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Journal: Acta crystallographica. Section C, Structural chemistry

24

A path to new synthons for application in crystal engineering is the replacement of a strong hydrogen-bond acceptor, like a C=O group, with a weaker acceptor, like a C=S group, in doubly or triply hydrogen-bonded synthons. For instance, if the C=O group at the 2-position of barbituric acid is changed into a C=S group, 2-thiobarbituric acid is obtained. Each of the compounds comprises two ADA hydrogen-bonding sites (D = donor and A = acceptor). We report the results of cocrystallization experiments of barbituric acid and 2-thiobarbituric acid, respectively, with 2,4-diaminopyrimidine, which contains a complementary DAD hydrogen-bonding site and is therefore capable of forming an ADA/DAD synthon with barbituric acid and 2-thiobarbituric acid. In addition, pure 2,4-diaminopyrimidine was crystallized in order to study its preferred hydrogen-bonding motifs. The experiments yielded one ansolvate of 2,4-diaminopyrimidine (pyrimidine-2,4-diamine, DAPY), C4H6N4, (I), three solvates of DAPY, namely 2,4-diaminopyrimidine-1,4-dioxane (2/1), 2C4H6N4·C4H8O2, (II), 2,4-diaminopyrimidine-N,N-dimethylacetamide (1/1), C4H6N4·C4H9NO, (III), and 2,4-diaminopyrimidine-1-methylpyrrolidin-2-one (1/1), C4H6N4·C5H9NO, (IV), one salt of barbituric acid, viz. 2,4-diaminopyrimidinium barbiturate (barbiturate is 2,4,6-trioxopyrimidin-5-ide), C4H7N4(+)·C4H3N2O3(-), (V), and two solvated salts of 2-thiobarbituric acid, viz. 2,4-diaminopyrimidinium 2-thiobarbiturate-N,N-dimethylformamide (½) (2-thiobarbiturate is 4,6-dioxo-2-sulfanylidenepyrimidin-5-ide), C4H7N4(+)·C4H3N2O2S(-)·2C3H7NO, (VI), and 2,4-diaminopyrimidinium 2-thiobarbiturate-N,N-dimethylacetamide (½), C4H7N4(+)·C4H3N2O2S(-)·2C4H9NO, (VII). The ADA/DAD synthon was succesfully formed in the salt of barbituric acid, i.e. (V), as well as in the salts of 2-thiobarbituric acid, i.e. (VI) and (VII). In the crystal structures of 2,4-diaminopyrimidine, i.e. (I)-(IV), R2(2)(8) N-H…N hydrogen-bond motifs are preferred and, in two structures, additional R3(2)(8) patterns were observed.

Concepts: Crystal, Ethanol, Barbiturate, Barbituric acid

24

A study of post-refinement absolute structure determination using previously published data was carried out using the CRYSTALS software package. We show that absolute structure determination may be carried out optimally using the analyses available in CRYSTALS, and that it is not necessary to have the separate procedures absolute structure determination and no interest in absolute structure as proposed by Flack [Chimia (2014), 68, 26-30].

Concepts: Scientific method, Chemistry, Sociology, Interior algebra

21

A novel phosphate, sodium zinc aluminium bis(phosphate), NaZnAl(PO4)2, was obtained under mild-temperature hydrothermal conditions at 553 K. The crystal structure has been studied using single-crystal X-ray experimental data. The pseudo-hexagonal phase NaZnAl(PO4)2 crystallizes in the monoclinic space group P21/c. Its unique crystal structure is based on a three-dimensional (3D) framework built by Zn-, Al- and P-centred tetrahedra sharing vertices. Channels parallel to the [101] and [-101] directions are limited by six- and eight-membered windows, and incorporate Na atoms. The new compound is discussed as a member of the morphotropic series AMM'PO4, where A = Na, K, Rb or NH4, M = Cu, Ni, Co, Fe, Zn or Mg and M' = Fe, Al or Ga. The title compound is the first Na representative within the series and is characterized by a 3D architecture of tetrahedra populated in an ordered manner by Zn2+, Al3+ and P5+ ions.

