1‐Carboxymethyl‐3‐methyl‐1H‐imidazol‐3‐ium chloride 2‐(3‐methyl‐1H‐imidazol‐3‐ium‐1‐yl)acetate monohydrate: a crystal stabilized by imidazolium zwitterions

The title compound, C₆H₉N₂O₂⁺·Cl⁻·C₆H₈N₂O₂·H₂O, contains one 2‐(3‐methyl‐1H‐imidazol‐3‐ium‐1‐yl)acetate inner salt molecule, one 1‐carboxymethyl‐3‐methyl‐1H‐imidazol‐3‐ium cation, one chloride ion and one water molecule. In the extended structure, chloride anions and water molecules are linked via O—H...Cl hydrogen bonds, forming an infinite one‐dimensional chain. The chloride anions are also linked by two weak C—H...Cl interactions to neighbouring methylene groups and imidazole rings. Two imidazolium moieties form a homoconjugated cation through a strong and asymmetric O—H...O hydrogen bond of 2.472 (2) Å. The IR spectrum shows a continuous D‐type absorption in the region below 1300 cm⁻¹ and is different to that of 1‐carboxymethyl‐3‐methylimidazolium chloride [Xuan, Wang & Xue (2012). Spectrochim. Acta Part A, 96 , 436–443].     

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.     

2,8‐Di­hydroxy‐1,3,7,9‐tetra­methyl‐6,12‐di­hydro­dipyrido­[1,2‐a:1′,2′‐d]pyrazine­diyl­ium dichloride dihydrate

The 2,8‐di­hydroxy‐1,3,7,9‐tetra­methyl‐6,12‐di­hydro­di­pyrido[1,2‐a:1′,2′‐d]pyrazine­diyl­ium dication possesses 2/m symmetry and lies in the mirror plane together with a chloride anion and the water O atom. The dication also lies on an inversion centre, i.e. C₁₆H₂₀N₂O₂²⁺·2Cl^?·2H₂O. Due to these symmetry constrictions the dication adopts an unexpected planar conformation. Molecules are linked by O—H?O and O—H?Cl hydrogen bonds to form chains, which are cross‐connected by C—H?Cl attractive interactions forming a complex three‐dimensional hydrogen‐bond network.     

Hydrogen‐bonding patterns in bis[2,4,6‐triazaniumylcyclohexane‐1,3,5‐tris(olate)‐κ3O,O′,O′′]germanium(IV) tetrachloride hexahydrate

A first preliminary report on the crystal structure of a hydrated salt formulated as [Ge(taci)₂]Cl₄·13H₂O (taci is 1,3,5‐triamino‐1,3,5‐trideoxy‐cis‐inositol) appeared more than 20 years ago [Ghisletta (1994). PhD thesis, ETH Zürich. Switzerland]. At that time it was not possible to discriminate unambiguously between the positions of some of the chloride ions and water O atoms, and disorder was thus postulated. In a new determination, a conclusive scheme of hydrogen bonding proves to be a particularly appealing aspect of the structure. Single crystals of the title compound, C₁₂H₃₀GeN₆O₆⁴⁺·4Cl⁻·6H₂O or [Ge(taci)₂]₂Cl₈·12H₂O, were grown from an aqueous solution by slow evaporation of the solvent. The two [Ge(taci)₂]⁴⁺ cations exhibit a double‐adamantane‐type structure with exclusive O‐atom coordination and approximate D_3d symmetry. The taci ligands adopt a zwitterionic form with deprotonated hydroxy groups and protonated amino groups. Both cations are hydrogen bonded to six water molecules. The structure of the hydration shell of the two cations is, however, slightly different. The {[Ge(taci)₂]·6H₂O}⁴⁺ aggregates are interlinked in all three dimensions by further hydrogen bonds of the types N—H...Cl...H—N, N—H...O(H)₂...H—N, (Ge)O...H—O(H)...H—N, N—H...O(H)—H...Cl...H—N, (Ge)O...H—O—H...Cl...H—N, N—H...O(H)—H...Cl...H—(H)O...H—N, (Ge)O...H—O—H...Cl...H—(H)O...H—N and Ge(O)...H—O—H...Cl...H—O—H...O(Ge).     

