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. C73, 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 hydrogen-bonding patterns in 1:1 cocrystals of 5-fluorouracil with 4-methylbenzoic acid and 3-nitrobenzoic acid.

The design of a pharmaceutical cocrystal is based on the identification of specific hydrogen-bond donor and acceptor groups in active pharmaceutical ingredients (APIs) in order to choose a `complementary interacting' molecule that can act as an efficient coformer. 5-Fluorouracil (5FU) is a pyrimidine derivative with two N-H donors and C=O acceptors and shows a diversity of hydrogen-bonding motifs. Two 1:1 cocrystals of 5-fluorouracil (5FU), namely 5-fluorouracil-4-methylbenzoic acid (5FU-MBA), C4H3FN2O2·C8H8O2, (I), and 5-fluorouracil-3-nitrobenzoic acid (5FU-NBA), C4H3FN2O2·C7H5NO4, (II), have been prepared and characterized by single-crystal X-ray diffraction. In (I), the MBA molecules form carboxylic acid dimers [R22(8) homosynthon]. Similarly, the 5FU molecules form two types of base pair via a pair of N-H...O hydrogen bonds [R22(8) homosynthon]. In (II), 5FU interacts with the carboxylic acid group of NBA via N-H...O and O-H...O hydrogen bonds, generating an R22(8) ring motif (heterosynthon). Furthermore, the 5FU molecules form base pairs [R22(8) homosynthon] via N-H...O hydrogen bonds. Both of the crystal structures are stabilized by C-H...F interactions.

Hydrogen-bonding patterns in 5-fluoro-cytosine-melamine co-crystal (4/1).

The asymmetric unit of the title compound, 4C4H4FN3O·C3H6N6, comprises of two independent 5-fluoro-cytosine (5FC) mol-ecules (A and B) and one half-mol-ecule of melamine (M). The other half of the melamine mol-ecule is generated by a twofold axis. 5FC mol-ecules A and B are linked through two different homosynthons [R 2 (2)(8) ring motif]; one is formed via a pair of N-H⋯O hydrogen bonds and the second via a pair of N-H⋯N hydrogen bonds. In addition to this pairing, the O atoms of 5FC mol-ecules A and B inter-act with the N2 amino group on both sides of the melamine mol-ecule, forming a DDAA array of quadruple hydrogen bonds and generating a supra-molecular pattern. The 5FC (mol-ecules A and B) and two melamine mol-ecules inter-act via N-H⋯O, N-H⋯N and N-H⋯O, N-H⋯N, C-H⋯F hydrogen bonds forming R 6 (6)(24) and R 4 (4)(15) ring motifs. The crystal structure is further strengthened by C-H⋯F, C-F⋯π and π-π stacking inter-actions.

Crystal structure of 3-acet-oxy-2-methyl-benzoic acid.

In the title mol-ecule, C10H10O4, the carb-oxy-lic acid group is twisted by 11.37 (15)° from the plane of the benzene ring and the acet-oxy group is twisted from this plane by 86.60 (17)°. In the crystal, mol-ecules are linked by pairs of O-H⋯O hydrogen bonds, forming inversion dimers with the expected R 2 (2)(8) graph-set motif.

Crystal structure of 4-[(5-methyl-isoxazol-3-yl)amino-sulfon-yl]anilinium 3,5-di-nitro-salicylate.

The title mol-ecular salt, C10H12N3O3S(+)·C7H3N2O7 (-), protonation occurs at the amino N atom attached to the benzene ring of sulfamethoxazole. In the anion, there is an intra-molecular O-H⋯O hydrogen bond and the cation is linked to the anion by an N-H⋯O hydrogen bond. In the extended structure, the cations and anions are linked via N-H⋯O, N-H⋯N and C-H⋯O hydrogen bonds, forming a three-dimensional framework.

Hydrogen bonding patterns in salts of derivatives of aminopyrimidine and thiobarbituric acid.

