Systematic Name Research Articles

Crystal structure and Hirshfeld-surface analysis of an etoxazole metabolite designated R13

The etoxazole metabolite R13, systematic name 4-(4-tert-butyl-2-ethoxyphenyl)-2-(2,6-difluorophenyl)oxazole (C21H21F2NO2), results from the oxidation of etoxazole, a chitin synthesis inhibitor belonging to the oxazoline class, widely used as an insecticide/acaricide since 1998. The structure of R13 features a central oxazole ring with attached 2,6-difluorophenyl and 4-t-butyl-2-ethoxyphenyl moieties. The overall conformation gives dihedral angles between these rings and the oxazole of 24.91 (5)° (with difluorophenyl) and 15.30 (6)° (with t-butyl-ethoxyphenyl), indicating an overall deviation from planarity. Additionally, torsion angles of the ethoxy and t-butyl groups define the orientation of these substituents relative to their benzene ring. In the crystal packing, no significant hydrogen bonds are present, but a Hirshfeld surface analysis highlights weak intermolecular contacts leading to π–π-stacked dimers linked by weak C—H...N contacts. The packing analysis confirms that most intermolecular interactions involve hydrogen atoms.

Crystal structure of AlPCl8

The crystal structure of aluminium phosphorus chloride (systematic name: phosphorus tetrachloride tetrachloridoaluminate), (PCl4)[AlCl4] or AlPCl8, was determined and refined using single-crystal X-ray diffraction data. The compound crystallizes in the orthorhombic space group Pbcm. The asymmetric unit comprises one Al atom, one P atom, and five Cl atoms. The structure is characterized by isolated AlCl4 and PCl4 tetrahedra, isostructural with FePCl8 and GaPCl8.

Structural multiplicity in a solvated hydrate of the antiretroviral protease inhibitor Lopinavir

Lopinavir is a potent protease inhibitor that is used as a first-line pharmaceutical drug for the treatment of HIV. The multi-component solvated Lopinavir crystal, systematic name (2S)-N-[(2S,4S,5S)-5-[2-(2,6-dimethylphenoxy)acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl]-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide–ethane-1,2-diol–water (8/3/7) 8C37H48N4O5·3C2H6O2·7H2O, was prepared using evaporative methods. The crystalline material obtained from this experimental synthesis was characterized and elucidated by single-crystal X-ray diffraction (SC-XRD). The crystal structure is unusual in that the unit cell contains 18 molecules. The stoichiometric ratio of this crystal is eight Lopinavir molecules [8(C37H48N4O5)], three ethane-1,2-diol molecules [3(C2H6O2)] and seven water molecules [7(H2O)]. The crystal packing features both bi- and trifurcated hydrogen bonds between atoms.

Revisiting a natural wine salt: calcium (2R,3R)-tartrate tetrahydrate.

The crystal structure of the salt calcium (2R,3R)-tartrate tetrahydrate {systematic name: poly[[diaqua[μ4-(2R,3R)-2,3-dihydroxybutanedioato]calcium(II)] dihydrate]}, {[Ca(C4H8O8)(H2O)2]·2H2O}n, is reported. The absolute configuration of the crystal was established unambiguously using anomalous dispersion effects in the diffraction patterns. High-quality data also allowed the location and free refinement of all the H atoms, and therefore to a careful analysis of the hydrogen-bond interactions.

Pinaverium bromide.

The structure of pinaverium bromide (systematic name: 4-[(2-bromo-4,5-di-meth-oxy-phen-yl)meth-yl]-4-{2-[2-(6,6-dimethyl-2-bi-cyclo-[3.1.1]hepta-nyl)eth-oxy]eth-yl}morpholin-4-ium bromide; C26H41Br2NO4), was determined at 110 K. It has monoclinic (P21) symmetry. It is of inter-est with respect to its anti-inflammatory properties. The asymmetric unit contains two independent mol-ecules, one of which exhibits disorder of the bi-cyclo terminal group (occupancy factors: 0.78 and 0.22).

Pyridinium tosyl-ate.

The title compound (systematic name: pyridinium 4-methyl-benzene-sulfonate), C5H6N+·C7H7O3S-, is the pyridinium salt of para-toluene-sulfonic acid. In the crystal, classical N-H⋯O hydrogen bonds as well as C-H⋯O contacts connect the cationic and anionic entities into sheets lying parallel to the ab plane.

Norfloxacinium nitrate.

In the title salt [systematic name: 4-(3-carb-oxy-1-ethyl-6-fluoro-4-oxo-1,4-di-hydro-quin-olin-7-yl)piperazin-1-ium nitrate], C16H19FN3O3 +·NO3 -, proton transfer from nitric acid to the N atom of the piperazine ring of norfloxacin has occurred to form a mol-ecular salt. In the extended structure, N-H⋯O hydrogen bonds link alternating cations and anions into [100] chains, which are reinforced by aromatic π-π stacking inter-actions between the quinoline moieties of the norfloxacinium cations.