Hydroxonium hydrate tris(2,4,6‐triamino‐1,3,5‐triazin‐1‐ium) bis[bis(pyridine‐2,6‐dicarboxylato)manganate(II/III)] hydroxide pyridine‐2,6‐dicarboxylic acid solvate pentahydrate

For charge balance in the title compound, (H₅O₂)(C₃H₇N₆)₃[Mn(C₇H₃NO₄)₂]₂(OH)·C₇H₅NO₄·5H₂O, it is assumed that the metal atom site is disordered Mn^II/Mn^III, probably due to partial air oxidation of the starting Mn^II species. The formula unit of the complex contains a hydroxonium hydrate cation, H₅O₂⁺, also known as the Zundel cation, with twofold symmetry. The O...O [2.445 (10) Å] and O...H distances [1.24 (2) Å] in the H₅O₂⁺ cation indicate a strong hydrogen bond. In addition, there is a hydroxide ion that is disordered with respect to a twofold rotation axis. One of the melaminium groups and the pyridine‐2,6‐dicarboxylate (pydc) ligand also reside on crystallographic twofold axes. The coordination environment of the Mn ion is distorted octahedral. Three intermolecular C=O...π interactions are observed, with distances of 3.536 (4), 3.262 (4) and 3.750 (4) Å between carboxylate C=O groups and the centroids of the aromatic rings of pydc and melaminium. There are numerous O—H...O, O—H...N, N—H...O, N—H...N and C—H...O hydrogen bonds. Most of the components of the structure are organized into one plane.     

4‐(3‐Azaniumylpropyl)morpholin‐4‐ium chloride hydrogen oxalate: an unusual example of a dication with different counter‐anions

The mixed organic–inorganic title salt, C₇H₁₈N₂O²⁺·C₂HO₄⁻·Cl⁻, forms an assembly of ionic components which are stabilized through a series of hydrogen bonds and charge‐assisted intermolecular interactions. The title assembly crystallizes in the monoclinic C2/c space group with Z = 8. The asymmetric unit consists of a 4‐(3‐azaniumylpropyl)morpholin‐4‐ium dication, a hydrogen oxalate counter‐anion and an inorganic chloride counter‐anion. The organic cations and anions are connected through a network of N—H...O, O—H...O and C—H...O hydrogen bonds, forming several intermolecular rings that can be described by the graph‐set notations R₃³(13), R₂¹(5), R₁²(5), R₂¹(6), R₂³(6), R₂²(8) and R₃³(9). The 4‐(3‐azaniumylpropyl)morpholin‐4‐ium dications are interconnected through N—H...O hydrogen bonds, forming C(9) chains that run diagonally along the ab face. Furthermore, the hydrogen oxalate anions are interconnected via O—H...O hydrogen bonds, forming head‐to‐tail C(5) chains along the crystallographic b axis. The two types of chains are linked through additional N—H...O and O—H...O hydrogen bonds, and the hydrogen oxalate chains are sandwiched by the 4‐(3‐azaniumylpropyl)morpholin‐4‐ium chains, forming organic layers that are separated by the chloride anions. Finally, the layered three‐dimensional structure is stabilized via intermolecular N—H...Cl and C—H...Cl interactions.     

Amino­pyrimidine–carboxyl­(ate) interactions in trimethoprim maleate,an antifolate drug

In the title cocrystal, trimethoprim maleate [2,4‐di­amino‐5‐(3,4,5‐tri­methoxy­benzyl)­pyrimidin‐1‐ium maleate], C₁₄H₁₉­N₄O₃⁺·­C₄H₃O₄^?, the trimethoprim mol­ecule is protonated at N1. The carboxyl group of the maleate ion makes a specific double hydrogen bond of type N—H?O with the 2‐amino group and the protonated N1 atom of the trimethoprim cation which is similar to the carboxyl­ate–trimethoprim cation interaction observed in the complex of di­hydro­folate reductase with trimethoprim. The pyrimidine moieties of trimethoprim cations are centrosymmetrically paired through a pair of N—H?N hydrogen bonds involving the 4‐amino group and the pyridinium N3 atom of a symmetry‐related molecule. One of the O atoms at the maleate carboxyl­ate group bridges the 2‐­amino and 4‐amino groups on either side of the paired trimethoprim cations. The other O atom of the carboxyl­ate group forms an intramolecular O—H?O hydrogen bond with the carboxyl group. These characteristic hydrogen bonds result in infinite two‐dimensional aggregation of rings into a supramolecular ladder, which is further crosslinked through weak C—H?O interactions with methoxy groups of neighbouring trimethoprim mol­ecules to form a layered structure.     

