Supramolecular networks in (9‐fluoro‐4H‐chromeno[4,3‐c]isoxazol‐3‐yl)methanol and its 9‐chloro analogue at 100 K

The title compounds, (9‐fluoro‐4H‐chromeno[4,3‐c]isoxazol‐3‐yl)methanol, C₁₁H₈FNO₃, (I), and (9‐chloro‐4H‐chromeno[4,3‐c]isoxazol‐3‐yl)methanol, C₁₁H₈ClNO₃, (II), crystallize in the orthorhombic space group Pbca with Z′ = 1 and the triclinic space group P with Z′ = 6, respectively. The simple replacement of F by Cl in the main molecular scaffold of (I) and (II) results in significant differences in the intermolecular interaction patterns and a corresponding change in the point‐group symmetry from D_2h to C_i = S₂. These striking differences are manifested through the presence of C—H...F and the absence of O—H...O and C—H...O interactions in (I), and the absence of C—H...Cl and the presence of O—H...O and C—H...O interactions in (II). However, the geometry of the synthons formed by the O—H...N and O—H...X (X = F or Cl) interactions observed in the constitution of the supramolecular networks of both (I) and (II) remains similar. Also, C—H...O interactions are not preferred in the presence of F in (I), while they are much preferred in the presence of Cl in (II).     

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.     

Hydrogen bonding in the bromide salts of 4‐aminobenzoic acid and 4‐aminoacetophenone

In the title compounds, 4‐carboxyanilinium bromide, C₇H₈NO₂⁺·Br⁻, (I), and 4‐acetylanilinium bromide, C₈H₁₀NO⁺·Br⁻, (II), each asymmetric unit contains a discrete cation with a protonated amino group and a halide anion. Both crystal structures are characterized by two‐dimensional hydrogen‐bonded networks. The ions in (I) are connected via N—H...Br, N—H...O and O—H...Br hydrogen bonds, with three characteristic graph‐set motifs, viz. C(8), C₂¹(4) and R₃²(8). The centrosymmetric hydrogen‐bonded R²₂(8) dimer motif characteristic of carboxylic acids is absent. The ions in (II) are connected via N—H...Br and N—H...O hydrogen bonds, with two characteristic graph‐set motifs, viz. C(8) and R₄²(8). The significance of this study lies in its illustration of the differences between the supramolecular aggregations in two similar compounds. The presence of the methyl group in (II) at the site corresponding to the hydroxyl group in (I) results in a significantly different hydrogen‐bonding arrangement.     

The effect of hydrogen bonding on the conformations of 2‐(1H‐indol‐3‐yl)‐2‐oxoacetamide and 2‐(1H‐indol‐3‐yl)‐N,N‐dimethyl‐2‐oxoacetamide

In the title compounds, C₁₀H₈N₂O₂, (I), and C₁₂H₁₂N₂O₂, (II), the two carbonyl groups are oriented with torsion angles of −149.3 (3) and −88.55 (15)°, respectively. The single‐bond distances linking the two carbonyl groups are 1.528 (4) and 1.5298 (17) Å, respectively. In (I), the molecules are linked by an elaborate system of N—H...O hydrogen bonds, which form adjacent R²₂(8) and R⁴₂(8) ring motifs to generate a ladder‐like construct. Adjacent ladders are further linked by N—H...O hydrogen bonds to build a three‐dimensional network. The hydrogen bonding in (II) is far simpler, consisting of helical chains of N—H...O‐linked molecules that follow the 2₁ screw of the b axis. It is the presence of an elaborate hydrogen‐bonding system in the crystal structure of (I) that leads to the different torsion angle for the orientation of the two adjacent carbonyl groups from that in (II).     

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.     

