Open-access and free articles in Acta Crystallographica Section C: Structural Chemistry
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Open-access and free articles in Acta Crystallographica Section C Structural Chemistry
Acta Crystallographica Section C Structural Chemistry
Structure and optical properties of a trimetallic cobalt–molybdenum–sodium metal–organic framework
The crystallization of a trimetallic cobalt–molybdenum–sodium metal–organic <!?tlsb=-0.05pt>framework, poly[μ-ben­zene-1,3,5-tri­car­box­yl­ato-tetra-μ-ox­ido-co­balt­mol­yb­de­num­tri­so­dium], UOW-10 or [Na3Co(MoO4)(BTC)]n, is achieved by solvothermal synthesis using benzene-1,3,5-tri­carb­oxy­lic acid (H3BTC, C9H6O6) as a ligand precursor, Na2MoO4·2H2O and Co(NO3)2·2H2O as metal sources, and N,N-di­methyl­formamide (DMF) as the solvent. 3D electron diffraction (3D ED) reveals that the structure crystallizes in the monoclinic space group P21/c, with lattice parameters of a = 9.718 (2), b = 18.250 (3), c = 6.892 (9) Å, α = γ = 90, β = 96.156 (15)°, V = 1214.7 (4) Å3 and Z = 4. The phase purity of the bulk sample was confirmed using syn­chro­tron powder X-ray diffraction. The organic ligands form a 2D layer, where cobalt and molybdenum are found, with sodium cations located between the layers. There are four crystallographically distinct sodium sites: three exhibit a distorted octa­hedral coordination geometry, while the remaining site is seven-coordinate. The cobalt has trigonal bipyramidal coordination geometry and molybdenum exhibits a tetra­hedral coordination geometry. Half the sodium cations in the structure forms 1D column-like motifs via shared oxygen edges along the crystallographic c axis, which are cross-linked in b by the cobalt and molybdenum sites via bridging O atoms, while the other half of the sodium cations form 2D ribbons in the ac plane, propagating along c, linked by sharing oxygen edges and faces. The optical properties of UOW-10 were investigated through the use of UV–Vis spectroscopy, showing a bandgap of 1.8 eV. Deconvolution of the features in the visible-light region reveals that four peaks are present, which can all be ascribed to the d–d transitions from the trigonal bipyramidal cobalt. By means of thermogravimetric analysis (TGA) and variable-tem­per­a­ture powder X-ray diffraction (VT-PXRD), it is demonstrated that the material has thermal stability to 410 °C, after which structure collapse occurs, leading to a mixture of Na2MoO4, CoO and Co3Mo above 900 °C.
3D ED; METAL-ORGANIC FRAMEWORK; COORDINATION POLYMER; SOLVOTHERMAL; MULTIVARIATE; CRYSTAL STRUCTURE
Acta Crystallographica Section C: Structural Chemistry
Charge-enhanced pyri­dyl tri­fluoro­borate organocatalysts: crystal structures and reactivity
The crystal structures of eleven 3- and 4-pyri­dyl borate salts with a variety of cations are reported. These are potassium tri­fluoro­(pyridin-3/4-yl)borate, K+·C5H4BF3N−, 1 and 2 (as the monohydrate), tetra­butyl­ammonium tri­fluoro­(pyridin-3/4-yl)borate, C16H36N+·C5H4BF3N−, 3 and 4, tetra­phenyl­phospho­nium tri­fluoro­(pyridin-3/4-yl)borate, C24H20P+·C5H4BF3N−, 5 and 6, tetra­kis­(3,5-di­meth­oxy­phen­yl)phospho­nium tri­fluoro­(pyridin-3/4-yl)borate, C32H36O8P+·C5H4BF3N−, 7 and 8, and tetra­kis­[4-(di­methyl­amino)­phen­yl]phospho­nium tri­fluoro­(pyridin-3/4-yl)borate, C32H40N4P+·C5H4BF3N−, 9 and 10, and the hemihydrate, C32H40N4P+·C5H4BF3N−·0.5H2O, 10h. The effects of the position of the pyridine N atom and the identity of the cations on the crystal packing of the salts are examined. The N⋯H and F⋯H anion–cation con­tacts and the Hirshfeld surface com­positions of the anions for the salts containing organic cations are com­pared to the reactivity of the salts in a low-polarity solvent to look for trends between solid-state features and solution-state reactivity.