Three salts, namely 2-amino-4,6-dimethylpyrimidin-1-ium thiobarbiturate trihydrate (I), 2-amino-4,6-dimethoxypyrimidin-1-ium thiobarbiturate dihydrate (II) and 2,4-diamino-5-(3',4',5'-trimethoxybenzyl)pyrimidin-1-ium thiobarbiturate (III), were synthesized and characterized by IR and X-ray diffraction techniques. The primary interaction between the acid and base happens via N-H...O hydrogen bonds in (II) and (III), and via water-mediated N-H...OW and OW-HW...S in (I). The water molecules present in compound (I) form a (H2O)12 water cluster via water-water interactions. In all three compounds (I)-(III), thiobarbiturate anions form self-complementary pairs with a robust R2(2)(8) motif via a pair of N-H...O/N-H...S hydrogen bonds. They mimic the nucleobase base pairs by utilizing the same groups (thymine/uracil uses N3-H and C4=O8 groups during the formation of Watson-Crick and Hoogsteen base pairs with adenine). Compound (I) forms a water-mediated base pair through N-H...OW hydrogen bonds and forms an R4(2)(12) motif. The formation of N-H...S hydrogen bonds, water-mediated base pairs and water-water interactions in these crystal systems offers scope for these systems to be considered as a model in the study of hydration of nucleobases and water-mediated nucleobase base pairs in macromolecules.

Crystal structure of 2-{[(2-chloro-phen-yl)imino]-meth-yl}phenol.

In the title compound, C13H10ClNO, the dihedral angle between the planes of the aromatic rings is 51.42 (9)° and an intra-molecular O-H⋯N hydrogen bond closes an S(6) ring. The Cl atom and the N atom are syn. No directional inter-actions beyond van der Waals contacts are observed in the crystal.

Crystal structure of N'-hy-droxy-pyrimidine-2-carboximidamide.

The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)° between the planes of the pyrimidine ring and the non-H atoms of the carboximidamide unit. The mol-ecule adopts an E configuration about the C=N double bond. In the crystal, adjacent mol-ecules are linked by pairs of N-H⋯O hydrogen bonds, forming inversion dimers with an R 2 (2)(10) ring motif. The dimers are further linked via N-H⋯N and O-H⋯N hydrogen bonds into a sheet structure parallel to the ac plane. The crystal structure also features N-H⋯O and weak C-H⋯O hydrogen bonds and offset π-π stacking inter-actions between adjacent pyrimidine rings [centroid-centroid distance = 3.622 (1) Å].

Design of co-crystals/salts of some Nitrogenous bases and some derivatives of thiophene carboxylic acids through a combination of hydrogen and halogen bonds.

BACKGROUND: The utility of N-heterocyclic bases to obtain molecular complexes with carboxylic acids is well studied. Depending on the solid state interaction between the N-heterocyclic base and a carboxylic acid a variety of neutral or ionic synthons are observed. Meanwhile, pyridines and pyrimidines have been frequently chosen in the area of crystal engineering for their multipurpose functionality. HT (hetero trimers) and LHT (linear heterotetramers) are the well known synthons that are formed in the presence of pyrimidines and carboxylic acids. RESULTS: Fourteen crystals involving various substituted thiophene carboxylic acid derivatives and nitrogenous bases were prepared and characterized by using single crystal X-ray diffraction. The 14 crystals can further be divided into two groups [1a-7a], [8b-14b] based on the nature of the nitrogenous base. Carboxylic acid to pyridine proton transfer has occurred in 3 compounds of each group. In addition to the commonly occurring hydrogen bond based pyridine/carboxylic acid and pyrimidine/carboxylic acid synthons which is the reason for assembly of primary motifs, various other interactions like Cl…Cl, Cl…O, C-H…Cl, C-H…S add additional support in organizing these supermolecules into extended architectures. It is also interesting to note that in all the compounds π-π stacking occurs between the pyrimidine-pyrimidine or pyridine-pyridine or acid-acid moieties rather than acid-pyrimidine/pyridine. CONCLUSIONS: In all the compounds (1a-14b) either neutral O-H…Npyridyl/pyrimidine or charge-assisted Npyridinium-H…Ocarboxylate hydrogen bonds are present. The HT (hetero trimers) and LHT (linear heterotetramers) are dominant in the crystal structures of the adducts containing N-heterocyclic bases with two proton acceptors (1a-7a). Similar type supramolecular ladders are observed in 5TPC44BIPY (8b), TPC44BIPY (9b), TPC44TMBP (11b). Among the seven compounds [8b-14b] the extended ligands are linear in all except for the TMBP (10b, 11b, 12b). The structure of each compound depends on the dihedral angle between the carboxyl group and the nitrogenous base. All these compounds indicate three main synthons that regularly occur, namely linear heterodimer (HD), heterotrimer (HT) and heterotetramer (LHT).

