Crystal structures of three 6-substituted coumarin-3-carboxamide derivatives.
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ABSTRACT:
SUBMITTER: Gomes LR
PROVIDER: S-EPMC4992908 | biostudies-other | 2016 Jul
REPOSITORIES: biostudies-other
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Crystal structures of three 6-substituted coumarin-3-carboxamide derivatives.
Gomes Lígia R LR Low John Nicolson JN Fonseca André A Matos Maria João MJ Borges Fernanda F
Acta crystallographica. Section E, Crystallographic communications 20160610 Pt 7
Three coumarin derivatives, viz. 6-methyl-N-(3-methyl-phen-yl)-2-oxo-2H-chromene-3-carboxamide, C18H15NO3 (1), N-(3-meth-oxy-phen-yl)-6-methyl-2-oxo-2H-chromene-3-carboxamide, C18H15NO4 (2), and 6-meth-oxy-N-(3-meth-oxy-phen-yl)-2-oxo-2H-chromene-3-carboxamide, C18H15NO5 (3), were synthesized and structurally characterized. The mol-ecules display intra-molecular N-H⋯O and weak C-H⋯O hydrogen bonds, which probably contribute to the approximate planarity of the mol-ecules. The supra-molecular stru ...[more]
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Project description:To explore the effect of the nature of substitutions on the structural parameters and hydrogen-bond inter-actions in N-acyl-hydrazone derivatives, the crystal structures of three ortho-substituted N-acyl-hydrazone derivatives, namely (E)-N-{2-[2-(2-chloro-benzyl-idene)hydrazin-yl]-2-oxoeth-yl}-4-methyl-benzene-sulfon-amide, C16H16ClN3O3S (I), (E)-N-{2-[2-(2-methyl-benzyl-idene)hydrazin-yl]-2-oxoeth-yl}-4-methyl-benzene-sulfonamide, C17H19N3O3S (II), and (E)-N-{2-[2-(2-nitro-benzyl-idene)hydrazin-yl]-2-oxoeth-yl}-4-methyl-benzene-sulfonamide, C16H16N4O5S (III), have been determined. The structures of the three compounds display similar mol-ecular conformations and hydrogen-bond patterns. The hydrazone part of the mol-ecule, C-C-N-N=C, is almost planar in all the compounds, with the C-C-N-N and C-N-N=C torsion angles being 179.5?(3) and 177.1?(3)°, respectively, in (I), -179.4?(2) and -177.1?(3)° in (II) and -179.7?(2) and 173.4?(2)° in (III). The two phenyl rings on either side of the chain are approximately parallel to each other. In the crystal, the mol-ecules are linked to each other via N-H?O hydrogen bonds, forming ribbons with R22(8) and R22(10) ring motifs. The introduction of electron-withdrawing groups (by a chloro or nitro group) to produce compounds (I) or (III) results in C-H?O hydrogen-bonding inter-actions involving the sulfonyl O atoms of adjacent ribbons, forming layers parallel to the ab plane in (I) or a three-dimensional network in (III). In (III), one O atom of the nitro group is disordered over two orientations with refined occupancy ratio of 0.836?(12):0.164?(12).
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Project description:In the first of the compounds reported herein, namely 6'-ferrocenyl-6a'-nitro-6',6a',6b',7',9',11a'-hexa-hydro-2H-spiro-[ace-naphthyl-ene-1,11'-chromeno[3',4':3,4]pyrrolo-[1,2-c]thia-zol]-2-one, [Fe(C5H5)(C29H21N2O4S)], (I), the thia-zolidine ring adopts a twist conformation on the methine N-C atoms. In the second compound, viz. 6'-(4-methoxy-phen-yl)-6a'-nitro-6',6a',6b',7',9',11a'-hexa-hydro-2H-spiro-[ace-naphthyl-ene-1,11'-chromeno[3',4':3,4]pyrrolo-[1,2-c]thia-zol]-2-one, [Fe(C5H5)(C26H19N2O5S)], (II), the thia-zolidine ring adopts an envelope conformation with a methine C atom as the flap. In both compounds, the pyrrolidine ring adopts a twist conformation on the thia-zolidine and tetra-hydro-pyran C atoms. The mean planes of the thia-zolidine and pyrrolidine rings subtend angles of 67.30?(1) and 62.95?(7)° in (I) and (II), respectively, while the mean plane of the pyrrolidine ring makes dihedral angles of 76.53?(1) and 87.74?(7)° with the ace-naphthyl-ene ring system in (I) and (II), respectively. In both compounds, an intra-molecular C-H?O hydrogen bond forms an S(7) ring motif. In the crystal of (I), mol-ecules are linked via two different C-H?O hydrogen bonds, forming chains along [001] and [100]. In (II), they are linked through C-H?O hydrogen bonds, forming dimers with an R 2 (2)(10) ring motif while C-H?? inter-actions link the mol-ecules in a head-to-tail fashion, forming chains along the a-axis direction.
