Supramolecular Synthon (supramolecular + synthon)

Distribution by Scientific Domains
Distribution within Chemistry


Selected Abstracts


Conformational polymorphism in a Schiff-base macrocyclic organic ligand: an experimental and theoretical study

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2010
Leonardo Lo Presti
Polymorphism in the highly flexible organic Schiff-base macrocycle ligand 3,6,9,17,20,23-hexa-azapentacyclo(23.3.1.111,15.02,6.016,20)triaconta-1(29),9,11,13,15(30),23,25,27-octaene (DIEN, C24H30N6) has been studied by single-crystal X-ray diffraction and both solid-state and gas-phase density functional theory (DFT) calculations. In the literature, only solvated structures of the title compound are known. Two new polymorphs and a new solvated form of DIEN, all obtained from the same solvent with different crystallization conditions, are presented for the first time. They all have symmetry, with the macrocycle positioned on inversion centres. The two unsolvated polymorphic forms differ in the number of molecules in the asymmetric unit Z,, density and cohesive energy. Theoretical results confirm that the most stable form is (II°), with Z, = 1.5. Two distinct molecular conformations have been found, named `endo' or `exo' according to the orientation of the imine N atoms, which can be directed towards the interior or the exterior of the macrocycle. The endo arrangement is ubiquitous in the solid state and is shared by two independent molecules which constitute an invariant supramolecular synthon in all the known crystal forms of DIEN. It is also the most stable arrangement in the gas phase. The exo form, on the other hand, appears only in phase (II°), which contains both the conformers. Similarities and differences among the occurring packing motifs, as well as solvent effects, are discussed with the aid of Hirshfeld surface fingerprint plots and correlated to the results of the energy analysis. A possible interconversion path in the gas phase between the endo and the exo conformers has been found by DFT calculations; it consists of a two-step mechanism with activation energies of the order of 30,40,kJ,mol,1. These findings have been related to the empirical evidence that the most stable phase (II°) is also the last appearing one, in accordance with Ostwald's rule. [source]


Basic forms of supramolecular self-assembly ­organized by parallel and antiparallel hydrogen bonds in the racemic crystal structures of six disubstituted and trisubstituted cyclopentane ­derivatives

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2001
Alajos Kálmán
A selection of stereoisomeric 2-hydroxy-1-cyclopentanecarboxamides, a 4- tert -butyl derivative and three tert -butyl derivatives of the respective carboxylic acid were subjected to X-ray crystallography. The optically active molecules (I),(VI) form racemic crystals. Each racemic structure is basically determined by two intermolecular hydrogen bonds of O,H,O=C,XH and O=C,X,H,OH types (X = O, NH). The partially similar patterns of close packing observed reflect five basic forms of supramolecular self-assembly. In the racemic crystals of chiral molecules, there are homo- and heterochiral chains of molecules formed by the principal (O,H,O=C) hydrogen bonds. These chains assemble either in a parallel or antiparallel mode. The parallel homochiral chains (hop) observed in structure (II), (1R*,2R*)-2-hydroxy-1-cyclopentanecarboxamide, demand the polar space group Pca21, while the parallel heterochiral chains (hep) are organized in antiparallel layers with space group P21/n in structure (VI), (1R*,2S*,5R*-5- tert -butyl-2-hydroxy-1-cyclopentanecarboxylic acid). Heterochiral chains in an antiparallel array (hea) are found in (I), (1R*,2S*)-2-hydroxy-1-cyclopentanecarboxamide, and (V) [(1R*,2S*4S*)-4- tert -butyl-2-hydroxy-1-cyclopentanecarboxylic acid, space group P21/c]. Structures (IV), (1R*,2S*,4R*)-4- tert -butyl-2-hydroxy-1-cyclopentanecarboxylic acid, and (III), (1R*,2R*,4S*)-4- tert -butyl-2-hydroxy-1-cyclopentanecarboxamide, reveal that homochiral chains in an antiparallel array (hoa; cross-linked by heterochiral dimers held together by the second hydrogen bonds) can be formed by either translation (space group P) or a screw axis (space group P21/c). These alternatives are denoted hoa1 and hoa2. Similarly, within each pattern (hea, hep and hop) two slightly different alternatives can be expected. The partial similarities in the identified five patterns of hydrogen bonding are described by graph-set notations. Structures (I), (IV) and (V) can be characterized by a common supramolecular synthon, while the highest degree of similarity is shown by the isostructurality of (I) and (V). [source]


