Cocrystals of 6‐propyl‐2‐thiouracil: N—H...O versus N—H...S hydrogen bonds

In order to investigate the relative stability of N—H...O and N—H...S hydrogen bonds, we cocrystallized the antithyroid drug 6‐propyl‐2‐thiouracil with two complementary heterocycles. In the cocrystal pyrimidin‐2‐amine–6‐propyl‐2‐thiouracil (1/2), C₄H₅N₃·2C₇H₁₀N₂OS, (I), the `base pair' is connected by one N—H...S and one N—H...N hydrogen bond. Homodimers of 6‐propyl‐2‐thiouracil linked by two N—H...S hydrogen bonds are observed in the cocrystal N‐(6‐acetamidopyridin‐2‐yl)acetamide–6‐propyl‐2‐thiouracil (1/2), C₉H₁₁N₃O₂·2C₇H₁₀N₂OS, (II). The crystal structure of 6‐propyl‐2‐thiouracil itself, C₇H₁₀N₂OS, (III), is stabilized by pairwise N—H...O and N—H...S hydrogen bonds. In all three structures, N—H...S hydrogen bonds occur only within R₂²(8) patterns, whereas N—H...O hydrogen bonds tend to connect the homo‐ and heterodimers into extended networks. In agreement with related structures, the hydrogen‐bonding capability of C=O and C=S groups seems to be comparable.     

Dibenzylammonium hydrogen maleate and a redetermination at 120 K of bis(dibenzylamino)methane

In dibenzylammonium hydrogen maleate [or dibenzylammonium (2Z)‐3‐carboxyprop‐2‐enoate], C₁₄H₁₆N⁺·C₄H₃O₄⁻, (I), the anion contains a fairly short and nearly linear O—H...O hydrogen bond, with an O...·O distance of 2.4603 (16) Å, but with the H atom clearly offset from the mid‐point of the O...O vector. The counter‐ions in (I) are linked by two N—H...O hydrogen bonds to form C₂²(6) chains and these chains are weakly linked into sheets by a C—H...O hydrogen bond. Bis(dibenzylamino)methane, C₂₉H₃₀N₂, (II), crystallizes with two independent molecules lying across twofold rotation axes in the space group C2/c, and the molecules are conformationally chiral; there are no direction‐specific intermolecular interactions in the crystal structure of (II).     

Three‐dimensional networks in bis(imidazolium) 2,2′‐dithiodibenzoate and 4‐methylimidazolium 2‐[(2‐carboxyphenyl)disulfanyl]benzoate

Cocrystallization of imidazole or 4‐methylimidazole with 2,2′‐dithiodibenzoic acid from methanol solution yields the title 2:1 and 1:1 organic salts, 2C₃H₅N₂⁺·C₁₄H₁₀O₄S₂²⁻, (I), and C₄H₇N₂⁺·C₁₄H₁₀O₄S₂⁻, (II), respectively. Compound (I) crystallizes in the monoclinic C2/c space group with the mid‐point of the S—S bond lying on a twofold axis. The component ions in (I) are linked by intermolecular N—H...O hydrogen bonds to form a two‐dimensional network, which is further linked by C—H...O hydrogen bonds into a three‐dimensional network. In contrast, by means of N—H...O, N—H...S and O—H...O hydrogen bonds, the component ions in (II) are linked into a tape and adjacent tapes are further linked by π–π, C—H...O and C—H...π interactions, resulting in a three‐dimensional network.     

An unusual conformation of gabapentin (Gpn) in Pyr‐Gpn‐NH‐NH‐Pyr stabilized by weak interactions

The crystal structure of N‐[(1‐{2‐oxo‐2‐[2‐(pyrazin‐2‐ylcarbonyl)hydrazin‐1‐yl]ethyl}cyclohexyl)methyl]pyrazine‐2‐carboxamide monohydrate (Pyr‐Gpn‐NN‐NH‐Pyr·H₂O), C₁₉H₂₃N₇O₃·H₂O, reveals an unusual trans–gauche (tg⁻) conformation for the gabapentin (Gpn) residue around the C^γ—C^β (θ₁) and C^β—C^α (θ₂) bonds. The molecular conformation is stabilized by intramolecular N—H...N hydrogen bonds and weak C—H...O interactions. The packing of the molecules in the crystal lattice shows a network of strong N—H...O and O—H...O hydrogen bonds together with weak C—H...O and π–π inteactions.     