Comparison of the crystal structures of the JAK1/2 inhibitor ruxolitinib and its hydrate and phosphate.

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.

Supramolecular interactions in cocrystals of benzoic acid derivatives with selective COX-2 inhibitor etoricoxib.

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.

The crystal structure of the ammonium salt of 2-aminomalonic acid.

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.

A 1:1 flavone cocrystal with cyclic trimeric perfluoro-o-phenyl-enemercury.

The title compound, systematic name tris-(μ2-perfluoro-o-phenyl-ene)(μ2-3-phenyl-4H-chromen-4-one)-triangulo-trimercury, [Hg3(C6F4)3(C15H10O2)], crystallizes in the monoclinic P21/n space group with one flavone (FLA) and one cyclic trimeric perfluoro-o-phenyl-enemercury (TPPM) mol-ecule per asymmetric unit. The FLA mol-ecule is located on one face of the TPPM acceptor and is linked in an asymmetric coordination of its carbonyl oxygen atom with two Hg centers of the TPPM macrocycle. The angular-shaped complexes pack in zigzag chains where they stack via two alternating TPPM-TPPM and FLA-FLA stacking patterns. The distance between the mean planes of the neighboring TPPM macrocycles in the stack is 3.445 (2) Å, and that between the benzo-γ-pyrone moieties of FLA is 3.328 (2) Å. The neighboring stacks are inter-digitated through the shortened F⋯F, CH⋯F and CH⋯π contacts, forming a dense crystal structure.

(S)-2-Carboxyethyl L-cysteinyl sulfone

The title compound {systematic name: (2S)-2-azaniumyl-3-[(2-carboxyethane)sulfonyl]propanoate}, C6H11NO6S, forms enantiopure crystals in the monoclinic space group P21 and exists as a zwitterion, with a protonated α-amino group and a deprotonated α-carboxyl group. Both the carboxyl groups and the amino group are involved in an extensive multicentered intermolecular hydrogen-bonding scheme. In the crystal, the diperiodic network of hydrogen bonds propagates parallel to (101) and involves interconnected heterodromic R 4 3(10) rings. Electrostatic forces are major contributors to the structure energy, which was estimated by DFT calculations as E total = −333.5 kJ mol−1.

Ethidium benzoate methanol monosolvate.

In the title salt solvate (systematic name: 8-amino-5-ethyl-6-phenyl-phenanthridin-5-ium benzoate methanol monosolvate), C21H20N3 +·C6H5CO2 -·CH3OH, two ethidium cations, C21H20N3 +, dimerize about a twofold axis through π-π inter-actions [inter-centroid separation = 3.6137 (4) Å]. The benzoate anions are connected through hydrogen bonding with the -NH2 groups of the ethidium cations and the -OH group of the MeOH mol-ecule. The MeOH mol-ecule also accepts a hydrogen bond from the -NH2 group of the ethidium cation. The result is a one-dimensional hydrogen-bonded chain along the b-axis direction.

Absolute structure determination of Berkecoumarin by X-ray and electron diffraction.

X-ray and electron diffraction methods independently identify the S-enantiomer of Berkecoumarin [systematic name: (S)-8-hydroxy-3-(2-hydroxypropyl)-6-methoxy-2H-chromen-2-one]. Isolated from Berkeley Pit Lake Penicillium sp., Berkecoumarin is a natural product with a light-atom composition (C13H14O5) that challenges in-house absolute structure determination by anomalous scattering. This study further demonstrates the utility of dynamical refinement of electron-diffraction data for absolute structure determination.

Structural Analysis of 3,5-Bistrifluoromethylhydrocinnamic Acid

The crystal structure of 3,5-bistrifluoromethylhydrocinnamic acid [systematic name: 3-[3,5-bis(trifluoromethyl)phenyl]propanoic acid], C11H8F6O2, has been determined and described. The structure was subject to the Hirshfeld surface-analysis and CE-B3LYP interaction-energies calculations. The title compound crystallises in the monoclinic P21/c space group with one molecule in the asymmetric unit. The propanoic acid side chain of the studied molecule has a bent conformation. The key supramolecular motif in the crystal structure is a centrosymmetric O–H∙∙∙O hydrogen-bonded dimer (R22(8) in the graph set notation). According to CE-B3LYP, the molecules involved in this motif exhibit the strongest pairwise interaction total energy (Etot = −67.9 kJ/mol). On the other hand, there are seven other interacting molecular pairs with significant Etot values in the range of −17 to −28 kJ/mol. In these, the energy is dominated by the dispersive contribution. A survey of the Cambridge Structural Database revealed that in other 3-phenylpropanoic acid structures, the middle dihedral angle of the propanoic acid side chain is always in the trans conformation. This contrasts the current structure where this dihedral angle is in the gauche conformation. According to the Density Functional Theory calculations in the gas phase (at the B3LYP/aug-cc-pvDZ level), the presence of the two CF3 groups (strong electron-withdrawing character) increases the population of the gauche conformers by a substituent electronic effect, and this may be a minor factor contributing to the appearance of this conformation observed in the solid state.

