The conformational analyses of 2‐amino‐N‐[2‐(dimethylphenoxy)ethyl]propan‐1‐ol derivatives in different environments

Four crystal structures of 2‐amino‐N‐(dimethylphenoxyethyl)propan‐1‐ol derivatives, characterized by X‐ray diffraction analysis, are reported. The free base (R,S)‐2‐amino‐N‐[2‐(2,3‐dimethylphenoxy)ethyl]propan‐1‐ol, C₁₃H₂₁NO₂, 1 , crystallizes in the space group P2₁/n, with two independent molecules in the asymmetric unit. The hydrochloride, (S)‐N‐[2‐(2,6‐dimethylphenoxy)ethyl]‐1‐hydroxypropan‐2‐aminium chloride, C₁₃H₂₂NO₂⁺·Cl^?, 2c , crystallizes in the space group P2₁, with one cation and one chloride anion in the asymmetric unit. The asymmetric unit of two salts of 2‐picolinic acid, namely, (R,S)‐N‐[2‐(2,3‐dimethylphenoxy)ethyl]‐1‐hydroxypropan‐2‐aminium pyridine‐2‐carboxylate, C₁₃H₂₂NO₂⁺·C₆H₄NO₂^?, 1p , and (R)‐N‐[2‐(2,6‐dimethylphenoxy)ethyl]‐1‐hydroxypropan‐2‐aminium pyridine‐2‐carboxylate, C₁₃H₂₂NO₂⁺·C₆H₄NO₂^?, 2p , consists of one cation and one 2‐picolinate anion. Salt 1p crystallizes in the triclinic centrosymmetric space group P, while salt 2p crystallizes in the space group P4₁2₁2. The conformations of the amine fragments are contrasted and that of 2p is found to have an unusual antiperiplanar arrangement about the ether group. The crystal packing of 1 and 2c is dominated by hydrogen‐bonded chains, while the structures of the 2‐picolinate salts have hydrogen‐bonded rings as the major features. In both salts with 2‐picolinic acid, the specific R₁²(5) hydrogen‐bonding motif is observed. Structural studies have been enriched by the generation of fingerprint plots derived from Hirshfeld surfaces.     

Influence of the position of the methyl substituent and N‐oxide formation on the geometry and intermolecular interactions of 1‐(phenoxyethyl)piperidin‐4‐ol derivatives

Aminoalkanol derivatives have attracted much interest in the field of medicinal chemistry as part of the search for new anticonvulsant drugs. In order to study the influence of the methyl substituent and N‐oxide formation on the geometry of molecules and intermolecular interactions in their crystals, three new examples have been prepared and their crystal structures determined by X‐ray diffraction. 1‐[(2,6‐Dimethylphenoxy)ethyl]piperidin‐4‐ol, C₁₅H₂₃NO₂, 1 , and 1‐[(2,3‐dimethylphenoxy)ethyl]piperidin‐4‐ol, C₁₅H₂₃NO₂, 2 , crystallize in the orthorhombic system (space groups P2₁2₁2₁ and Pbca, respectively), with one molecule in the asymmetric unit, whereas the N‐oxide 1‐[(2,3‐dimethylphenoxy)ethyl]piperidin‐4‐ol N‐oxide monohydrate, C₁₅H₂₃NO₃·H₂O, 3 , crystallizes in the monoclinic space group P2₁/c, with one N‐oxide molecule and one water molecule in the asymmetric unit. The geometries of the investigated compounds differ significantly with respect to the conformation of the O—C—C linker, the location of the hydroxy group in the piperidine ring and the nature of the intermolecular interactions, which were investigated by Hirshfeld surface and corresponding fingerprint analyses. The crystal packing of 1 and 2 is dominated by a network of O—H…N hydrogen bonds, while in 3 , it is dominated by O—H…O hydrogen bonds and results in the formation of chains.     

