Acta Crystallographica Section C Structural Chemistry最新文献

{"title":"Comparison of the crystal structures of the JAK1/2 inhibitor ruxolitinib and its hydrate and phosphate.","authors":"Ziyu Peng, Long Ye","doi":"10.1107/S2053229624006740","DOIUrl":"10.1107/S2053229624006740","url":null,"abstract":"<p><p>Ruxolitinib {RUX; systematic name: (3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile, C₁₇H₁₈N₆} is an orally bioavailable JAK1/2 inhibitor approved for treating intermediate- or high-risk myelofibrosis (MF) and high-risk polycythemia vera (PV). Recent patents claim that RUX can exist in many different forms, information for which is important for the clinical utilization of RUX, especially for the formulation and bioavailability of the drug. But there has been no detailed study on its forms so far. Herein crystals of RUX and its dihydrate (RUX-2H; C₁₇H₁₈N₆·2H₂O) and phosphate (RUX-P; systematic name: 4-{1-[(1R)-2-cyano-1-cyclopentylethyl]-1H-pyrazol-4-yl}-7H-pyrrolo[2,3-d]pyrimidin-3-ium dihydrogen phosphate, C₁₇H₁₉N₆⁺·H₂PO₄^-) were prepared successfully and their structures studied in detail for the first time. Our study shows that the three crystals of RUX differ in the orientation of the pyrimidine ring relative to the pyrazole ring of the RUX molecule, and in their hydrogen-bond interactions. The water molecules in RUX-2H and the dihydrogen phosphate anion in RUX-P enrich the hydrogen-bond networks in these forms. The expected proton transfer occurs in RUX phosphate and the protonated N atom is engaged in a charge-assisted hydrogen bond with the counter-anion. Hydrogen-bonding interactions dominate in the crystal packing of the three forms. The detailed conformations and packing of the three forms were compared through the calculation of both Hirshfeld surfaces and fingerprint plots.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"440-447"},"PeriodicalIF":0.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756506","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":"3-[(Benzo-1,3-dioxol-5-yl)amino]-4-methoxycyclobut-3-ene-1,2-dione: polymorphism and twinning of a precursor to an antimycobacterial squaramide.","authors":"Paul R Palme, Richard Goddard, Adrian Richter, Peter Imming, Rüdiger W Seidel","doi":"10.1107/S2053229624006211","DOIUrl":"10.1107/S2053229624006211","url":null,"abstract":"<p><p>The title compound, 3-[(benzo-1,3-dioxol-5-yl)amino]-4-methoxycyclobut-3-ene-1,2-dione, C₁₂H₉NO₅ (3), is a precursor to an antimycobacterial squaramide. Block-shaped crystals of a monoclinic form (3-I, space group P2₁/c, Z = 8, Z' = 2) and needle-shaped crystals of a triclinic form (3-II, space group P-1, Z = 4, Z' = 2) were found to crystallize concomitantly. In both crystal forms, R₂²(10) dimers assemble through N-H...O=C hydrogen bonds. These dimers are formed from crystallographically unique molecules in 3-I, but exhibit crystallographic C_i symmetry in 3-II. Twinning by pseudomerohedry was encountered in the crystals of 3-II. The conformations of 3 in the solid forms 3-I and 3-II are different from one another but are similar for the unique molecules in each polymorph. Density functional theory (DFT) calculations on the free molecule of 3 indicate that a nearly planar conformation is preferred.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"375-382"},"PeriodicalIF":0.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533362","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":"The pattern of bifurcated hydrogen bonds in thiourea cocrystals with diazine derivatives: experimental and quantum theoretical studies.","authors":"Kinga Wzgarda-Raj, Adrian Olszewski, Marcin Palusiak","doi":"10.1107/S2053229624006259","DOIUrl":"10.1107/S2053229624006259","url":null,"abstract":"<p><p>Cocrystals of thiourea with pyrazine N-oxide as thiourea-pyrazine N-oxide (2/1), C₄H₄N₂O·2CH₄N₂S, (I), and with phenazine as thiourea-phenazine (6/7), 7C₁₂H₈N₂·6CH₄N₂S, (II), both crystallize in the monoclinic space group P2₁/c. In the crystalline state, molecules of both components are linked by N-H...N hydrogen bonds. In addition, there are R₂²(8) hydrogen-bond synthons between thiourea molecules in both crystal structures. Furthermore, bifurcated hydrogen bonds between the -NH groups in the thiourea molecule and the N and O atoms in the N-oxide ring [in (I)], as well as the N atom in the central phenazine ring [in (II)], play a significant role in both structures. This emerging motif was thoroughly examined using quantum chemistry methods.