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Crystal structures of three N-(pyridine-2-carbon-yl)pyridine-2-carboxamides as potential ligands for supra-molecular chemistry.

ABSTRACT: The synthesis and single-crystal X-ray structures of three N-(pyridine-2-carbon-yl)pyridine-2-carboxamide imides, with or without F atoms on the 3-position of the pyridine rings are reported, namely, N-(pyridine-2-carbon-yl)pyridine-2-carboxamide, C₁₂H₉N₃O₂ (1), N-(3-fluoro-pyridine-2-carbon-yl)pyridine-2-carboxamide, C₁₂H₈FN₃O₂ (2), and 3-fluoro-N-(3-fluoro-pyridine-2-carbon-yl)pyridine-2-carboxamide, C₁₂H₇F₂N₃O₂ (3). The above-mentioned compounds were synthesized by a mild, general procedure with an excellent yield, providing straightforward access to symmetrical and/or asymmetrical heterocyclic ureas. The crystal structures of 1 and 2 are isomorphous, showing similar packing arrangements, i.e. double layers of parallel (face-to-face) mol-ecules alternating with analogous, but perpendicularly oriented, double layers. In contrast, the crystal structure of 3, containing a fluoro- group at the 3-position of both pyridine rings, shows mol-ecular arrangements in a longitudinal, tubular manner along the c axis, with the aromatic pyridine and carbon-yl/fluorine moieties facing towards each other.

SUBMITTER: Xu X

PROVIDER: S-EPMC8423013 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Crystal structures of three <i>N</i>-(3-acetyl-phen-yl)quinoline-2-carboxamides.

Project description:In the title compounds, N-(5-acetyl-2-methyl-phen-yl)quinoline-2-carboxamide [C19H16N2O2, (I)], N-(5-acetyl-2-bromo-phen-yl)quinoline-2-carboxamide [C18H13BrN2O2, (II)] and N-(5-acetyl-2-ethynylphen-yl)quinoline-2-carboxamide [C20H14N2O2, (III)], the quinoline ring system is essentially planar and forms a dihedral angles of 3.68 (5) (I), 5.59 (7) (II) and 1.87 (6)° (III) with the acetyl-substituted ring. The mol-ecular structures of (I) and (III) each feature an intra-molecular N-H⋯N hydrogen bond, forming an S(5) ring, while in (II) an intra-molecular bifurcated N-H⋯(N,Br) hydrogen bond forms two S(5) rings. In the crystals, weak C-H⋯O hydrogen bonds link mol-ecules of (I) into C(7) chains long [010], mol-ecules of (II) into chains of R22(8) rings along [110] and mol-ecules of (III) into C(8) chains along [010]. In (I), there are no significant π-π stacking inter-actions under 4 Å, but in both (II) and (III), π-π inter-actions link the weak hydrogen-bonded chains into layers parallel to (001) [centroid-centroid disttances of 3.748 (1) Å in (II) and 3.577 (1), 3.784 (1) and 3.780 (1) Å in (III)].

| S-EPMC5458296 | biostudies-literature

The crystal structures of three pyrazine-2,5-dicarb-oxamides: three-dimensional supra-molecular structures.

Project description:The complete mol-ecules of the title compounds, N2,N5-bis-(pyridin-2-ylmeth-yl)pyrazine-2,5-dicarboxamide, C18H16N6O2 (I), 3,6-dimethyl-N2,N5-bis-(pyridin-2-yl-meth-yl)pyrazine-2,5-dicarboxamide, C20H20N6O2 (II), and N2,N5-bis-(pyridin-4-ylmeth-yl)pyrazine-2,5-dicarboxamide, C18H16N6O2 (III), are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each mol-ecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7)° in (I), 75.83 (8)° in (II) and by 82.71 (6)° in (III). In the crystal of (I), mol-ecules are linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (II), mol-ecules are also linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the (10-1) plane. As in (I), the layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (III), mol-ecules are again linked by N-H⋯N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π-π inter-actions [inter-centroid distance = 3.739 (1) Å]. The sheets are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. Compound (I) crystallizes in the monoclinic space group P21/c. Another monoclinic polymorph, space group C2/c, has been reported on by Cockriel et al. [Inorg. Chem. Commun. (2008), 11, 1-4]. The mol-ecular structures of the two polymorphs are compared.

| S-EPMC5418794 | biostudies-literature

Extracting Crystal Chemistry from Amorphous Carbon Structures.