Concomitant polymorphism in the stereoselective synthesis of a β‐benzyl‐β‐hydroxyaspartate analogue

Two concomitant polymorphs, (I) and (II), of a β‐benzyl‐β‐hydroxyaspartate analogue [systematic name: dibenzyl 2‐benzyl‐2‐hydroxy‐3‐(4‐methylphenylsulfonamido)succinate], C₃₂H₃₁NO₇S, crystallize from a mixture of ethyl acetate and cyclohexane at ambient temperature. The structure of (I) has triclinic (P) symmetry and that of (II) monoclinic (P2₁/c) symmetry. Both crystal structures are made up of a stacking of homochiral racemic dimers (2S,3S and 2R,3R) which are internally connected by a similar R₂²(9) hydrogen‐bonding pattern consisting of intermolecular N—H...O and O—H...O hydrogen bonds. The centroid of the racemic dimer lies on an inversion centre. The main structural difference between the two polymorphs is the conformational orientation of two of the four aromatic rings present in the molecule. Polymorph (II) is found to be twinned by reticular merohedry with twin index 3 and twin fractions 0.854 (1) and 0.146 (1).     

Supramolecular architectures of succinates of 1‐hydroxypropan‐2‐aminium derivatives

Aminoalkanol and aroxyalkyl derivatives are known as potential anticonvulsants. Two new salts, namely bis{(R,S)‐N‐[2‐(2,6‐dimethylphenoxy)ethyl]‐1‐hydroxypropan‐2‐aminium} succinate ( 1s ), C₁₃H₂₂NO₂⁺·0.5C₄H₄O₄²⁻, and bis{(S)‐(+)‐N‐[2‐(2,6‐dimethylphenoxy)ethyl]‐1‐hydroxypropan‐2‐aminium} succinate ( 2s ), C₁₃H₂₂NO₂⁺·0.5C₄H₄O₄²⁻, have been prepared and characterized by single‐crystal X‐ray diffraction. The N atoms are protonated by proton transfer from succinic acid. Salt 1s crystallizes in the space group P2₁/n with one cation and half an anion in the asymmetric unit across an inversion centre, while ( 2s ) crystallizes in the space group P2₁ with four cations and two anions in the asymmetric unit. The hydroxy group of the cation of 1s is observed in two R/S disorder positions. The crystals of these two salts display similar supramolecular architectures (i.e. two‐dimensional networks), built mainly by intermolecular N⁺—H…O^δ− and O—H…O^δ− hydrogen bonds, where `δ−' represents a partial charge. The succinate anions are engaged in hydrogen bonds, not only with protonated N atoms, but also with hydroxy groups.     

Five solvates of a multicomponent pharmaceutical salt formed by berberine and diclofenac

A multicomponent pharmaceutical salt formed by the isoquinoline alkaloid berberine (5,6‐dihydro‐9,10‐dimethoxybenzo[g]‐1,3‐benzodioxolo[5,6‐a]quinolizinium, BBR) and the nonsteroidal anti‐inflammatory drug diclofenac {2‐[2‐(2,6‐dichloroanilino)phenyl]acetic acid, DIC} was discovered. Five solvates of the pharmaceutical salt form were obtained by solid‐form screening. These five multicomponent solvates are the dihydrate (BBR–DIC·2H₂O or C₂₀H₁₈NO₄⁺·C₁₄H₁₀Cl₂NO₂^?·2H₂O), the dichloromethane hemisolvate dihydrate (BBR–DIC·0.5CH₂Cl₂·2H₂O or C₂₀H₁₈NO₄⁺·C₁₄H₁₀Cl₂NO₂^?·0.5CH₂Cl₂·2H₂O), the ethanol monosolvate (BBR–DIC·C₂H₅OH or C₂₀H₁₈NO₄⁺·C₁₄H₁₀Cl₂NO₂^?·C₂H₅OH), the methanol monosolvate (BBR–DIC·CH₃OH or C₂₀H₁₈NO₄⁺·C₁₄H₁₀Cl₂NO₂^?·CH₃OH) and the methanol disolvate (BBR–DIC·2CH₃OH or C₂₀H₁₈NO₄⁺·C₁₄H₁₀Cl₂NO₂^?·2CH₃OH), and their crystal structures were determined. All five solvates of BBR–DIC (1:1 molar ratio) were crystallized from different organic solvents. Solvent molecules in a pharmaceutical salt are essential components for the formation of crystalline structures and stabilization of the crystal lattices. These solvates have strong intermolecular O…H hydrogen bonds between the DIC anions and solvent molecules. The intermolecular hydrogen‐bond interactions were visualized by two‐dimensional fingerprint plots. All the multicomponent solvates contained intramolecular N—H…O hydrogen bonds. Various π–π interactions dominate the packing structures of the solvates.     

