scholarly journals Syntheses and crystal structures of two piperine derivatives

2020 ◽  
Vol 76 (5) ◽  
pp. 646-650
Author(s):  
Toshinari Ezawa ◽  
Yutaka Inoue ◽  
Isamu Murata ◽  
Mitsuaki Suzuki ◽  
Koichi Takao ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Geometrical Parameters ◽  
Amide Hydrogen ◽  
Extended Structure ◽  
Π Stacking ◽  
Derivatives Of

The title compounds, 5-(2H-1,3-benzodioxol-5-yl)-N-cyclohexylpenta-2,4-dienamide, C18H21NO3 (I), and 5-(2H-1,3-benzodioxol-5-yl)-1-(pyrrolidin-1-yl)penta-2,4-dien-1-one C16H17NO3 (II), are derivatives of piperine, which is known as a pungent component of pepper. Their geometrical parameters are similar to those of the three polymorphs of piperine, which indicate conjugation of electrons over the length of the molecules. The extended structure of (I) features N—H...O amide hydrogen bonds, which generate C(4) [010] chains. The crystal of (II) features aromatic π–π stacking, as for two of three known piperine polymorphs.

Polymorphs of phenazine hexacyanoferrate(II) hydrate: supramolecular isomerism in a 2D hydrogen-bonded network

2021 ◽  
Vol 77 (2) ◽  
pp. 211-218
Author(s):  
Ivica Cvrtila ◽  
Vladimir Stilinović
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Two Dimensional ◽  
Structural Motifs ◽  
Supramolecular Isomerism ◽  
Other Hand ◽  
Π Stacking ◽  
Hydrogen Bonded

The crystal structures of two polymorphs of a phenazine hexacyanoferrate(II) salt/cocrystal, with the formula (Hphen)3[H2Fe(CN)6][H3Fe(CN)6]·2(phen)·2H2O, are reported. The polymorphs are comprised of (Hphen)2[H2Fe(CN)6] trimers and (Hphen)[(phen)2(H2O)2][H3Fe(CN)6] hexamers connected into two-dimensional (2D) hydrogen-bonded networks through strong hydrogen bonds between the [H2Fe(CN)6]2− and [H3Fe(CN)6]− anions. The layers are further connected by hydrogen bonds, as well as through π–π stacking of phenazine moieties. Aside from the identical 2D hydrogen-bonded networks, the two polymorphs share phenazine stacks comprising both protonated and neutral phenazine molecules. On the other hand, the polymorphs differ in the conformation, placement and orientation of the hydrogen-bonded trimers and hexamers within the hydrogen-bonded networks, which leads to different packing of the hydrogen-bonded layers, as well as to different hydrogen bonding between the layers. Thus, aside from an exceptional number of symmetry-independent units (nine in total), these two polymorphs show how robust structural motifs, such as charge-assisted hydrogen bonding or π-stacking, allow for different arrangements of the supramolecular units, resulting in polymorphism.

scholarly journals Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Small Molecule ◽  
Base Pair ◽  
Base Pairs ◽  
Standard Pattern ◽  
Planar Structures ◽  
Structural Database ◽  
Derivatives Of

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

scholarly journals Crystal structures of two 6-(2-hydroxybenzoyl)-5H-thiazolo[3,2-a]pyrimidin-5-ones

2015 ◽  
Vol 71 (7) ◽  
pp. 766-771
Author(s):  
Ligia R. Gomes ◽  
John Nicolson Low ◽  
Fernando Cagide ◽  
Fernanda Borges
Keyword(s):  
Hydrogen Bond ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Dihedral Angles ◽  
Stacking Interactions ◽  
Mechanism Of Formation ◽  
Π Stacking ◽  
Heterocyclic Moiety

The title compounds, 6-(2-hydroxybenzyl)-5H-thiazolo[3,2-a]pyrimidin-5-one, C13H8N2O3S, (1), and 6-(2-hydroxybenzyl)-3-methyl-5H-thiazolo[3,2-a]pyrimidin-5-one, C14H10N2O3S, (2), were synthesized when a chromone-3-carboxylic acid, activated with (benzotriazol-1-yloxy)tripyrrolidinylphosphonium hexafluoridophosphate (PyBOP), was reacted with a primary heteromamine. Instead of the expected amidation, the unusual title thiazolopyrimidine-5-one derivatives were obtained serendipitously and a mechanism of formation is proposed. Both compounds present an intramolecular O—H...O hydrogen bond, which generates anS(6) ring. The dihedral angles between the heterocyclic moiety and the 2-hydroxybenzoyl ring are 55.22 (5) and 46.83 (6)° for (1) and (2), respectively. In the crystals, the molecules are linked by weak C—H...O hydrogen bonds and π–π stacking interactions.