Project description:Carbon allotropes have been explored intensively by ab?initio crystal structure prediction, but such methods are limited by the large computational cost of the underlying density functional theory (DFT). Here we show that a novel class of machine-learning-based interatomic potentials can be used for random structure searching and readily predicts several hitherto unknown carbon allotropes. Remarkably, our model draws structural information from liquid and amorphous carbon exclusively, and so does not have any prior knowledge of crystalline phases: it therefore demonstrates true transferability, which is a crucial prerequisite for applications in chemistry. The method is orders of magnitude faster than DFT and can, in principle, be coupled with any algorithm for structure prediction. Machine-learning models therefore seem promising to enable large-scale structure searches in the future.

| S-EPMC5413819 | biostudies-other

The crystal structures of four N-(4-halophen-yl)-4-oxo-4H-chromene-3-carboxamides.

Project description:Four N-(4-halophen-yl)-4-oxo-4H-chromene-3-carboxamides (halo = F, Cl, Br and I), N-(4-fluoro-phen-yl)-4-oxo-4H-chromene-3-carboxamide, C16H10FNO3, N-(4-chloro-phen-yl)-4-oxo-4H-chromene-3-carboxamide, C16H10ClNO3, N-(4-bromo-phen-yl)-4-oxo-4H-chromene-3-carboxamide, C16H10BrNO3, N-(4-iodo-phen-yl)-4-oxo-4H-chromene-3-carboxamide, C16H10INO3, have been structurally characterized. The mol-ecules are essentially planar and each exhibits an anti conformation with respect to the C-N rotamer of the amide and a cis geometry with respect to the relative positions of the Carom-Carom bond of the chromone ring and the carbonyl group of the amide. The structures each exhibit an intra-molecular hydrogen-bonding network comprising an N-H⋯O hydrogen bond between the amide N atom and the O atom of the carbonyl group of the pyrone ring, forming an S(6) ring, and a weak Carom-H⋯O inter-action with the O atom of the carbonyl group of the amide as acceptor, which forms another S(6) ring. All four compounds have the same supra-molecular structure, consisting of R 2 (2)(13) rings that are propagated along the a-axis direction by unit translation. There is π-π stacking involving inversion-related mol-ecules in each structure.

| S-EPMC4331845 | biostudies-literature

Crystal structures of three platinacyclic complexes bearing isopropyl eugenoxyacetate and pyridine derivatives.

Project description:Three new platinum(II) complexes bearing a eugenol and a pyridine derivative, namely (η2-2-allyl-4-meth-oxy-5-{[(propan-2-yl-oxy)carbon-yl]meth-oxy}phenyl-κC 1)chlorido-(pyridine-κN)platinum(II), [Pt(C15H19O4)Cl(C5H5N)], (I), (η2-2-allyl-4-meth-oxy-5-{[(propan-2-yl-oxy)carbon-yl]meth-oxy}phenyl-κC 1)chlorido-(4-methyl-pyridine-κN)platinum(II), [Pt(C15H19O4)Cl(C6H7N)], (II), and (η2-2-allyl-4-meth-oxy-5-{[(propan-2-yl-oxy)carbon-yl]meth-oxy}phenyl-κC 1)chlorido(pyridine-4-carb-oxy-lic acid-κN)platinum(II), [Pt(C15H19O4)Cl(C6H5NO2)], (III), have been synthesized and further characterized by single-crystal X-ray diffraction. The PtII atoms exhibit the usual distorted square-planar coordination and are surrounded by one Cl atom, one N atom, and a C atom and C=C double bond of the eugenol ligand. The donor N atom of the pyridine ligand occupies a cis position with respect to the double bond. Complexes (I) and (II) crystallize isomorphously in space group P and display a similar crystal packing characterized by C-H⋯O hydrogen bonding, C-H⋯π and π-π inter-actions. However, the presence of the additional methyl group in the 4-methyl-pyridine ligand in (II) disturbs the π-π inter-actions. The crystal packing of (III) is characterized by O-H⋯O hydrogen bonding, resulting in the formation of chains of mol-ecules connected in a head-to-tail fashion and running in the [101] direction. The IC50 values for the HepG2 and KB cell lines are 150.9, 122.3 µM for (I) and 138.9, 93.2 µM for (II), respectively.

| S-EPMC7336793 | biostudies-literature

The crystal structures of three clozapinium salts: different mol-ecular configurations, and supra-molecular assembly in one, two and three dimensions.