10‐Benzyl‐4‐oxo‐2,3,4,10‐tetrahydropyrimido[4,5‐b]quinolin‐2‐iminium chloride sesquihydrate: a polarized electronic structure within a complex hydrogen‐bonded sheet structure

In the title compound, C₁₈H₁₅N₄O⁺·Cl⁻·1.5H₂O, one water site is fully ordered with unit occupancy while the other, which lies close to an inversion centre in the space group C2/c, has only 0.5 occupancy. The cation exhibits bond fixation in the fused carbocyclic ring and electronic polarization in the terminal heterocyclic ring. The components are linked into complex sheets by a combination of N—H...O, N—H...Cl, O—H...O, O—H...Cl and C—H...O hydrogen bonds.     

Chlorido[N,N′‐dibenzyl‐N′′‐(trichloroacetyl)phosphoramidato‐κ2O,O′](1,10‐phenanthroline‐κ2N,N′)copper(II)

In the title complex, [Cu(C₁₆H₁₆Cl₃N₃O₂P)Cl(C₁₂H₈N₂)], the Cu^II cation presents a square‐pyramidal environment, where the CuO₂N₂ base is formed by two O atoms from carbonyl and phosphoryl groups, and by two N atoms from a 1,10‐phenanthroline molecule. A coordinated Cl atom occupies the apex. N—H...Cl hydrogen bonds link the molecules into one‐dimensional chains. The trichloromethyl group is rotationally disordered over two positions, with occupancies of 0.747 (7) and 0.253 (7).     

catena‐Poly[[[1‐benzoyl‐2‐(2‐hydroxyethyl)‐3‐(2‐pyridyl)guanidine]chloridocopper(II)] chloride 0.61‐hydrate]

The title copper(II) complex, {[CuCl(C₁₅H₁₆N₄O₂)]Cl·0.61H₂O}_n, is a one‐dimensional zigzag coordination polymer structure extending along the (010) direction. The Cu^II atom has a square‐pyramidal geometry, where the basal plane is formed by two cis N atoms and one O atom from the ligand, and by a Cl atom. The apical position is occupied by a carbonyl O atom from a symmetry‐related molecule. In the crystal structure, there are O—H...Cl and N—H...Cl hydrogen bonds, which link parallel polymer chains along the c direction, so building a two‐dimensional structure via the interstitial Cl atoms.     

2′‐Deoxy‐5‐propynyluridine: a nucleoside with two conformations in the asymmetric unit

The title compound, 1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐(prop‐1‐ynyl)pyrimidin‐2,4(1H,3H)‐dione, C₁₂H₁₄N₂O₅, shows two conformations in the crystalline state: conformer 1 adopts a C2′‐endo (close to ²E; S‐type) sugar pucker and an anti nucleobase orientation [χ = −134.04 (19)°], while conformer 2 shows an S sugar pucker (twisted C2′‐endo–C3′‐exo), which is accompanied by a different anti base orientation [χ = −162.79 (17)°]. Both molecules show a +sc (gauche, gauche) conformation at the exocyclic C4′—C5′ bond and a coplanar orientation of the propynyl group with respect to the pyrimidine ring. The extended structure is a three‐dimensional hydrogen‐bond network involving intermolecular N—H...O and O—H...O hydrogen bonds. Only O atoms function as H‐atom acceptor sites.     

Water‐induced pseudo‐quadruple hydrogen‐bonding motifs in xanthine–inorganic acid complexes

In xanthinium nitrate hydrate [systematic name: 2,6‐dioxo‐1,2,3,6‐tetrahydro‐9H‐purin‐7‐ium nitrate monohydrate], C₅H₅N₄O₂⁺·NO₃⁻·H₂O, (I), and xanthinium hydrogen sulfate hydrate [systematic name: 2,6‐dioxo‐1,2,3,6‐tetrahydro‐9H‐purin‐7‐ium hydrogen sulfate monohydrate], C₅H₅N₄O₂⁺·HSO₄⁻·H₂O, (II), the xanthine molecules are protonated at the imine N atom with the transfer of an H atom from the inorganic acid. The asymmetric unit of (I) contains a xanthinium cation, a nitrate anion and one water molecule, while that of (II) contains two crystallographically independent xanthinium cations, two hydrogen sulfate anions and two water molecules. A pseudo‐quadruple hydrogen‐bonding motif is formed between the xanthinium cations and the water molecules via N—H...O and O—H...O hydrogen bonds in both structures, and leads to the formation of one‐dimensional polymeric tapes. These cation–water tapes are further connected by the respective anions and aggregate into two‐dimensional hydrogen‐bonded sheets in (I) and three‐dimensional arrangements in (II).     

