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A 2:1 co-crystal of p-nitro-benzoic acid and N,N'-bis-(pyridin-3-ylmeth-yl)ethanedi-amide: crystal structure and Hirshfeld surface analysis.

ABSTRACT: The title 2:1 co-crystal, 2C7H5NO4·C14H14N4O2, in which the complete di-amide mol-ecule is generated by crystallographic inversion symmetry, features a three-mol-ecule aggregate sustained by hydroxyl-O-H?N(pyrid-yl) hydrogen bonds. The p-nitro-benzoic acid mol-ecule is non-planar, exhibiting twists of both the carb-oxy-lic acid and nitro groups, which form dihedral angles of 10.16?(9) and 4.24?(4)°, respectively, with the benzene ring. The di-amide mol-ecule has a conformation approximating to a Z shape, with the pyridyl rings lying to either side of the central, almost planar di-amide residue (r.m.s. deviation of the eight atoms being 0.025?Å), and forming dihedral angles of 77.22?(6)° with it. In the crystal, three-mol-ecule aggregates are linked into a linear supra-molecular ladder sustained by amide-N-H?O(nitro) hydrogen bonds and orientated along [10-4]. The ladders are connected into a double layer via pyridyl- and benzene-C-H?O(amide) inter-actions, which, in turn, are connected into a three-dimensional architecture via ?-? stacking inter-actions between pyridyl and benzene rings [inter-centroid distance = 3.6947?(8)?Å]. An evaluation of the Hirshfeld surfaces confirm the importance of inter-molecular inter-actions involving oxygen atoms as well as the ?-? inter-actions.

SUBMITTER: Syed S

PROVIDER: S-EPMC4704746 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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N,N'-Bis(pyridin-3-ylmeth-yl)ethanedi-amide monohydrate: crystal structure, Hirshfeld surface analysis and computational study.

Project description:The mol-ecular structure of the title bis-pyridyl substituted di-amide hydrate, C14H14N4O2·H2O, features a central C2N2O2 residue (r.m.s. deviation = 0.0205 Å) linked at each end to 3-pyridyl rings through methyl-ene groups. The pyridyl rings lie to the same side of the plane, i.e. have a syn-periplanar relationship, and form dihedral angles of 59.71 (6) and 68.42 (6)° with the central plane. An almost orthogonal relationship between the pyridyl rings is indicated by the dihedral angle between them [87.86 (5)°]. Owing to an anti disposition between the carbonyl-O atoms in the core, two intra-molecular amide-N-H⋯O(carbon-yl) hydrogen bonds are formed, each closing an S(5) loop. Supra-molecular tapes are formed in the crystal via amide-N-H⋯O(carbon-yl) hydrogen bonds and ten-membered {⋯HNC2O}2 synthons. Two symmetry-related tapes are linked by a helical chain of hydrogen-bonded water mol-ecules via water-O-H⋯N(pyrid-yl) hydrogen bonds. The resulting aggregate is parallel to the b-axis direction. Links between these, via methyl-ene-C-H⋯O(water) and methyl-ene-C-H⋯π(pyrid-yl) inter-actions, give rise to a layer parallel to (10); the layers stack without directional inter-actions between them. The analysis of the Hirshfeld surfaces point to the importance of the specified hydrogen-bonding inter-actions, and to the significant influence of the water mol-ecule of crystallization upon the mol-ecular packing. The analysis also indicates the contribution of methyl-ene-C-H⋯O(carbon-yl) and pyridyl-C-H⋯C(carbon-yl) contacts to the stability of the inter-layer region. The calculated inter-action energies are consistent with importance of significant electrostatic attractions in the crystal.

| S-EPMC6944093 | biostudies-literature

A 2:1 co-crystal of 2-methyl-benzoic acid and N,N'-bis-(pyridin-4-ylmeth-yl)ethanedi-amide: crystal structure and Hirshfeld surface analysis.

Project description:The asymmetric unit of the title 2:1 co-crystal, 2C8H8O2·C14H14N4O2, comprises an acid mol-ecule in a general position and half a di-amide mol-ecule, the latter being located about a centre of inversion. In the acid, the carb-oxy-lic acid group is twisted out of the plane of the benzene ring to which it is attached [dihedral angle = 28.51 (8)°] and the carbonyl O atom and methyl group lie approximately to the same side of the mol-ecule [hy-droxy-O-C-C-C(H) torsion angle = -27.92 (17)°]. In the di-amide, the central C4N2O2 core is almost planar (r.m.s. deviation = 0.031 Å), and the pyridyl rings are perpendicular, lying to either side of the central plane [central residue/pyridyl dihedral angle = 88.60 (5)°]. In the mol-ecular packing, three-mol-ecule aggregates are formed via hy-droxy-O-H⋯N(pyrid-yl) hydrogen bonds. These are connected into a supra-molecular layer parallel to (12[Formula: see text]) via amide-N-H⋯O(carbon-yl) hydrogen bonds, as well as methyl-ene-C-H⋯O(amide) inter-actions. Significant π-π inter-actions occur between benzene/benzene, pyrid-yl/benzene and pyrid-yl/pyridyl rings within and between layers to consolidate the three-dimensional packing.

