Evaluation of N—H…S and N—H…π interactions in O,O′‐diethyl N‐(2,4,6‐trimethylphenyl)thiophosphate: a combination of X‐ray crystallographic and theoretical studies

In the crystal structure of O,O′‐diethyl N‐(2,4,6‐trimethylphenyl)thiophosphate, C₁₃H₂₂NO₂PS, two symmetrically independent thiophosphoramide molecules are linked through N—H…S and N—H…π hydrogen bonds to form a noncentrosymmetric dimer, with Z′ = 2. The strengths of the hydrogen bonds were evaluated using density functional theory (DFT) at the M06‐2X level within the 6‐311++G(d,p) basis set, and by considering the quantum theory of atoms in molecules (QTAIM). It was found that the N—H…S hydrogen bond is slightly stronger than the N—H…π hydrogen bond. This is reflected in differences between the calculated N—H stretching frequencies of the isolated molecules and the frequencies of the same N—H units involved in the different hydrogen bonds of the hydrogen‐bonded dimer. For these hydrogen bonds, the corresponding charge transfers, i.e. lp (or π)→σ*, were studied, according to the second‐order perturbation theory in natural bond orbital (NBO) methodology. Hirshfeld surface analysis was applied for a detailed investigation of all the contacts participating in the crystal packing.     

Synthesis and characterization of a novel long‐alkyl‐chain ester‐substituted benzimidazole gelator and its octan‐1‐ol solvate

The synthesis of a novel benzimidazole derivative with a long‐chain‐ester substituent, namely methyl 8‐[4‐(1H‐benzimidazol‐2‐yl)phenoxy]octanoate, (3), is reported. Ester (3) shows evidence of aggregation in solution and weak gelation ability with toluene. The octan‐1‐ol solvate, methyl 8‐[4‐(1H‐benzimidazol‐2‐yl)phenoxy]octanoate octan‐1‐ol monosolvate, C₂₂H₂₆N₂O₃·C₈H₁₈O, (4), exhibits a four‐molecule hydrogen‐bonded motif in the solid state, with N—H…O hydrogen bonds between benzimidazole molecules and O—H…N hydrogen bonds between the octan‐1‐ol solvent molecules and the benzimidazole unit. The alkyl chains of the ester and the octan‐1‐ol molecules are in unfolded conformations. The phenylene ring is canted by 10.27 (6)° from the plane of the benzimidazole ring system. H…C contacts make up 20.7% of the Hirshfeld surface coverage. Weak C—H…π interactions involving the benzimidazole alkyl chain and three aromatic rings are observed.     

The hydrogen‐bonded complex bis(tert‐butylammonium) 2,6‐dichlorophenolate 2,4‐dichlorophenol–2,4‐dichlorophenolate tetrahydrofuran disolvate containing a chiral R53(10) hydrogen‐bonded ring as a supramolecular synthon

A fixed hydrogen‐bonding motif with a high probability of occurring when appropriate functional groups are involved is described as a `supramolecular hydrogen‐bonding synthon'. The identification of these synthons may enable the prediction of accurate crystal structures. The rare chiral hydrogen‐bonding motif R₅³(10) was observed previously in a cocrystal of 2,4,6‐trichlorophenol, 2,4‐dichlorophenol and dicyclohexylamine. In the title solvated salt, 2C₄H₁₂N⁺·C₆H₃Cl₂O⁻·(C₆H₃Cl₂O⁻·C₆H₄Cl₂O)·2C₄H₈O, five components, namely two tert‐butylammonium cations, one 2,4‐dichlorophenol molecule, one 2,4‐dichlorophenolate anion and one 2,6‐dichlorophenolate anion, are bound by N—H…O and O—H…O hydrogen bonds to form a hydrogen‐bonded ring, with the graph‐set motif R₅³(10), which is further associated with two pendant tetrahydrofuran molecules by N—H…O hydrogen bonds. The hydrogen‐bonded ring has internal symmetry, with a twofold axis running through the centre of the 2,6‐dichlorophenolate anion, and is isostructural with a previous and related structure formed from 2,4‐dichlorophenol, dicyclohexylamine and 2,4,6‐trichlorophenol. In the title crystal, helical columns are built by the alignment and twisting of the chiral hydrogen‐bonded rings, along and across the c axis, and successive pairs of rings are associated with each other through C—H…π interactions. Neighbouring helical columns are inversely related and, therefore, no chirality is sustained, in contrast to the previous case.     