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"434-439"},"PeriodicalIF":0.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141722848","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":"How to grow crystals for X-ray crystallography.","authors":"Roger D Sommer","doi":"10.1107/S2053229624006624","DOIUrl":"10.1107/S2053229624006624","url":null,"abstract":"<p><p>Growing high-quality crystals remains a necessary part of crystallography and many other techniques. This article tabulates and describes several techniques and variations that will help individuals grow high-quality crystals in preparation for crystallographic techniques and other endeavors, such as form screening. The discussion is organized to focus on low-tech approaches available in any laboratory.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"337-342"},"PeriodicalIF":0.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756507","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 of organotin(IV) heterocycles containing a xanthenyl group by a Barbier approach via ultrasound activation: synthesis, crystal structure and Hirshfeld surface analysis.","authors":"J Viridiana García-González, José G Alvarado-Rodríguez, Noemí Andrade-López, Esmeralda Zamora-Martínez, Vojtech Jancik, Diego Martínez-Otero","doi":"10.1107/S2053229624006946","DOIUrl":"10.1107/S2053229624006946","url":null,"abstract":"<p><p>A series of organotin heterocycles of general formula [{Me₂C(C₆H₃CH₂)₂O}SnR₂] [R = methyl (Me, 4), n-butyl (n-Bu, 5), benzyl (Bn, 6) and phenyl (Ph, 7)] was easily synthesized by a Barbier-type reaction assisted by the sonochemical activation of metallic magnesium. The ¹¹⁹Sn{¹H} NMR data for all four compounds confirm the presence of a central Sn atom in a four-coordinated environment in solution. Single-crystal X-ray diffraction studies for 17,17-dimethyl-7,7-diphenyl-15-oxa-7-stannatetracyclo[11.3.1.0^5,16.0^9,14]heptadeca-1,3,5(16),9(14),10,12-hexaene, [Sn(C₆H₅)₂(C₁₇H₁₆O)], 7, at 100 and 295 K confirmed the formation of a mononuclear eight-membered heterocycle, with a conformation depicted as boat-chair, resulting in a weak Sn...O interaction. The Sn and O atoms are surrounded by hydrophobic C-H bonds. A Hirshfeld surface analysis of 7 showed that the eight-membered heterocycles are linked by weak C-H...π, π-π and H...H noncovalent interactions. The pairwise interaction energies showed that the cohesion between the heterocycles are mainly due to dispersion forces.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"357-365"},"PeriodicalIF":0.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756508","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":"Using cocrystals as a tool to study non-crystallizing molecules: crystal structure, Hirshfeld surface analysis and computational study of the 1:1 cocrystal of (E)-N-(3,4-difluorophenyl)-1-(pyridin-4-yl)methanimine and acetic acid.","authors":"Addi Dana Sánchez-Pacheco, Eduardo H Huerta, Josué Benjamín Espinosa-Camargo, Evelyn Valeria Rodríguez-Nájera, Diego Martínez-Otero, Simón Hernández-Ortega, Jesús Valdés-Martínez","doi":"10.1107/S2053229624005187","DOIUrl":"10.1107/S2053229624005187","url":null,"abstract":"<p><p>Using a 1:1 cocrystal of (E)-N-(3,4-difluorophenyl)-1-(pyridin-4-yl)methanimine with acetic acid, C₁₂H₈F₂N₂·C₂H₄O₂, we investigate the influence of F atoms introduced to the aromatic ring on promoting π-π interactions. The cocrystal crystallizes in the triclinic space group P1. Through crystallographic analysis and computational studies, we reveal the molecular arrangement within this cocrystal, demonstrating the presence of hydrogen bonding between the acetic acid molecule and the pyridyl group, along with π-π interactions between the aromatic rings. Our findings highlight the importance of F atoms in promoting π-π interactions without necessitating full halogenation of the aromatic ring.