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Project description:The title compounds, [(1R,3R,4R,5R,6S)-4,5-bis-(acet-yloxy)-7-oxo-2-oxabi-cyclo[4.2.0]octan-3-yl]methyl acetate, C14H18O8, (I), [(1S,4R,5S,6R)-5-acet-yloxy-7-hy-droxy-imino-2-oxobi-cyclo-[4.2.0]octan-4-yl acetate, C11H15NO6, (II), and [(3aR,5R,6R,7R,7aS)-6,7-bis-(acet-yloxy)-2-oxo-octa-hydro-pyrano[3,2-b]pyrrol-5-yl]methyl acetate, C14H19NO8, (III), are stable bicyclic carbohydrate derivatives. They can easily be synthesized in a few steps from commercially available glycals. As a result of the ring strain from the four-membered rings in (I) and (II), the conformations of the carbohydrates deviate strongly from the ideal chair form. Compound (II) occurs in the boat form. In the five-membered lactam (III), on the other hand, the carbohydrate adopts an almost ideal chair conformation. As a result of the distortion of the sugar rings, the configurations of the three bicyclic carbohydrate derivatives could not be determined from their NMR coupling constants. From our three crystal structure determinations, we were able to establish for the first time the absolute configurations of all new stereocenters of the carbohydrate rings.
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Project description:A series of thio-phenes substituted in positions 2 and 5 by imine groups have been synthesized using a solvent-free approach, and their crystal structures determined. The substituents are chiral groups, and the expected absolute configuration for each mol-ecule was confirmed by refinement of the Flack parameter. The compounds are 2,5-bis-[(S)-(+)-(1,2,3,4-tetra-hydro-naphthalen-1-yl)imino]-thio-phene, C26H26N2S, (I), 2,5-bis-{[(R)-(-)-1-(4-meth-oxy-phen-yl)eth-yl]imino-meth-yl}thio-phene, C24H26N2O2S, (II), 2,5-bis-{[(R)-(-)-1-(4-fluoro-phen-yl)eth-yl]imino-meth-yl}thio-phene, C22H20F2N2S, (III), and 2,5-bis-{[(S)-(+)-1-(4-chloro-phen-yl)eth-yl]imino-meth-yl}thio-phene, C22H20Cl2N2S, (IV). A common feature of all four mol-ecules is the presence of twofold symmetry. For (I), which crystallizes in the triclinic space group P1, this symmetry is non-crystallographic, but for (II) in C2 and the isomorphous structures (III) and (IV) that crystallize in P21212, the twofold symmetry is crystallographically imposed with one half of each mol-ecule in the asymmetric unit. The comparable mol-ecular symmetry in the four structures is also reflected in similar packing, with mol-ecules aggregated to form chains through weak C-H⋯S inter-actions.
| S-EPMC4778840 | biostudies-literature
Project description:A series of novel coumarin-3-carboxamide derivatives were designed and synthesized to evaluate their biological activities. The compounds showed little to no activity against gram-positive and gram-negative bacteria but specifically showed potential to inhibit the growth of cancer cells. In particular, among the tested compounds, 4-fluoro and 2,5-difluoro benzamide derivatives (14b and 14e, respectively) were found to be the most potent derivatives against HepG2 cancer cell lines (IC50 = 2.62-4.85 μM) and HeLa cancer cell lines (IC50 = 0.39-0.75 μM). The activities of these two compounds were comparable to that of the positive control doxorubicin; especially, 4-flurobenzamide derivative (14b) exhibited low cytotoxic activity against LLC-MK2 normal cell lines, with IC50 more than 100 μM. The molecular docking study of the synthesized compounds revealed the binding to the active site of the CK2 enzyme, indicating that the presence of the benzamide functionality is an important feature for anticancer activity.