Five pseudopolymorphs of 6‐amino‐2‐thiouracil: absence of N—H...S hydrogen bonds

In order to study the preferred hydrogen‐bonding pattern of 6‐amino‐2‐thiouracil, C₄H₅N₃OS, (I), crystallization experiments yielded five different pseudopolymorphs of (I), namely the dimethylformamide disolvate, C₄H₅N₃OS·2C₃H₇NO, (Ia), the dimethylacetamide monosolvate, C₄H₅N₃OS·C₄H₉NO, (Ib), the dimethylacetamide sesquisolvate, C₄H₅N₃OS·1.5C₄H₉NO, (Ic), and two different 1‐methylpyrrolidin‐2‐one sesquisolvates, C₄H₅N₃OS·1.5C₅H₉NO, (Id) and (Ie). All structures contain R₂¹(6) N—H...O hydrogen‐bond motifs. In the latter four structures, additional R₂²(8) N—H...O hydrogen‐bond motifs are present stabilizing homodimers of (I). No type of hydrogen bond other than N—H...O is observed. According to a search of the Cambridge Structural Database, most 2‐thiouracil derivatives form homodimers stabilized by an R₂²(8) hydrogen‐bonding pattern, with (i) only N—H...O, (ii) only N—H...S or (iii) alternating pairs of N—H...O and N—H...S hydrogen bonds.     

Two three‐dimensional networks in the binary molecular adducts 4‐methylimidazolium hydrogen terephthalate and bis(4‐methylimidazolium) terephthalate

Both the 1:1 and 2:1 molecular adducts of 4‐methylimidazole (4‐MeIm) and terephthalic acid (H₂TPA) are organic salts, viz. C₄H₇N₂⁺·C₈H₅O₄⁻, (I), and 2C₄H₇N₂⁺·C₈H₄O₄²⁻, (II), respectively. The component ions in (I) are linked by N—H...O and O—H...O hydrogen bonds into continuous two‐dimensional layers built from R₆⁴(32) hydrogen‐bond motifs running parallel to the (100) plane. These adjacent two‐dimensional layers are in turn linked by a combination of C—H...O, C—H...π and π–π interactions into a three‐dimensional network. In the crystal structure of (II), with the anion located on an inversion centre, only N—H...O hydrogen bonds result in two‐dimensional layers built from R₈⁸(42) hydrogen‐bond motifs running parallel to the (102) plane. Being similar to those in (I), these layers are also linked by means of C—H...O, C—H...π and π–π interactions, forming a three‐dimensional network. This study indicates that, on occasion, a change of the reactant concentration can exert a pivotal influence on the construction of supramolecular structures based on hydrogen bonds.     

Charge‐assisted hydrogen‐bonded supramolecular networks in acetoguanaminium hydrogen phthalate,acetoguanaminium hydrogen maleate and acetoguanaminium 3‐hydroxypicolinate monohydrate

In 2,4‐diamino‐6‐methyl‐1,3,5‐triazin‐1‐ium (acetoguanaminium) hydrogen phthalate, C₄H₈N₅⁺·C₈H₅O₄⁻, (I), acetoguanaminium hydrogen maleate, C₄H₈N₅⁺·C₄H₃O₄⁻, (II), and acetoguanaminium 3‐hydroxypicolinate monohydrate, C₄H₈N₅⁺·C₆H₄NO₃⁻·H₂O, (III), the acetoguanaminium cations interact with the carboxylate groups of the corresponding anions via a pair of nearly parallel N—H...O hydrogen bonds, forming R₂²(8) ring motifs. In (II) and (III), N—H...N base‐pairing is observed, while there is none in (I). In (II), a series of fused R₃²(8), R₂²(8) and R₃²(8) hydrogen‐bonded rings plus fused R₂²(8), R₆²(12) and R₂²(8) ring motifs occur alternately, aggregating into a supramolecular ladder‐like arrangement. In (III), R₂²(8) motifs occur on either side of a further ring formed by pairs of N—H...O hydrogen bonds, forming an array of three fused hydrogen‐bonded rings. In (I) and (II), the anions form a typical intramolecular O—H...O hydrogen bond with graph set S(7), whereas in (III) an intramolecular hydrogen bond with graph set S(6) is formed.     

Hydrogen‐bonded two‐ and three‐dimensional polymeric structures in the ammonium salts of 3,5‐dinitrobenzoic acid, 4‐nitrobenzoic acid and 2,4‐dichlorobenzoic acid