A comparative study of the packing of two polymorphs of the nickel(II) pincer complex [2,6‐bis(di‐tert‐butylphosphinoyl)‐4‐(3,5‐dinitrobenzoyloxy)phenyl‐κ3P,C1,P′]chloridonickel(II)

Pincer complexes can act as catalysts in organic transformations and have potential applications in materials, medicine and biology. They exhibit robust structures and high thermal stability attributed to the tridentate coordination of the pincer ligands and the strong σ metal–carbon bond. Nickel derivatives of these ligands have shown high catalytic activities in cross‐coupling reactions and other industrially relevant transformations. This work reports the crystal structures of two polymorphs of the title Ni^II POCOP pincer complex, [Ni(C₂₉H₄₁N₂O₈P₂)Cl] or [NiCl{C₆H₂‐4‐[OCOC₆H₄‐3,5‐(NO₂)₂]‐2,6‐(OP^tBu₂)₂}]. Both pincer structures exhibit the Ni^II atom in a distorted square‐planar coordination geometry with the POCOP pincer ligand coordinated in a typical tridentate manner via the two P atoms and one arene C atom via a C—Ni σ bond, giving rise to two five‐membered chelate rings. The coordination sphere of the Ni^II centre is completed by a chloride ligand. The asymmetric units of both polymorphs consist of one molecule of the pincer complex. In the first polymorph, the arene rings are nearly coplanar, with a dihedral angle between the mean planes of 27.9 (1)°, while in the second polymorph, this angle is 82.64 (1)°, which shows that the arene rings are almost perpendicular to one another. The supramolecular structure is directed by the presence of weak C—H…O=X (X = C or N) interactions, forming two‐ and three‐dimensional chain arrangements.     

2‐Ethyl‐6‐methylpyridin‐3‐ol and its salt bis(2‐ethyl‐3‐hydroxy‐6‐methylpyridinium) succinate

The title compounds, C₈H₁₁NO, (I), and 2C₈H₁₂NO⁺·C₄H₄O₄²⁻, (II), both crystallize in the monoclinic space group P2₁/c. In the crystal structure of (I), intermolecular O—H...N hydrogen bonds combine the molecules into polymeric chains extending along the c axis. The chains are linked by C—H...π interactions between the methylene H atoms and the pyridine rings into polymeric layers parallel to the ac plane. In the crystal structure of (II), the succinate anion lies on an inversion centre. Its carboxylate groups interact with the 2‐ethyl‐3‐hydroxy‐6‐methylpyridinium cations via intermolecular N—H...O hydrogen bonds with the pyridine ring H atoms and O—H...O hydrogen bonds with the hydroxy H atoms to form polymeric chains, which extend along the [01] direction and comprise R₄⁴(18) hydrogen‐bonded ring motifs. These chains are linked to form a three‐dimensional network through nonclassical C—H...O hydrogen bonds between the pyridine ring H atoms and the hydroxy‐group O atoms of neighbouring cations. π–π interactions between the pyridine rings and C—H...π interactions between the methylene H atoms of the succinate anion and the pyridine rings are also present in this network.     

Investigation of the effect of the N‐oxidation process on the interaction of selected pyridine compounds with biomacromolecules: structural,spectral, theoretical and docking studies