Supramolecular architecture of metal-organic frameworks involving dinuclear copper paddle-wheel complexes.

The two centrosymmetric dinuclear copper paddle-wheel complexes tetrakis(µ-4-hydroxybenzoato-κ(2)O:O')bis[aquacopper(II)] dimethylformamide disolvate dihydrate, [Cu2(C7H5O3)4(H2O)2]·2C3H7NO·2H2O, (I), and tetrakis(µ-4-methoxybenzoato-κ(2)O:O')bis[(dimethylformamide-κO)copper(II)], [Cu2(C8H7O3)4(C3H7NO)2], (II), crystallize with half of the dinuclear paddle-wheel cage unit in the asymmetric unit and, in addition, complex (I) has one dimethylformamide (DMF) and one water solvent molecule in the asymmetric unit. In both (I) and (II), two Cu(II) ions are bridged by four syn,syn-η(1):η(1):µ carboxylate groups, showing a paddle-wheel cage-type structure with a square-pyramidal coordination geometry. The equatorial positions of (I) and (II) are occupied by the carboxylate groups of 4-hydroxy- and 4-methoxybenzoate ligands, and the axial positions are occupied by aqua and DMF ligands, respectively. The three-dimensional supramolecular metal-organic framework of (I) consists of three different R2(2)(20) and an R4(4)(36) ring motif formed via O-H···O and OW-HW···O hydrogen bonds. Complex (II) simply packs as molecular species.

Tetraammine(carbonato-κ(2) O,O')cobalt(III) perchlorate.

In the title complex, [Co(CO3)(NH3)4]ClO4, both the cation and anion lie on a mirror plane. The Co(III) ion is coordinated by two NH3 ligands and a chelating carbonato ligand in the equatorial sites and by two NH3 groups in the axial sites, forming a distorted octa-hedral geometry. In the crystal, N-H⋯O hydrogen bonds connect the anions and cations, forming a three-dimensional network.

2-Amino-4,6-di-methyl-pyrimidine-sorbic acid (1/1).

In the crystal of the title compound, C6H9N3·C6H8O2, the 2-amino-4,6-di-methyl-pyrimidine and sorbic acid mol-ecules are linked through N-H⋯O and O-H⋯N hydrogen bonds, which generate a cyclic bimolecular heterosynthon with an R 2 (2)(8) graph-set motif. Further, two inversion-related pyrimidine mol-ecules are base-paired via a pair of N-H⋯N hydrogen bonds, forming a cyclic bimolecular homosynthon with a graph-set of R 2 (2)(8). A discrete hetero tetra-meric supra-molecular unit along the b axis is formed by the fusion of two heterosynthons and one homosynthon. An aromatic π-π inter-action [centroid-centroid distance = 3.7945 (16) Å] is observed between these tetra-meric units.

Synthesis, characterization and X-ray structural studies of four copper (II) complexes containing dinuclear paddle wheel structures.

