Acta Crystallographica Section C Structural Chemistry最新文献

{"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":" ","pages":"262-263"},"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":"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":" ","pages":"297-301"},"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}

{"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":" ","pages":"319-330"},"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":" ","pages":"264-277"},"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":"The crystal structure of the ammonium salt of 2-aminomalonic acid.","authors":"Dirk Hollenwäger, Alexander Nitzer, Valentin Bockmair, Andreas J Kornath","doi":"10.1107/S2053229624005576","DOIUrl":"10.1107/S2053229624005576","url":null,"abstract":"<p><p>The salt ammonium 2-aminomalonate (systematic name: ammonium 2-azaniumylpropanedioate), NH₄⁺·C₃H₄NO₄^-, was synthesized in diethyl ether from the starting materials malonic acid, ammonia and bromine. The salt was recrystallized from water as colourless blocks. In the solid state, intramolecular medium-strong N-H...O, weak C-H...O and weak C-H...N hydrogen bonds build a three-dimensional network.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"291-296"},"PeriodicalIF":0.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426035","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 structural investigation of salts of 2-amino-3-methylpyridine with carboxylic acid derivatives: an experimental and theoretical study.","authors":"Hemalatha Balasubramanian, Aarifa Muhammed Ashraf, Srikanth Karuppannan, Kumaradhas Poomani","doi":"10.1107/S2053229624005473","DOIUrl":"10.1107/S2053229624005473","url":null,"abstract":"<p><p>The salts bis(2-amino-3-methylpyridinium) fumarate dihydrate, 2C₆H₉N₂⁺·C₄H₂O₂^2-·2H₂O (I), and 2-amino-3-methylpyridinium 5-chlorosalicylate, C₆H₉N₂⁺·C₇H₄ClO₃^- (II), were synthesized from 2-amino-3-methylpyridine with fumaric acid and 5-chlorosalicylic acid, respectively. The crystal structures of these salts were characterized by single-crystal X-ray diffraction, revealing protonation in I and II by the transfer of a H atom from the acid to the pyridine base. In the crystals of both I and II, N-H...O interactions form an R₂²(8) ring motif. Hirshfeld surface analysis distinguishes the interactions present in the crystal structures of I and II, and the two-dimensional (2D) fingerprint plot analysis shows the percentage contribution of each type of interaction in the crystal packing. The volumes of the crystal voids of I (39.65 ų) and II (118.10 ų) have been calculated and reveal that the crystal of I is more mechanically stable than II. Frontier molecular orbital (FMO) analysis predicts that the band gap energy of II (2.6577 eV) is lower compared to I (4.0035 eV). The Quantum Theory of Atoms In Molecules (QTAIM) analysis shows that the pyridinium-carboxylate N-H...O interaction present in I is stronger than the other interactions, whereas in II, the hydroxy-carboxylate O-H...O interaction is stronger than the pyridinium-carboxylate N-H...O interaction; the bond dissociation energies also confirm these results. The positive Laplacian [∇²ρ(r) > 0] of these interactions shows that the interactions are of the closed shell type. An in-silico ADME (Absorption, Distribution, Metabolism and Excretion) study predicts that both salts will exhibit good pharmacokinetic properties and druglikeness.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"302-310"},"PeriodicalIF":0.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426034","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":"Interfacial behaviour of short-chain fluorocarbon surfactants at the n-hexane/water interface: a molecular dynamics study.","authors":"Ke Chen, Xianwu Jing, Huali Zhang, Yujie Wang, Yezhong Wang, Wuping Xie, Chungang Shuai, Bo Wen, Nanqiao Zhang, Peiyu Zhang, Hao Wu, Shan Li, Lijia Wang","doi":"10.1107/S205322962400528X","DOIUrl":"10.1107/S205322962400528X","url":null,"abstract":"<p><p>The utilization of long-chain fluorocarbon surfactants is restricted due to environmental regulations, prompting a shift in the focus of research towards short-chain fluorocarbon surfactants. The present study employs molecular dynamics techniques to model the behaviour of potassium perfluorobutylsulfonate (PFBS) at the n-hexane/water interface, aiming to investigate the efficacy of short-chain fluorocarbon surfactants in enhancing oil recovery. The findings suggest that ionized PFBS^- has the ability to autonomously migrate to the oil/water interface, forming a layered thin film, with the sulfonic acid group being submerged in water, while the fluorocarbon chain is oriented towards the oil phase. This phenomenon aligns with the fundamental concept of surfactants in reducing interfacial tension between oil and water. The spontaneous dispersion process is supported by changes in the number of water molecules surrounding each PFBS^- anion, as is well indicated by the number density distribution within the simulation box. Based on the analysis conducted by IGMH (Independent Gradient Model based on Hirshfeld partition), it was determined that sulfonic acid molecules are capable of forming hydrogen bonds with water molecules, whereas the interaction between fluorocarbon chains and the oil phase is predominantly characterized by weak van der Waals interactions.