Two new N‐oxide compounds, namely glycinium 2‐carboxy‐1‐(λ¹‐oxidaneyl)‐1λ⁴‐pyridine‐6‐carboxylate–glycine–water (1/1/1), C₂H₆NO₂⁺·C₇H₄NO₅^?·C₂H₅NO₂·H₂O or [(2,6‐HpydcO)(HGLY)(GLY)(H₂O)], 1 , and methyl 6‐carboxy‐1‐(λ¹‐oxidaneyl)‐1λ⁴‐pyridine‐2‐carboxylate, C₈H₇NO₅ or 2,6‐HMepydcO, 2 , were prepared and identified by elemental analysis, FT–IR, Raman spectroscopy and single‐crystal X‐ray diffraction. The X‐ray analysis of 1 revealed an ionic compound containing a 2,6‐HpydcO^? anion, a glycinium cation, a neutral glycine molecule and a water molecule. Compound 2 is a neutral compound with two independent units in its crystal structure. In addition to the hydrogen bonds, the crystal network is stabilized by π–π stacking interactions of the types pyridine–carboxylate and carboxylate–carboxylate. The thermodynamic stability and charge‐distribution patterns for isolated molecules of 2,6‐H₂pydcO and 2,6‐HMepydcO, and their two similar derivatives, pyridine‐2,6‐dicarboxylic acid (2,6‐H₂pydc) and dimethyl 1‐(λ¹‐oxidaneyl)‐1λ⁴‐pyridine‐2,6‐dicarboxylate (2,6‐Me₂pydcO), were studied by density functional theory (DFT) and natural bond orbital (NBO) analysis, respectively. The ability of these compounds and their analogues to interact with nine selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS and Top II) was investigated using docking calculations.     

(1‐{[2‐(6‐Methoxynaphthalen‐1‐yl)ethyl]amino}ethylidene)oxidanium bromide monohydrate

The title salt, C₁₅H₁₈NO₂⁺·Br⁻·H₂O, is an analogue of the antidepressant drug agomelatine. The cation is protonated at the carbonyl O atom of its amide group. The side chain at the 1‐position adopts an extended conformation, with all non‐H atoms lying in the same plane as the naphthalene ring. This is in contrast with the crystal structures known for three agomelatine polymorphs, and also with two known cocrystals containing agomelatine. The structure displays three types of hydrogen bond, namely C=O—H...O, N—H...Br and O—H...Br, which define a two‐dimensional network parallel to the (100) plane. The naphthalene rings interdigitate in a `zipper‐like' fashion between these hydrogen‐bonded networks, forming an offset arrangement. Direct face‐to‐face π–π contacts between naphthalene rings are not present in the structure.     

2,6‐Di­phenyl­pyridine‐4‐carboxyl­ic acid

The distinctive feature of the crystal structure of 2,6‐di­phenyl­pyridine‐4‐carboxyl­ic acid, C₁₈H₁₃NO₂, is the formation of intermolecular O—H?O hydrogen bonds that lead to the formation of centrosymmetric cyclic dimers with R(8) topology. Molecules related by translation along the b axis exhibit strong π–π stacking of aromatic rings, with an average interplanar distance of 3.3 Å.     

A novel binucleating macrocyclic ligand with two alcohol pendants

A novel binucleating 24‐membered macrocyclic ligand, 6,20‐bis(2‐hydroxy­ethyl)‐3,6,9,17,20,23‐hex­aza­tri­cyclo­[23.3.1.1^11,15]triaconta‐1(29),11(30),12,14,25,27‐hexaene (L), was synthesized and crystallized as the tetra­hydro­bromide salt, i.e. 6,20‐bis(2‐hydroxy­ethyl)‐6,20‐di­aza‐3,9,17,23‐hexa­azoniatri­cyclo­[23.3.1.1^11,15]­triaconta‐1(29),11(30),­12,14,25,27‐hexaene tetrabromide tetrahydrate, C₂₈H₅₀N₆O₂⁴⁺·­4Br^?·4H₂O. A crystallographic inversion center is located in the macrocyclic cavity and the two hydroxy­ethyl pendants are on opposite sides of the macrocyclic plane. The benzene rings of the macrocycle are parallel to each other and a π–π‐stacking interaction exists between the benzene rings of adjacent macrocycles, which are separated by 3.791 (9) Å. An infinite intermolecular hydrogen‐bond network stabilizes the crystal.     

Crystallographic and computational studies of a new organoarsenate compound: o‐anisidinium dihydroarsenate

The crystal structure and the results of theoretical calculations for the new organoarsenate salt o‐anisidinium dihydroarsenate (systematic name: 2‐methoxyanilinium dihydrogen arsenate), C₇H₁₀NO⁺·H₂AsO₄^?, are reported. The salt, crystallizing in the triclinic space group P, was synthesized using a solution method and was characterized by single‐crystal X‐ray diffraction analysis. It possesses a layered supramolecular architecture in the crystal. The intermolecular interactions were studied using Hirshfeld surface analysis which confirmed that hydrogen bonds and H…H contacts play dominant roles in the crystal structure of the investigated system. An analysis of the electronic structure and molecular modelling using charge distribution confirms the good electrophilic reactivity of the title compound.     