The structures of ammonium 3,5‐dinitrobenzoate, NH₄⁺·C₇H₃N₂O₆⁻, (I), ammonium 4‐nitrobenzoate dihydrate, NH₄⁺·C₇H₄NO₄⁻·2H₂O, (II), and ammonium 2,4‐dichlorobenzoate hemihydrate, NH₄⁺·C₇H₃Cl₂O₂⁻·0.5H₂O, (III), have been determined and their hydrogen‐bonded structures are described. All three salts form hydrogen‐bonded polymeric structures, viz. three‐dimensional in (I) and two‐dimensional in (II) and (III). With (I), a primary cation–anion cyclic association is formed [graph set R₄³(10)] through N—H...O hydrogen bonds, involving a carboxylate group with both O atoms contributing to the hydrogen bonds (denoted O,O′‐carboxylate) on one side and a carboxylate group with one O atom involved in two hydrogen bonds (denoted O‐carboxylate) on the other. Structure extension involves N—H...O hydrogen bonds to both carboxylate and nitro O‐atom acceptors. With structure (II), the primary inter‐species interactions and structure extension into layers lying parallel to (001) are through conjoined cyclic hydrogen‐bonding motifs, viz.R₄³(10) (one cation, an O,O′‐carboxylate group and two water molecules) and centrosymmetric R₄²(8) (two cations and two water molecules). The structure of (III) also has conjoined R₄³(10) and centrosymmetric R₄²(8) motifs in the layered structure but these differ in that the first motif involves one cation, an O,O′‐carboxylate group, an O‐carboxylate group and one water molecule, and the second motif involves two cations and two O‐carboxylate groups. The layers lie parallel to (100). The structures of salt hydrates (II) and (III), displaying two‐dimensional layered arrays through conjoined hydrogen‐bonded nets, provide further illustration of a previously indicated trend among ammonium salts of carboxylic acids, but the anhydrous three‐dimensional structure of (I) is inconsistent with that trend.     

Hydro­gen‐bonded supramolecular motifs in 4,4′‐bipyridinium 8‐hydroxy‐7‐iodo­quinoline‐5‐sulfonate dihydrate

In the title compound, C₁₀H₉N₂⁺·C₉H₅INO₄S⁻·2H₂O, the 4,4′‐bi­pyridine mol­ecule is protonated at one of the pyridine N atoms. These moieties self‐assemble into a supramolecular chain along the a axis through N—H⋯N hydrogen bonds. The quinolinol OH group acts as a donor with respect to a sulfonate O atom [O—H⋯O(sulfonate)] and acts as an acceptor with respect to a C—H group of ferron [C—H⋯O(hydroxy)], forming a supramolecular chain along the b axis. These two types of supramolecular chains (one type made up of bi­pyridine motifs and the other made up of sulfoxine motifs) interact viaπ–π stacking, generating a three‐dimensional framework. These chains are further crosslinked by C—­H⋯O hydrogen bonds and O—H⋯O hydrogen bonds involving water mol­ecules.     

Hydrogen bonding and π–π stacking in 6‐hydroxy­biochanin A monohydrate

In the lattice of the title compound (systematic name: 5,6,7‐trihydroxy‐4′‐meth­oxy­isoflavone monohydrate), C₁₆H₁₂O₆·H₂O, the isoflavone mol­ecules are linked into chains through R₄³(17) motifs composed via O—H⋯O and C—H⋯O hydrogen bonds. Centrosymmetric R₄²(14) motifs assemble the chains into sheets. Hydrogen‐bonding and aromatic π–π stacking inter­actions lead to the formation of a three‐dimensional network structure.     

4‐(3,5‐Dimethyl‐1H‐pyrazol‐4‐ylmethyl)‐3,5‐dimethyl‐1H‐pyrazol‐2‐ium dihydrogen phosphate: a combined X‐ray and DFT study

The molecular structure of the title salt, C₁₁H₁₇N₄⁺·H₂PO₄⁻, has been determined from single‐crystal X‐ray analysis and compared with the structure calculated by density functional theory (DFT) at the BLYP level. The crystal packing in the title compound is stabilized primarily by intermolecular N—H...O, O—H...N and O—H...O hydrogen bonds and π–π stacking interactions, and thus a three‐dimensional supramolecular honeycomb network consisting of R₄²(10), R₄⁴(14) and R₄⁴(24) ring motifs is established. The HOMO–LUMO energy gap (1.338 eV; HOMO is the highest occupied molecular orbital and LUMO is the lowest unoccupied molecular orbital) indicates a high chemical reactivity for the title compound.     