ORGANOCATALYSTS; CRYSTAL STRUCTURE; CHARGE-ENHANCED REACTIVITY; PYRIDYL TRIFLUOROBORATE SALT; ORGANIC CATION
Structures and electronic properties of cobalt(II) selone coordination com­plexes
The structural chemistry of seleno­urea ligands is quite diverse, though examples of their coordination to cobalt are rare. In this study, the solid-state structures of the seleno­urea 1,3-di­ethyl­im­id­a­zole-2-selone, C7H12N2Se, and the cobalt com­plexes di­chlorido­bis­(1,3-di­ethyl­im­id­a­zole-2-selone-κSe)cobalt(II), [CoCl2(C7H12N2Se)2] (1), and di­chlorido­bis­(1,3-diiso­propyl­im­id­a­zole-2-selone-κSe)cobalt(II), [CoCl2(C9H16N2Se)2] (2), are presented. Two crystallization methods for the coordination com­plexes are utilized. The structures of com­plexes 1 and 2 are com­pared with the few existing examples in the literature, revealing a similar trend for terminal binding modes, rather than bridging modes which are often seen for late d-block metal com­plexes. Density functional theory calculations reveal a trend in cobalt–selenium bond strengths for 1,3-dialkyl-substituted im­id­a­zole-2-selones of Me ≃ Et < iPr.
SELENOUREA LIGAND; COBALT(II) COMPLEX; COORDINATION CHEMISTRY; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; THERMOCHEMISTRY
Effect of the size of halide ligands on the crystal structures of halide-bibridged polymers of HgX2 with 4-ethyl­pyridine
Halide-bridged polymers are a type of coordination polymer whereby halide ligands act as bridging ligands between the metal centres. The crystal structures of three halide-bibridged polymers of the formula [Hg(μ-X)2(4-Etpy)]n, namely, catena-poly[[(4-ethyl­pyridine)­mercury(II)]-di-μ-halido], ob­tained through the combination of the organic ligand 4-ethyl­pyridine (4-Etpy, C7H9N) and HgX2 (X = Cl, Br or I), were determined. In these structures, abbreviated as 4epHgCl, 4epHgBr and 4epHgI, respectively, the HgII ion ex­hibits a coordination number of five. All three structures were found to display a similar one-dimensional scalloped polymeric chain with halide ligands bridging pairs of HgII ions in a bidentate fashion; however, 4epHgI differs from the other two structures in terms of the packing arrangement of the polymer. The change of the halide ligand to the larger iodide ligand disrupts the formation of the regular halide-bibridged polymeric chain observed in the chloride and bromide analogues, with 4epHgI displaying pseudo-bridging in the polymer chain.
COORDINATION POLYMERS; CRYSTAL STRUCTURE; HALIDE-BIBRIDGED POLYMERS; MERCURY; ETHYLPYRIDINE; ORGANIC-INORGANIC HYBRID
Weak hy­dro­gen bonding in the structures of three double-acyl­ated amino­anti­pyrines
The structures of three doubly-acyl­ated 4-amino­anti­pyrine (AP) com­pounds where the aryl substituent is varied are reported and analysed in terms of their relative conformation, inter­molecular inter­actions and overall packing; these are N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-di­hydro-1H-pyrazol-4-yl)-4-methyl-N-[(4-methyl­phen­yl)carbon­yl]benzamide, C27H25N3O3, N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-di­hydro-1H-pyrazol-4-yl)-N-[(furan-2-yl)carbon­yl]furan-2-carbox­am­ide, C21H17N3O5, and N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-di­hydro-1H-py­ra­zol-4-yl)-N-[(thio­phen-2-yl)carbon­yl]thio­phene-2-carboxamide, C21H17N3O3S2. The com­pounds were crystallized using the encapsulated nanodroplet crystallization (ENaCt) protocol. Where previous singly-acyl­ated AP com­pounds pro­duced structures with obvious classical hy­dro­gen-bonding motifs, the doubly-acyl­ated derivatives lack classical donors and therefore exhibit weak C—H hy­dro­gen bonds and inter­actions involving the π-system. All three AP com­pounds form bifurcated C—H⋯O inter­actions having either dimer or chain motifs, with the other structure-directing inter­actions being dependant on the nature of the aryl substituent.