BACKGROUND: Various dinuclear copper (II) complexes with octahedral geometry have been reported. The majority of these complexes contain N containing aromatic rings as axial ligands. There are also a few cases where the solvent used in the reaction occupies the axial position of the dinuclear copper (II) complex. This may occur by planned synthesis or some times by serendipity. Here we report some four copper (II) complexes containing solvent and or N containing heterocyclic ring as the axial ligand. RESULTS: Four compounds, each containing dinuclear Copper (II) units (with the most robust, frequently occurring paddle wheel structures) were synthesized and characterised by single crystal X-ray diffraction and by IR spectroscopy. The compounds 1 & 2 have the general formula Cu2(RCOO) 4(L)2 [(for (1) RCOO= 4-Chloro Benzoate, L= Isopropanol; for 2 RCOO= Benzoate, L= 2-Amino-4,6-dimethyl pyrimidine )] while 3 & 4 have the general formula, Cu2(RCOO) 4(S)2 Cu2(RCOO) 4(L)2 [RCOO=5-Chloro-thiophene-2-carboxylate L= 2-Amino-4,6-dimethyl pyrimidine, for 3 S= ethanol; for 4 S= methanol ]. A wide range of hydrogen bonds (of the O-H…O, N-H…O and N-H…N type) and π-π stacking interactions are present in the crystal structures. CONCLUSIONS: All compounds contain the dinuclear units, in which two Cu (II) ions are bridged by four syn, syn-η1:η1:µ carboxylates, showing a paddle-wheel cage type with a distorted octahedral geometry. The compounds 1 &2 contain a single dimeric unit while 3 &4 contain two dimeric units. The structures 3 and 4 are very interesting co-crystals of two paddle wheel molecules. Also it is interesting to note that the compounds 3 &4 are isostructural with similar cell parameters. Both the compounds 3 &4 differ in the solvent molecule coordinated to copper in one of the dimeric units. In all the four compounds, each of the copper dimers has an inversion centre. Every copper has a distorted octahedral centre, formed by four oxygen atoms (from different carboxylate) in the equatorial sites. The two axial positions are occupied by copper and the corresponding ligand.

2-Amino-4,6-dimethyl-pyrimidin-1-ium 2,3,5-triiodo-benzoate 2,3,5-triiodo-benzoic acid monosolvate.

In the crystal structure of the title compound, C(6)H(10)N(3) (+)·C(7)H(2)I(3)O(2) (-)·C(7)H(3)I(3)O(2), two R(2) (2)(8) motifs are observed. One is generated by the inter-action of the 2-amino-4,6-dimethyl-pyrimidin-1-ium cation with the carboxyl-ate group of the 2,3,5-triiodo-benzoate anion via N-H⋯O hydrogen bonds. The other R(2) (2)(8) motif is formed by the inter-action of two centrosymmentrically related pyrimidine moieties through N-H⋯N hydrogen bonds. The two motifs combine to form a linear heterotetra-meric unit. Heterotetra-meric units are linked by a carbox-yl-carboxyl-ate O-H⋯O hydrogen bond (involving the O-H group of neutral 2,3,5-triiodo-benzoic acid and an O atom of the anion), forming a supra-molecular chain along the a axis. In addition, components are held by weak I⋯O interactions in the range 3.023 (5) to 3.382 (5) Šand I⋯I inter-actions in the range 3.6327 (7) to 4.0025 (8) Å.

2,4-Diamino-6-methyl-1,3,5-triazin-1-ium tetra-fluoro-borate.

In the crystal structure of the title salt, C(4)H(8)N(5) (+)·BF(4) (-), centrosymmetrically related cations undergo base pairing via a pair of N-H⋯N hydrogen bonds, forming an R(2) (2)(8) ring motif. The cations and anions inter-act via N-H⋯F hydrogen bonds, generating supra-molecular layers parallel to ([Formula: see text]20), which are in turn linked into a three-dimensional network, forming rings of R(6) (6)(24) graph-set motif. The crystal structure is further stabilized by π-π stacking inter-actions [centroid-centroid distance = 3.3361 (12) Å].

2-Amino-4,6-dimeth-oxy-pyrimidin-1-ium p-toluene-sulfonate.