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.     

Mechanochemical synthesis and X‐ray structural characterization of three 3‐nitrophenol cocrystals with three aminal cage azaadamantanes: the role of the stereoelectronic effect on intermolecular hydrogen‐bonding patterns

The structures of the cocrystalline adducts of 3‐nitrophenol (3‐NP) with 1,3,5,7‐tetraazatricyclo[3.3.1.1^3,7]decane [HMTA, ( 1 )] as the 2:1:1 hydrate, 2C₆H₅NO₃·C₆H₁₂N₄·H₂O, ( 1a ), with 1,3,6,8‐tetraazatricyclo[4.3.1.1^3,8]undecane [TATU ( 2 )] as the 2:1 cocrystal, 2C₆H₅NO₃·C₇H₁₄N₄, ( 2a ), and with 1,3,6,8‐tetraazatricyclo[4.4.1.1^3,8]dodecane [TATD, ( 3 )] as the 2:1 cocrystal, 2C₆H₅NO₃·C₈H₁₆N₄, ( 3a ), are reported. In the binary crystals ( 2a ) and ( 3a ), the 3‐nitrophenol molecules are linked via O—H…N hydrogen bonds into aminal cage azaadamantanes. In ( 1a ), the structure is stabilized by O—H…N and O—H…O hydrogen bonds, and generates ternary cocrystals. There are C—H…O hydrogen bonds present in all three cocrystals, and in ( 1a ), there are also C—H…O and C—H…π interactions present. The presence of an ethylene bridge in the structures of ( 2 ) and ( 3 ) defines the formation of a hydrogen‐bonded motif in the supramolecular architectures of ( 2a ) and ( 3a ). The differences in the C—N bond lengths of the aminal cage structures, as a result of hyperconjugative interactions and electron delocalization, were analysed. These three cocrystals were obtained by the solvent‐free assisted grinding method. Crystals suitable for single‐crystal X‐ray diffraction were grown by slow evaporation from a mixture of hexanes.     

Supramolecular architectures in cytosinium 6‐chloronicotinate monohydrate and 5‐bromo‐6‐methylisocytosinium hydrogen sulfate

Aminopyrimidine derivatives are biologically important as they are components of nucleic acids and drugs. The crystals of two new salts, namely cytosinium 6‐chloronicotinate monohydrate, C₄H₆N₃O⁺·C₆H₃ClNO₂⁻·H₂O, ( I ), and 5‐bromo‐6‐methylisocytosinium hydrogen sulfate (or 2‐amino‐5‐bromo‐4‐oxo‐6‐methylpyrimidinium hydrogen sulfate), C₅H₇BrN₃O⁺·HSO₄⁻, ( II ), have been prepared and characterized by single‐crystal X‐ray diffraction. The pyrimidine ring of both compounds is protonated at the imine N atom. In hydrated salt ( I ), the primary R₂²(8) ring motif (supramolecular heterosynthon) is formed via a pair of N—H…O(carboxylate) hydrogen bonds. The cations, anions and water molecule are hydrogen bonded through N—H…O, N—H…N, O—H…O and C—H…O hydrogen bonds, forming R₂²(8), R₃²(7) and R₅⁵(21) motifs, leading to a hydrogen‐bonded supramolecular sheet structure. The supramolecular double sheet structure is formed via water–carboxylate O—H…O hydrogen bonds and π–π interactions between the anions and the cations. In salt ( II ), the hydrogen sulfate ions are linked via O—H…O hydrogen bonds to generate zigzag chains. The aminopyrimidinium cations are embedded between these zigzag chains. Each hydrogen sulfate ion bridges two cations via pairs of N—H…O hydrogen bonds and vice versa, generating two R₂²(8) ring motifs (supramolecular heterosynthon). The cations also interact with one another via halogen–halogen (Br…Br) and halogen–oxygen (Br…O) interactions.     