Probing the supramolecular interaction synthons of 1-benzofuran-2,3-dicarboxylic acid in its monoanionic form

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2009
Rajesh Koner
1-Benzofuran-2,3-dicarboxylic acid (C10H6O5) is a dicarboxylic acid ligand which can readily engage in organometallic complexes with various metal ions. This ligand is characterized by an intramolecular hydrogen bond between the two carboxyl residues, and, as a monoanionic species, readily forms supramolecular adducts with different organic and inorganic cations. These are a 1:1 adduct with the dimethylammonium cation, namely dimethylammonium 3-carboxy-1-benzofuran-2-carboxylate, C2H8N+·C10H5O5,, (I), a 2:1 complex with Cu2+ ions in which four neutral imidazole molecules also coordinate the metal atom, namely bis(3-carboxy-1-benzofuran-2-carboxylato-,O3)tetrakis(1H -imidazole-,N3)copper(II), [Cu(C10H5O5)2(C3H4N2)4], (II), and a 4:1 adduct with [La(H2O)7]3+ ions, namely heptaaquabis(3-carboxy-1-benzofuran-2-carboxylato-,O3)lanthanum 3-carboxy-1-benzofuran-2-carboxylate 1-benzofuran-2,3-dicarboxylic acid solvate tetrahydrate, [La(C10H5O5)2(H2O)7](C10H5O5)·C10H6O5·4H2O, (III). In the crystal structure, complex (II) resides on inversion centres, while complex (III) resides on axes of twofold rotation. The crystal packing in all three structures reveals ,,, stacking interactions between the planar aromatic benzofuran residues, as well as hydrogen bonding between the components. The significance of this study lies in the first crystallographic characterization of the title framework, which consistently exhibits the presence of an intramolecular hydrogen bond and a consequent monoanionic-only nature. It shows further that the anion can coordinate readily to metal cations as a ligand, as well as acting as a monovalent counter-ion. Finally, the aromaticity of the flat benzofuran residue provides an additional supramolecular synthon that directs and facilitates the crystal packing of compounds (I),(III). [source]


Van der Waals and Polar Intermolecular Contact Distances: Quantifying Supramolecular Synthons

CHEMISTRY - AN ASIAN JOURNAL, Issue 5 2008
Parthasarathy Ganguly Prof.
Abstract Crystal structures are viewed as being determined by ranges and constraints on interatomic contact distances between neighboring molecules. These distances are considered to arise from environment-dependent atomic sizes, that is, larger sizes for isotropic, van der Waals type contacts and smaller sizes for more-polar, possibly ionic contacts. Although the idea of different, or anisotropic, radii for atoms is not new, we developed a method of obtaining atomic sizes that is based on a theoretical framework. Using different atomic sizes for the same atom in different environments, we were able to rationalize some structural observations and anomalies. For example, benzene with the Pbca structure may be described in terms of two types of C,,,H interactions: a longer contact largely of the van der Waals type, and a shorter, structure-determining type (C,,,,,H,+), which we term "n-polar". Our approach is illustrated with three examples: 1),the equivalence in crystal packing of fluorobenzene, benzonitrile, pyridine N -oxide, and pyridine/HF 1:1 molecular complex, all of which take the not-so-common tetragonal P41212 space group and are practically isomorphous; 2),the similarity of the Pa3 acetylene and Pbca benzene crystal structures; and 3),the equivalence between an increase in pressure and an increase in the "n-polar" contacts in Pbca benzene; in other words, the equivalence between hydrostatic pressure and chemical pressure. In the context of crystal engineering, we describe a method whereby the topological information conveyed in a supramolecular synthon is recast in a more quantitative manner. A particular synthon, and in turn the crystal structure to which it leads, is viable within small ranges of distances of its constituent atoms, and these distances are determined by chemical factors. [source]