Project description:The structures of three salts derived from clozapine, 8-chloro-11-(4-methyl-piperazin-1-yl)-5H-dibenzo[b,e][1,4]diazepine, are reported, namely, clo-za-pin-ium 3,5-di-nitro-benzoate dimethyl sulfoxide monosolvate, C18H20ClN4 (+)·C7H3N2O6 (-)·C2H6OS, (I), where the dimethyl sulfoxide component is disordered over two sets of atomic sites having occupancies 0.627 (2) and 0.373 (2); clo-za-pin-ium hydrogen maleate 0.21-hydrate, C18H20ClN4 (+)·C4H3O4 (-)·0.21H2O, (II), and clozapinium 2-hy-droxy-benzoate, C18H20ClN4 (+)·C7H5O3 (-), (III). In all three salts, the protonation site is the methyl-ated N atom of the piperazine ring, and the dimensions and conformations of the fused tricyclic system are very similar. However, differences are apparent in the piperazine component: in both compounds (II) and (III), the unprotonated N atom of this ring has a pyramidal geometry, but in compound (I) this atom has a planar geometry. In compound (III), both N-substituents in this ring occupy equatorial sites, but in compound (II) the fused tricyclic system occupies an axial site of the piperazine ring. The independent components of compound (I) are linked within the selected asymmetric unit by a combination of N-H⋯O and C-H⋯O hydrogen bonds, and these hydrogen-bonded aggregates are linked into chains by an aromatic π-π stacking inter-action. In compound (II), the components are linked into sheets by a combination of O-H⋯O, N-H⋯O and C-H⋯O hydrogen bonds, and in compound (III), a combination of N-H⋯O, C-H⋯O and C-H⋯N hydrogen bonds links the components into a three-dimensional framework structure. Comparisons are made with some similar compounds.

| S-EPMC4438793 | biostudies-literature

Crystal structures of three N-ar-yl-2,2,2-tri-bromo-acetamides.

Project description:Three N-ar-yl-2,2,2-tri-bromo-acetamides, namely, 2,2,2-tri-bromo-N-(2-fluoro-phen-yl)-acetamide, C8H5Br3FNO, (I), 2,2,2-tri-bromo-N-[3-(tri-fluoro-methyl)-phen-yl]-acetamide, C9H5Br3F3NO, (II) and 2,2,2-tri-bromo-N-(4-fluoro-phen-yl)-acetamide, C8H5Br3FNO, (III) were synthesized and their crystal structures were analysed. In the crystal structure of (I), C-Br⋯πar-yl inter-actions connect the mol-ecules into dimers, which in turn are connected via Br⋯Br contacts [3.6519 (12) Å], leading to the formation of a one-dimensional ladder-type architecture. The crystal structure of (II) features chains linked by N-H⋯O and C-H⋯O hydrogen bonds. Two such chains are inter-linked to form ribbons through Br⋯Br [3.6589 (1) Å] and Br⋯F [3.0290 (1) Å] inter-actions. C-Br⋯πar-yl and C-F⋯πar-yl inter-actions between the ribbons extend the supra-molecular architecture of (II) from one dimension to two. In (III), the mol-ecules are connected into R 2 (2)(8) dimers via pairs of C-H⋯F inter-actions and these dimers form ribbons through Br⋯Br [3.5253 (1) Å] contacts. The ribbons are further inter-linked into columns via C-Br⋯O=C contacts, forming a two-dimensional architecture.

| S-EPMC4555380 | biostudies-literature

Crystal structures of three N-(aryl-sulfon-yl)-4-fluoro-benzamides.