meso‐5,5,7,12,12,14‐Hexamethyl‐1,4‐diaza‐8,11‐diazoniacyclotetradecane bis(2‐naphthoate) ethanol disolvate: centrosymmetric five‐component aggregates linked into sheets by C—H⃛π(arene) hydrogen bonding

The title compound is an ethanol‐solvated salt, C₁₆H₃₈N₄²⁺·2C₁₁H₇O₂⁻·2C₂H₆O, in which the cation lies across a centre of inversion in P2₁/c. The ions are linked by N—H⃛O hydrogen bonds [H⃛O = 1.70 and 2.30 Å, N⃛O = 2.624 (2) and 3.136 (2) Å, and N—H⃛O = 178 and 151°], and the ethanol mol­ecule is linked to the anion by an O—H⃛O hydrogen bond [H⃛O = 1.90 Å, O⃛O = 2.728 (2) Å and O—H⃛O = 171°], to form a centrosymmetric five‐component aggregate. C—H⃛O hydrogen bonds and aromatic π–π‐stacking interactions are absent, but the aggregates are linked into sheets by a single C—H⃛π(arene) hydrogen bond.     

trans‐Bis(dimethyl sulfoxide‐κO)bis(3‐oxo‐3,4‐dihydroquinoxaline‐2‐carboxylato‐κ2N1,O2)copper(II)

The title compound, [Cu(C₉H₅N₂O₃)₂(C₂H₆OS)₂], consists of octahedrally coordinated Cu^II ions, with the 3‐oxo‐3,4‐dihydroquinoxaline‐2‐carboxylate ligands acting in a bidentate manner [Cu—O = 1.9116 (14) Å and Cu—N = 2.1191 (16) Å] and a dimethyl sulfoxide (DMSO) molecule coordinated axially via the O atom [Cu—O = 2.336 (5) and 2.418 (7) Å for the major and minor disorder components, respectively]. The whole DMSO molecule exhibits positional disorder [0.62 (1):0.38 (1)]. The octahedron around the Cu^II atom, which lies on an inversion centre, is elongated in the axial direction, exhibiting a Jahn–Teller effect. The ligand exhibits tautomerization by H‐atom transfer from the hydroxyl group at position 3 to the N atom at position 4 of the quinoxaline ring of the ligand. The complex molecules are linked through an intermolecular N—H...O hydrogen bond [N...O = 2.838 (2) Å] formed between the quinoxaline NH group and a carboxylate O atom, and by a weak intermolecular C—H...O hydrogen bond [3.392 (11) Å] formed between a carboxylate O atom and a methyl C atom of the DMSO ligand. There is a weak intramolecular C—H...O hydrogen bond [3.065 (3) Å] formed between a benzene CH group and a carboxylate O atom.     

7‐Deaza‐2′‐deoxyinosine: a nucleoside showing ambiguous base‐pairing properties against the four canonical DNA constituents

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐3,7‐dihydro‐4H‐pyrrolo[2,3‐d]pyrimidin‐4‐one], C₁₁H₁₃N₃O₄, represents an acid‐stable derivative of 2′‐deoxyinosine. It exhibits an anti glycosylic bond conformation, with a χ torsion angle of 113.30 (15)°. The furanose moiety adopts an S‐type sugar pucker ⁴T₃, with P = 221.8 (1)° and τ_m = 40.4 (1)°. The conformation at the exocyclic C4′—C5′ bond of the furanose ring is ap (trans), with γ = 167.14 (10)°. The extended structure forms a three‐dimensional hydrogen‐bond network involving O—H...O, N—H...O and C—H...O hydrogen bonds. The title compound forms an uncommon hydrogen bond between a CH group of the pyrrole system and the ring O atom of the sugar moiety of a neighbouring molecule.     

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.     