Comparison of the structure of (E)-2-(2-benzylidenehydrazinylidene)quinoxaline with those of its chloro- and bromobenzylidene analogues

2013 ◽  
Vol 69 (8) ◽  
pp. 920-926
Author(s):  
Ligia Rebelo Gomes ◽  
John Nicolson Low ◽  
Ana S. M. C. Rodrigues ◽  
James L. Wardell ◽  
Marcus V. N. de Souza ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Supramolecular Structures ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Hydrogen Bond Interactions ◽  
Π Stacking ◽  
Derivatives Of

(E)-2-(2-Benzylidenehydrazinylidene)quinoxaline, C15H12N4, crystallized with two molecules in the asymmetric unit. The structures of six halogen derivatives of this compound were also investigated: (E)-2-[2-(2-chlorobenzylidene)hydrazinylidene]quinoxaline, C15H11ClN4; (E)-2-[2-(3-chlorobenzylidene)hydrazinylidene]quinoxaline, C15H11ClN4; (E)-2-[2-(4-chlorobenzylidene)hydrazinylidene]quinoxaline, C15H11ClN4; (E)-2-[2-(2-bromobenzylidene)hydrazinylidene]quinoxaline, C15H11BrN4; (E)-2-[2-(3-bromobenzylidene)hydrazinylidene]quinoxaline, C15H11BrN4; (E)-2-[2-(4-bromobenzylidene)hydrazinylidene]quinoxaline, C15H11BrN4. The 3-Cl and 3-Br compounds are isomorphous, as are the 4-Cl and 4-Br compounds. In all of these compounds, it was found that the supramolecular structures are governed by similar predominant patterns,viz.strong intermolecular N—H...N(pyrazine) hydrogen bonds supplemented by weak C—H...N(pyrazine) hydrogen-bond interactions in the 2- and 3-halo compounds and by C—H...Cl/Br interactions in the 4-halo compounds. In all compounds, there are π–π stacking interactions.

(E)-N′-(4-Chlorobenzylidene)-, (E)-N′-(4-bromobenzylidene)- and (E)-N′-[4-(diethylamino)benzylidene]- derivatives of 4-hydroxybenzohydrazide

2012 ◽  
Vol 68 (10) ◽  
pp. o408-o412 ◽  
Author(s):  
Ashokkumar Subashini ◽  
Kandasamy Ramamurthi ◽  
Helen Stoeckli-Evans
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Dihedral Angles ◽  
Two Dimensional ◽  
Aromatic Rings ◽  
Space Group ◽  
Π Interactions ◽  
Centroid Distance ◽  
Benzene Rings ◽  
Derivatives Of

The 4-chloro- [C14H11ClN2O2, (I)], 4-bromo- [C14H10BrN2O2, (II)] and 4-diethylamino- [C18H21N3O2, (III)] derivatives of benzylidene-4-hydroxybenzohydrazide, all crystallize in the same space group (P21/c), (I) and (II) also being isomorphous. In all three compounds, the conformation about the C=N bond isE. The molecules of (I) and (II) are relatively planar, with dihedral angles between the two benzene rings of 5.75 (12) and 9.81 (17)°, respectively. In (III), however, the same angle is 77.27 (9)°. In the crystal structures of (I) and (II), two-dimensional slab-like networks extending in theaandcdirections are formedviaN—H...O and O—H...O hydrogen bonds. The molecules stack head-to-tailviaπ–π interactions involving the aromatic rings [centroid–centroid distance = 3.7622 (14) Å in (I) and 3.8021 (19) Å in (II)]. In (III), undulating two-dimensional networks extending in thebandcdirections are formedviaN—H...O and O—H...O hydrogen bonds. The molecules stack head-to-headviaπ–π interactions involving inversion-related benzene rings [centroid–centroid distances = 3.6977 (12) and 3.8368 (11) Å].