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Project description:The crystal structures of three benzimidazole esters containing aryl or heterocyclic substituents at position 2 are reported, and all three exhibit disorder of mol-ecular entities. In ethyl 1-methyl-2-[4-(prop-2-yn-oxy)phen-yl]-1H-benzimidazole-5-carboxyl-ate, C20H18N2O3, (I), the prop-2-yn-1-oxyphenyl unit is disordered over two sets of atomic sites having effectively equal occupancies, 0.506 (5) and 0.494 (5). The propyl substituent in ethyl 1-propyl-2-(pyren-1-yl)-1H-benzimidazole-5-carboxyl-ate, C29H24N2O2, (II), is disordered over two sets of atomic sites having occupancies 0.601 (8) and 0.399 (8), and the ester unit in ethyl 1-methyl-2-(5-chloro-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1H-benzimidazole-5-carboxyl-ate, C21H19ClN4O2 (III), is disordered over two sets of atomic sites having occupancies 0.645 (7) and 0.355 (7). In each of the C-H⋯π(arene) hydrogen bonds in (I), the donor and acceptor form parts of different disorder components, so that no continuous aggregation is possible. The mol-ecules of (II) are linked by a single C-H⋯O hydrogen bond into C(10) chains, which are linked into sheets by a π-π stacking inter-action, whereas those of (III) are just linked into C(13) chains, again by a single C-H⋯O hydrogen bond. Comparisons are made with the structures of some related compounds.
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Project description:The title compounds, C27H20O6, (I) [systematic name: methyl 7-oxo-14-phenyl-1H,7H,14H-pyrano[3,2-c:5,4-c']dichromene-14a(6bH)-carboxyl-ate], C24H22O5, (II) [systematic name: methyl 1-oxo-6-phenyl-2,3,4,12b-tetra-hydro-1H,6H-chromeno[3,4-c]chromene-6a(7H)-carboxyl-ate], and C25H23N3O4, (III) [systematic name: 6-(4-ethyl-phen-yl)-2,4-dimethyl-1,3-dioxo-2,3,4,12b-tetra-hydro-1H,6H-chromeno[4',3':4,5]pyrano[2,3-d]pyrimidine-6a(7H)-carbo-nitrile], are pyran-ochromene derivatives. The central pyran rings (B) of compounds (I) and (III) adopt half-chair conformations, whereas that of compound (II) adopts a sofa conformation. The pyran rings (A) of the chromene ring systems of compounds (II) and (III) adopt half-chair conformations, while that of compound (I) adopts a sofa conformation. The mean plane of the central pyran rings (B) make dihedral angles of 70.02 (6), 61.52 (6) and 69.12 (7)°, respectively, with the mean planes of the chromene moieties (C+A) of compounds (I), (II) and (III). The bicyclic coumarin ring system (C+A+B+E) in compound (I) is almost planar (r.m.s. deviation = 0.042 Å). The carbo-nitrile side chain in compound (III) is very nearly linear, with the C-C N angle being 176.6 (2)°. The cyclo-hexene ring (E), fused with the central pyran ring (B) in compound (II) adopts a sofa conformation. In the mol-ecular structures of compounds (II) and (III), there are C-H⋯O short contacts, which generate S(7) ring motifs. In the crystal structures of the title compounds, mol-ecules are linked by C-H⋯O hydrogen bonds, which generate mol-ecular sheets parallel to the ab plane, with R 4 (3)(28) loops in (I), inversion dimers with R 2 (2)(10) loops in (II) and chains along [010] with R 2 (2)(12) ring motifs in (III). In the crystal structures of (I) and (III), there are also C-H⋯π inter-actions present, leading to the formation of a three-dimensional framework in (II) and to sheets parallel to (101) in (III).
