Acta Crystallographica Section C Structural Chemistry最新文献

{"title":"7-(4-Chlorophenyl)-1-hydroxy-5-methylpyrido[3,4-d]pyridazin-4(3H)-one: synthesis, solvatomorphism, in vitro anti-inflammatory and cytotoxic activity studies and in silico analysis.","authors":"Anna Wójcicka, Iwona Bryndal, Magdalena Krupińska, Aleksandra Wolska, Jakub Milewski, Anna Pyra, Lilianna Becan, Marcin Mączyński, Agnieszka Matera-Witkiewicz","doi":"10.1107/S2053229625001858","DOIUrl":"10.1107/S2053229625001858","url":null,"abstract":"<p><p>The newly obtained compound 7-(4-chlorophenyl)-1-hydroxy-5-methylpyrido[3,4-d]pyridazin-4(3H)-one (CPM) was crystallized as two new variable solvates, namely, the dimethyl sulfoxide monosolvate, C₁₄H₁₀ClN₃O₂·C₂H₆SO (I), and the sesquisolvate, C₁₄H₁₀ClN₃O₂·1.5C₂H₆SO (II), and their structures were confirmed by single-crystal X-ray diffraction analysis. In previous work, 1-hydroxy-5-methyl-7-phenylpyrido[3,4-d]pyridazin-4(3H)-one (PM) was found to display anticancer activity. In the next step of our studies, we synthesized a new derivative of PM, introducing a Cl atom into the PM structure, obtaining CPM, which showed not only anticancer but also anti-inflammatory activity. CPM and the new semi-products of each step of the synthesis were examined by ¹H NMR, ¹³C NMR and FT-IR spectroscopic analyses, and mass spectrometry. CPM forms (I) and (II) crystallize in the triclinic P1 and monoclinic C2/c space groups, respectively, and differ in the stoichiometry of the CPM and DMSO molecules in the crystal lattice, being 1:1 and 1:1.5 for (I) and (II), respectively. A powder X-ray diffraction analysis was performed only for solvate (I) due to the lack of stability of solvate (II). The potential cytotoxicity of CPM was evaluated against the normal cell lines L929 and RPTEC, as well as the cancer cell lines A172, AGS, CACO-2 and HepG2. The anti-inflammatory activity of CPM was also evaluated using colorimetric assay for the inhibition of COX-1 and COX-2. The same biological tests were carried out for PM to compare the activities of both compounds. The biological studies revealed that CPM does not exhibit more activity than PM. Moreover, in silico analysis of the bioavailability and molecular docking were performed.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"198-211"},"PeriodicalIF":0.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"8-Ethynyl-2'-deoxyisoguanosine with two tautomeric forms in the unit cell: crystal structure, packing and Hirshfeld surface analysis.","authors":"Dasharath Kondhare, Simone Budow-Busse, Constantin G Daniliuc, Peter Leonard","doi":"10.1107/S2053229625001998","DOIUrl":"10.1107/S2053229625001998","url":null,"abstract":"<p><p>Isoguanine nucleosides constructed by different heterocyclic skeletons play a significant role in the context of genetic code expansion, as well as for purine-purine base pairing. However, with respect to structure analysis, only limited information is available on this class of nucleosides. In this study, the single-crystal X-ray structure of 8-ethynyl-2'-deoxyisoguanosine, C₁₂H₁₃N₅O₄·C₁₂H₁₃N₅O₄·2H₂O (1), has been investigated. In the crystal of 1, the N1-H and N3-H tautomers exist together. They are connected by O3'-H to O3' hydrogen bonds. The conformation at the glycosylic bond is syn for both tautomeric forms. This conformation is stabilized by intramolecular hydrogen bonds from N3 or N3-H of the pyrimidine ring to the 5'-OH group of the sugar residue. For both tautomers, the sugar conformation adopts a C2'-endo-C3'-exo twist (²T₃; S-type), with P = 165.0 and 163.9°. A synclinal orientation is observed around the C4-C5' bond. Crystal packing is controlled by a tridentate purine-purine pair of 8-ethynyl-2'-deoxyisoguanosine that is enabled by a tautomeric shift of the proton from N1 to N3 of the nucleobase. Additional stability to the 3D network is contributed by water molecules connecting different layers in the solid state. A Hirshfeld surface analysis was performed confirming the existence of the purine-purine pair and the impact of the water molecules on hydrogen bonding. To the best of our knowledge, this is the first X-ray analysis on a nucleoside with two different tautomeric forms in the crystal unit that form a purine-purine base pair.