Supramolecular hydrogen‐bonding patterns in the organic–inorganic hybrid compound bis(4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium) tetrathiocyanatozinc(II)–4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–water (1/2/2)

Zinc thiocyanate complexes have been found to be biologically active compounds. Zinc is also an essential element for the normal function of most organisms and is the main constituent in a number of metalloenzyme proteins. Pyrimidine and aminopyrimidine derivatives are biologically very important as they are components of nucleic acids. Thiocyanate ions can bridge metal ions by employing both their N and S atoms for coordination. They can play an important role in assembling different coordination structures and yield an interesting variety of one‐, two‐ and three‐dimensional polymeric metal–thiocyanate supramolecular frameworks. The structure of a new zinc thiocyanate–aminopyrimidine organic–inorganic compound, (C₆H₉ClN₃)₂[Zn(NCS)₄]·2C₆H₈ClN₃·2H₂O, is reported. The asymmetric unit consist of half a tetrathiocyanatozinc(II) dianion, an uncoordinated 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium cation, a 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine molecule and a water molecule. The Zn^II atom adopts a distorted tetrahedral coordination geometry and is coordinated by four N atoms from the thiocyanate anions. The Zn^II atom is located on a special position (twofold axis of symmetry). The pyrimidinium cation and the pyrimidine molecule are not coordinated to the Zn^II atom, but are hydrogen bonded to the uncoordinated water molecules and the metal‐coordinated thiocyanate ligands. The pyrimidine molecules and pyrimidinium cations also form base‐pair‐like structures with an R₂²(8) ring motif via N—H…N hydrogen bonds. The crystal structure is further stabilized by intermolecular N—H…O, O—H…S, N—H…S and O—H…N hydrogen bonds, by intramolecular N—H…Cl and C—H…Cl hydrogen bonds, and also by π–π stacking interactions.     

The synergistic co‐operation of N—H…O=P hydrogen bonds and C—H…OX weak intermolecular interactions (X is =P or —C) in the (CH3O)2P(O)(NH–NHC6F5) amidophosphoester: a combined X‐ray crystallographic and theoretical study

The asymmetric unit of O,O′‐dimethyl [(2,3,4,5,6‐pentafluorophenyl)hydrazinyl]phosphonate, C₈H₈F₅N₂O₃P, is composed of two symmetry‐independent molecules with significant differences in the orientations of the C₆F₅ and OMe groups. In the crystal structure, a one‐dimensional assembly is mediated from classical N—H…O hydrogen bonds, which includes R₂²(8), D(2) and some higher‐order graph‐set motifs. By also considering weak C—H…O=P and C—H…O—C intermolecular interactions, a two‐dimensional network extends along the ab plane. The strengths of the hydrogen bonds were evaluated using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6‐311G(d,p) level of theory. The LP(O) to σ*(NH) and σ*(CH) charge‐transfer interactions were examined according to second‐order perturbation theory in natural bond orbital (NBO) methodology. The hydrogen‐bonded clusters of molecules, including N—H…O and C—H…O interactions, were constructed as input files for the calculations and the strengths of the hydrogen bonds are as follows: N—H…O [R₂²(8)] > N—H…O [D(2)] > C—H…O. The decomposed fingerprint plots show that the contribution portions of the F…H/H…F contacts in both molecules are the largest.     

Different supramolecular architectures mediated by different weak interactions in the crystals of three N‐aryl‐2,5‐dimethoxybenzenesulfonamides

The synthesis and evaluation of the pharmacological activities of molecules containing the sulfonamide moiety have attracted interest as these compounds are important pharmacophores. The crystal structures of three closely related N‐aryl‐2,5‐dimethoxybenzenesulfonamides, namely N‐(2,3‐dichlorophenyl)‐2,5‐dimethoxybenzenesulfonamide, C₁₄H₁₃Cl₂NO₄S, (I), N‐(2,4‐dichlorophenyl)‐2,5‐dimethoxybenzenesulfonamide, C₁₄H₁₃Cl₂NO₄S, (II), and N‐(2,4‐dimethylphenyl)‐2,5‐dimethoxybenzenesulfonamide, C₁₆H₁₉NO₄S, (III), are described. The asymmetric unit of (I) consists of two symmetry‐independent molecules, while those of (II) and (III) contain one molecule each. The molecular conformations are stabilized by different intramolecular interactions, viz. C—H…O interactions in (I), N—H…Cl and C—H…O interactions in (II), and C—H…O interactions in (III). The crystals of the three compounds display different supramolecular architectures built by various weak intermolecular interactions of the types C—H…O, C—H…Cl, C—H…π(aryl), π(aryl)–π(aryl) and Cl…Cl. A detailed Hirshfeld surface analysis of these compounds has also been conducted in order to understand the relationship between the crystal structures. The d _norm and shape‐index surfaces of (I)–(III) support the presence of various intermolecular interactions in the three structures. Analysis of the fingerprint plots reveals that the greatest contribution to the Hirshfeld surfaces is from H…H contacts, followed by H…O/O…H contacts. In addition, comparisons are made with the structures of some related compounds. Putative N—H…O hydrogen bonds are observed in 29 of the 30 reported structures, wherein the N—H…O hydrogen bonds form either C (4) chain motifs or R ₂²(8) rings. Further comparison reveals that the characteristics of the N—H…O hydrogen‐bond motifs, the presence of other interactions and the resultant supramolecular architecture is largely decided by the position of the substituents on the benzenesulfonyl ring, with the nature and position of the substituents on the aniline ring exerting little effect. On the other hand, the crystal structures of (I)–(III) display several weak interactions other than the common N—H…O hydrogen bonds, resulting in supramolecular architectures varying from one‐ to three‐dimensional depending on the nature and position of the substituents on the aniline ring.     