21

A cocrystal and a molecular salt of β-alanine and DL-tartaric acid, C3H8NO2+·C4H4O6-, of the same chemical composition, were studied over a wide temperature range by single-crystal and powder X-ray diffraction. Neither the interconversion between the two phases nor any polymorphic transitions were observed in the temperature range from 100 K to the melting points. This contrasts with the solvent-mediated phase transition from the salt to the cocrystal in a slurry that has been documented earlier.

0

The use of supramolecular synthons as a strategy to control crystalline structure is a crucial factor in developing new solid forms with physicochemical properties optimized by design. However, to achieve this objective, it is necessary to understand the intermolecular interactions in the context of crystal packing. The feasibility of a given synthon depends on its flexibility to combine the drug with a variety of coformers. In the present work, the imidazole-hydroxy synthon is investigated using as the target molecule benzoylmetronidazole [BZMD; systematic name 2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl benzoate], whose imidazole group seems to be a suitable acceptor for hydrogen bonds. Thus, coformers with carboxylic acid and phenol groups were chosen. According to the availability of binding sites presented in the coformer, and considering the proposed synthon and hydrogen-bond complementarity as major factors, different drug-coformer stoichiometric ratios were explored (1:1, 2:1 and 3:1). Thirteen new solid forms (two salts and eleven cocrystals) were produced, namely BZMD-benzoic acid (1/1), C13H13N3O4·C7H6O2, BZMD-β-naphthol (1/1), C13H13N3O4·C10H8O, BZMD-4-methoxybenzoic acid (1/1), C13H13N3O4·C8H8O3, BZMD-3,5-dinitrobenzoic acid (1/1), C13H13N3O4·C7H4N2O6, BZMD-3-aminobenzoic acid (1/1), C13H13N3O4·C7H7NO2, BZMD-salicylic acid (1/1), C13H13N3O4·C7H6O3, BZMD-maleic acid (1/1) {as the salt 1-[2-(benzoyloxy)ethyl]-2-methyl-5-nitro-1H-imidazol-3-ium 3-carboxyprop-2-enoate}, C13H14N3O4+·C4H3O4-, BZMD-isophthalic acid (1/1), C13H13N3O4·C8H6O4, BZMD-resorcinol (2/1), 2C13H13N3O4·C6H6O2, BZMD-fumaric acid (2/1), C13H13N3O4·0.5C4H4O4, BZMD-malonic acid (2/1), 2C13H13N3O4·C3H2O4, BZMD-2,6-dihydroxybenzoic acid (1/1) {as the salt 1-[2-(benzoyloxy)ethyl]-2-methyl-5-nitro-1H-imidazol-3-ium 2,6-dihydroxybenzoate}, C13H14N3O4+·C7H5O4-, and BZMD-3,5-dihydroxybenzoic acid (3/1), 3C13H13N3O4·C7H6O4, and their crystalline structures elucidated, confirming the robustness of the selected synthon.

0

Two one-dimensional (1D) coordination polymers (CPs), namely catena-poly[[[aqua(2,2'-bipyridine-κ2N,N')(nitrato-κO)copper(II)]-μ-1,3-bis(pyridin-4-yl)propane-κ2N:N'] nitrate], {[Cu(NO3)(C10H8N2)(C13H14N2)(H2O)]·NO3}n (1), and catena-poly[[[aqua(nitrato-κO)(1,10-phenanthroline-κ2N,N')copper(II)]-μ-1,3-bis(pyridin-4-yl)propane-κ2N:N'] nitrate], {[Cu(NO3)(C12H8N2)(C13H14N2)(H2O)]·NO3}n (2), have been synthesized using [Cu(NO3)(NN)(H2O)2]NO3, where NN = 2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen), as a linker in a 1:1 molar ratio. The CPs were characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis and single-crystal X-ray structure determination. The 1,3-bis(pyridin-4-yl)propane (dpp) ligand acts as a bridging ligand, leading to the formation of a 1D polymer. The octahedral coordination sphere around copper consists of two N atoms from bpy for 1 or phen for 2, two N atoms from dpp, one O atom from water and one O atom from a coordinated nitrate anion. Each structure contains two crystallographically independent chains in the asymmetric unit and the chains are linked via hydrogen bonds into a three-dimensional network.

