Acta Crystallographica Section C Structural Chemistry最新文献

{"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":null,"pages":null},"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":null,"pages":null},"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":"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":null,"pages":null},"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":"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":null,"pages":null},"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":"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":null,"pages":null},"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":"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":null,"pages":null},"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}

{"title":"Data collection is your last experiment.","authors":"Tim Gruene","doi":"10.1107/S2053229624005254","DOIUrl":"10.1107/S2053229624005254","url":null,"abstract":"<p><p>Exciting developments are unfolding in the realm of chemical crystallography, especially with the profound impact of electron diffraction and the remarkable progress it has witnessed in recent years.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417172","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 structural characterizations of three carbonyl(α-diimine)hydrido(triphenylphosphine)ruthenium(II) complexes with derivatives of 1,10-phenanthroline.","authors":"Waldemar Wysocki, Anna Kamecka, Zbigniew Karczmarzyk","doi":"10.1107/S2053229624005898","DOIUrl":"10.1107/S2053229624005898","url":null,"abstract":"<p><p>Three new ruthenium(II) polypyridyl complexes containing α-diimine ligands, namely, carbonylhydrido(1,10-phenanthroline-κ²N,N)bis(triphenylphosphine-κP)ruthenium(II) hexafluorophosphate, [RuH(C₁₂H₈N₂)(C₁₈H₁₅P)₂(CO)]PF₆, carbonylhydrido(2,9-dimethyl-1,10-phenanthroline-κ²N,N)bis(triphenylphosphine-κP)ruthenium(II) hexafluorophosphate, and carbonylhydrido(4,7-dimethyl-1,10-phenanthroline-κ²N,N)bis(triphenylphosphine-κP)ruthenium(II) hexafluorophosphate, both [RuH(C₁₄H₁₂N₂)(C₁₈H₁₅P)₂(CO)]PF₆, were synthesized and characterized by spectroscopic and X-ray diffraction methods. In these complexes, the ruthenium(II) ion adopts a distorted octahedral geometry. There are no intermolecular hydrogen bonds in the crystal structures of the analysed complexes and Hirshfeld surface analysis showed that the H...H contacts constitute a high percentage, close to 50%, of the intermolecular interactions.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454578","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":"TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules.","authors":"Anil Kumar, Kunal Kumar Jha, Barbara Olech, Tomasz Goral, Maura Malinska, Krzysztof Woźniak, Paulina Maria Dominiak","doi":"10.1107/S2053229624005357","DOIUrl":"10.1107/S2053229624005357","url":null,"abstract":"<p><p>3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data. TAAM refinement on both experimental and simulated data clearly improves the model fitting statistics (R factors and residual electrostatic potential) compared to IAM refinement. This shows that TAAM better represents the experimental electrostatic potential of organic crystals than IAM. Furthermore, we compared the geometrical parameters and atomic displacement parameters (ADPs) resulting from the experimental refinements with the simulated refinements, with the periodic density functional theory (DFT) calculations and with published X-ray and neutron crystal structures. The TAAM refinements on the 3D ED data did not improve the accuracy of the bond lengths between the non-H atoms. The experimental 3D ED data provided more accurate H-atom positions than the IAM refinements on the X-ray diffraction data. The IAM refinements against 3D ED data had a tendency to lead to slightly longer X-H bond lengths than TAAM, but the difference was statistically insignificant. Atomic displacement parameters were too large by tens of percent for L-alanine and α-glycine. Most probably, other unmodelled effects were causing this behaviour, such as radiation damage or dynamical scattering.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454579","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":"Preferential crystallization of (±)-pinenyllithium·TMEDA.","authors":"Alexander N Erickson, Curtis Haltiwanger, Masoumeh Rahim, Charles M Garner","doi":"10.1107/S2053229624004662","DOIUrl":"10.1107/S2053229624004662","url":null,"abstract":"<p><p>(±)-Pinenyllithium·TMEDA or (tetramethylethylenediamine-κ²N,N')(η³-6,6-dimethyl-2-methylenebicyclo[3.1.1]heptyl)lithium, [Li(C₁₀H₁₅)(C₆H₁₆N₂)], is readily prepared from β-pinene, butyllithium and TMEDA, and the racemic material preferentially crystallizes even from 96:4 (92% ee) mixtures of (-)- and (+)-β-pinene, respectively. The structure is monomeric, with the geminal-dimethyl bridge of the bicyclic structure shielding one face of the allyl system, restricting the lithium to the opposite face and preventing the Li-allyl-Li aggregation observed with some other allyllithium systems. The symmetry of the allyl system, bond lengths, bond angles and out-of-plane deviations are compared to existing structures. In addition, a much older structure of this complex is compared to this very recent one.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426033","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}