| S-EPMC4778829 | biostudies-literature

The 1:2 co-crystal formed between N,N'-bis(pyridin-4-ylmeth-yl)ethanedi-amide and benzoic acid: crystal structure, Hirshfeld surface analysis and computational study.

Project description:The crystal and mol-ecular structures of the title 1:2 co-crystal, C14H14N4O2·2C7H6O2, are described. The oxalamide mol-ecule has a (+)-anti-periplanar conformation with the 4-pyridyl residues lying to either side of the central, almost planar C2N2O2 chromophore (r.m.s. deviation = 0.0555 Å). The benzoic acid mol-ecules have equivalent, close to planar conformations [C6/CO2 dihedral angle = 6.33 (14) and 3.43 (10)°]. The formation of hy-droxy-O-H⋯N(pyrid-yl) hydrogen bonds between the benzoic acid mol-ecules and the pyridyl residues of the di-amide leads to a three-mol-ecule aggregate. Centrosymmetrically related aggregates assemble into a six-mol-ecule aggregate via amide-N-H⋯O(amide) hydrogen bonds through a 10-membered {⋯HNC2O}2 synthon. These are linked into a supra-molecular tape via amide-N-H⋯O(carbon-yl) hydrogen bonds and 22-membered {⋯HOCO⋯NC4NH}2 synthons. The contacts between tapes to consolidate the three-dimensional architecture are of the type methyl-ene-C-H⋯O(amide) and pyridyl-C-H⋯O(carbon-yl). These inter-actions are largely electrostatic in nature. Additional non-covalent contacts are identified from an analysis of the calculated Hirshfeld surfaces.

| S-EPMC6944079 | biostudies-literature

Crystal structure, Hirshfeld surface analysis and computational study of the 1:2 co-crystal formed between N,N'-bis-[(pyridin-4-yl)meth-yl]ethanedi-amide and 3-chloro-benzoic acid.

Project description:The asymmetric unit of the title 1:2 co-crystal, C14H14N4O2·2C7H5ClO2, comprises a half-mol-ecule of oxalamide (4 LH2), being located about a centre of inversion, and a mol-ecule of3-chloro-benzoic acid (3-ClBA) in a general position. From symmetry, the 4 LH2 mol-ecule has a (+)anti-periplanar conformation with the 4-pyridyl residues lying to either side of the central, planar C2N2O2 chromophore with the dihedral angle between the core and pyridyl ring being 74.69?(11)°; intra-molecular amide-N-H?O(amide) hydrogen bonds are noted. The 3-ClBA mol-ecule exhibits a small twist as seen in the C6/CO2 dihedral angle of 8.731?(12)°. In the mol-ecular packing, three-mol-ecule aggregates are formed via carb-oxy-lic acid-O-H?N(pyrid-yl) hydrogen bonding. These are connected into a supra-molecular tape along [111] through amide-N-H?O(carbon-yl) hydrogen bonding. Additional points of contact between mol-ecules include pyridyl and benzoic acid-C-H?O(amide), methyl-ene-C-H?O(carbon-yl) and C-Cl??(pyrid-yl) inter-actions so a three-dimensional architecture results. The contributions to the calculated Hirshfeld surface are dominated by H?H (28.5%), H?O/O?H (23.2%), H?C/C?H (23.3%), H?Cl/Cl?H (10.0%) and C?Cl/C?Cl (6.2%) contacts. Computational chemistry confirms the C-Cl?? inter-action is weak, and the importance of both electrostatic and dispersion terms in sustaining the mol-ecular packing despite the strong electrostatic term provided by the carb-oxy-lic acid-O-H?N(pyrid-yl) hydrogen bonds.

| S-EPMC7274012 | biostudies-literature

The co-crystal N,N'-bis-[(pyridin-1-ium-2-yl)meth-yl]ethane-dithio-amide bis-(2,6-di-nitro-benzoate)-2,6-di-nitro-benzoic acid (1/4).