CRYSTAL STRUCTURE; ARYLATION; CRYSTAL PACKING; WEAK HYDROGEN BONDS; [PI]-INTERACTIONS; ENACT; 4-AMINOANTIPYRINE
Structural insights into transition-metal–amino­diphosphine (PNP) com­plexes bearing [MCln(PNP)2] (M = Co, Ru, Cr or Mo; n = 1 or 2) cores in the solid state
The mol­ecular structures of two novel cobalt amino­diphosphine (PNP) com­plexes (1 and 2) are reported, namely, bis­[bis­(di­phenyl­phosphan­yl)(pent­yl)amine-κ2P,P′]chlorido­cobalt(III) di-μ-chlorido-bis­[di­chlorido­cobalt(II)], [CoCl(C29H31NP2)2][Co2Cl6], and bis­[bis­(di­phenyl­phosphan­yl)(propan-2-yl)amine-κ2P,P′]chlorido­cobalt(III) di-μ-chlorido-bis­[di­chlorido­cobalt(II)], [CoCl(C27H27NP2)2][Co2Cl6], featuring variation in the N-atom substituent, i.e. n-pentyl in com­plex 1 and isopropyl in com­plex 2. The asymmetric unit of com­plex 1 contains a five-coordinated cationic [CoCl{κ2-P,P-(N)-C5H11}2]2+ species and a [Co2(μ2-Cl)2Cl4]2− anion, while com­plex 2 includes a five-coordinated cation [CoCl{κ2-P,P-(N)-C3H7}2], half a [Co2(μ2-Cl)2Cl4]2− anion, and disordered diethyl ether and di­chloro­methane solvent mol­ecules. The impact of ligand-induced strain, particularly due to the small bite angles of the PNP amino­diphosphine ligands, was examined in the context of geometric constraints and their influence on stability and reactivity. A Cambridge Structural Database (CSD) survey, along with a noncovalent inter­action (NCI) analysis of the analogous [TMCln(PNP)2] (where TM = transition metal and n = 1 or 2) core, revealed an inverse correlation between P—TM—P bite angles and N⋯TM contact distances. This correlation is attributed to the influence of the van der Waals radius of the metal: smaller metals allow wider bite angles and stronger N⋯TM contacts, whereas larger metals favour narrower bite angles and longer N⋯TM distances. NCI analysis indicated significant steric repulsion at the TM⋯N contacts, reflecting strain imposed by ligand geometry. A com­parison of sign(λ2)ρ eigenvalues suggests that Mo—P bonds exhibit weaker attractive inter­actions relative to Co—P and Ru—P bonds, with Cr—P bonds being the weakest. These findings provide po­inters to structural and electronic factors governing coordination in PNP-ligated transition-metal com­plexes, offering rational design and catalytic and material applications.
COBALT AMINODIPHOSPHINE COMPLEXES; CRYSTAL STRUCTURE; CSD SURVEY; NONCOVALENT INTERACTIONS
Solving molecular organic crystal structures from powders
POWDER X-RAY DIFFRACTION; REAL-SPACE STRUCTURE SOLUTION; ORGANIC MOLECULES; COMMENTARY
Origin of phase relative stability and phase transformation in an S-ibu­pro­fen–nicotinamide cocrystal
The crystal structure of the metastable form of S-ibu­pro­fen–nicotinamide cocrystals, C13H18O2·C6H6N2O, was solved from powder X-ray diffraction. This form was obtained by melting a molar mixture of S-ibu­pro­fen and nicotinamide at 100 °C, and then cooling. The high-resolution powder X-ray diffraction pattern of this new phase was recorded at room tem­per­a­ture using synchrotron radiation at SOLEIL Synchrotron (France). A hypothetical structure was ob­tained from the Monte-Carlo simulated annealing method and confirmed by Rietveld refinement. The symmetry is monoclinic (space group P21, No. 4) and the unit cell contains four mol­ecules, two of nicotinamide and two of S-ibu­pro­fen. Density functional theory (DFT) energy minimization simulation was performed in order to locate the H atoms. The determination of the crystallographic structure of this metastable form allowed an explanation of the main mechanisms at the origin of the relative stability of the two forms of the S-ibu­pro­fen–nicotinamide cocrystals. This also made it possible to explain the transition mechanism between the two forms with tem­per­a­ture.