Supramolecular Complexes Self-assembled by Copper(II) Carboxylate and Monohelical Pyridylamino Ligand

CHINESE JOURNAL OF CHEMISTRY, Issue 3 2006
Li-Jun Zhou
Abstract Two novel supramolecular complexes [Cu(bpapa)(dhbd)]·CH3OH (1) and [Cu(bpapa)(ma)]·ma (2) (bpapa=bis[6-(2-pyridylamino)pyrid-2-yl]amine, dhbd=2,3-dihydroxybutanedioate dianion, ma=, -methacrylate) were rationally designed, synthesized and characterized by single crystal X-ray diffraction, IR, electronic spectroscopy and thermogravimetric analyses. Complex 1 was the first oligo- , -pyridylamino complex based on hydroxypolycarboxylate and self-assembled into a 3D honeycomb configuration network with open channels and tubes containing 1D ladder-shaped double chains formed by hydrogen bonds and aromatic ,-, stacking interactions. Complex 2 constructed a 2D supramolecular network extended by 1D chains from dimeric supramolecular synthon through noncovalent supramolecular interactions. In the two complexes, the chelating monohelical ligand adopted all- anti configuration. Density functional theory calculations were applied to 1 and 2. [source]


Supramolecular association in proton-transfer adducts containing benzamidinium cations.

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2010

Four organic salts, namely benzamidinidium orotate (2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylate) hemihydrate, C7H9N2+·C5H3N2O4,·0.5H2O (BenzamH+·Or,), (I), benzamidinium isoorotate (2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate) trihydrate, C7H9N2+·C5H3N2O4,·3H2O (BenzamH+·Isor,), (II), benzamidinium diliturate (5-nitro-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate) dihydrate, C7H9N2+·C4H2N3O5,·2H2O (BenzamH+·Dil,), (III), and benzamidinium 5-nitrouracilate (5-nitro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ide), C7H9N2+·C4H2N3O4, (BenzamH+·Nit,), (IV), have been synthesized by a reaction between benzamidine (benzenecarboximidamide or Benzam) and the appropriate carboxylic acid. Proton transfer occurs to the benzamidine imino N atom. In all four acid,base adducts, the asymmetric unit consists of one tautomeric aminooxo anion (Or,, Isor,, Dil, and Nit,) and one monoprotonated benzamidinium cation (BenzamH+), plus one-half (which lies across a twofold axis), three and two solvent water molecules in (I), (II) and (III), respectively. Due to the presence of protonated benzamidine, these acid,base complexes form supramolecular synthons characterized by N+,H...O, and N+,H...N, (±)-charge-assisted hydrogen bonds (CAHB). [source]


Uncommon isonicotinamide supramolecular synthons in copper(II) complexes directed by nitrate and perchlorate anions

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2009
Marijana ?akovi
The title compounds, trans -diaquabis(nitrato-,O)bis(pyridine-4-carboxamide-,N1)copper(II), [Cu(NO3)2(C6H6N2O)2(H2O)2], (I), and trans -diaquatetrakis(pyridine-4-carboxamide-,N1)copper(II) bis(perchlorate), [Cu(C6H6N2O)4(H2O)2](ClO4)2, (II), are composed of mononuclear coordination entities involving CuII ions and isonicotinamide. In (I), the centrosymmetric tetragonally distorted octahedral copper(II) environment contains trans -related isonicotinamide and water molecules in the equatorial plane and two nitrate ions occupying the axial sites. In (II), the equatorial plane of the C2 -symmetric distorted octahedron is built up of four isonicotinamide ligands, while water molecules occupy the axial positions. The complex molecules of (I) and (II) are linked into three-dimensional supramolecular frameworks by O,H...O and N,H...O hydrogen bonds. The nitrate and perchlorate ions are building blocks that disturb the robust R22(8) amide supramolecular motif commonly found in crystal structures of copper,isonicotinamide complexes. [source]