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Project description:Crystal structures of CYP2B35 and CYP2B37 from the desert woodrat were solved in complex with 4-(4-chlorophenyl)imidazole (4-CPI). The closed conformation of CYP2B35 contained two molecules of 4-CPI within the active site, whereas the CYP2B37 structure demonstrated an open conformation with three 4-CPI molecules, one within the active site and the other two in the substrate access channel. To probe structure-function relationships of CYP2B35, CYP2B37, and the related CYP2B36, we tested the O-dealkylation of three series of related substrates-namely, 7-alkoxycoumarins, 7-alkoxy-4-(trifluoromethyl)coumarins, and 7-alkoxy-4-methylcoumarins-with a C1-C7 side chain. CYP2B35 showed the highest catalytic efficiency (kcat/KM) with 7-heptoxycoumarin as a substrate, followed by 7-hexoxycoumarin. In contrast, CYP2B37 showed the highest catalytic efficiency with 7-ethoxy-4-(trifluoromethyl)coumarin (7-EFC), followed by 7-methoxy-4-(trifluoromethyl)coumarin (7-MFC). CYP2B35 had no dealkylation activity with 7-MFC or 7-EFC. Furthermore, the new CYP2B-4-CPI-bound structures were used as templates for docking the 7-substituted coumarin derivatives, which revealed orientations consistent with the functional studies. In addition, the observation of multiple -Cl and -NH-π interactions of 4-CPI with the aromatic side chains in the CYP2B35 and CYP2B37 structures provides insight into the influence of such functional groups on CYP2B ligand binding affinity and specificity. To conclude, structural, computational, and functional analysis revealed striking differences between the active sites of CYP2B35 and CYP2B37 that will aid in the elucidation of new structure-activity relationships.
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Project description:Three hexahydroquinoline derivatives were synthesized and crystallized in an effort to study the structure–activity relationships of these calcium-channel antagonists. n these hexahydroquinoline derivatives, common structural features such as a flat-boat conformation of the 1,4-dihydropyridine (1,4-DHP) ring, an envelope conformation of the fused cyclohexanone ring, and a substituted phenyl group at the pseudo-axial position are retained. Hydrogen bonds are the main contributors to the packing of the molecules in these crystals. Three hexahydroquinoline derivatives were synthesized and crystallized in an effort to study the structure–activity relationships of these calcium-channel antagonists. The derivatives are ethyl 4-(2-methoxyphenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C22H27NO4, (I), ethyl 4-(4-methoxyphenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C22H27NO4, (II), and ethyl 4-(3,4-dihydroxyphenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C21H24NO5, (III). In these hexahydroquinoline derivatives, common structural features such as a flat-boat conformation of the 1,4-dihydropyridine (1,4-DHP) ring, an envelope conformation of the fused cyclohexanone ring, and a substituted phenyl group at the pseudo-axial position are retained. Hydrogen bonds are the main contributors to the packing of the molecules in these crystals.
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Project description:The crystal structures of three benzamide derivatives, viz. N-(6-hy-droxy-hex-yl)-3,4,5-tri-meth-oxy-benzamide, C16H25NO5, (1), N-(6-anilinohex-yl)-3,4,5-tri-meth-oxy-benzamide, C22H30N2O4, (2), and N-(6,6-di-eth-oxy-hex-yl)-3,4,5-tri-meth-oxy-benzamide, C20H33NO6, (3), are described. These compounds differ only in the substituent at the end of the hexyl chain and the nature of these substituents determines the differences in hydrogen bonding between the mol-ecules. In each mol-ecule, the m-meth-oxy substituents are virtually coplanar with the benzyl ring, while the p-meth-oxy substituent is almost perpendicular. The carbonyl O atom of the amide rotamer is trans related with the amidic H atom. In each structure, the benzamide N-H donor group and O acceptor atoms link the mol-ecules into C(4) chains. In 1, a terminal -OH group links the mol-ecules into a C(3) chain and the combined effect of the C(4) and C(3) chains is a ribbon made up of screw related R 2 (2)(17) rings in which the ?O-H? chain lies in the centre of the ribbon and the tri-meth-oxy-benzyl groups forms the edges. In 2, the combination of the benzamide C(4) chain and the hydrogen bond formed by the terminal N-H group to an O atom of the 4-meth-oxy group link the mol-ecules into a chain of R 2 (2)(17) rings. In 3, the mol-ecules are linked only by C(4) chains.
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