Bis(adamantan‐1‐aminium) tetrachloridozincate(II) 18‐crown‐6 monohydrate clathrate

The structure of the title compound [systematic name: bis(adamantan‐1‐aminium) tetrachloridozincate(II)–1,4,7,10,13,16‐hexaoxacyclooctadecane–water (1/1/1)], (C₁₀H₁₈N)₂[ZnCl₄]·C₁₂H₂₄O₆·H₂O, consists of supramolecular rotator–stator assemblies and ribbons of hydrogen bonds parallel to [010]. The assemblies are composed of one protonated adamantan‐1‐aminium cation and one crown ether molecule (1,4,7,10,13,16‐hexaoxacyclooctadecane) to give an overall [(C₁₀H₁₈N)(18‐crown‐6)]⁺ cation. The –NH₃⁺ group of the cation nests in the crown and links to the crown‐ether O atoms through N—H...O hydrogen bonds. The 18‐crown‐6 ring adopts a pseudo‐C_3v conformation. The second adamantan‐1‐aminium forms part of ribbons of adamantan‐1‐aminium–water–tetrachloridozincate units which are interconnected by O—H...Cl, N—H...O and N—H...Cl hydrogen bonds via three different continuous rings with R₅⁴(12), R₄³(10) and R₃³(8) motifs.     

4‐Carboxypyridinium perchlorate 18‐crown‐6 dihydrate clathrate and 4‐carboxypyridinium tetrafluoroborate 18‐crown‐6 dihydrate clathrate

Mixtures of 4‐carboxypyridinium perchlorate or 4‐carboxypyridinium tetrafluoroborate and 18‐crown‐6 (1,4,7,10,13,16‐hexaoxacyclooctadecane) in ethanol and water solution yielded the title supramolecular salts, C₆H₆NO₂⁺·ClO₄⁻·C₁₂H₂₄O₆·2H₂O and C₆H₆NO₂⁺·BF₄⁻·C₁₂H₂₄O₆·2H₂O. Based on their similar crystal symmetries, unit cells and supramolecular assemblies, the salts are essentially isostructural. The asymmetric unit in each structure includes one protonated isonicotinic acid cation and one crown ether molecule, which together give a [(C₆H₆NO₂)(18‐crown‐6)]⁺ supramolecular cation. N—H...O hydrogen bonds between the protonated N atoms and a single O atom of each crown ether result in the 4‐carboxypyridinium cations `perching' on the 18‐crown‐6 molecules. Further hydrogen‐bonding interactions involving the supramolecular cation and both water molecules form a one‐dimensional zigzag chain that propagates along the crystallographic c direction. O—H...O or O—H...F hydrogen bonds between one of the water molecules and the anions fix the anion positions as pendant upon this chain, without further increasing the dimensionality of the supramolecular network.     

Charge‐assisted hydrogen bonding in salts of 2‐amino‐1H‐benzimidazole with 3‐phenylpropynoic acid and oct‐2‐ynoic acid

The 100 K structures of two salts, namely 2‐amino‐1H‐benzimidazolium 3‐phenylpropynoate, C₇H₈N₃⁺·C₉H₅O₂⁻, (I), and 2‐amino‐1H‐benzimidazolium oct‐2‐ynoate, C₇H₈N₃⁺·C₈H₁₁O₂⁻, (II), both have monoclinic symmetry (space group P2₁/c) and display N—H...O hydrogen bonding. Both structures show packing with corrugated sheets of hydrogen‐bonded molecules lying parallel to the [001] direction. Two hydrogen‐bonded ring motifs can be identified and described with graph sets R²₂(8) and R⁴₄(16), respectively, in both (I) and (II). Computational chemistry calculations performed on both compounds show that the hydrogen‐bonded ion pairs are more energetically favourable in the crystal structure than their hydrogen–bonded neutral molecule counterparts.     

An optically resolved crystal of thiomalate: (S)‐1‐phenylethanaminium (R)‐thiomalate

The asymmetric unit of the optically resolved title salt, C₈H₁₂N⁺·C₄H₅O₄S⁻, contains a 1‐phenylethanaminium monocation and a thiomalate (3‐carboxy‐2‐sulfanylpropanoate) monoanion. The absolute configurations of the cation and the anion are determined to be S and R, respectively. In the crystal, cation–anion N—H...O hydrogen bonds, together with anion–anion O—H...O and S—H...O hydrogen bonds, construct a two‐dimensional supramolecular sheet parallel to the ab plane. The two‐dimensional sheet is linked with the upper and lower sheets through C—H...π interactions to stack along the c axis.     

