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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 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.

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The important role of pyrazine (pz) and its derivatives in fields such as biochemistry and pharmacology, as well as in the study of magnetic properties, is surveyed. Recognition of these properties without extensive investigations into their structural properties is not possible. This review summarizes interactions that exist between these organic compounds by themselves in the solid state, as well as those in coordination polymers with metal ions and in polyoxometalate-based hybrids. Complexes based on pyrazine ligands can generate metal-organic framework (MOF) structures that bind polyoxometalates (POMs) through covalent and noncovalent interactions. Some biological and magnetic properties involving these compounds are considered and the effect of hydrogen bonding on their supramolecular architectures is highlighted.

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A new electroneutral half-sandwich tantalum(V) dichlorido complex containing pentamethylcyclopentadienyl (Cp*) and the double-deprotonated version of the Schiff base 2-ethoxy-6-{(E)-[(2-hydroxyphenyl)imino]methyl}phenol (H2L) as ligands, namely cis-dichlorido(2-ethoxy-6-{(E)-[(2-oxidophenyl)imino]methyl}phenolato-κ3O,N,O')(η5-pentamethylcyclopentadienyl)tantalum(V), [Ta(C10H15)(C15H13NO3)Cl2] or [Ta(η5-Cp*)(L)Cl2], has been prepared and thoroughly characterized by elemental analysis, IR and NMR spectroscopy, mass spectrometry, density functional theory (DFT) calculations and single-crystal X-ray diffraction. The molecular structure revealed that the TaV centre is coordinated by a η5-Cp* ligand, two monodentate chlorido ligands and one O,N,O'-tridentate L2- ligand. The crystal structure is stabilized by C-H…C, C-H…Cl and C…C intermolecular interactions. Moreover, the complex shows notable in vitro cytotoxicity against the A2780 human ovarian carcinoma cell line, with IC50 = 14.4 µM, which is higher than that of the conventional platinum-based anticancer drug cisplatin (IC50 = 20.1 µM).

0

Pyrazole (pz)-derived ligands can, besides exhibiting a strong coordination ability toward different metal ions, exhibit a great diversity in their coordination geometry and nuclearity, which can be achieved by varying the type and position of the pz substituents. The present study reports the synthesis and crystal structure of two binuclear complexes, namely bis(μ-4-nitro-1H-imidazol-1-ide-5-carboxylato)-κ3N1,O:N2;κ3N2:N1,O-bis[aqua(dimethylformamide-κO)copper(II)], [Cu2(C4HN3O4)2(C3H7NO)2(H2O)2], (II), and bis(μ-4-nitro-1H-imidazol-1-ide-5-carboxylato)-κ2N1,O:N2;κ2N2:N1,O-bis[triaquacobalt(II)] dihydrate, [Co2(C4HN3O4)2(H2O)6]·2H2O, (III). These compounds represent rare examples of metal complexes comprising 3,4-substituted pz derivatives as a bridging ligand and also the first crystal structures of transition-metal complexes with ligands derived from 4-nitropyrazole-3-carboxylic acid. Recently, the crystal structures of the same ligand in the neutral and mixed neutral/anionic forms have been reported. We present here the third form of this ligand, where it is present in a fully deprotonated anionic form within a salt, i.e. ammonium 4-nitropyrazole-3-carboxylate, NH4+·C4H2N3O4-, (I). Single-crystal X-ray diffraction revealed that in the present complexes, the CuII and CoII centres adopt distorted square-pyramidal and octahedral geometries, respectively. In both cases, the N,N',O-coordinated pz ligand shows simultaneously chelating and bridging coordination modes, leading to the formation of a nearly planar six-membered M2N4 metallocycle. In all three crystal structures, the supramolecular arrangement is controlled by strong hydrogen bonds which primarily engage the carboxylate O atoms as acceptors, while the nitro group adopts the role of an acceptor only in structures with an increased number of donors, as is the case with CoII complex (III). The electrostatic potential, as a descriptor of reactivity, was also calculated in order to examine the changes in ligand electrostatic preferences upon coordination to metal ions.