CRYSTAL ENGINEERING; CRYSTAL STRUCTURE; COCRYSTAL; IBUPROFEN; NICOTINAMIDE; POWDER X-RAY DIFFRACTION; PXRD; SOLEIL SYNCHROTRON; DFT
Crystallographic and physicochemical characterization of salcaprozoic acid: a structural basis for SNAC-enabled drug delivery systems
Salcaprozate sodium (SNAC) is a clinically approved oral permeation enhancer, notably used in the formulation of oral semaglutide. Despite its pharmaceutical importance, the crystallographic information of SNAC or its free acid form, salcaprozoic acid {systematic name: 8-[(2-hy­droxy­phen­yl)formamido]­octa­noic acid, C15H21NO4, denoted HNAC}, has not been reported previously. Here, we present the first crystallographic and physicochemical characterization of HNAC using single-crystal X-ray diffraction and com­plementary analytical techniques. The structure reveals the mol­ecular conformation, hy­dro­gen-bonding network and packing features of HNAC, supported by a com­plementary solid-state dataset. These findings provide fundamental insights into the structural and physicochemical properties of this physiologically relevant form of SNAC.
SALCAPROZOIC ACID; SALCAPROZATE SODIUM; SNAC; HNAC; CRYSTAL STRUCTURE; DRUG DELIVERY SYSTEM; ORAL PERMEATION ENHANCER
Structural adaptability and hy­dro­gen bonding in a dissymmetric pyrimidine thio­ether ligand
Dissymmetric ligands have garnered inter­est due to their ability to simultaneously coordinate to multiple different acceptors. Herein, we report the syn­thesis of a dissymmetric thio­ether N,N′-bidentate ligand, namely, 2-[(6-chloro­pyrimidin-4-yl)sulfan­yl]pyrimidine-4,6-di­amine (C8H7ClN6S, L1), along with its hydrated form (C8H7ClN6S·H2O). In addition, we describe the structure of a nitrate salt of the protonated ligand {4,6-di­amino-2-[(6-chloro­pyrimidin-4-yl)sulfan­yl]pyrimidin-1-ium nitrate, C8H8ClN6S+·NO3−} and a cobalt(II) com­plex of L1 (di­chlorido­{2-[(6-chloro­pyrimidin-4-yl-κN3)sulfan­yl]pyrimidine-4,6-di­amine-κN3}cobalt(II), [CoCl2(C8H7ClN6S)]). The structures of all four com­pounds were determined by single-crystal X-ray diffraction and Hirshfeld surface analyses were performed. These analyses reveal unengaged hy­dro­gen-bond donors and acceptors in both the neutral ligand and its water solvate, while protonation or metal coordination induces a conformational change that en­ables full engagement of hy­dro­gen-bond donors. These structural insights have implications for the mol­ecular design of ligands in ion-sensing applications.
CRYSTAL STRUCTURE; PYRIMIDINE THIOETHER LIGAND; HYDROGEN BONDING; COORDINATION CHEMISTRY; HIRSHFELD SURFACE ANALYSIS; STRUCTURE ADAPTABILITY; DISYMMETRIC
A good-practice guide to solving and refining mol­ecular organic crystal structures from laboratory powder X-ray diffraction data
This article focuses on a specific real-space methodology for solving and refining mol­ecular organic crystal structures, developed by the authors and collaborators. It outlines a practical route from polycrystalline samples to refined crystal structures, emphasizing efficient global optimization by DASH and the robust refinement capabilities of TOPAS. The approach prioritizes laboratory-to-laboratory reproducibility via a standardized workflow that addresses key challenges in mol­ecular organic crystal structure determination.
MOLECULAR CRYSTAL STRUCTURES; CRYSTAL STRUCTURE SOLUTION AND REFINEMENT; POWDER X-RAY DIFFRACTION; GOOD PRACTICE; DASH; TOPAS-ACADEMIC
Protonated deca­fluoro­benzo­phenone and the deca­fluoro­benzo­phenone–arsenic penta­fluoride adduct
The reaction of deca­fluoro­benzo­phenone [perfluoro­benzo­phenone, (C6F5)2CO] with AsF5 in anhydrous HF yields the protonated salt [bis­(2,3,4,5,6-penta­fluoro­phen­yl)methyl­idene]oxidanium hexa­fluorido­arsenate, (C6F5)2COH+[AsF6]−, whereas its reaction with AsF5 in SO2 affords the Lewis acid–base adduct deca­fluoro­benzo­phenone–arsenic penta­fluoride, (C6F5)2CO·AsF5. In both com­pounds, the deca­fluoro­benzo­phenone moiety exhibits an elongated C=O bond [1.274 (2) and 1.2526 (15) Å in the salt and adduct, respectively]. The crystal structure of (C6F5)2COH+[AsF6]− features a short O—H⋯F hy­dro­gen bond between the cation and the anion, and the crystal structure of (C6F5)2CO·AsF5 represents a rare example of a ketone coordinated to the strong Lewis acid AsF5.