Structure and absolute configuration of natural fungal product beauveriolide I, isolated from Cordyceps javanica, determined by 3D electron diffraction.

Beauveriolides, including the main beauveriolide I {systematic name: (3R,6S,9S,13S)-9-benzyl-13-[(2S)-hexan-2-yl]-6-methyl-3-(2-methylpropyl)-1-oxa-4,7,10-triazacyclotridecane-2,5,8,11-tetrone, C27H41N3O5}, are a series of cyclodepsipeptides that have shown promising results in the treatment of Alzheimer's disease and in the prevention of foam cell formation in atherosclerosis. Their crystal structure studies have been difficult due to their tiny crystal size and fibre-like morphology, until now. Recent developments in 3D electron diffraction methodology have made it possible to accurately study the crystal structures of submicron crystals by overcoming the problems of beam sensitivity and dynamical scattering. In this study, the absolute structure of beauveriolide I was determined by 3D electron diffraction. The cyclodepsipeptide crystallizes in the space group I2 with lattice parameters a = 40.2744 (4), b = 5.0976 (5), c = 27.698 (4) Å and β = 105.729 (6)°. After dynamical refinement, its absolute structure was determined by comparing the R factors and calculating the z-scores of the two possible enantiomorphs of beauveriolide I.

Crystal structure of the tetra-ethyl-ammonium salt of the non-steroidal anti-inflammatory drug nimesulide (polymorph II).

The crystal structure of the tetra-ethyl-ammonium salt of the non-steroidal anti-inflammatory drug nimesulide (polymorph II) (systematic name: tetra-ethyl-ammonium N-methane-sulfonyl-4-nitro-2-phen-oxy-anilinide), C8H20N+·C13H11N2O5S-, was determined using single-crystal X-ray diffraction. The title compound crystallizes in the monoclinic space group P21/c with one tetra-ethyl-ammonium cation and one nimesulide anion in the asymmetric unit. In the crystal, the ions are linked by C-H⋯N and C-H⋯O hydrogen bonds and C-H⋯π inter-actions. There are differences in the geometry of both the nimesulide anion and the tetra-ethyl-ammonium cation in polymorphs I [Rybczyńska & Sikorski (2023 ▸). Sci. Rep. 13, 17268] and II of the title compound.

Omadacycline dihydrate, C29H40N4O7·2H2O, from X-ray powder diffraction data.

The crystal structure of the title compound {systematic name: (4S,4aS,5aR,12aR)-4,7-bis-(di-methyl-amino)-9-[(2,2-di-methyl-propyl-amino)-meth-yl]-1,10,11,12a-tetra-hydroxy-3,12-dioxo-4a,5,5a,6-tetra-hydro-4H-tetra-cene-2-carb-oxamide dihydrate, C29H40N4O7·2H2O} has been solved and refined using synchrotron X-ray powder diffraction data: it crystallizes in space group R3 with a = 24.34430 (7), c = 14.55212 (4) Å, V = 7468.81 (2) Å3 and Z = 9. Most of the hydrogen bonds are intra-molecular, but two classical N-H⋯O inter-molecular hydrogen bonds (along with probable weak C-H⋯O and C-H⋯N hydrogen bonds) link the mol-ecules into a three-dimensional framework. The framework contains voids, which contain disordered water mol-ecules. Keto-enol tautomerism is apparently important in this mol-ecule, and the exact mol-ecular structure is ambiguous.

Crystal structure, Hirshfeld surface analysis and DFT study of N-(2-nitro-phen-yl)male-imide.

The title compound [systematic name: 1-(2-nitro-phen-yl)pyrrole-2,5-dione], C10H6N2O4, crystallizes in the monoclinic system (space group P21/n) with two mol-ecules in the asymmetric unit, which are linked by C-H⋯O hydrogen bonds. Hirshfeld surface analysis showed that the most significant contributions to the crystal packing are from H⋯O/O⋯H, H⋯C/C⋯H and H⋯H inter-actions, which contribute 54.7%, 15.2% and 15.6%, respectively. A DFT study was conducted using three different levels of theory [(B3LYP/6-311+G(d,p), wB97XD/Def2TZVPP and LC-wpbe/6-311(2 d,2p)] in order to determine the stability, structural and electronic properties of the title mol-ecule with a view to its potential applications and photochemical and copolymer properties.

A triclinic polymorph of miconazole

The crystal structure of the new triclinic polymorph of miconazole {MIC; C18H14Cl4N2O; systematic name: (RS)-1-[2-(2,4-dichlorobenzyloxy)-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole} is reported and compared with the monoclinic form of solvent-free miconazole previously reported [Kaspiaruk & Chęcińska (2022). Acta Cryst. C78, 343–350]. A comparison shows a different orientation of imidazole and one dichlorophenyl ring between polymorphic molecules. In the crystal structure of the title compound, only weak halogen bonds and C—H...π(arene) interactions are found. Hirshfeld surface analysis and energy framework calculations complement the comparison of the two polymorphic forms of the miconazole drug.