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.     

(S)‐5‐Benzylimidazolidine‐2,4‐dione monohydrate

The crystal structure of the title compound, C₁₀H₁₀N₂O₂·H₂O, also known as l ‐5‐benzylhydantoin monohydrate, is described in terms of two‐dimensional supramolecular arrays built up from infinite chains assembled via N—H...O and O—H...O hydrogen bonds among the organic molecules and solvent water molecules, with graph‐set R³₃(10)C(5)C²₂(6). The hydrogen‐bond network is reinforced by stacking of the layers through C—H...π interactions.     

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.     

3‐[(Diphenylphosphinothioyl)oxy]‐N‐methylpropan‐1‐aminium diphenylphosphanylthioate

The title salt, C₁₆H₂₁NOPS⁺·C₁₂H₁₀OPS, was synthesized from the reaction between 3‐(methylamino)propan‐1‐ol and PPh₂(S)Cl in the presence of Et₃N. Its structure has been identified using spectroscopic methods and X‐ray analysis. Single crystals were obtained from ethanol by slow evaporation. In the asymmetric unit, a cation–anion pair is formed through an intermolecular N—H...O [N...O = 2.6974 (18) Å] hydrogen bond. The molecules are packed through N—H...O and N—H...S hydrogen bonds in the crystal and these hydrogen bonds are responsible for the high melting point. The P atoms of the anion and cation both have distorted tetrahedral environments.     

(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.     

Sodium tris(glycinium) bis(hexafluorosilicate) glycine trisolvate

The title compound, Na⁺·3C₂H₆NO₂⁺·2SiF₆²⁻·3C₂H₅NO₂, arose from an unexpected reaction of glycine and HF with the glass container. It is an unusual hybrid organic–inorganic network built up from chains of vertex‐sharing NaF₄O₂ and SiF₆ octahedra. A pair of glycinium/glycine molecules bridges the chains into a sheet via a centrosymmetric O...H...O link. The other organic species interact with the network by an extensive N—H...F hydrogen‐bond network, including bifurcated and trifurcated bonds. Finally, an extremely short C—H...O interaction (H...O = 2.25 Å) is seen in the crystal structure. The Na atom has site symmetry .     

Cocrystals of 1,4‐diethynylbenzene with 1,3‐diacetylbenzene and benzene‐1,4‐dicarbaldehyde exhibiting strong nonconventional alkyne–carbonyl C—H…O hydrogen bonds between the components

Weak interactions between organic molecules are important in solid‐state structures where the sum of the weaker interactions support the overall three‐dimensional crystal structure. The sp‐C—H…N hydrogen‐bonding interaction is strong enough to promote the deliberate cocrystallization of a series of diynes with a series of dipyridines. It is also possible that a similar series of cocrystals could be formed between molecules containing a terminal alkyne and molecules which contain carbonyl O atoms as the potential hydrogen‐bond acceptor. I now report the crystal structure of two cocrystals that support this hypothesis. The 1:1 cocrystal of 1,4‐diethynylbenzene with 1,3‐diacetylbenzene, C₁₀H₆·C₁₀H₁₀O₂, (1), and the 1:1 cocrystal of 1,4‐diethynylbenzene with benzene‐1,4‐dicarbaldehyde, C₁₀H₆·C₈H₆O₂, (2), are presented. In both cocrystals, a strong nonconventional ethynyl–carbonyl sp‐C—H…O hydrogen bond is observed between the components. In cocrystal (1), the C—H…O hydrogen‐bond angle is 171.8 (16)° and the H…O and C…O hydrogen‐bond distances are 2.200 (19) and 3.139 (2) Å, respectively. In cocrystal (2), the C—H…O hydrogen‐bond angle is 172.5 (16)° and the H…O and C…O hydrogen‐bond distances are 2.25 (2) and 3.203 (2) Å, respectively.     

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).     