0

Excellent fluorescence properties are exhibited by d10 metal compounds. The novel three-dimensional ZnII coordination framework, poly[[{μ2-bis[4-(2-methyl-1H-imidazol-1-yl)phenyl] ether-κ2N3:N3'}(μ2-furan-2,5-dicarboxylato-κ2O2:O5)zinc(II)] 1.76-hydrate], {[Zn(C6H2O5)(C20H18N4O)]·1.76H2O}n, has been prepared and characterized using IR spectroscopy, elemental analysis and single-crystal X-ray diffraction. The crystal structure analysis revealed that the compound exhibits a novel fourfold interpenetrating diamond-like network. This polymer also displays a strong fluorescence emission in the solid state at room temperature.

0

The title coordination polymer, poly[bis[μ3-4-(3,2':6',3'‘-terpyridin-4’-yl)benzoato]cadmium(II)], [Cd(C22H14N3O2)2]n or [Cd(3-cptpy)2]n, (I), has been synthesized solvothermally and characterized by IR spectroscopy, thermogravimetric analysis, and single-crystal and powder X-ray diffraction. The structure is composed of 3-cptpy- ligands bridging Cd atoms, with each Cd atom coordinated by six ligands and each ligand coordinating to three Cd atoms. Each Cd atom is in a slightly distorted trans-N2O4 octahedral environment, forming a two-dimensional layer structure with a (3,6)-connected topology. Layers are linked to each other by π-π stacking, resulting in a three-dimensional supramolecular framework. The strong luminescence and good thermal stability of (I) indicate that it can potentially be used as a luminescence sensor. The compound also shows a highly selective and sensitive response to 2,4,6-trinitrophenol through the luminescence quenching effect.

0

The self-assembly of ditopic bis(1H-imidazol-1-yl)benzene ligands (LH) and the complex (2,2'-bipyridyl-κ2N,N')bis(nitrato-κO)palladium(II) affords the supramolecular coordination complex tris[μ-bis(1H-imidazol-1-yl)benzene-κ2N3:N3']-triangulo-tris[(2,2'-bipyridyl-κ2N,N')palladium(II)] hexakis(hexafluoridophosphate) acetonitrile heptasolvate, [Pd3(C10H8N2)3(C12H10N4)3](PF6)6·7CH3CN, 2. The structure of 2 was characterized in acetonitrile-d3 by 1H/13C NMR spectroscopy and a DOSY experiment. The trimeric nature of supramolecular coordination complex 2 in solution was ascertained by cold spray ionization mass spectrometry (CSI-MS) and confirmed in the solid state by X-ray structure analysis. The asymmetric unit of 2 comprises the trimetallic Pd complex, six PF6- counter-ions and seven acetonitrile solvent molecules. Moreover, there is one cavity within the unit cell which could contain diethyl ether solvent molecules, as suggested by the crystallization process. The packing is stabilized by weak inter- and intramolecular C-H…N and C-H…F interactions. Interestingly, the crystal structure displays two distinct conformations for the LH ligand (i.e. syn and anti), with an all-syn-[Pd] coordination mode. This result is in contrast to the solution behaviour, where multiple structures with syn/anti-LH and syn/anti-[Pd] are a priori possible and expected to be in rapid equilibrium.