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"230-237"},"PeriodicalIF":0.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-crystal structure of the spicy capsaicin.","authors":"Matic Lozinšek","doi":"10.1107/S2053229625001706","DOIUrl":"10.1107/S2053229625001706","url":null,"abstract":"<p><p>The crystal structure of capsaicin (C₁₈H₂₇NO₃), or trans-8-methyl-N-vanillylnon-6-enamide, the natural product responsible for the spiciness of chilli peppers, was determined using low-temperature single-crystal X-ray diffraction. The reported crystal structure is in good agreement with previous determinations based on powder X-ray diffraction data. The localization and free refinement of all H atoms revealed that each capsaicin molecule is hydrogen bonded to four other molecules, with the O-H and N-H groups acting as hydrogen-bond donors, and the C=O group serving as a bifurcated hydrogen-bond acceptor.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"188-192"},"PeriodicalIF":0.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fast event-based electron counting for small-molecule structure determination by MicroED.","authors":"Niko Vlahakis, Songrong Qu, Logan S Richards, Lygia Silva de Moraes, Duilio Cascio, Hosea M Nelson, Jose A Rodriguez","doi":"10.1107/S2053229624012300","DOIUrl":"10.1107/S2053229624012300","url":null,"abstract":"<p><p>Electron counting helped realize the resolution revolution in single-particle cryoEM and is now accelerating the determination of MicroED structures. Its advantages are best demonstrated by new direct electron detectors capable of fast (kilohertz) event-based electron counting (EBEC). This strategy minimizes the inaccuracies introduced by coincidence loss (CL) and promises rapid determination of accurate structures. We used the Direct Electron Apollo camera to leverage EBEC technology for MicroED data collection. Given its ability to count single electrons, the Apollo collects high-quality MicroED data from organic small-molecule crystals illuminated with incident electron beam flux densities as low as 0.01-0.045 e^-/Ų/s. Under even the lowest flux density (0.01 e^-/Ų/s) condition, fast EBEC data produced ab initio structures of a salen ligand (268 Da) and biotin (244 Da). Each structure was determined from a 100° wedge of data collected from a single crystal in as few as 50 s, with a delivered fluence of only ∼0.5 e^-/Ų. Fast EBEC data collected with a fluence of 2.25 or 3.33 e^-/Ų also facilitated a 1.5 Å structure of thiostrepton (1665 Da). While refinement of these structures appeared unaffected by CL, a CL adjustment applied to EBEC data further improved the distribution of intensities measured from the salen ligand and biotin crystals. However, CL adjustment only marginally improved the refinement of their corresponding structures, signaling the already high counting accuracy of detectors with counting rates in the kilohertz range. Overall, by delivering low-dose structure-worthy data, fast EBEC collection strategies open new possibilities for high-throughput MicroED.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"116-130"},"PeriodicalIF":0.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis and crystal structure of a nickel(II) 2'-deoxy-6-thioguanosine nitrate complex.","authors":"Samira O Hribesh, William Clegg, Ross W Harrington, Andrew Houlton, Andrew R Pike","doi":"10.1107/S2053229625001500","DOIUrl":"10.1107/S2053229625001500","url":null,"abstract":"<p><p>The reaction of Ni(NO₃)₂·6H₂O with the thio-modified nucleoside 2'-deoxy-6-thioguanosine (d-tG, C₁₀H₁₃N₅O₃S) in methanol in a 1:1.3 stoichiometric ratio deposited the title compound, [Ni(d-tG)₃](NO₃)₂·2H₂O, as green crystals. Despite the <1:3 Ni-ligand ratio used in the synthesis, the deoxy-thioguanosine binds to form three N⁷,S⁶-coordinated five-membered chelate rings with individual Ni^II ions in mononuclear complexes rather than bridge metal centres into more extended oligomeric or polymeric structures.