SUPERACID MEDIUM; PROTONATION; DECAFLUOROBENZOPHENONE; ASF5 ADDUCT; CRYSTAL STRUCTURE; PROTONATED KETONE
The disordered structure of sparsentan: energy calculations for com­peting chain con­for­mations
The crystalline form of sparsentan (SST) (systematic name: 2-{4-[(2-butyl-4-oxo-1,3-di­aza­spiro­[4.4]non-1-en-3-yl)meth­yl]-2-(eth­oxy­meth­yl)phen­yl}-N-(4,5-dimethyl-1,2-oxazol-3-yl)benzene­sulfonamide), C32H40N4O5S, was produced and characterized using single-crystal and powder X-ray diffraction, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and IR spectroscopy. The SST mol­ecule displays positional disorder in three different sections. Viability tests of alternative disorder models involved the calculation of energetic contributions to analyse each possible mol­ecular con­for­mation within its crystal environment and identify the energetically most favourable con­for­mations in the lattice.
CRYSTAL STRUCTURE; DISORDER; ENERGY CALCULATIONS; CONFORMATION; PHARMACEUTICAL; FLEXIBLE MOLECULE; SPARSENTAN; SST
Ce, Gd and Yb accumulation in microalgae: an L-edge XAS study
The extraction and separation of rare earth elements (lanthanides) can be difficult due to their chemical similarities. Biological processes can have very selective activity towards different elements. We investigated the use of microalgae for this purpose by looking at the inter­action of Ce, Gd and Yb with the microalga Chlamydomonas reinhardtii, which has been induced to form polyphosphate granules. X-ray absorption spectroscopy with XANES and EXAFS at the Ce L3-edge, Gd L3-edge and Yb L3-edge was used to characterize the inter­action between the lanthanides and the phosphate-containing algae. All three of the lanthanides, added as the chloride salt to the algae, appeared to react to form phosphate com­pounds. These form both in the presence of phosphate granules or when there is only a low level of P present. CePO4 could be determined by XANES, but the structures of GdPO4 and YbPO4 were determined by EXAFS analysis without reference to the XAS spectra of the standard com­pounds. It is proposed that C. reinhardtii or other similar microalgae may be useful in the selective removal of rare earths from solution.
CRYSTAL STRUCTURE; LANTHANIDE; XAFS; EXAFS; GD L3-EDGE; CE L3-EDGE; YB L3-EDGE; RARE EARTH REMOVAL
Syn- and anti-rotamers of the ortho-stereoisomer [Pt{(o-BrC6F4)N(CH2)2NEt2}Cl(py)]
The crystal structure of the ortho-isomer trans-[N-(2-bromo-3,4,5,6-tetrafluorophenyl)-N′,N′-diethylethane-1,2-diaminato(1−)]chloridopyridineplatinum(II), [PtBr0.1(C12H14BrF4N2)Cl0.9(C5H5N)][PtBr0.4(C12H14BrF4N2)Cl0.6(C5H5N)] or [Pt{(o-BrC6F4)N(CH2)2NEt2}Cl(py)], 1o, revealed syn and anti rotamers in a 1:1 ratio in the solid state. 1o crystallizes in the centrosymmetric space group P1. The Pt-coordinated Cl ligand exhibits partial occupancy with Br, predominantly in the syn-rotamer. Notably, agostic inter­actions are observed between the Pt centre and a H atom of one of the ethyl groups. The ortho-isomer 1o was successfully isolated as a side product from the reaction of [Pt{H2N(CH2)2NEt2}Cl2], Tl2CO3 and C6F5Br. While the para-isomer [Pt{(p-BrC6F4)N(CH2)2NEt2}Cl(py)], 1p, is the main product, the higher solubility of 1o facilitates its isolation.