Crystallographic characterization of three cathinone hydrochlorides new on the NPS market: 1-(4-methylphenyl)-2-(pyrrolidin-1-yl)hexan-1-one (4-MPHP), 4-methyl-1-phenyl-2-(pyrrolidin-1-yl)pentan-1-one (α-PiHP) and 2-(methylamino)-1-(4-methylphenyl)pentan-1-one (4-MPD)

Cathinones belong to a group of compounds of great interest in the new psychoactive substances (NPS) market. Constant changes to the chemical structure made by the producers of these compounds require a quick reaction from analytical laboratories in ascertaining their characteristics. In this article, three cathinone derivatives were characterized by X-ray crystallography. The investigated compounds were confirmed as: 1-[1-(4-methylphenyl)-1-oxohexan-2-yl]pyrrolidin-1-ium chloride ( 1 , C₁₇H₂₆NO⁺·Cl^?, the hydrochloride of 4-MPHP), 1-(4-methyl-1-oxo-1-phenylpentan-2-yl)pyrrolidin-1-ium chloride ( 2 ; C₁₆H₂₄NO⁺·Cl^?, the hydrochloride of α-PiHP) and methyl[1-(4-methylphenyl)-1-oxopentan-2-yl]azanium chloride ( 3 ; C₁₃H₂₀NO⁺·Cl^?, the hydrochloride of 4-MPD). All the salts crystallize in a monoclinic space group: 1 and 2 in P2₁/c, and 3 in P2₁/n. To the best of our knowledge, this study provides the first detailed and comprehensive crystallographic data on salts 1 – 3 .     

Desvenlafaxine succinate monohydrate

The title compound {systematic name: [2‐(1‐hydroxycyclohexyl)‐2‐(4‐hydroxyphenyl)ethyl]dimethylammonium 3‐carboxypropanoate monohydrate}, C₁₆H₂₆NO₂⁺·C₄H₅O₄⁻·H₂O, is a succinate salt of O‐desmethylvenlafaxine (desvenlafaxine). The present structure is one of four reported polymorphs of this salt, which is a new antidepressant drug. The carboxyl group of the succinate anion adopts a rare anti conformation and is engaged in a very short O—H...O⁻ hydrogen‐bond contact. Both cations and anions are involved separately in the formation of distinct O—H...O hydrogen‐bonded networks. Desvenlafaxine cations and water molecules self‐assemble to generate a honeycomb layer, while the succinate anions form a linear tape structure. These hydrogen‐bonded networks are interlinked via N—H...O and O—H...O hydrogen bonds. The hydrogen‐bonding network is so strong that desolvation and melting occur together at approximately 402 K. Thus, the crystal structure may be used to understand the thermal stability and solubility of the compound at the molecular level.     

1:1 Complex of 4‐nitro­benzoic acid and 4‐nitro­pyridine N‐oxide

In the title co‐crystal, C₇H₅NO₄·C₅H₄N₂O₃, the two components are linked by an intermolecular hydrogen bond between the O—H and N—O groups [O?O 2.577 (3) Å]. The interplanar angle between the planes of the rings of the mol­ecules is 5.3 (2)°. The rings are stacked in the crystal with a mean interplanar distance of 3.279 (3) Å.     

Two succinic acid derivatives of 2‐ethyl‐6‐methylpyridin‐3‐ol

Crystals of bis(2‐ethyl‐3‐hydroxy‐6‐methylpyridinium) succinate–succinic acid (1/1), C₈H₁₂NO⁺·0.5C₄H₄O₄²⁻·0.5C₄H₆O₄, (I), and 2‐ethyl‐3‐hydroxy‐6‐methylpyridinium hydrogen succinate, C₈H₁₂NO⁺·C₄H₅O₄⁻, (II), were obtained by reaction of 2‐ethyl‐6‐methylpyridin‐3‐ol with succinic acid. The succinate anion and succinic acid molecule in (I) are located about centres of inversion. Intermolecular O—H...O, N—H...O and C—H...O hydrogen bonds are responsible for the formation of a three‐dimensional network in the crystal structure of (I) and a two‐dimensional network in the crystal structure of (II). Both structures are additionally stabilized by π–π interactions between symmetry‐related pyridine rings, forming a rod‐like cationic arrangement for (I) and cationic dimers for (II).     