Hydrogen‐bonded supramolecular networks of N,N′‐bis(4‐pyridylmethyl)oxalamide and 4,4′‐{[oxalylbis(azanediyl)]dimethylene}dipyridinium dinitrate

The molecule of N,N′‐bis(4‐pyridylmethyl)oxalamide, C₁₄H₁₄N₄O₂, (I) or 4py‐ox, has an inversion center in the middle of the oxalamide group. Adjacent molecules are then linked through intermolecular N—H...N and C—H...O hydrogen bonds, forming an extended supramolecular network. 4,4′‐{[Oxalylbis(azanediyl)]dimethylene}dipyridinium dinitrate, C₁₄H₁₆N₄O₂²⁺·2NO₃⁻, (II), contains a diprotonated 4py‐ox cation and two nitrate counter‐anions. Each nitrate ion is hydrogen bonded to four 4py‐ox cations via intermolecular N—H...O and C—H...O interactions. Adjacent 4py‐ox cations are linked through weak C—H...O hydrogen bonding between an α‐pyridinium C atom and an oxalamide O atom, forming a two‐dimensional extended supramolecular network.     

catena‐Poly[[diaquadiisothiocyanatoiron(II)]‐μ‐4,4′‐bi‐1,2,4‐triazole]: a one‐dimensional coordination polymer

In the title complex, [Fe(NCS)₂(C₄H₂N₆)₂(H₂O)₂]_n, the Fe^II atom is on an inversion centre and the 4,4′‐bi‐1,2,4‐triazole (btr) group is bisected by a twofold axis through the central N—N bond. The coordination geometry of the Fe^II atom is elongated distorted FeN₄O₂ octahedral, where the cation is coordinated by two N atoms from the triazole rings of two btr groups, two N atoms from NCS⁻ ligands and two water molecules. Btr is a bidentate ligand, coordinating one Fe^II atom through a peripheral N atom of each triazole ring, leading to a one‐dimensional polymeric (chain) structure extending along [101]. The chains are further connected through a network of O—H...N and C—H...S hydrogen bonds.     

(E)‐4‐[(2‐Carbamoylhydrazinylidene)methyl]‐3‐hydroxy‐5‐hydroxymethyl‐2‐methylpyridin‐1‐ium nitrate

The title compound, C₉H₁₃N₄O₃⁺·NO₃⁻, is the first structurally characterized Schiff base derived from semicarbazide and pyridoxal. Unusually for an unsubstituted semicarbazone, the compound adopts a syn conformation, in which the carbonyl O atom is in a cis disposition relative to the azomethine N atom. This arrangement is supported by a pair of hydrogen bonds between the organic cation and the nitrate anion. The cation is essentially planar, with only a hydroxymethyl O atom deviating significantly from the mean plane of the remaining atoms (r.m.s. deviation of the remaining non‐H atoms = 0.01 Å). The molecules are linked into flat layers by N—H...O and C—H...O hydrogen bonds. O—H...O hydrogen bonds involving the hydroxymethyl group as a donor interconnect the layers into a three‐dimensional structure.     

Bis{tris[(1H‐benzimidazol‐3‐ium‐2‐yl)methyl]amine} tetraaquaocta‐μ2‐chlorido‐octachloridopentacadmate(II) monohydrate

The title compound, (C₂₄H₂₄N₇)₂[Cd₅Cl₁₆(H₂O)₄]·H₂O, contains a [Cd₅Cl₁₆(H₂O)₄]⁶⁻ anion, two triply protonated tris[(1H‐benzimidazol‐3‐ium‐2‐yl)methyl]amine cations and one solvent water molecule. The structure of the anion is a novel chloride‐bridged pentanuclear cluster. The five unique Cd^II centres have quite different coordination environments. Two of the central hexacoordinated Cd^II cations have a CdOCl₅ chromophore, in which each Cd^II cation is ligated by four bridging chloride ligands, one terminal chloride ligand and one water molecule, adopting a distorted octahedral environment. The third central Cd^II cation is octahedrally coordinated by four bridging chloride ligands and two water molecules. Finally, the two terminal Cd^II cations are pentacoordinated by two bridging and three terminal chloride ligands and adopt a trigonal–bipyramidal geometry. A three‐dimensional supramolecular network is formed through intra‐ and intermolecular O—H...O, O—H...Cl, N—H...Cl and N—H...O hydrogen bonds and π–π interactions between the cations and anions.<!?tpb=20.6pt>