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"343-348"},"PeriodicalIF":0.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299205/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533365","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":"Supramolecular interactions in cocrystals of benzoic acid derivatives with selective COX-2 inhibitor etoricoxib.","authors":"Yu Heng Ma, Kang Yang, Yan Ling Qian, Wei Pu Hong, Kai Yue Zhang, Zhen Wei Tao, Hui Meng, Wen Jing Ma","doi":"10.1107/S2053229624006193","DOIUrl":"10.1107/S2053229624006193","url":null,"abstract":"<p><p>The structures of three 1:1 cocrystal forms of etoricoxib {ETR; systematic name: 5-chloro-2-(6-methylpyridin-3-yl)-3-[4-(methylsulfonyl)phenyl]pyridine, C₁₈H₁₅ClN₂O₂S} have been synthesized and characterized by single-crystal X-ray diffraction; these are etoricoxib-benzoic acid (1/1), C₁₈H₁₅ClN₂O₂S·C₇H₆O₂ (ETR-Bz), etoricoxib-4-fluorobenzoic acid (1/1), C₁₈H₁₅ClN₂O₂S·C₇H₅FO₂ (ETR-PFB), and etoricoxib-4-nitrobenzoic acid (1/1), C₁₈H₁₅ClN₂O₂S·C₇H₅NO₄ (ETR-PNB). Powder X-ray diffraction and thermal differential scanning calorimetry-thermogravimetry (DSC-TG) techniques were also used to characterize these multicomponent systems. Due to the influence of the corresponding acids, ETR shows different conformations. Furthermore, the energetic contributions of the supramolecular motifs have been established by energy framework studies of the stabilizing interaction forces and are consistent with the thermal stability of the cocrystals.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"366-374"},"PeriodicalIF":0.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533363","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":"Crystal structure elucidation of a geminal and vicinal bis(trifluoromethanesulfonate) ester.","authors":"Thomas Pickl, Julian Zuber, Johannes Stephan, Alexander Pöthig","doi":"10.1107/S2053229624005230","DOIUrl":"10.1107/S2053229624005230","url":null,"abstract":"<p><p>Geminal and vicinal bis(trifluoromethanesulfonate) esters are highly reactive alkylene synthons used as potent electrophiles in the macrocyclization of imidazoles and the transformation of bypyridines to diquat derivatives via nucleophilic substitution reactions. Herein we report the crystal structures of methylene (C₃H₂F₆O₆S₂) and ethylene bis(trifluoromethanesulfonate) (C₄H₄F₆O₆S₂), the first examples of a geminal and vicinal bis(trifluoromethanesulfonate) ester characterized by single-crystal X-ray diffraction (SC-XRD). With melting points slightly below ambient temperature, both reported bis(trifluoromethanesulfonate)s are air- and moisture-sensitive oils and were crystallized at 277 K to afford two-component non-merohedrally twinned crystals. The dominant interactions present in both compounds are non-classical C-H...O hydrogen bonds and intermolecular C-F...F-C interactions between trifluoromethyl groups. Molecular electrostatic potential (MEP) calculations by DFT-D3 helped to quantify the polarity between O...H and F...F contacts to rationalize the self-sorting of both bis(trifluoromethanesulfonate) esters in polar (non-fluorous) and non-polar (fluorous) domains within the crystal structure.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"278-283"},"PeriodicalIF":0.