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Calix[4]arene and oxacalix[4]arene derivatives have eight possible conformations in the up and down directions of their four aromatic rings from the mean plane of a bridged central ring, the conformations of which determine the functionality of the host frameworks. Despite being a known compound for five decades, oxacalix[4]arene, C24H16O4, has not been characterized previously by crystallographic methods. It crystallizes from hexane/CH2Cl2 solution to give two polymorphs, i.e. prismatic and block-shaped crystals as twisted 1,3-alternate structures with S4 and C2 symmetry, respectively. These were previously suggested as the prefered stable conformations by density functional theory (DFT) calculations.

0

The molecular structure of the anti-aging agent J147 [systematic name: (E)-N-(2,4-dimethylphenyl)-2,2,2-trifluoro-N'-(3-methoxybenzylidene)acetohydrazide], C18H17F3N2O2, has been determined at 150 K. The crystal structure corresponds to the minimum-energy conformation in the gas phase calculated by density functional theory (DFT). 15 other conformations have been calculated and compared with the minimum, denoted 1111. NMR spectroscopic data have been obtained and compared with those from Gauge Independent Atomic Orbital (GIAO) calculations. DFT calculations allow the reduction of the 16 possible rotamers to the four most stable (i.e. 1111, 1112, 1121 and 1222); in addition, the calculated barriers connecting these minima are low enough to permit their interconversion. Comparison of the NMR spectroscopic results, both experimental and calculated, point to the 1121 isomer being present in chloroform solution.

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The assembly of metal-organic frameworks (MOFs) with metal ions and organic ligands is currently attracting considerable attention in crystal engineering and materials science due to their intriguing architectures and potential applications. A new three-dimensional MOF, namely poly[[diaqua(μ8-para-terphenyl-3,3',5,5'-tetracarboxylato)dizinc(II)] dimethylformamide disolvate monohydrate], {[Zn2(C22H10O8)(H2O)2]·2C3H7NO·H2O}n, was synthesized by the self-assembly of Zn(NO3)2·6H2O and para-terphenyl-3,3',5,5'-tetracarboxylic acid (H4TPTC) under solvothermal conditions. The compound was structurally characterized by FT-IR spectroscopy, elemental analysis and single-crystal X-ray diffraction analysis. Each ZnII ion is located in a square-pyramidal geometry and is coordinated by four carboxylate O atoms from four different TPTC4- ligands. Pairs of adjacent equivalent ZnII ions are bridged by four carboxylate groups, forming [Zn2(O2CR)4] (R = terphenyl) paddle-wheel units. One aqua ligand binds to each ZnII centre along the paddle-wheel axis. Each [Zn2(O2CR)4] paddle wheel is further linked to four terphenyl connectors to give a three-dimensional framework with NBO-type topology. The thermal stability and solid-state photoluminescence properties of the title compound have also been investigated.

0

The crystal structures of seven α-aryl-α-hydroxyphosphonates synthesized by the Pudovik reaction of substituted benzaldehydes and dialkyl phosphites, namely dimethyl [(hydroxy)(phenyl)methyl]phosphonate, C9H13O4P, dimethyl [(3,4-dimethoxyphenyl)(hydroxy)methyl]phosphonate, C11H17O6P, dimethyl (1-hydroxy-1-phenylethyl)phosphonate, C10H15O4P, dimethyl [1-hydroxy-1-(4-nitrophenyl)ethyl]phosphonate, C10H14NO6P, dibenzyl [hydroxy(2-nitrophenyl)methyl]phosphonate, C21H20NO6P, dibenzyl [(3-chlorophenyl)(hydroxy)methyl]phosphonate, C21H20ClO4P, and dibenzyl [hydroxy(4-methylphenyl)methyl]phosphonate, C22H23O4P, were studied to gain a better understanding of the organization in this type of molecule in the solid state. The crystals obtained for this series of compounds show a balance between C-OH…O=P chain-linked packing and the dimeric types of hydrogen-bond bridges of intermolecular pairs of such functions. The description is based on primary graph-set descriptors. Using graph-set descriptors one level deeper (i.e. secondary graph sets of the C-H…O type) revealed a similarity in the graph-set descriptors, suggesting a fine interplay of substituent- and shape-dependent effects on strong-weak interactions. It seems that the formation of chains or dimers is governed not only by the presence of a tertiary Cα atom, but also by the nature and crowding of the ortho substituents of the α-aryl group.