicomponent systems of flucytosine: structural elucidation and their impact on stability.","authors":"Manimurugan Kanagavel, Sridhar Balasubramanian, Sunil Kumar Nechipadappu","doi":"10.1107/S2052520624010278","DOIUrl":"https://doi.org/10.1107/S2052520624010278","url":null,"abstract":"<p><p>New cocrystals and a salt-cocrystal intermediate system involving the antifungal drug flucytosine (FCY) and various coformers including caffeic acid (CAF), 2-chloro-4-nitrobenzoic acid (CNB), hydroquinone (HQN), resorcinol (RES) and catechol (CAL), are reported. The crystal structures of the prepared multicomponent systems were determined through SC-XRD analysis and characterized by different solid-state techniques. All FCY multicomponent systems crystallize in anhydrous form with different stoichiometric ratios. The cocrystals FCY-HQN, FCY-RES and FCY-CAL crystallize in 2:0.5, 2:0.5 and 3:2 stoichiometric ratios respectively. In contrast, FCY-CAF and FCY-CNB crystallize in a 1:1 stoichiometric ratio. The FCY-CAF cocrystal is formed via an acid-pyrimidine heterosynthon. Due to the partial proton transfer from the acid group of CNB to FCY, a three-point homosynthon is observed between two FCY molecules and the molecules interact via an N-H...O hydrogen bond between FCY and CNB. In FCY phenolic cocrystals, a single-point O-H...O hydrogen bond is observed. The formation of cocrystals and salt-cocrystal intermediate was further confirmed by difference Fourier map analysis and bond angle differences. Except for FCY-CAL, all the multicomponent systems were reproduced in the bulk scale for further characterization. A detailed Crystal Structural Database search was carried out on the multicomponent systems of FCY with acid coformers and we evaluated the formation of cocrystals/salt based on the ΔpK_a values, the difference in the bond distances and bond angles. Additionally, the prepared multicomponent systems exhibited hydration stability for one month under accelerated conditions [40 (2) °C and relative humidity 90-95 (5)%].</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765436","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":"Crystal structure and compressibility of magnesium chloride heptahydrate found under high pressure.","authors":"Keishiro Yamashita, Kazuki Komatsu, Takanori Hattori, Shinichi Machida, Hiroyuki Kagi","doi":"10.1107/S205252062400903X","DOIUrl":"10.1107/S205252062400903X","url":null,"abstract":"<p><p>The odd hydration number has so far been missing in the water-rich magnesium chloride hydrate series (MgCl₂·nH₂O). In this study, magnesium chloride heptahydrate, MgCl₂·7H₂O (or MgCl₂·7D₂O), which forms at high pressures above 2 GPa and high temperatures above 300 K, has been identified. Its structure has been determined by a combination of in-situ single-crystal X-ray diffraction at 2.5 GPa and 298 K and powder neutron diffraction at 3.1 GPa and 300 K. The single-crystal specimen was grown by mixing alcohols to prevent nucleation of undesired crystalline phases. The results show orientational disorder of water molecules, which was also examined using density functional theory calculations. The disorder involves the reconnection of hydrogen bonds, which differs from those in water ice phases and known disordered salt hydrates. Shrinkage by compression occurs mainly in one direction. In the plane perpendicular to this most compressible direction, oxygen and chlorine atoms are in a hexagonal-like arrangement.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492802","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":"Density functional theory investigation of the phase transition, elastic and thermal characteristics for AuMTe₂(M = Ga, In) chalcopyrite compounds.","authors":"N Boucerredj, F Semari, S Ghemid, H Oughaddou, R Khenata, A Bouhemadou, M Boucharef, H Meradji, Z Chouahda, S Bin-Omran, S Goumri-Said","doi":"10.1107/S2052520624010473","DOIUrl":"https://doi.org/10.1107/S2052520624010473","url":null,"abstract":"<p><p>We explored the pressure-induced structural phase transitions and elastic properties of AuMTe₂ (M = Ga, In) using the full-potential linearized augmented plane wave method within the framework of density functional theory, applying both generalized gradient and local density approximations. Thermodynamic properties were further assessed through the quasi-harmonic model. We determined the transition pressures for the phase shift from the chalcopyrite structure to the NaCl rock-salt phase in both AuGaTe₂ and AuInTe₂. Additionally, we calculated and analyzed mechanical properties, such as bulk modulus, shear modulus, Young's modulus, Poisson's ratio, elastic anisotropy, ductility versus brittleness, and hardness for the polycrystalline forms of AuMTe₂ (M = Ga, In). The study also examined how temperature and pressure affect the Debye temperature, heat capacities, thermal expansion, entropy, bulk modulus, Grüneisen parameter, and hardness, utilizing the quasi-harmonic Debye model.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765327","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}