Polymorphism in 2‐(4‐hydroxy‐2,6‐dimethylanilino)‐5,6‐dihydro‐4H‐1,3‐thiazin‐3‐ium chloride

Details of the structures of two conformational polymorphs of the title compound, C₁₂H₁₇N₂OS⁺·Cl⁻, are reported. In form (I) (space group P), the two N—H groups of the cation are in a trans conformation, while in form (II) (space group P2₁/c), they are in a cis arrangement. This results in different packing and hydrogen‐bond arrangements in the two forms, both of which have extended chains lying along the a direction. In form (I), these chains are composed of centrosymmetric R₄²(18) (N—H...Cl and O—H...Cl) hydrogen‐bonded rings and R₂²(18) (N—H...O) hydrogen‐bonded rings. In form (II), the chains are formed by centrosymmetric R₄²(18) (N—H...Cl and O—H...Cl) hydrogen‐bonded rings and by R₄²(12) (N—H...Cl) hydrogen‐bonded rings.     

Hydrogen‐bonding motifs in 3‐carboxyanilinium bromide and iodide

In the title compounds, C₇H₈NO₂⁺·Br⁻, (I), and C₇H₈NO₂⁺·I⁻, (II), the asymmetric unit contains a discrete 3‐carboxyanilinium cation, with a protonated amine group, and a halide anion. The compounds are not isostructural, and the crystal structures of (I) and (II) are characterized by different two‐dimensional hydrogen‐bonded networks. The ions in (I) are connected into ladder‐like ribbons via N—H...Br hydrogen bonds, while classic cyclic O—H...O hydrogen bonds between adjacent carboxylic acid functions link adjacent ribbons to give three characteristic graph‐set motifs, viz. C₂¹(4), R₄²(8) and R₂²(8). The ions in (II) are connected via N—H...I, N—H...O and O—H...I hydrogen bonds, also with three characteristic graph‐set motifs, viz. C(7), C₂¹(4) and R₄²(18), but an O—H...O interaction is not present.     

Comparison of the hydrogen‐bond patterns in 2‐amino‐1,3,4‐thiadiazolium hydrogen oxalate, 2‐amino‐1,3,4‐thiadiazole–succinic acid (1/2), 2‐amino‐1,3,4‐thiadiazole–glutaric acid (1/1) and 2‐amino‐1,3,4‐thiadiazole–adipic acid (1/1)

The X‐ray single‐crystal structure determinations of the chemically related compounds 2‐amino‐1,3,4‐thiadiazolium hydrogen oxalate, C₂H₄N₃S⁺·C₂HO₄⁻, (I), 2‐amino‐1,3,4‐thiadiazole–succinic acid (1/2), C₂H₃N₃S·2C₄H₆O₄, (II), 2‐amino‐1,3,4‐thiadiazole–glutaric acid (1/1), C₂H₃N₃S·C₅H₈O₄, (III), and 2‐amino‐1,3,4‐thiadiazole–adipic acid (1/1), C₂H₃N₃S·C₆H₁₀O₄, (IV), are reported and their hydrogen‐bonding patterns are compared. The hydrogen bonds are of the types N—H...O or O—H...N and are of moderate strength. In some cases, weak C—H...O interactions are also present. Compound (II) differs from the others not only in the molar ratio of base and acid (1:2), but also in its hydrogen‐bonding pattern, which is based on chain motifs. In (I), (III) and (IV), the most prominent feature is the presence of an R₂²(8) graph‐set motif formed by N—H...O and O—H...N hydrogen bonds, which are present in all structures except for (I), where only a pair of N—H...O hydrogen bonds is present, in agreement with the greater acidity of oxalic acid. There are nonbonding S...O interactions present in all four structures. The difference electron‐density maps show a lack of electron density about the S atom along the S...O vector. In all four structures, the carboxylic acid H atoms are present in a rare configuration with a C—C—O—H torsion angle of ∼0°. In the structures of (II)–(IV), the C—C—O—H torsion angle of the second carboxylic acid group has the more common value of ∼|180|°. The dicarboxylic acid molecules are situated on crystallographic inversion centres in (II). The Raman and IR spectra of the title compounds are presented and analysed.