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"165-169"},"PeriodicalIF":0.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Foreword to the special issue Crystallography in Latin America: a vibrant community.","authors":"Maria Rosales-Hoz, Renata Diniz","doi":"10.1107/S205322962500083X","DOIUrl":"10.1107/S205322962500083X","url":null,"abstract":"<p><p>This collection highlights the diversity and quality of research conducted by Latin American scientists, and emphasizes the interdisciplinary nature of crystallography, highlighting its connections with other research fields and presenting innovative and thought-provoking studies.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"114-115"},"PeriodicalIF":0.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis and characterization of coumarin-derived sulfur analogues using Lawesson's reagent.","authors":"Neliswa Mama, Stiaan Schoeman, Lisa Myburgh, Eric C Hosten","doi":"10.1107/S2053229625000956","DOIUrl":"10.1107/S2053229625000956","url":null,"abstract":"<p><p>The synthesis and characterization of six novel coumarin derivatives containing O and S atoms are described here, namely, ethyl 2-oxo-2H-chromene-3-carboxylate, C₁₂H₁₀O₄ (S1a), ethyl 2-sulfanylidene-2H-chromene-3-carboxylate, C₁₂H₁₀O₃S (S2a), ethyl 2-sulfanylidene-2H-chromene-3-carbothioate, C₁₂H₁₀O₂S₂ (S3a), ethyl 8-methoxy-2-oxo-2H-chromene-3-carboxylate, C₁₃H₁₂O₅ (S1b), ethyl 8-methoxy-2-sulfanylidene-2H-chromene-3-carboxylate, C₁₃H₁₂O₄S (S2b), and ethyl 8-methoxy-2-sulfanylidene-2H-chromene-3-carbothioate, C₁₃H₁₂O₃S₂ (S3b). Compounds S1a/b were synthesized in good yields following the Knoevenagel condensation method. The thiocarbonyl analogues of these compounds, S2a/b and S3a/b, were obtained using Lawesson's reagent as a thionating compound. The structures of S2a/b and S3a/b were confirmed using FT-IR, ¹H and ¹³C NMR, and UV-Vis spectroscopy, and single-crystal X-ray diffraction. Hirshfeld surface and energy framework analyses show that stacked π-π ring interactions occur for all the structures obtained here, and various hydrogen-bond interactions link the stacks to form three-dimensional energy frameworks.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"170-180"},"PeriodicalIF":0.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rb₂Ca₂Si₂O₇: a new alkali alkaline-earth silicate based on [Si₂O₇]^6- anions.","authors":"Volker Kahlenberg","doi":"10.1107/S2053229625001196","DOIUrl":"10.1107/S2053229625001196","url":null,"abstract":"<p><p>Synthesis experiments were conducted in the ternary Rb₂O-CaO-SiO₂ system, resulting in the formation of a hitherto unknown compound with the composition Rb₂Ca₂Si₂O₇, i.e. dirubidium dicalcium pyrosilicate. Single crystals of sufficient size and quality were recovered from a starting mixture with an Rb₂O:CaO:SiO₂ molar ratio of 2:1:3. The educts were confined in a lid-covered platinum crucible and gradually cooled from 1050 °C at a rate of 0.3 °C min^-1 to 800 °C before being finally quenched in air to ambient conditions. The crystal structure was investigated at -80 and 15 °C from single-crystal X-ray diffraction data, with structure determination performed using direct methods. The compound was found to be of orthorhombic symmetry, belonging to the space group Pmmn (No. 59), with a = 5.7363 (6), b = 13.8532 (12), c = 9.9330 (10) Å, V = 789.34 (13) ų and Z = 4 (at 15 °C). The final refinement calculations at ambient temperature converged at R1 = 0.030 and wR2 = 0.076 for 773 observed reflections with I > 2σ(I). The silicate anion is based on pyrosilicate units of composition [Si₂O₇]^6- with point-group symmetry m (C_s). Charge compensation is achieved by the incorporation of rubidium and calcium cations distributed among a total of five independent sites within the asymmetric unit. Two of the nontetrahedrally coordinated