scholarly journals Different N—H...π interactions in two indole derivatives

2016 ◽  
Vol 72 (5) ◽  
pp. 699-703 ◽  
Author(s):  
Jamie R. Kerr ◽  
Laurent Trembleau ◽  
John M. D. Storey ◽  
James L. Wardell ◽  
William T. A. Harrison
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interaction ◽  
Aromatic Ring ◽  
Stacking Interactions ◽  
Indole Derivatives ◽  
Asymmetric Unit ◽  
Π Interactions ◽  
Π Stacking

We describe the syntheses and crystal structures of two indole derivatives, namely 6-isopropyl-3-(2-nitro-1-phenylethyl)-1H-indole, C19H20N2O2, (I), and 2-(4-methoxyphenyl)-3-(2-nitro-1-phenylethyl)-1H-indole, C23H20N2O3, (II); the latter crystallizes with two molecules (AandB) with similar conformations (r.m.s. overlay fit = 0.139 Å) in the asymmetric unit. Despite the presence of O atoms as potential acceptors for classical hydrogen bonds, the dominant intermolecular interaction in each crystal is an N—H...π bond, which generates chains in (I) andA+AandB+Binversion dimers in (II). A different aromatic ring acts as the acceptor in each case. The packing is consolidated by C—H...π interactions in each case but aromatic π–π stacking interactions are absent.

scholarly journals Crystal structures of 4-methyl-2-oxo-2H-chromene-7,8-diyl diacetate and 4-methyl-2-oxo-2H-chromene-7,8-diyl bis(pent-4-ynoate)

2016 ◽  
Vol 72 (5) ◽  
pp. 704-708
Author(s):  
Akintunde Akinyemi ◽  
Courtney Thomas ◽  
Willis Marsh ◽  
Ray J. Butcher ◽  
Jerry P. Jasinski ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Triple Bond ◽  
The Other ◽  
Coumarin Derivatives ◽  
Extended Conformation ◽  
Π Stacking ◽  
Planar Part ◽  
Centrosymmetric Dimers

In the structures of the two title coumarin derivatives, C14H12O6, (1), and C20H16O6, (2), one with acetate and the other with pent-4-ynoate substituents, both the coumarin rings are almost planar. In (1), both acetate substituents are significantly rotated out of the coumarin plane to minimize steric repulsions. One acetate substituent is disordered over two equivalent conformations, with occupancies of 0.755 (17) and 0.245 (17). In (2), there are two pent-4-ynoate substituents, the C[triple-bond]C group of one being disordered over two positions with occupancies of 0.55 (2) and 0.45 (2). One of the pent-4-ynoate substituents is in an extended conformation, while the other is in a bent conformation. In this derivative, the planar part of both pent-4-ynoate substituents deviate from the coumarin plane. The packing of (1) is dominated by π–π stacking involving the coumarin rings and weak C—H...O contacts link the parallel stacks in the [101] direction. In contrast, in (2) the packing is dominated byR22(24) hydrogen bonds, involving the acidicspH atom and the oxo O atom, which link the molecules into centrosymmetric dimers. The bent conformation of one of the pent-4-ynoate substituents prevents the coumarin rings from engaging in π–π stacking.

scholarly journals Template or ligand? Different structural behaviours of aromatic amines in combination with zincophosphite networks

2018 ◽  
Vol 74 (10) ◽  
pp. 1411-1416 ◽  
Author(s):  
William Holmes ◽  
David B. Cordes ◽  
Alexandra M. Z. Slawin ◽  
William T. A. Harrison
Keyword(s):  
Data Collection ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Aromatic Amines ◽  
Water Molecules ◽  
Extended Structure ◽  
Π Interactions ◽  
Vertex Sharing

The solution-mediated syntheses and crystal structures of catena-poly[bis(2-amino-3-hydroxypyridinium) [zinc-di-μ-phosphonato] dihydrate], {(C5H7N2O)[Zn(HPO3)2]·2H2O} n , (I), and poly[(benzene-1,2-diamine)(μ5-phosphonato)zinc], [Zn(HPO3)(C6H8N2)] n , (II) are described. The extended structure of (I) features [010] anionic chains of vertex-sharing ZnO4 tetrahedra and HPO3 pseudopyramids; these chains are characterized by disorder over major [occupancy 0.7962 (13)] and minor [0.2038 (13)] components, which can be superimposed on each other by a nominal translational shift. The 2-amino-3-hydroxypyridinium cations and water molecules of crystallization interact with the ZnPO chains by way of numerous O—H...O and N—H...O hydrogen bonds. The structure of (II) features a direct Zn—N bond to the neutral 1,2-diaminobenzene species as part of ZnO3N tetrahedra as well as HPO3 pseudopyramids. The Zn- and P-centred groupings are linked through their O-atom vertices into infinite (010) sheets and the structure is consolidated by N—H...O hydrogen bonds and N—H...π interactions. The crystal of (I) chosen for data collection was found to be an inversion twin in a 0.56 (2):0.44 (2) domain ratio.