CRYSTAL STRUCTURE; PLATINUM ANTICANCER AGENT; SYN AND ANTI ROTAMERS; AGOSTIC INTERACTIONS; SYNCHROTRON
Concomitant colour polymorphs of (Z)-N-(4-fluoro­phen­yl)-2-oxo­propane­hydrazonoyl chloride
The title com­pound, (Z)-N-(fluoro­phen­yl)-2-oxo­propane­hydrazonoyl chloride, C9H8ClFN2O, was found to form concomitant colour polymorphs upon recrystallization from acetone. Block-shaped pale-orange crystals of form I (space group P21/n, No. 14) and prism-shaped yellow crystals of form II (space group P21/c, No. 14) both belong to the monoclinic crystal system. N—H⋯O hy­dro­gen bonds resulting in zigzag chains [graph-set descriptor C(6)] are the dominating inter­molecular inter­actions in both crystal forms. The hy­dro­gen-bonded zigzag chains so formed extend by 21 screw symmetry in form I and by c-glide symmetry in form II, and are arranged in layers, which are more corrugated in form II than in form I. The polymorphs are virtually indistinguishable by their calculated densities, packing indices and melting points. Form I sublimes to yield crystals of form II, whereas form II sublimes to afford crystals of the same polymorph with characteristic crystal morphology.
HYDRAZONOYL CHLORIDE; HYDROGEN BONDING; COLOUR POLYMORPHISM; HIRSHFELD ATOM REFINEMENT; CRYSTAL STRUCTURE
Good data with `bad' reflections: the employment of non-spherical scattering factors in the redetermination of the structure of O-ethyl N-phenyl­carbamate
The structure of O-ethyl N-phenyl­thio­carbamate, C9H11NOS (2), has been redetermined, confirming the results obtained in three earlier structure determinations. The higher data quality provided by modern diffractomers has enabled a reliable analysis (absent from the earlier reports) of the hy­dro­gen bonding. However, conventional refinement of the structure of 2 was unsatisfactory because of the large number of extremely badly-fitting reflections, leading to many checkCIF `ALERT A' messages that might be detrimental to ease of publication. A refinement using nonspherical scattering factors effectively eliminated this problem. There are three independent mol­ecules of 2 in the asymmetric unit; two are directly connected by two N—H⋯S hy­dro­gen bonds, forming a dimer with the well-known R22(8) motif. The other mol­ecule forms a topologically identical but inversion-symmetric dimer. Each type of dimer occupies a different region parallel to the ac plane (mol­ecule 1, y ≃ 0; mol­ecules 2 and 3, y ≃ 1 \over 3 and 2 \over 3). All three molecules lie in planes parallel to (031). The title com­pound is effectively isotypic to 1-ethyl-3-phenyl­thio­urea (another known structure for which the hy­dro­gen bonding was not analysed) because its EtNH group, like the EtO group of 2, is not involved in hy­dro­gen bonding.
THIOUREA; CARBAMATE; HYDROGEN BONDING; NONSPHERICAL SCATTERING FACTORS; CRYSTAL STRUCTURE
The cleavage of indinavir sulfate: synthesis and characterization of a cis-1-amino-2-indanol salt
The HIV-1 protease inhibitor indinavir sulfate was cleaved via a one-pot reflux synthesis using 1-propanol, yielding the salt bis(2-hydroxy-2,3-dihydro-1H-inden-1-aminium) sulfate, 2C9H12NO+·SO42−. Single-crystal X-ray diffraction (SC-XRD) revealed that the salt crystallizes in the monoclinic space group P21. The structure consists of two conformationally distinct cations and one sulfate anion, stabilized through an extensive hydrogen-bonding network. Thermal analysis showed minor solvent loss around 200 °C, followed by a two-step decomposition process commencing at 306.6 °C. Hirshfeld surface analysis revealed dominant O⋯H/H⋯O (44.4–41.0%) and H⋯H (45.2–40.1%) intermolecular contacts, with minor contributions from C⋯H/H⋯C and C⋯O/O⋯C interactions. These contact percentages were calculated for each of the two independent cations. The van der Waals surface area (687.30 Å2) accounts for 71.43% of the unit cell. These results provide structural and thermal evidence for the transformation of indinavir sulfate under alcoholytic conditions, highlighting the formation and stabilization of the resulting salt.