Hydrogen‐bonding and C—H⋯π interactions in 7‐hydroxy‐3‐methoxy‐4‐methyl‐5,6,7,8‐tetrahydro­pyrido­[1,2‐c]pyrimidin‐1(9H)‐one

In the title compound, C₁₀H₁₄N₂O₃, a pyrimidine ring is fused with a piperidine ring. The pyrimidine ring is planar, whereas the piperidine ring adopts a half‐chair conformation. The molecules of the title compound are connected via O—H⋯O intermolecular hydrogen bonds into infinite zigzag chains. The pyrimidine ring is involved in three C—H⋯π interactions, which link the hydrogen‐bonded chains into a three‐dimensional framework.     

Weak hydrogen and halogen bonding in 4‐[(2,2‐difluoroethoxy)methyl]pyridinium iodide and 4‐[(3‐chloro‐2,2,3,3‐tetrafluoropropoxy)methyl]pyridinium iodide

To enable a comparison between a C—H…X hydrogen bond and a halogen bond, the structures of two fluorous‐substituted pyridinium iodide salts have been determined. 4‐[(2,2‐Difluoroethoxy)methyl]pyridinium iodide, C₈H₁₀F₂NO⁺·I⁻, (1), has a –CH₂OCH₂CF₂H substituent at the para position of the pyridinium ring and 4‐[(3‐chloro‐2,2,3,3‐tetrafluoropropoxy)methyl]pyridinium iodide, C₉H₉ClF₄NO⁺·I⁻, (2), has a –CH₂OCH₂CF₂CF₂Cl substituent at the para position of the pyridinium ring. In salt (1), the iodide anion is involved in one N—H…I and three C—H…I hydrogen bonds, which, together with C—H…F hydrogen bonds, link the cations and anions into a three‐dimensional network. For salt (2), the iodide anion is involved in one N—H…I hydrogen bond, two C—H…I hydrogen bonds and one C—Cl…I halogen bond; additional C—H…F and C—F…F interactions link the cations and anions into a three‐dimensional arrangement.     

2‐Ethyl‐1‐[5‐(4‐methylphenyl)pyrazol‐3‐yl]‐3‐(thiophene‐2‐carbonyl)isothiourea: molecular ribbons containing three types of hydrogen‐bonded ring

The title compound, C₁₈H₁₈N₄OS₂, was prepared by reaction of S,S‐diethyl 2‐thenoylimidodithiocarbonate with 5‐amino‐3‐(4‐methylphenyl)‐1H‐pyrazole using microwave irradiation under solvent‐free conditions. In the molecule, the thiophene unit is disordered over two sets of atomic sites, with occupancies of 0.814 (4) and 0.186 (4), and the bonded distances provide evidence for polarization in the acylthiourea fragment and for aromatic type delocalization in the pyrazole ring. An intramolecular N—H...O hydrogen bond is present, forming an S(6) motif, and molecules are linked by N—H...O and N—H...N hydrogen bonds to form a ribbon in which centrosymmetric R₂²(4) rings, built from N—H...O hydrogen bonds and flanked by inversion‐related pairs of S(6) rings, alternate with centrosymmetric R₂²(6) rings built from N—H...N hydrogen bonds.     