scholarly journals Crystal structure of 3-bromo-2-hydroxybenzoic acid

2015 ◽  
Vol 71 (5) ◽  
pp. 531-535 ◽  
Author(s):  
Gerhard Laus ◽  
Volker Kahlenberg ◽  
Thomas Gelbrich ◽  
Sven Nerdinger ◽  
Herwig Schottenberger
Keyword(s):  
Crystal Structure ◽  
Salicylic Acid ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Title Compound ◽  
Hydroxybenzoic Acid ◽  
Compound C ◽  
Derivatives Of ◽  
Centrosymmetric Dimers ◽  
Ring Motif

Mutual carboxyl–carboxyl O—H...O hydrogen bonds link the molecules of the title compound, C7H5BrO3, into centrosymmetric dimers which display a centralR22(8) ring motif. In addition, there is an intramolecular hydroxyl–carboxyl O—H...O interaction present. A comparison with the crystal structures of 59 other substituted derivatives of salicylic acid shows that both the centrosymmetric carboxyl–carboxyl O—H...O dimer and the stacking mode of molecules along the shortaaxis observed in the title structure are frequent packing motifs in this set.

scholarly journals Crystal structures of tetramethylammonium (2,2′-bipyridine)tetracyanidoferrate(III) trihydrate and poly[[(2,2′-bipyridine-κ2N,N′)di-μ2-cyanido-dicyanido(μ-ethylenediamine)(ethylenediamine-κ2N,N′)cadmium(II)iron(II)] monohydrate]

2016 ◽  
Vol 72 (5) ◽  
pp. 741-746
Author(s):  
Songwuit Chanthee ◽  
Wikorn Punyain ◽  
Supawadee Namuangrak ◽  
Kittipong Chainok
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Layer Structure ◽  
Three Dimensional ◽  
Building Blocks ◽  
Chain Structure ◽  
Water Molecules ◽  
Two Dimensional ◽  
Lattice Water ◽  
Π Stacking

The crystal structures of the building block tetramethylammonium (2,2′-bipyridine-κ2N,N′)tetracyanidoferrate(III) trihydrate, [N(CH3)4][Fe(CN)4(C10H8N2)]·3H2O, (I), and a new two-dimensional cyanide-bridged bimetallic coordination polymer, poly[[(2,2′-bipyridine-κ2N,N′)di-μ2-cyanido-dicyanido(μ-ethylenediamine-κ2N:N′)(ethylenediamine-κ2N,N′)cadmium(II)iron(II)] monohydrate], [CdFe(CN)4(C10H8N2)(C2H8N2)2]·H2O, (II), are reported. In the crystal of (I), pairs of [Fe(2,2′-bipy)(CN)4]−units (2,2′-bipy is 2,2′-bipyridine) are linked together through π–π stacking between the pyridyl rings of the 2,2′-bipy ligands to form a graphite-like structure parallel to theabplane. The three independent water molecules are hydrogen-bonded alternately with each other, forming a ladder chain structure withR44(8) andR66(12) graph-set ring motifs, while the disordered [N(CH3)4]+cations lie above and below the water chains, and the packing is stabilized by weak C—H...O hydrogen bonds. The water chains are further linked with adjacent sheets into a three-dimensional networkviaO—H...O hydrogen bonds involving the lattice water molecules and the N atoms of terminal cyanide groups of the [Fe(2,2′-bipy)(CN)4]−building blocks, forming anR44(12) ring motif. Compound (II) features a two-dimensional {[Fe(2,2′-bipy)(CN)4Cd(en)2]}nlayer structure (en is ethylenediamine) extending parallel to (010) and constructed from {[Fe(2,2′-bipy)(CN)4Cd(en)]}nchains interlinked by bridging en ligands at the Cd atoms. Classical O—H...N and N—H...O hydrogen bonds involving the lattice water molecule and N atoms of terminal cyanide groups and the N—H groups of the en ligands are observed within the layers. The layers are further connectedviaπ–π stacking interactions between adjacent pyridine rings of the 2,2′-bipy ligands, completing a three-dimensional supramolecular structure.

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