CRYSTAL STRUCTURE; INDINAVIR; SOLVATION CRYSTALLIZATION; SALT CRYSTAL STRUCTURE; SLOW EVAPORATION; THERMAL ANALYSIS; SURFACE ANALYSIS; CHEMICAL TRANSFORMATIONS
Synthesis, structure and blue-light emission of a zero-dimensional zinc halide with the 4-(4-chloro­phen­yl)pyridinium cation
Exploring blue emission lead-free halides with high photoluminescence quan­tum yields (PLQYs) is a significant and challenging issue for luminescent materials. Herein, a zero-dimensional (0D) organic–inorganic hybrid halide, namely, bis­[4-(4-chloro­phen­yl)pyridinium] tetra­bromido­zincate, (C11H9ClN)2[ZnBr4] or [HCPP]2[ZnBr4] [CPP is 4-(4-chloro­phen­yl)pyridine], was synthesized through acid solution evaporation. The com­pound crystallizes in the monoclinic space group C2/c. The asymmetric unit consists of a [ZnBr4]2− dianion cluster and two monoprotonated [HCPP]+ cations. The [ZnBr4]2− unit presents an almost undistorted tetra­hedral geometry. The [HCPP]+ cations adopt nearly coplanar conformations with small dihedral angles of 5.05 (3)°; there are relatively strong π–π inter­actions between adjacent [HCPP]+ cations due to slipped parallel packing, with a distance of 3.81 (1) Å. Significantly, this halide exhibits highly efficient blue-light emission (385–500 nm) with a PLQY of 56.35%.
PYRIDINIUM; TETRABROMIDOZINCATE; CRYSTAL STRUCTURE; ZINC HYBRID HALIDE; PYRIDINE CATION; BLUE EMISSION
Structure of l-arginine and detection of trace dl-arginine by 3D ED
3D electron crystallography has emerged as a method with great potential for the structure determination of small mol­ecules and macromolecules com­plementing traditional single-crystal X-ray crystallography and powder X-ray diffraction (PXRD). It offers the unique capability of determining the structures of small mol­ecules and macromolecules from micro- and nanocrystals. In this study, using 3D electron diffraction (3D ED), we determined the single-crystal structure of commercially sourced arginine directly from its bottle. The 3D ED analysis of micro-sized single crystals identified two distinct forms: the l-arginine enanti­omer and the racemic mixture dl-arginine. At the time of writing, neither the Cambridge Structural Database nor the Crystallographic Open Database contain a single-crystal structure of isolated l-arginine (sum formula C6H14N4O2), which has been solved in this work by 3D ED. We also present a com­parison of the structures of these mol­ecules solved by 3D ED and PXRD.
CRYSTAL STRUCTURE; L-ARGININE; 3D ELECTRON CRYSTALLOGRAPHY; 3D ED; TRACE IMPURITY
As the electron diffraction technique MicroED gains momentum and is in­creasingly embraced by researchers in both academia and industry, we have the opportunity to familiarize ourselves with the characteristics of MicroED data and results. The number of refined structures and their associated data is steadily growing and becoming more accessible to the scientific community, offering valuable insights into the significance and quality of MicroED-derived structures. Additionally, the growing body of experience is helping to identify best practices for the technique. In this summary, we highlight key lessons learned from these data and propose gold standards for the community to consider adopting.
MICROED; ELECTRON DIFFRACTION; QUALITY INDICATOR; BEST PRACTICES; CRYOEM; GOLD STANDARDS
High-pressure crystal structure of n-hexyl­amine
A primary amine, n-hexyl­amine (HA, C6H15N), has been studied at high pressure by single-crystal X-ray diffraction. The structure of this com­pound has been determined, at ambient tem­per­a­ture, from the freezing pressure up to 1.40 GPa. HA at high pressure crystallizes in the space group Pca21, which was already found at ambient pressure and low tem­per­a­ture. The com­pressibility of the N—H⋯N hy­dro­gen bonds has been com­pared with that of the shortest C—H⋯N and H⋯H inter­molecular distances, revealing that the H⋯H distances exhibit the highest degree of com­pressibility among them.
HEXYLAMINE; CRYSTAL STRUCTURE; N-H...N HYDROGEN BONDS; ALIPHATIC AMINES; IN-SITU CRYSTALLIZATION; HIGH PRESSURE; COMPRESSIBILITY
Ca(BF4)2·xH2O redefined from powder diffraction as hy­dro­gen-bonded Ca(H2O)4(BF4)2 ribbons
The crystal structure of the calcium bis(tetra­fluoro­borate) hydrate Ca(BF4)2·xH2O has been determined from laboratory powder diffraction data. The water mol­ecules all belong to [CaO4F4] square anti­prisms sharing F corners with [BF4] tetra­hedra, forming a mono-dimensional structure of infinite ribbons inter­connected by H⋯F and H⋯O hy­dro­gen bonds. No place is found for inter­stitial water mol­ecules, so that the com­pound has to be reformulated as Ca(H2O)4(BF4)2, which is isostructural with calcium perchlorate tetra­hydrate, Ca(ClO4)2·4H2O.