Project description:The asymmetric unit of title co-crystal, C14H16N4S2 (2+)·2C7H3N2O6 (-)·4C7H4N2O6, comprises a centrosymmetric dipyridinium dication, a 2,6-di-nitro-benzoate anion and two independent 2,6-di-nitro-benzoic acid mol-ecules. The pyridin-ium rings are each approximately perpendicular to the central di-thio-amide unit [dihedral angle = 80.67?(12)°]. The carboxyl-ate/carb-oxy-lic acid groups are approximately perpendicular to the benzene ring to which they are attached [dihedral angles = 78.85?(16), 81.46?(19) and 71.28?(15)°]. By contrast, the major twist exhibited by a nitro group is manifested in a dihedral angle of 32.66?(17)°. The most prominent feature of the crystal packing is linear supra-molecular chains along [1-10], featuring O-H?O(carboxyl-ate) and pyridinium-N-H?O hydrogen bonds. These are consolidated into a three-dimensional architecture by thio-amide-nitro N-H?O, C-H?O and ?-? [inter-centroid distance = 3.524?(2)?Å] inter-actions. One of the nitro O atoms was refined over two sites; the major site was 0.65?(7) occupied.

| S-EPMC3790379 | biostudies-literature

Crystal structures of {?2-N,N'-bis-[(pyridin-3-yl)meth-yl]ethanedi-amide}tetra-kis-(di-methyl-carbamodi-thio-ato)dizinc(II) di-methyl-formamide disolvate and {?2-N,N'-bis-[(pyridin-3-yl)meth-yl]ethanedi-amide}tetra-kis-(di-n-propyl-carbamodi-thio-ato)dizinc(II).

Project description:The title structures, [Zn2(C3H6NS2)4(C14H14N4O2)]·2C3H7NO (I) and [Zn2(C7H14NS2)4(C14H14N4O2)] (II), each feature a bidentate, bridging bipyridyl-type ligand encompassing a di-amide group. In (I), the binuclear compound is disposed about a centre of inversion, leading to an open conformation, while in (II), the complete mol-ecule is completed by the application of a twofold axis of symmetry so that the bridging ligand has a U-shape. In each of (I) and (II), the di-thio-carbamate ligands are chelating with varying degrees of symmetry, so the zinc atom is within an NS4 set approximating a square-pyramid for (I) and a trigonal-bipyramid for (II). The solvent di-methyl-formaide (DMF) mol-ecules in (I) connect to the bridging ligand via amide-N-H?O(DMF) and various amide-, DMF-C-H?O(amide, DMF) inter-actions. The resultant three-mol-ecule aggregates assemble into a three-dimensional architecture via C-H??(pyridyl, chelate ring) inter-actions. In (II), undulating tapes sustained by amide-N-H?O(amide) hydrogen bonding lead to linear supra-molecular chains with alternating mol-ecules lying to either side of the tape; no further directional inter-actions are noted in the crystal.

| S-EPMC5730304 | biostudies-literature

Crystal structure, Hirshfeld surface analysis and computational study of the 1:2 co-crystal formed between N,N'-bis-(pyridin-4-ylmeth-yl)ethane-diamide and 4-chloro-benzoic acid.

Project description:The asymmetric unit of the title 1:2 co-crystal, C14H14N4O2·2C7H5ClO2, comprises two half mol-ecules of oxalamide (4 LH2), as each is disposed about a centre of inversion, and two mol-ecules of 4-chloro-benzoic acid (CBA), each in general positions. Each 4 LH2 mol-ecule has a (+)anti-periplanar conformation with the pyridin-4-yl residues lying to either side of the central, planar C2N2O2 chromophore with the dihedral angles between the respective central core and the pyridyl rings being 68.65 (3) and 86.25 (3)°, respectively, representing the major difference between the independent 4 LH2 mol-ecules. The anti conformation of the carbonyl groups enables the formation of intra-molecular amide-N-H⋯O(amide) hydrogen bonds, each completing an S(5) loop. The two independent CBA mol-ecules are similar and exhibit C6/CO2 dihedral angles of 8.06 (10) and 17.24 (8)°, indicating twisted conformations. In the crystal, two independent, three-mol-ecule aggregates are formed via carb-oxy-lic acid-O-H⋯N(pyrid-yl) hydrogen bonding. These are connected into a supra-molecular tape propagating parallel to [100] through amide-N-H⋯O(amide) hydrogen bonding between the independent aggregates and ten-membered {⋯HNC2O}2 synthons. The tapes assemble into a three-dimensional architecture through pyridyl- and methyl-ene-C-H⋯O(carbon-yl) and CBA-C-H⋯O(amide) inter-actions. As revealed by a more detailed analysis of the mol-ecular packing by calculating the Hirshfeld surfaces and computational chemistry, are the presence of attractive and dispersive Cl⋯C=O inter-actions which provide inter-action energies approximately one-quarter of those provided by the amide-N-H⋯O(amide) hydrogen bonding sustaining the supra-molecular tape.

| S-EPMC7001830 | biostudies-literature

2-({[(Pyridin-1-ium-2-ylmeth-yl)carbamo-yl]form-amido}-meth-yl)pyridin-1-ium bis-(3,5-di-carb-oxy-benzoate): crystal structure and Hirshfeld surface analysis.