Crystallographic study of self‐organization in the solid state including quasi‐aromatic pseudo‐ring stacking interactions in 1‐benzoyl‐3‐(3,4‐dimethoxyphenyl)thiourea and 1‐benzoyl‐3‐(2‐hydroxypropyl)thiourea

1‐Benzoylthioureas contain both carbonyl and thiocarbonyl functional groups and are of interest for their biological activity, metal coordination ability and involvement in hydrogen‐bond formation. Two novel 1‐benzoylthiourea derivatives, namely 1‐benzoyl‐3‐(3,4‐dimethoxyphenyl)thiourea, C₁₆H₁₆N₂O₃S, (I), and 1‐benzoyl‐3‐(2‐hydroxypropyl)thiourea, C₁₁H₁₄N₂O₂S, (II), have been synthesized and characterized. Compound (I) crystallizes in the space group P , while (II) crystallizes in the space group P 2₁/c . In both structures, intramolecular N—H…O hydrogen bonding is present. The resulting six‐membered pseudo‐rings are quasi‐aromatic and, in each case, interact with phenyl rings via stacking‐type interactions. C—H…O, C—H…S and C—H…π interactions are also present. In (I), there is one molecule in the asymmetric unit. Pairs of molecules are connected via two intermolecular N—H…S hydrogen bonds, forming centrosymmetric dimers. In (II), there are two symmetry‐independent molecules that differ mainly in the relative orientations of the phenyl rings with respect to the thiourea cores. Additional strong hydrogen‐bond donor and acceptor –OH groups participate in the formation of intermolecular N—H…O and O—H…S hydrogen bonds that join molecules into chains extending in the [001] direction.     

How the oxazole fragment influences the conformation of the tetraoxazocane ring in a cyclohexanespiro‐3′‐(1,2,4,5,7‐tetraoxazocane): single‐crystal X‐ray and theoretical study

Single crystals of (2S,5R)‐2‐isopropyl‐5‐methyl‐7‐(5‐methylisoxazol‐3‐yl)cyclohexanespiro‐3′‐(1,2,4,5,7‐tetraoxazocane), C₁₆H₂₆N₂O₅, have been studied via X‐ray diffraction. The tetraoxazocane ring adopts a boat–chair conformation in the crystalline state, which is due to intramolecular interactions. Conformational analysis of the tetraoxazocane fragment performed at the B3LYP/6‐31G(d,2p) level of theory showed that there are three minima on the potential energy surface, one of which corresponds to the conformation realized in the solid state, but not to a global minimum. Analysis of the geometry and the topological parameters of the electron density at the (3,?1) bond critical points (BCPs), and the charge transfer in the tetraoxazocane ring indicated that there are stereoelectronic effects in the O—C—O and N—C—O fragments. There is a two‐cross hyperconjugation in the N—C—O fragment between the lone electron pair of the N atom (lpN) and the antibonding orbital of a C—O bond (σ*_C—O) and vice versa between lpO and σ*_C—N. The oxazole substituent has a considerable effect on the geometry and the topological parameters of the electron density at the (3,?1) BCPs of the tetraoxazocane ring. The crystal structure is stabilized via intermolecular C—H…N and C—H…O hydrogen bonds, which is unambiguously confirmed with PIXEL calculations, a quantum theory of atoms in molecules (QTAIM) topological analysis of the electron density at the (3,?1) BCPs and a Hirshfeld analysis of the electrostatic potential. The molecules form zigzag chains in the crystal due to intermolecular C—H…N interactions being electrostatic in origin. The molecules are further stacked due to C—H…O hydrogen bonds. The dispersion component in the total stabilization energy of the crystal lattice is 68.09%.     

Design of two series of 1:1 cocrystals involving 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine and carboxylic acids