FLUOROBORATE; CALCIUM; HYDRATE; POWDER DIFFRACTION; AB INITIO
Synthesis and structure analysis of a cobalt(III) coordination com­pound obtained from a redox-active phenolate ligand and cobalt(II)
Exploration of the structure and inter­actions of 4-(di­methyl­amino)-3-methyl­phenyl N-methyl­car­bam­ate (Aminocarb)
Amino­carb [4-(di­methyl­amino)-3-methyl­phenyl N-methyl­car­bam­ate, C11H16N2O2], a synthetic pesticide, was crystallized and characterized by single-crystal and powder X-ray diffraction. In the solid state, the mol­ecules have a strong chain N—H⋯O hy­dro­gen bond with a strength of −29.37 kJ mol−1 and a short C—H⋯π contact that build a wave-like three-dimensional structure. The structural stability and inter­molecular inter­action of Amino­carb were investigated using differential scanning calorimetry (DSC) and density functional theory (DFT). The results show that the com­pound is chemically stable, and the two dominating inter­actions are electrostatic and dispersion energies. An electrostatic potential map reveals the binding sites of the mol­ecules for reactivity. The understanding of the structural stability and interactions in Aminocarb provided in this study could be used to design new compounds with improved solubility and bioavailability. The dimethylamino group and the methyl group on the carbamate could be modified with other alkyl groups, which might reduce the Aminocarb toxicity, thereby leading to the development of safe, efficient and cost-effective compounds.
CRYSTAL STRUCTURE; NONCOVALENT INTERACTIONS; DENSITY FUNCTIONAL THEORY; DFT; AMINOCARB; SYNTHETIC PESTICIDE
Electron diffraction in structural chemistry
ELECTRON DIFFRACTION; STRUCTURAL DETERMINATION
Transformations of thio­carbonyls into alkenes via Barton–Kellogg olefination
The transformation of a thio­carbonyl com­pound into an alkene by stepwise treatment with a diazo com­pound and tri­phenyl­phosphane is known as Barton–Kellogg olefination. As a model reaction, 4,4′-di­meth­oxy­thio­benzo­phenone and diazo­cyclo­hexane were used to prepare [bis­(4-meth­oxy­phen­yl)methylid­ene]­cyclo­hexane, C21H24O2. The crystal structure of the latter, as well as that of the inter­mediate thiirane, 2,2-bis­(4-meth­oxy­phen­yl)-1-thia­spiro­[2.5]octane, C21H24O2S, have been determined and their mol­ecular conformations and geometries are generally consistent with those of related structures in the literature. Variations in the influence of four substituents on crowded thiirane rings are minimal and the main differences are noted in the presence of bulky tert-butyl substituents. The conformation of the inter­mediate thiirane is influenced by weak intra­molecular C—H⋯S inter­actions. A three-dimensional supra­molec­u­lar structure of the methyl­ene cyclo­hexane com­pound results from the combination of three distinct weak C—H⋯π inter­actions. Under similar reaction conditions, 5-phenyl-3H-1,2-di­thiole-3-thione has been transformed into 3-[bis­(4-meth­oxy­phen­yl)methylid­ene]-5-phenyl-3H-1,2-di­thiole, C24H20O2S2, by treatment with bis­(4-meth­oxy­phen­yl)diazo­methane. The crystal structure of the 1,2-di­thiole product reveals a mol­ecule with an all-trans 2,4-hexa­diene core, in which the Csp2—Csp2 bond lengths display an alternating character that suggests little delocalization of the double bonds. The 1,2-di­thiole ring is nearly planar, with just a slight puckering into an envelope form. Two weak C—H⋯π and one C—H⋯O inter­action link the mol­ecules into thick two-dimensional supra­molecular layers.
CRYSTAL STRUCTURE; DITHIOLE; THIIRANE; BARTON-KELLOGG; OLEFINATION
Single-crystal structure of the spicy capsaicin
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&z-dbnd;O group serving as a bifurcated hy­dro­gen-bond acceptor.
CAPSAICIN; CAPSAICINOID; CAPSICUM; CRYSTAL STRUCTURE; SINGLE-CRYSTAL X-RAY DIFFRACTION; NATURAL PRODUCT
Rb2Ca2Si2O7: a new alkali alkaline-earth silicate based on [Si2O7]6− anions
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) Å3 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 (Cs). 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.
CRYSTAL STRUCTURE; RB2CA2SI2O7; PYROSILICATE; SOROSILICATE; RUBIDIUM; CALCIUM