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417171","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":"Conformational disorder in the crystal structure of methyl 2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (methyl β-chitobioside) methanol monosolvate.","authors":"Pradip Shit, Timothy Tetrault, Wenhui Zhang, Mi Kyung Yoon, Allen G Oliver, Anthony S Serianni","doi":"10.1107/S2053229624005199","DOIUrl":"10.1107/S2053229624005199","url":null,"abstract":"<p><p>Methyl 2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside (methyl β-chitobioside), (IV), crystallizes from aqueous methanol at room temperature to give a structure (C₁₇H₃₀N₂O₂₂·CH₃OH) containing conformational disorder in the exocyclic hydroxymethyl group of one of its βGlcNAc residues. As observed in other X-ray structures of disaccharides containing β-(1→4) O-glycosidic linkages, inter-residue hydrogen bonding between O3H of the βGlcNAc bearing the OCH₃ aglycone and O5 of the adjacent βGlcNAc is observed based on the 2.79 Å internuclear distance between the O atoms. The structure of (IV) was compared to that determined previously for 2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-deoxy-β-D-glucopyranose (β-chitobiose), (III). The O-glycosidic linkage torsion angles, phi (φ) and psi (ψ), in (III) and (IV) differ by 6-8°. The N-acetyl side chain conformation in (III) and (IV) shows some context dependence, with the C1-C2-N-C_car torsion angle 10-15° smaller for the βGlcNAc residue involved in the internal O-glycosidic linkage. In (IV), conformational disorder is observed in the exocyclic hydroxymethyl (-CH₂OH) group in the βGlcNAc residue bearing the OCH₃ aglycone, and a fitting of the electron density indicates an approximate 50:50 distribution of the gauche-gauche (gg) and gauche-trans (gt) conformers in the lattice. Similar behavior is not observed in (III), presumably due to the different packing structure in the vicinity of the -CH₂OH substituent that affects its ability to hydrogen bond to proximal donors/acceptors. Unlike (IV), a re-examination of the previously reported electron density of (III) revealed conformational disorder in the N-acetyl side chain attached to the reducing-end βGlcNAc residue caused by rotation about the C2-N bond.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"331-336"},"PeriodicalIF":0.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465438","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":"Formation of extended polyiodides at large cation templates.","authors":"Alexander J Blake, Carlo Castellano, Vito Lippolis, Enrico Podda, Martin Schröder","doi":"10.1107/S2053229624004194","DOIUrl":"10.1107/S2053229624004194","url":null,"abstract":"<p><p>By studying the structures of (μ-1,4,10,13-tetrathia-7,16-diazacyclooctadecane)bis[iodidopalladium(II)] diiodide penta(diiodine), [Pd₂I₂(C₁₂H₂₆N₂S₄)](I)₂·5I₂ or [Pd₂I₂([18]aneN₂S₄)](I)₂·(I₂)₅, and 4,7,13,16,21,24-hexaoxa-1,10-diazoniabicyclo[8.8.8]hexacosane triiodide iodide hemipenta(diiodine) dichloromethane monosolvate, C₁₈H₃₈N₂O₆²⁺·I₃^-·I^-·2.5I₂·CH₂Cl₂ or [H₂([2.2.2]cryptand)](I₃)(I)(I₂)_2.5·CH₂Cl₂, we confirm the structural variety of extended polyiodides achievable upon changing the shape, charge and dimensions of the cation template, by altering the synthetic strategy adopted and/or the experimental conditions. Although it is still often difficult to characterize discrete [I_2m+n]^n- polyiodides higher than I₃^- on the basis of structural parameters, such as I-I bond distances, FT-Raman spectroscopy appears to identify them as aggregates of I₂, I^- and (symmetric or slightly asymmetric) I₃^- building blocks linked by I...I interactions of varying strengths. However, because FT-Raman spectroscopy carries no information about the topological features of extended polyiodides, the two techniques should therefore be applied in combination to enhance the analysis of this kind of compounds.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"311-318"},"PeriodicalIF":0.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454577","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}