Ethyl 6‐acetylamino‐6,7‐dihydro‐5H‐dibenzo[a,c]cycloheptene‐6‐carboxylate

The title compound, C₂₀H₂₁NO₃, is a derivative of Aib (α‐­aminoisobutyric acid) and is cyclized at the C^α position by bi­phenyl rings. The seven‐membered ring possesses C2 symmetry. The C^α cyclization causes the backbone to assume a helical conformation in the crystal structure. The packing of the mol­ecules is stabilized by intermolecular C—H?O, C—H?π and N—H?O hydrogen bonds.     

Two polymorphs of 2,5‐dichloro‐3,6‐bis(dibenzylamino)‐p‐hydroquinone with flexible dibenzylamino groups

We obtained two conformational polymorphs of 2,5‐dichloro‐3,6‐bis(dibenzylamino)‐p‐hydroquinone, C₃₄H₃₀Cl₂N₂O₂. Both polymorphs have an inversion centre at the centre of the hydroquinone ring (Z′ = ), and there are no significant differences between their bond lengths and angles. The most significant structural difference in the molecular conformations was found in the rotation of the phenyl rings of the two crystallographically independent benzyl groups. The crystal structures of the polymorphs were distinguishable with respect to the arrangement of the hydroquinone rings and the packing motif of the phenyl rings that form part of the benzyl groups. The phenyl groups of one polymorph are arranged in a face‐to‐edge motif between adjacent molecules, with intermolecular C—H…π interactions, whereas the phenyl rings in the other polymorph form a lamellar stacking pattern with no significant intermolecular interactions. We suggest that this partial conformational difference in the molecular structures leads to the significant structural differences observed in their molecular arrangements.     

Crystal structure and Hirshfeld surface analysis of a salt of antineoplastic kinase inhibitor vandetanib

A salt of vandetanib, namely, 4-({4-[(4-bromo-2-fluorophenyl)amino]-6-methoxyquinazolin-7-yl}methoxy)-1-methylpiperazin-1-ium 2-(butylamino)-4-phenoxy-6-sulfamoylbenzoate acetonitrile monosolvate, C₂₂H₂₅BrFN₄O₂⁺·C₁₇H₁₉N₂O₅S⁻·C₂H₃N, composed of kinase inhibitor vandetanib and sulfamyl diuretic bumetanide in a 1:1 molar ratio, is reported. There is proton transfer between the piperidine ring of vandetanib and the carboxyl group of bumetanide to form the salt. In the vandetanib cation, the arene and pyrimidine rings are not coplanar, their planes subtending a dihedral angle of 60.47 (14)°. The roles of the intermolecular interactions in the crystal packing were clarified using Hirshfeld surface analysis, and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H…H (40.5%), O…H/H…C (20.7%), C…H/ H…C (18.8%) and N…C/C…N (9.0%) contacts.     

Alogliptin and its benzoate salt

The crystal structure of the free base of the antidiabetic drug alogliptin [systematic name: 2‐({6‐[(3R)‐3‐aminopiperidin‐1‐yl]‐3‐methyl‐2,4‐dioxo‐1,2,3,4‐tetrahydropyrimidin‐1‐yl}methyl)benzonitrile], C₁₈H₂₁N₅O₂, displays a two‐dimensional N—H...O hydrogen‐bonded network. It contains two independent molecules, which have the same conformation but differ in their hydrogen‐bond connectivity. In the crystal structure of the benzoate salt (systematic name: (3R)‐1‐{3‐[(2‐cyanophenyl)methyl]‐1‐methyl‐2,6‐dioxo‐1,2,3,6‐tetrahydropyrimidin‐4‐yl}piperidin‐3‐aminium benzoate), C₁₈H₂₂N₅O₂⁺·C₇H₅O₂⁻, the NH₃⁺ group of the cation is engaged in three intermolecular N—H...O hydrogen bonds to yield a hydrogen‐bonded layer structure. The benzoate salt and the free base differ fundamentally in the conformations of their alogliptin moieties.