Two solid phases of pyrimidin‐1‐ium hydrogen chloranilate monohydrate determined at 225 and 120 K

The crystal structures of two solid phases of the title compound, C₄H₅N₂⁺·C₆HCl₂O₄⁻·H₂O, have been determined at 225 and 120 K. In the high‐temperature phase, stable above 198 K, the transition temperature of which has been determined by ³⁵Cl nuclear quadrupole resonance and differential thermal analysis measurements, the three components are held together by O—H...O, N...H...O, C—H...O and C—H...Cl hydrogen bonds, forming a centrosymmetric 2+2+2 aggregate. In the N...H...O hydrogen bond formed between the pyrimidin‐1‐ium cation and the water molecule, the H atom is disordered over two positions, resulting in two states, viz. pyrimidin‐1‐ium–water and pyrimidine–oxonium. In the low‐temperature phase, the title compound crystallizes in the same monoclinic space group and has a similar molecular packing, but the 2+2+2 aggregate loses the centrosymmetry, resulting in a doubling of the unit cell and two crystallographically independent molecules for each component in the asymmetric unit. The H atom in one N...H...O hydrogen bond between the pyrimidin‐1‐ium cation and the water molecule is disordered, while the H atom in the other hydrogen bond is found to be ordered at the N‐atom site with a long N—H distance [1.10 (3) Å].     

2,2′‐Bipyridinium(1+) bromide monohydrate

In the crystal structure of 2,2′‐bipyridinium(1+) bromide monohydrate, C₁₀H₉N₂⁺·Br⁻·H₂O, the cation has a cisoid conformation with an intramolecular N—H⋯N hydrogen bond. The cation also forms an N—H⋯O hydrogen bond to an adjacent water mol­ecule, which in turn forms O—H⋯Br⁻ hydrogen bonds to adjacent Br⁻ anions. In this way, a chain is formed extending along the b axis. Additional interactions (C—H⋯Br⁻ and π–π) serve to stabilize the structure further.     

N—H...O and O—H...O hydrogen‐bonded supramolecular networks in 4‐chloroanilinium, 2‐hydroxyanilinium and 3‐hydroxyanilinium hydrogen phthalates

The title salts, 4‐chloroanilinium hydrogen phthalate (PCAHP), C₆H₇ClN⁺·C₈H₅O₄⁻, 2‐hydroxyanilinium hydrogen phthalate (2HAHP), C₆H₈NO⁺·C₈H₅O₄⁻, and 3‐hydroxyanilinium hydrogen phthalate (3HAHP), C₆H₈NO⁺·C₈H₅O₄⁻, all crystallize in the space group P2₁/c. The asymmetric unit of 2HAHP contains two independent ion pairs. The hydrogen phthalate ions of 2HAHP and 3HAHP show a short intramolecular O—H...O hydrogen bond, with O...O distances ranging from 2.3832 (15) to 2.3860 (14) Å. N—H...O and O—H...O hydrogen bonds, together with short C—H...O contacts in PCAHP and 3HAHP, generate extended hydrogen‐bond networks. PCAHP forms a two‐dimensional supramolecular sheet extending in the (100) plane, whereas 2HAHP has a supramolecular chain running parallel to the [100] direction and 3HAHP has a two‐dimensional network extending parallel to the (001) plane.     

Bis(dl‐cysteinium) oxalate

In the title compound, 2C₃H₈NO₂S⁺·C₂O₄²⁻, the oxalate anion occupies an inversion centre and is coordinated to cysteine molecules of different chirality (l and d ) via O—H...O and N—H...O hydrogen bonds, the resulting cysteine–oxalate stoichiometry in the crystal structure being 2:1. The oxalate anion is completely deprotonated, whereas cysteine has a positively charged –NH₃⁺ group and a neutral protonated carboxyl group. The structure is built from infinite hydrogen‐bonded triple layers, consisting of an oxalate layer in the middle with layers of l ‐ and d ‐cysteine molecules on either side. The thiol groups are at the external sides of the layers and form S—H...O hydrogen bonds with the carboxyl groups of neighbouring cysteine molecules. An interesting feature of the structure is the occurrence of short S...S contacts between SH groups of molecules in neighbouring layers, which form not S—H...S but S—H...O intermolecular hydrogen bonds. Due to the effects of crystal packing and intermolecular hydrogen‐bond formation, the conformation of the cysteine cation in the title structure is different from that calculated theoretically for an individual cation, as well as from those of cysteine zwitterions in crystals of pure cysteine.     