In the title salt, C(6)H(10)N(3)O(2) (+)·C(7)H(7)O(3)S(-), the 2-amino-4,6-dimeth-oxy-pyrimidinium cation inter-acts with the sulfonate group of the p-toluene-sulfonate anion via a pair of N-H⋯O hydrogen bonds, forming a cyclic hydrogen-bonded R(2) (2)(8) motif, which in the crystal is linked by further intemolecular N-H⋯O hydrogen bonds, forming supra-molecular chains along the c axis. Furthermore, neighboring chains are inter-linked via weak C-H⋯O hydrogen bonds and C-H⋯π inter-actions, forming layers.

2,6,6-Trimethyl-cyclo-hexene-1-carbaldehyde oxime.

In the crystal of the title compound C(10)H(17)NO, synthesized by the reaction of ß-cyclo-citral with hydroxyl-amine hydro-chloride, inversion-related mol-ecules are linked by a pair of O-H⋯N hydrogen-bonding inter-actions between the oxime functionalities, forming R(2) (2)(6) loops. The molecular conformation is stabilized by intra-molecular methyl C-H⋯N inter-actions. The cyclohexene ring has the typical half-chair conformation.

2-Meth-oxy-anilinium 3-hy-droxy-2,4,6-trinitro-phenolate.

The cation and anion of the title mol-ecular salt, C(7)H(10)NO(+)·C(6)H(2)N(3)O(8) (-), are linked via an N-H⋯O hydrogen bond. An intra-molecular O-H⋯O hydrogen bond is also found in the anion. In the crystal, the anions self-assemble via O-H⋯O hydrogen bonds, forming a C(9) supra-molecular chain the b axis. Further inter-molecular N-H⋯O inter-actions also occur.

Supramolecular architectures of two novel organic-inorganic hybrid materials containing identical monomeric uranyl units.

Two isostructural uranyl complexes have been crystallized with different bipyridyl cations to yield the compounds hemi(4,4'-bipyridinium) tris(5-chlorothiophene-2-carboxylato)dioxidouranate(VI) monohydrate, (C(10)H(10)N(2))(0.5)[U(C(5)H(2)ClO(2)S)(3)O(2)]·H(2)O, (I), and hemi[4,4'-(ethane-1,2-diyl)dipyridinium] tris(5-chlorothiophene-2-carboxylato)dioxidouranate(VI) monohydrate, (C(12)H(14)N(2))(0.5)[U(C(5)H(2)ClO(2)S)(3)O(2)]·H(2)O, (II). In the [UO(2)X(3)](-) complexes (X is 5-chlorothiophene-2-carboxylate), the uranyl O atoms occupy the two axial positions and the equatorial positions are occupied by six O atoms of the three X ions so that each U atom is eight coordinated in a puckered hexagonal-bipyramidal structure. In both compounds, the metal centres are linked by classical O-H...O and N-H...O hydrogen bonds involving the coordinated ligands, the diprotonated organic linker cation (which rests on a centre of inversion at the mid-point of the central C-C bond) and water molecules. The crystal structures are further stabilized by weak C-H...O and π-π stacking interactions, forming similar three-dimensional supramolecular architectures, forming a two-dimensional network parallel to the (100) plane in (I) and a three-dimensional network in (II).

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, C(4)H(8)N(5)(+) x C(8)H(5)O(4)(-), (I), acetoguanaminium hydrogen maleate, C(4)H(8)N(5)(+) x C(4)H(3)O(4)(-), (II), and acetoguanaminium 3-hydroxypicolinate monohydrate, C(4)H(8)N(5)(+) x C(6)H(4)NO(3)(-) x H(2)O, (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 R(2)(2)(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 R(3)(2)(8), R(2)(2)(8) and R(3)(2)(8) hydrogen-bonded rings plus fused R(2)(2)(8), R(6)(2)(12) and R(2)(2)(8) ring motifs occur alternately, aggregating into a supramolecular ladder-like arrangement. In (III), R(2)(2)(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.