cation sites (M4 and M5) are exclusively occupied by calcium cations, which are surrounded by six O atoms in the form of octahedra or trigonal prisms, respectively. The rubidium cations on the M1-M3 sites show more complex coordination environments. The M2 site, for example, is characterized by a tricapped trigonal prism polyhedron. Notably, the M3 site exhibits a 50% population of Ca²⁺ and Rb⁺, respectively. The compound shows closer structural resemblances with K₂Ca₂Si₂O₇ and can be derived from a hexagonal aristotype with space-group symmetry P6₃/mmc by displacements of the atoms. The corresponding distortion modes can be classified by certain irreducible representations of the high-symmetry parent phase. Structural investigations were completed by determining the thermal expansion tensor for the temperature interval between -80 and 15 °C.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"146-155"},"PeriodicalIF":0.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis, crystal structure elucidation, theoretical characterization and thermochemistry analysis of the potential anticancer drug BFS.","authors":"Marta Hoelm, Kinga Wzgarda-Raj, Zdzislaw Kinart, Bartlomiej Kost, Marek Brzezinski, Paulina Staniec","doi":"10.1107/S2053229625001299","DOIUrl":"10.1107/S2053229625001299","url":null,"abstract":"<p><p>The potential anticancer drug for leukemia, butane-1,4-diyl bis(2,2,2-trifluoroethane-1-sulfonate) (BFS), C₈H₁₂F₆O₆S₂, a fluorine analogue of busulfan, was synthesized and analyzed for the first time using various experimental and theoretical techniques, including NMR spectroscopy, single-crystal X-ray diffraction, thermochemistry and computational methods. Crystallographic analysis revealed that BFS crystallizes in the monoclinic space group P2₁/n, with its structure stabilized by covalent bonding, torsional flexibility and hydrogen bonding. Efficient packing and symmetry interactions balance density and stability. Theoretical calculations, using molecular mechanics, semi-empirical methods and density functional theory (DFT), with functionals such as M06-2X-D3, M08-HX-D3, CAM-B3LYP-D3 and B97D3, confirmed that BFS adopts a compact geometry stabilized by intramolecular hydrogen bonds, consistent with spectroscopic measurements. Gravimetric analysis was used to estimate the solubility of BFS in water at room temperature.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"156-164"},"PeriodicalIF":0.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Magnesium and potassium scorpionate complexes based on dihydrobis(pyrazolyl)borate.","authors":"Marcos A Loroño-González, Daniel J Loroño-González","doi":"10.1107/S2053229625000750","DOIUrl":"10.1107/S2053229625000750","url":null,"abstract":"<p><p>The first X-ray crystal structure is reported for [dihydrobis(pyrazol-1-yl)borato-κ²N,N']tris(tetrahydrofuran-κO)magnesium(II) tetrabenzylborate, [Mg(C₆H₈BN₄)(C₄H₈O)₃][B(C₇H₇)₄)], (I), which was obtained by reacting crude [K(C₆H₈BN₄)] with an equimolar amount of (PhCH₂)MgCl in tetrahydrofuran at room temperature and was isolated as a side product. The crystal structure analysis reveals the existence of a pronounced boat-shaped central Mg(N-N)₂B moiety with a weak pseudo-axial B-H...Mg interaction. The existence of a novel counter-ion, [B(C₇H₇)₄)]^-, has been demonstrated by the first evidence of reactivity between KBH₄ and (PhCH₂)MgCl (in a 1:4 molar ratio) to give a polymeric potassium tetrabenzylborate, poly[[μ₄-dihydrobis(pyrazol-1-yl)borato-κ²N,N']potassium(I)], [K{B(C₇H₇)₄}]_n, (II), with predominant (η⁶-C₆H₅)...K, and (η³-C₆H₅)...K interactions. Density functional theory (DFT) calculations were conducted to determine the energy, the frontier molecular orbitals (HOMO and LUMO) and the molecular electrostatic potential (MEP) in order to explain the stability of the structures in the experimental results for complexes (I) and (II).</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"131-139"},"PeriodicalIF":0.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}