Two series of a total of ten cocrystals involving 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine with various carboxylic acids have been prepared and characterized by single‐crystal X‐ray diffraction. The pyrimidine unit used for the cocrystals offers two ring N atoms (positions N1 and N3) as proton‐accepting sites. Depending upon the site of protonation, two types of cations are possible [Rajam et al. (2017). Acta Cryst. C 73 , 862–868]. In a parallel arrangement, two series of cocrystals are possible depending upon the hydrogen bonding of the carboxyl group with position N1 or N3. In one series of cocrystals, i.e. 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–3‐bromothiophene‐2‐carboxylic acid (1/1), 1 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–5‐chlorothiophene‐2‐carboxylic acid (1/1), 2 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–2,4‐dichlorobenzoic acid (1/1), 3 , and 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–2‐aminobenzoic acid (1/1), 4 , the carboxyl hydroxy group (–OH) is hydrogen bonded to position N1 (O—H…N1) of the corresponding pyrimidine unit (single point supramolecular synthon). The inversion‐related stacked pyrimidines are doubly bridged by the carboxyl groups via N—H…O and O—H…N hydrogen bonds to form a large cage‐like tetrameric unit with an R₄²(20) graph‐set ring motif. These tetrameric units are further connected via base pairing through a pair of N—H…N hydrogen bonds, generating R₂²(8) motifs (supramolecular homosynthon). In the other series of cocrystals, i.e. 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–5‐methylthiophene‐2‐carboxylic acid (1/1), 5 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–benzoic acid (1/1), 6 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–2‐methylbenzoic acid (1/1), 7 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–3‐methylbenzoic acid (1/1), 8 , 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–4‐methylbenzoic acid (1/1), 9 , and 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–4‐aminobenzoic acid (1/1), 10 , the carboxyl group interacts with position N3 and the adjacent 4‐amino group of the corresponding pyrimidine ring via O—H…N and N—H…O hydrogen bonds to generate the robust R₂²(8) supramolecular heterosynthon. These heterosynthons are further connected by N—H…N hydrogen‐bond interactions in a linear fashion to form a chain‐like arrangement. In cocrystal 1 , a Br…Br halogen bond is present, in cocrystals 2 and 3 , Cl…Cl halogen bonds are present, and in cocrystals 5 , 6 and 7 , Cl…O halogen bonds are present. In all of the ten cocrystals, π–π stacking interactions are observed.     

Supramolecular interactions in salts/cocrystals involving pyrimidine derivatives of sulfonate/carboxylic acid

The crystal structures of three compounds involving aminopyrimidine derivatives are reported, namely, 5-fluorocytosinium sulfanilate–5-fluorocytosine–4-azaniumylbenzene-1-sulfonate (1/1/1), C₄H₅FN₃O⁺·C₆H₆NO₃S⁻·C₄H₄FN₃O·C₆H₇NO₃S, I , 5-fluorocytosine–indole-3-propionic acid (1/1), C₄H₄FN₃O·C₁₁H₁₁NO₂, II , and 2,4,6-triaminopyrimidinium 3-nitrobenzoate, C₄H₈N₅⁺·C₇H₄NO₄⁻, III , which have been synthesized and characterized by single-crystal X-ray diffraction. In I , there are two 5-fluorocytosine (5FC) molecules (5FC-A and 5FC-B) in the asymmetric unit, with one of the protons disordered between them. 5FC-A and 5FC-B are linked by triple hydrogen bonds, generating two fused rings [two R₂²(8) ring motifs]. The 5FC-A molecules form a self-complementary base pair [R₂²(8) ring motif] via a pair of N—H…O hydrogen bonds and the 5FC-B molecules form a similar complementary base pair [R₂²(8) ring motif]. The combination of these two types of pairing generates a supramolecular ribbon. The 5FC molecules are further hydrogen bonded to the sulfanilate anions and sulfanilic acid molecules via N—H…O hydrogen bonds, generating R₄⁴(22) and R⁶₆(36) ring motifs. In cocrystal II , two types of base pairs (homosynthons) are observed via a pair of N—H…O/N—H…N hydrogen bonds, generating R₂²(8) ring motifs. The first type of base pair is formed by the interaction of an N—H group and the carbonyl O atom of 5FC molecules through a couple of N—H…O hydrogen bonds. Another type of base pair is formed via the amino group and a pyrimidine ring N atom of the 5FC molecules through a pair of N—H…N hydrogen bonds. The base pairs (via N—H…N hydrogen bonds) are further bridged by the carboxyl OH group of indole-3-propionic acid and the O atom of 5FC through O—H…O hydrogen bonds on either side of the R₂²(8) motif. This leads to a DDAA array. In salt III , one of the N atoms of the pyrimidine ring is protonated and interacts with the carboxylate group of the anion through N—H…O hydrogen bonds, leading to the primary ring motif R₂²(8). Furthermore, the 2,4,6-triaminopyrimidinium (TAP) cations form base pairs [R₂²(8) homosynthon] via N—H…N hydrogen bonds. A carboxylate O atom of the 3-nitrobenzoate anion bridges two of the amino groups on either side of the paired TAP cations to form another ring [R₃²(8)]. This leads to the generation of a quadruple DADA array. The crystal structures are further stabilized by π–π stacking ( I and III ), C—H…π ( I and II ), C—F…π ( I ) and C—O…π ( II ) interactions.     