An unusual two‐dimensional hydrogen‐bonding network in bis(2,9‐dimethyl‐1,10‐phenanthrolin‐1‐ium) peroxodisulfate dihydrate

The title compound, 2C₁₄H₁₃N₂⁺·S₂O₈²⁻·2H₂O, is a protonated amine salt which is formed from two rather uncommon ionic species, namely a peroxodisulfate (pds²⁻) anion, which lies across a crystallographic inversion centre, and a 2,9‐dimethyl‐1,10‐phenanthrolin‐1‐ium (Hdmph⁺) cation lying in a general position. Each pds²⁻ anion binds to two water molecules through strong water–peroxo O—H...O interactions, giving rise to an unprecedented planar network of hydrogen‐bonded macrocycles which run parallel to (100). The atoms of the large R₈⁸(30) rings are provided by four water molecules bridging in fully extended form (...H—O—H...) and four pds²⁻ anions alternately acting as long (...O—S—O—O—S—O...) and short (...O—S—O...) bridges. The Hdmph⁺ cations, in turn, bind to these units through hydrogen bonds involving their protonated N atoms. In addition, the crystal structure also contains π–π and aromatic–peroxo C—H...O interactions.     

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.     

(6‐Oxido‐2‐oxo‐1,2‐dihydropyrimidine‐5‐carboxylato‐κ2O5,O6)bis[2‐(2‐pyridyl)‐1H‐benzimidazole‐κ2N2,N3]manganese(II) monohydrate

In the title compound, [Mn(C₅H₂N₂O₄)(C₁₂H₉N₃)₂]·H₂O, the Mn^II centre is surrounded by three bidentate chelating ligands, namely, one 6‐oxido‐2‐oxo‐1,2‐dihydropyrimidine‐5‐carboxylate (or uracil‐5‐carboxylate, Huca²⁻) ligand [Mn—O = 2.136 (2) and 2.156 (3) Å] and two 2‐(2‐pyridyl)‐1H‐benzimidazole (Hpybim) ligands [Mn—N = 2.213 (3)–2.331 (3) Å], and it displays a severely distorted octahedral geometry, with cis angles ranging from 73.05 (10) to 105.77 (10)°. Intermolecular N—H...O hydrogen bonds both between the Hpybim and the Huca²⁻ ligands and between the Huca²⁻ ligands link the molecules into infinite chains. The lattice water molecule acts as a hydrogen‐bond donor to form double O...H—O—H...O hydrogen bonds with the Huca²⁻ O atoms, crosslinking the chains to afford an infinite two‐dimensional sheet; a third hydrogen bond (N—H...O) formed by the water molecule as a hydrogen‐bond acceptor and a Hpybim N atom further links these sheets to yield a three‐dimensional supramolecular framework. Possible partial π–π stacking interactions involving the Hpybim rings are also observed in the crystal structure.     

Three‐dimensional hydrogen‐bonded framework structures in flunarizinium nicotinate and flunarizinediium bis(4‐toluenesulfonate) dihydrate

The structures of two salts of flunarizine, namely 1‐bis[(4‐fluorophenyl)methyl]‐4‐[(2E)‐3‐phenylprop‐2‐en‐1‐yl]piperazine, C₂₆H₂₆F₂N₂, are reported. In flunarizinium nicotinate {systematic name: 4‐bis[(4‐fluorophenyl)methyl]‐1‐[(2E)‐3‐phenylprop‐2‐en‐1‐yl]piperazin‐1‐ium pyridine‐3‐carboxylate}, C₂₆H₂₇F₂N₂⁺·C₆H₄NO₂⁻, (I), the two ionic components are linked by a short charge‐assisted N—H...O hydrogen bond. The ion pairs are linked into a three‐dimensional framework structure by three independent C—H...O hydrogen bonds, augmented by C—H...π(arene) hydrogen bonds and an aromatic π–π stacking interaction. In flunarizinediium bis(4‐toluenesulfonate) dihydrate {systematic name: 1‐[bis(4‐fluorophenyl)methyl]‐4‐[(2E)‐3‐phenylprop‐2‐en‐1‐yl]piperazine‐1,4‐diium bis(4‐methylbenzenesulfonate) dihydrate}, C₂₆H₂₈F₂N₂²⁺·2C₇H₇O₃S⁻·2H₂O, (II), one of the anions is disordered over two sites with occupancies of 0.832 (6) and 0.168 (6). The five independent components are linked into ribbons by two independent N—H...O hydrogen bonds and four independent O—H...O hydrogen bonds, and these ribbons are linked to form a three‐dimensional framework by two independent C—H...O hydrogen bonds, but C—H...π(arene) hydrogen bonds and aromatic π–π stacking interactions are absent from the structure of (II). Comparisons are made with some related structures.