Project description:The asymmetric unit of the title salt, C14H16N4O2 (2+)·2C9H5O6 (-), comprises half a dication, being located about a centre of inversion, and one anion, in a general position. The central C4N2O2 group of atoms in the dication are almost planar (r.m.s. deviation = 0.009 Å), and the carbonyl groups lie in an anti disposition to enable the formation of intra-molecular amide-N-H⋯O(carbon-yl) hydrogen bonds. To a first approximation, the pyridinium and amide N atoms lie to the same side of the mol-ecule [Npy-C-C-Namide torsion angle = 34.8 (2)°], and the anti pyridinium rings are approximately perpendicular to the central part of the mol-ecule [dihedral angle = 68.21 (8)°]. In the anion, one carboxyl-ate group is almost coplanar with the ring to which it is connected [Cben-Cben-Cq-O torsion angle = 2.0 (3)°], whereas the other carboxyl-ate and carb-oxy-lic acid groups are twisted out of the plane [torsion angles = 16.4 (3) and 15.3 (3)°, respectively]. In the crystal, anions assemble into layers parallel to (10-4) via hy-droxy-O-H⋯O(carbon-yl) and charge-assisted hy-droxy-O-H⋯O(carboxyl-ate) hydrogen bonds. The dications are linked into supra-molecular tapes by amide-N-H⋯O(amide) hydrogen bonds, and thread through the voids in the anionic layers, being connected by charge-assisted pyridinium-N-O(carboxyl-ate) hydrogen bonds, so that a three-dimensional architecture ensues. An analysis of the Hirshfeld surface points to the importance of O-H⋯O hydrogen bonding in the crystal structure.

| S-EPMC4770948 | biostudies-literature

<i>N</i>,<i>N</i>'-Bis(pyridin-4-ylmeth-yl)oxalamide benzene monosolvate: crystal structure, Hirshfeld surface analysis and computational study.

Project description:The asymmetric unit of the title 1:1 solvate, C14H14N4O2·C6H6 [systematic name of the oxalamide mol-ecule: N,N'-bis-(pyridin-4-ylmeth-yl)ethanedi-amide], comprises a half mol-ecule of each constituent as each is disposed about a centre of inversion. In the oxalamide mol-ecule, the central C2N2O2 atoms are planar (r.m.s. deviation = 0.0006 Å). An intra-molecular amide-N-H⋯O(amide) hydrogen bond is evident, which gives rise to an S(5) loop. Overall, the mol-ecule adopts an anti-periplanar disposition of the pyridyl rings, and an orthogonal relationship is evident between the central plane and each terminal pyridyl ring [dihedral angle = 86.89 (3)°]. In the crystal, supra-molecular layers parallel to (10) are generated owing the formation of amide-N-H⋯N(pyrid-yl) hydrogen bonds. The layers stack encompassing benzene mol-ecules which provide the links between layers via methyl-ene-C-H⋯π(benzene) and benzene-C-H⋯π(pyrid-yl) inter-actions. The specified contacts are indicated in an analysis of the calculated Hirshfeld surfaces. The energy of stabilization provided by the conventional hydrogen bonding (approximately 40 kJ mol-1; electrostatic forces) is just over double that by the C-H⋯π contacts (dispersion forces).

| S-EPMC6690468 | biostudies-literature

Benzoic acid-3,4-bis-[(pyridin-3-ylmeth-yl)amino]-cyclo-but-3-ene-1,2-dione (1/2).

Project description:In the title co-crystal, C(16)H(14)N(4)O(2)·2C(7)H(6)O(2), the 3,4-bis-[(pyridin-3-ylmeth-yl)amino]-cyclo-but-3-ene-1,2-dione squareamide mol-ecules assemble into chains along the b axis via N-H?O hydrogen bonds. The benzoic acid mol-ecules then hydrogen bond to the pyridine rings via O-H?N hydrogen bonds, supported by weaker C-H?O hydrogen bonds, forming extended ribbons. The asymmetric unit consists of a half squareamide mol-ecule, sitting on a special position around a twofold axis, and one benzoic acid mol-ecule on a general position.

| S-EPMC3275061 | biostudies-literature

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