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Packing Motifs (packing + motif)

Distribution by Scientific Domains
Chemistry100%

Selected Abstracts

Hantzsch 1,4-dihydropyridine esters and analogs: candidates for generating reproducible one-dimensional packing motifs

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2009
R. S. Rathore
Examination of the symmetric Hantzsch 1,4-dihydropyridine ester derivatives of the prototypical nifedipine molecule indicates the tendency of this class of molecule to form a common packing motif. Crystal structure analysis of 2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylic diesters and analogs reveals that they form extended chains, characterized as the C(6) packing motif, via intermolecular (amine) N,H...O=C (C3,C5 carbonyl) hydrogen bonds. In addition, all the prepared derivatives also satisfy the basic structural requirements for their high binding efficiency to the receptor. The reproducible C(6) packing motif observed among these compounds has a use in the design of solid-state materials. [source]

N,N -Diethyl- N,-[(E)-4-pyridylmethylene]benzene-1,4-diamine: a combined X-ray and density functional theory study

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009
Rüdiger W. Seidel
The crystal structure of the title compound, C16H19N3, comprises neutral molecules of a dipolar Schiff base chromophore. A density functional theory (DFT) optimized structure at the B3LYP/6-31G(d) level is compared with the molecular structure in the solid state. The compound crystallizes in the noncentrosymmetric space group Pna21 with a herring-bone packing motif and is therefore a potential candidate for nonlinear optical effects in the bulk. [source]

Incorporation of a disaccharide nucleoside into the backbone of double-stranded DNA: crystallization and preliminary X-ray diffraction

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2005
Kristof Van Hecke
Incorporation of a disaccharide nucleoside into double-stranded DNA can be considered as a chemical (non-enzymatic) alternative for site-specific cleavage of DNA. Crystals of the sequence d(CGCGAATT*CGCG), where * is an incorporated ribose, were obtained by hanging-drop vapour diffusion and diffracted to 2.6,Å. The crystals belong to the orthorhombic space group P2221, with unit-cell parameters a = 41.52, b = 57.63, c = 81.39,Å, indicating a new crystal packing motif for an oligonucleotide dodecamer sequence. [source]

Hybrid Organic/Inorganic Supramolecular Conductors D2[Au(CN)4] [D = Diiodo(ethylenedichalcogeno)tetrachalcogenofulvalene], Including a New Ambient Pressure Superconductor

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 30 2007
Tatsuro Imakubo
Abstract Five diiodo(ethylenedichalcogeno)tetrachalcogenofulvalenes, DIEDSS {2-(5,6-dihydro[1,3]diselenolo[4,5- b][1,4]diselenin-2-ylidene)-4,5-diiodo-1,3-dithiole}, DIET-STF {2-(4,5-diiodo-1,3-diselenol-2-ylidene)-5,6-dihydro[1,3]dithiolo[4,5- b][1,4]dithiine}, DIEDS-STF {2-(4,5-diiodo-1,3-diselenol-2-ylidene)-5,6-dihydro[1,4]diselenino[2,3- d][1,3]dithiole}, DIETSe {2-(4,5-diiodo-1,3-diselenol-2-ylidene)-5,6-dihydro[1,3]diselenolo[4,5- b][1,4]dithiine}, and DIEDSSe {2-(4,5-diiodo-1,3-diselenol-2-ylidene)-5,6-dihydro[1,3]diselenolo[4,5- b][1,4]diselenine},have been synthesized without the use of the highly toxic reagent CSe2, and their Au(CN)4 salts have been prepared by electrochemical oxidation. Characteristic I···N iodine bonds are constructed in all crystals, and their packing motifs are classified into two groups by the difference in the space group symmetry. The salt of DIEDSS crystallizes in the monoclinic C2/c space group and a novel helical supramolecular architecture is constructed by the strong and directional I···N iodine bond. On the other hand, the rest of the four salts crystallize in the triclinic P space group and their donor packing motifs belong to the so-called ,-type. Conducting properties of the ,-type salts strongly depend on the number and positions of the selenium atoms on the donor molecule. The salts based on the diselenadithiafulvalene (DSDTF) derivatives, DIET-STF and DIEDS-STF, show metal,semiconductor transition and the salt of fully selenated ,-donor DIEDSSe shows stable metallic behavior down to 1.6 K. On the other hand, (DIETSe)2[Au(CN)4] is semimetallic down to low temperature and the superconducting transition occurs at around 2 K (onset).(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]

Crystal Structures of Conformationally Locked Cyclitols: An Analysis of Hydrogen-Bonded Architectures and their Implications in Crystal Engineering

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 3 2007
Goverdhan Mehta
Abstract A qualitative study has been carried out on selected polycyclitols to evaluate the potential of conformational locking of hydroxy groups in lending predictability to the O,H···O hydrogen-bonding network observed in the crystal structures of such compounds. The polycyclitols employed in this study are conformationally locked with all the hydroxy groups destined to be axial owing to the trans ring fusion(s) in the polycyclic carbon framework. The consequent formation of intramolecular O,H···O hydrogen bonds between the 1,3- syn diaxial hydroxy groups now permits any packing pattern in the polycyclitols to be described in terms of a small group of intramolecularly bonded molecular motifs linked to their respective neighbors by four O,H···O bonds. By using this model and the results of CSD analyses of polyols as a guide, the O,H···O hydrogen-bonded packing motifs most likely to be observed in the crystal structure of each polycyclitol were proposed and compared with those obtained experimentally. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]