Project description:The crystal structures of three N-aryl-sulfonyl-4-fluoro-benzamides, namely 4-fluoro-N-(2-methyl-phenyl-sulfon-yl)benzamide, C14H12FNO3S, (I), N-(2-chloro-phenyl-sulfon-yl)-4-fluorobenzamide, C13H9ClFNO3S, (II), and N-(4-chloro-phenyl-sulfon-yl)-4-fluoro-benzamide monohydrate, C13H9ClFNO3S·H2O, (III), are described and compared with related structures. The asymmetric unit of (I) contains two independent mol-ecules (A and B), while that of (II) contains just one mol-ecule, and that of (III) contains a mol-ecule of water in addition to one main mol-ecule. The dihedral angle between the benzene rings is 82.83 (11)° in mol-ecule A and 85.01 (10)° in mol-ecule B of (I), compared to 89.91 (10)° in (II) and 81.82 (11)° in (III). The crystal structure of (I) features strong N-H⋯O hydrogen bonds between the A and B mol-ecules, resulting in an R 4 (4)(16) tetra-meric unit. These tetra-meric units are connected into sheets in the bc plane by various C-H⋯O inter-actions, and adjacent sheets are further inter-linked via C-H⋯πar-yl inter-actions, forming a three-dimensional architecture. The crystal structure is further stabilized by πar-yl-πar-yl and S=O⋯πar-yl inter-actions. In the crystal of (II), mol-ecules are connected into R 2 (2)(8) and R 2 (2)(14) dimers via N-H⋯O hydrogen bonds and C-H⋯O inter-actions, respectively; the dimers are further inter-connected via a weak C=O⋯πar-yl inter-action, leading to the formation of chains along [1-10]. In the crystal of (III), N-H⋯O and O-H⋯O hydrogen bonds involving both the main mol-ecule and the solvent water mol-ecule results in the formation of sheets parallel to the bc plane. The sheets are further connected by C-H⋯O inter-actions and weak C-Cl⋯πar-yl, C-F⋯πar-yl and S=O⋯πar-yl inter-actions, forming a three-dimensional architecture.

| S-EPMC4910346 | biostudies-literature

Two coordination modes of Cu(II) in a binuclear complex with N-(pyridin-2-yl-carbon-yl)pyridine-2-carboxamidate ligands.

Project description:In the title dinuclear complex, (acetonitrile-1?N)[?-N-(pyri-din-2-ylcarbonyl)pyridine-2-carboxamidato-1:2?(5)N,N',N'':O,O'][N-(pyridin-2-ylcarbonyl)pyridine-2-carboxamidato-2?(3)N,N',N'']bis(trifluoromethanesulfonato-1?O)dicopper(II), [Cu(2)(C(12)H(8)N(3)O(2))(2)(CF(3)O(3)S)(2)(CH(3)CN)], one of the Cu(II) ions is five-coordinated in a distorted square-pyramidal N(3)O(2) environment provided by two N-(pyridin-2-ylcarbon-yl)pyridine-2-carboxamidate (bpca) ligands, while the second Cu(II) ion is six-coordinated in a distorted octa-hedral N(4)O(2) environment provided by one bpca ligand, two trifluoro-methansulfonate ligands and one acetonitrile mol-ecule. Weak inter-molecular C-H?O and C-H?F hydrogen bonds and ?-? stacking inter-actions with centroid-centroid distances of 3.6799?(15) and 3.8520?(16)?Å stabilize the crystal packing and lead to a three-dimensional network.

| S-EPMC3470158 | biostudies-literature

Crystal structure of 4-(anthracen-9-yl)pyridine.

Project description:The title compound, C19H13N, which crystallizes in the monoclinic C2/c space group with one half-mol-ecule in the asymmetric unit, was synthesized by Suzuki-Miyaura cross-coupling reaction of 9-bromo-anthracene with pyridin-4-ylboronic acid and purified by column chromatography on silica gel. Light-yellow crystals of 4-(anthracen-9-yl)-pyridine suitable for X-ray diffraction were collected by the solvent evaporation method. In the crystal, pairs of mol-ecules are connected by inter-molecular C-H⋯π (pyridine) inter-actions [d(H7⋯Cg) = 2.7391 (2) Å], forming cyclic centrosymmetric dimers, further resulting in an infinite one-dimensional linear chain along the c-axis direction. Weak face-to-face π-π stacking inter-actions [d(Cg⋯Cg) = 3.6061 (2) Å] link neighboring lamellar networks into the supra-molecular structure.

| S-EPMC8183450 | biostudies-literature

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