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"284-290"},"PeriodicalIF":0.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417173","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":"Relationship between synthesis method-crystal structure-melting properties in cocrystals: the case of caffeine-citric acid.","authors":"Mathieu Guerain, Hubert Chevreau, Yannick Guinet, Laurent Paccou, Erik Elkaïm, Alain Hédoux","doi":"10.1107/S205322962400319X","DOIUrl":"10.1107/S205322962400319X","url":null,"abstract":"<p><p>The influence of the crystal synthesis method on the crystallographic structure of caffeine-citric acid cocrystals was analyzed thanks to the synthesis of a new polymorphic form of the cocrystal. In order to compare the new form to the already known forms, the crystal structure of the new cocrystal (C₈H₁₀N₄O₂·C₆H₈O₇) was solved by powder X-ray diffraction thanks to synchrotron experiments. The structure determination was performed using `GALLOP', a recently developed hybrid approach based on a local optimization with a particle swarm optimizer, particularly powerful when applied to the structure resolution of materials of pharmaceutical interest, compared to classical Monte-Carlo simulated annealing. The final structure was obtained through Rietveld refinement, and first-principles density functional theory (DFT) calculations were used to locate the H atoms. The symmetry is triclinic with the space group P-1 and contains one molecule of caffeine and one molecule of citric acid per asymmetric unit. The crystallographic structure of this cocrystal involves different hydrogen-bond associations compared to the already known structures. The analysis of these hydrogen bonds indicates that the cocrystal obtained here is less stable than the cocrystals already identified in the literature. This analysis is confirmed by the determination of the melting point of this cocrystal, which is lower than that of the previously known cocrystals.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"221-229"},"PeriodicalIF":0.8,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11150877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140848792","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":"Crystal structures, electron spin resonance, and thermogravimetric analysis of three mixed-valence copper cyanide polymers.","authors":"Peter W R Corfield, Ahmed Elsayed, Tristan DaCunha, Christopher Bender","doi":"10.1107/S2053229624003371","DOIUrl":"10.1107/S2053229624003371","url":null,"abstract":"<p><p>The crystal structures of three mixed-valence copper cyanide alkanolamine polymers are presented, together with thermogravimetric analysis (TGA) and electron spin resonance (ESR) data. In all three structures, a Cu^II moiety on a crystallographic center of symmetry is coordinated by two alkanolamines and links two Cu^ICN chains via cyanide bridging groups to form diperiodic sheets. The sheets are linked together by cuprophilic Cu^I-Cu^I interactions to form a three-dimensional network. In poly[bis(μ-3-aminopropanolato)tetra-μ-cyanido-dicopper(I)dicopper(II)], [Cu₄(CN)₄(C₃H₈NO)₂]_n, 1, propanolamine bases have lost their hydroxyl H atoms and coordinate as chelates to two Cu^II atoms to form a dimeric Cu^II moiety bridged by the O atoms of the bases with Cu^II atoms in square-planar coordination. The ESR spectrum is very broad, indicating exchange between the two Cu^II centers. In poly[bis(2-aminopropanol)tetra-μ-cyanido-dicopper(I)copper(II)], [Cu₃(CN)₄(C₃H₉NO)₂]_n, 2, and poly[bis(2-aminoethanol)tetra-μ-cyanido-dicopper(I)copper(II)], [Cu₃(CN)₄(CH₇NO)₂]_n, 3, a single Cu^II atom links the Cu^ICN chains together via CN bridges. The chelating alkanolamines are not ionized, and the OH groups form rather long bonds in the axial positions of the octahedrally coordinated Cu^II atoms. The coordination geometries of Cu^II in 2 and 3 are almost identical, except that the Cu-O distances are longer in 2 than in 3, which may explain their somewhat different ESR spectra. Thermal decomposition in 2 and 3, but not in 1, begins with the loss of HCN(g), and this can be correlated with the presence of OH protons on the ligands in 2 and 3, which are not present in 1.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":" ","pages":"212-220"},"PeriodicalIF":0.8,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11150880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140847586","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":"3D ED/MicroED entering a new era.","authors":"Mauro Gemmi","doi":"10.1107/S205322962400490X","DOIUrl":"10.1107/S205322962400490X","url":null,"abstract":"<p><p>Aragon et al. [Acta Cryst. (2024), C80, 179-189], by reporting the discussion and the final conclusions of a round table held during a symposium at the National Center for CryoEM Access and Training, well describe all the advances that have been made for the application of 3D ED/MicroED to pharmaceutical and macromolecular nanocrystals and propose possible future scenarios.</p>","PeriodicalId":7115,"journal":{"name":"Acta Crystallographica Section C Structural Chemistry","volume":"80 Pt 6","pages":"177-178"},"PeriodicalIF":0.8,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11150876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141247336","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}