0

Three asymmetric diosmium(I) carbonyl sawhorse complexes have been prepared by microwave heating. One of these complexes is of the type Os2(μ-O2CR)(μ-O2CR')(CO)4L2, with two different bridging carboxylate ligands, while the other two complexes are of the type Os2(μ-O2CR)2(CO)5L, with one axial CO ligand and one axial phosphane ligand. The mixed carboxylate complex Os2(μ-acetate)(μ-propionate)(CO)4[P(p-tolyl)3]2, (1), was prepared by heating Os3(CO)12 with a mixture of acetic and propionic acids, isolating Os2(μ-acetate)(μ-propionate)(CO)6, and then replacing two CO ligands with two phosphane ligands. This is the first example of an Os2 sawhorse complex with two different carboxylate bridges. The syntheses of Os2(μ-acetate)2(CO)5[P(p-tolyl)3], (3), and Os2(μ-propionate)2(CO)5[P(p-tolyl)3], (6), involved the reaction of Os3(CO)12 with the appropriate carboxylic acid to initially produce Os2(μ-carboxylate)2(CO)6, followed by treatment with refluxing tetrahydrofuran (THF) to form Os2(μ-carboxylate)2(CO)5(THF), and finally addition of tri-p-tolylphosphane to replace the THF ligand with the P(p-tolyl)3 ligand. Neutral complexes of the type Os2(μ-O2CR)2(CO)5L had not previously been subjected to X-ray crystallographic analysis. The more symmetrical disubstituted complexes, i.e. Os2(μ-formate)2(CO)4[P(p-tolyl)3]2, (8), Os2(μ-acetate)2(CO)4[P(p-tolyl)3]2, (4), and Os2(μ-propionate)2(CO)4[P(p-tolyl)3]2, (7), as well as the previously reported symmetrical unsubstituted complexes Os2(μ-acetate)2(CO)6, (2), and Os2(μ-propionate)2(CO)6, (5), were also prepared in order to examine the influence of axial ligand substitution on the Os-Os bond distance in these sawhorse molecules. Eight crystal structures have been determined and studied, namely μ-acetato-1κO:2κO'-μ-propanoato-1κO:2κO'-bis[tris(4-methylphenyl)phosphane]-1κP,2κP'-bis(dicarbonylosmium)(Os-Os) dichloromethane monosolvate, [Os2(C2H3O2)(C3H5O2)(C21H21P)2(CO)4]·CH2Cl2, (1), bis(μ-acetato-1κO:2κO')bis(tricarbonylosmium)(Os-Os), [Os2(C2H3O2)2(CO)6], (2) (redetermined structure), bis(μ-acetato-1κO:2κO')pentacarbonyl-1κ2C,2κ3C-[tris(4-methylphenyl)phosphane-1κP]diosmium(Os-Os), [Os2(C2H3O2)2(C21H21P)(CO)5], (3), bis(μ-acetato-1κO:2κO')bis[tris(4-methylphenyl)phosphane]-1κP,2κP-bis(dicarbonylosmium)(Os-Os) p-xylene sesquisolvate, [Os2(C2H3O2)2(C21H21P)2(CO)4]·1.5C8H10, (4), bis(μ-propanoato-1κO:2κO')bis(tricarbonylosmium)(Os-Os), [Os2(C3H5O2)2(CO)6], (5), pentacarbonyl-1κ2C,2κ3C-bis(μ-propanoato-1κO:2κO')[tris(4-methylphenyl)phosphane-1κP]diosmium(Os-Os), [Os2(C3H5O2)2(C21H21P)(CO)5], (6), bis(μ-propanoato-1κO:2κO')bis[tris(4-methylphenyl)phosphane]-1κP,2κP-bis(dicarbonylosmium)(Os-Os) dichloromethane monosolvate, [Os2(C3H5O2)2(C21H21P)2(CO)4]·CH2Cl2, (7), and bis(μ-formato-1κO:2κO')bis[tris(4-methylphenyl)phosphane]-1κP,2κP-bis(dicarbonylosmium)(Os-Os), [Os2(CHO2)2(C21H21P)2(CO)4], (8).