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]

Hantzsch 1,4-dihydropyridine esters and analogs: candidates for generating reproducible one-dimensional packing motifs

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2009
R. S. Rathore
Examination of the symmetric Hantzsch 1,4-dihydropyridine ester derivatives of the prototypical nifedipine molecule indicates the tendency of this class of molecule to form a common packing motif. Crystal structure analysis of 2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylic diesters and analogs reveals that they form extended chains, characterized as the C(6) packing motif, via intermolecular (amine) N,H...O=C (C3,C5 carbonyl) hydrogen bonds. In addition, all the prepared derivatives also satisfy the basic structural requirements for their high binding efficiency to the receptor. The reproducible C(6) packing motif observed among these compounds has a use in the design of solid-state materials. [source]

Herringbone array of hydrogen-bonded ribbons in 2-ethoxybenzamide from high-resolution X-ray powder diffraction

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2009
Silvina Pagola
In 2-ethoxybenzamide, C9H11NO2, the amide substituents are linked into centrosymmetric head-to-head hydrogen-bonded dimers. Additional hydrogen bonds between adjacent dimers give rise to ribbon-like packing motifs, which extend along the c axis and possess a third dimension caused by twisting of the 2-ethoxyphenyl substituent with respect to the hydrogen-bonded amide groups. The ribbons are arranged in a T-shaped herringbone pattern and cohesion between them is achieved by van der Waals forces. [source]

Two packing motifs based upon chains of edge-sharing PbI6 octa­hedra

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2006
Andreas Lemmerer
The compounds catena -poly[p -phenyl­enediammonium [[diiodo­lead(II)]-di-,-iodo] dihydrate], {(C6H10N2)[PbI4]·2H2O}n, (I), and catena -poly[bis­(3,5-dimethyl­anilinium) [[diiodo­lead(II)]-di-,-iodo]], {(C8H12N)2[PbI4]}n, (II), crystallize as organic,inorganic hybrids. As such, the structures consist of chains of [PbI2], units extending along the c axis in (I) and along the b axis in (II). The asymmetric unit in (I) contains one Pb atom on a site of 2/m symmetry, two I atoms and a water molecule on mirror planes, and a p -phenyl­enediammonium mol­ecule that sits around a site of 2/m symmetry with the C and N atoms on a mirror plane. In (II), the Pb atom is on a twofold axis and the two I atoms are on general positions. Each Pb atom is octa­hedrally coordinated to six I atoms, arranged as chains of edge-sharing octa­hedra. Both compounds undergo hydrogen-bonding inter­actions between the ammonium groups and the I atoms. In addition, there are hydrogen bonds between the water mol­ecules and the ammonium groups and halides in (I), and between the ammonium groups and the ring systems in (II). [source]

Molecular Conformation and Packing of Peptide , Hairpins in the Solid State: Structures of Two Synthetic Octapeptides Containing 1-Aminocycloalkane-1-Carboxylic Acid Residues at the i+2 Position of the , Turn

CHEMISTRY - A EUROPEAN JOURNAL, Issue 12 2005
Veldore Vidya Harini
Abstract Peptide ,-hairpin formation is facilitated by centrally positioned D -Pro-Xxx segments. The synthetic peptides Boc-Leu-Phe-Val- D -Pro-Ac6c-Leu-Phe-Val-OMe (1) and Boc-Leu-Phe-Val- D -Pro-Ac8c-Leu-Phe-Val-OMe (2) were synthesized in order to explore the role of bulky 1-aminocycloalkane-1-carboxylic acid residues (Acnc, where n is the number of carbon atoms in the ring), at the i+2 position of the nucleating , turn in peptide , hairpins. Peptides 1 and 2 crystallize in the monoclinic space group P21 with two molecules in the asymmetric unit. The crystal structures of 1 and 2 provide conformational parameters for four peptide hairpin molecules. In all cases, the central segments adopts a type II, ,-turn conformation, and three of the four possible cross-strand hydrogen bonds are observed. Fraying of the hairpins at the termini is accompanied by the observation of NH,,,, interaction between the Leu(1)NH group and Phe(7) aromatic group. Cross strand stabilizing interactions between the facing residues Phe(2) and Phe(7) are suggested by the observed orientation of aromatic rings. Anomalous far-UV CD spectra observed in solution suggest that close proximity of the Phe rings is maintained even in isolated molecules. In both peptides 1 and 2, the asymmetric unit consists of approximately orthogonal hairpins, precluding the formation of a planar ,-sheet arrangement in the solid state. Solvent molecules, one dioxane and one water in 1, three water molecules in 2, mediate peptide association. A comparison of molecular conformation and packing motifs in available ,-hairpin structures permits delineation of common features. The crystal structures of ,-hairpin peptides provide a means of visualizing different modes of ,-sheet packing, which may be relevant in developing models for aggregates of polypeptides implicated in disease situations. [source]