trans‐Diaquabis(nicotinamide‐κN)bis(salicylato‐κO)cobalt(II)

The title compound, [Co(C₇H₅O₃)₂(C₆H₆N₂O)₂(H₂O)₂], forms a three‐dimensional hydrogen‐bonded supramolecular structure. The Co^II ion is in an octahedral coordination environment comprising two pyridyl N atoms, two carboxylate O atoms and two O atoms from water molecules. Intermolecular N—H...O and O—H...O hydrogen bonds produce R₂²(8), R₂²(12) and R₂²(14) rings, which lead to two‐dimensional chains. An extensive three‐dimensional supramolecular network of C—H...O, N—H...O and O—H...O hydrogen bonds and C—H...π interactions is responsible for crystal structure stabilization. This study is an example of the construction of a supramolecular assembly based on hydrogen bonds in mixed‐ligand metal complexes.     

4,6‐Diaminopyrimidine‐2(1H)‐thione hemihydrate: a three‐dimensional hydrogen‐bonded framework

In the title compound, C₄H₆N₄S·0.5H₂O, there are two independent pyrimidinethione units, both of which lie across mirror planes in the space group Cmca. Hence, the H atoms bonded to the ring N atoms in each molecule are disordered over two symmetry‐related sites, each having an occupancy of 0.5. The water molecule lies across a twofold rotation axis parallel to [010]. The molecular components of (I) are linked by seven independent hydrogen bonds, of N—H...N, N—H...S, N—H...O and O—H...S types. A combination of disordered N—H...N hydrogen bonds and ordered N—H...S hydrogen bonds links the pyrimidinethione units into a continuous tubular structure. The water molecule acts as both a double donor of hydrogen bonds and a double acceptor, forming hydrogen bonds with components of four distinct pyrimidinethione tubes, thus linking these tubes into a three‐dimensional structure.     

Contrasting the supramolecular structures in the isomeric pair 5‐bromo‐3‐nitrosalicylaldehyde phenylhydrazone and 3‐bromo‐5‐nitrosalicylaldehyde phenylhydrazone

Isomeric 5‐bromo‐3‐nitrosalicylaldehyde phenylhydrazone and 3‐bromo‐5‐nitrosalicylaldehyde phenylhydrazone, C₁₃H₁₀BrN₃O₃, both crystallize with two molecules in the asymmetric unit. In both isomers, an intramolecular O—H...N hydrogen bond links the hydroxy group and the imine N atom. In the 5‐bromo‐3‐nitro isomer, there are two independent N—H...O hydrogen‐bonded chains, each molecule in the asymmetric unit forming its own chain. These chains are then linked to form a three‐dimensional framework by a combination of weak C—H...O, C—H...Br, C—H...π and π–π stacking interactions. In the 3‐bromo‐5‐nitro isomer, N—H...O hydrogen bonds link the independent molecules alternately into a zigzag chain, which is reinforced by a weak C—H...O interaction. Individual chains are linked by a C—H...Br interaction and a three‐dimensional framework is generated by π–π stacking interactions.     

A three‐dimensional hydrogen‐bonded framework in 2‐amino‐6‐(N‐methylanilino)pyrimidin‐4(3H)‐one and a ribbon of fused hydrogen‐bonded rings in 2‐amino‐6‐(N‐methylanilino)‐5‐nitropyrimidin‐4(3H)‐one

The molecular dimensions of both 2‐amino‐6‐(N‐methylanilino)pyrimidin‐4(3H)‐one, C₁₁H₁₂N₄O, (I), and 2‐amino‐6‐(N‐methylanilino)‐5‐nitropyrimidin‐4(3H)‐one, C₁₁H₁₁N₅O₃, (II), are consistent with considerable polarization of the molecular–electronic structures. The molecules of (I) are linked into a three‐dimensional framework by a combination of one N—H...N hydrogen bond, two independent N—H...O hydrogen bonds and one C—H...π(arene) hydrogen bond. The molecules of (II) are linked into ribbons containing three types of edge‐fused ring by the combination of two independent three‐centre N—H...(O)₂ hydrogen bonds.