Eight Schiff bases derived from various salicylaldehydes: phenol–imine and keto–amine forms, conformational disorder, and supramolecular assembly in one and two dimensions

2018 ◽  
Vol 74 (10) ◽  
pp. 1094-1104 ◽  
Author(s):  
Marisiddaiah Girisha ◽  
Belakavadi K. Sagar ◽  
Hemmige S. Yathirajan ◽  
Ravindranath S. Rathore ◽  
Manpreet Kaur ◽  
...  

Structures are reported for eight Schiff bases derived from various salicylaldehydes: five are newly synthesized and re-investigations are reported for three previously reported structures, leading, in each case, to some revision of previous conclusions. In (E)-N-(3,4-dimethylisoxazol-5-yl)-4-[(2-hydroxybenzylidene)amino]benzenesulfonamide, C18H17N3O4S, (I), and (E)-4-[(5-bromo-2-hydroxy-3-methoxybenzylidene)amino]-N-(3,4-dimethylisoxazol-5-yl)benzenesulfonamide. C19H18BrN3O5S, (II), the isoxazole rings adopt different orientations relative to the rest of the molecules, despite the additional substituents in (II) being in the aryl ring remote from the isoxazole unit. The molecules of both (E)-4-bromo-2-[(2-hydroxyphenylimino)methyl]-6-methoxyphenol, C14H12BrNO3, (III), and (E)-4-bromo-2-methoxy-6-[(2-methoxyphenylimino)methyl]phenol, C15H14BrNO3, (IV), are both effectively planar; while (III) adopts the phenol–imine constitution, (IV) adopts the keto–amine constitution. (E)-2-Methoxy-6-[(2-methoxyphenylimino)methyl]phenol, C15H15NO3, (V), which was determined previously using powder X-ray data assuming the phenol–imine constitution, has now been refined from single-crystal X-ray data, confirming the phenol–imine constitution. In (E)-3-benzoyl-2-[(5-fluoro-2-hydroxybenzylidene)amino]-4,5,6,7-tetrahydrobenzo[b]thiophene, C22H18FNO2S, (VI), the fused carbocyclic ring exhibits conformational disorder; both disorder components, having populations of 0.705 (4) and 0.295 (4), adopt half-chair conformations. The isostructural (E)-3-benzoyl-2-[(2-hydroxybenzylidene)amino)]-4,5,6,7-tetrahydrobenzo[b]thiophene, C22H19NO2S, (VII), which was originally reported as having a fully ordered structure [Kauret al.(2014).Acta Cryst.E70, o476–o477], has been rerefined using the original data set and found to exhibit the same type of disorder as found in (VI), with disordered populations having occupancies of 0.851 (3) and 0.149 (3). The triclinic polymorph of (E)-[(2-hydroxyphenylimino)methyl]phenol, C13H11NO2, (VIII), which crystallizes withZ′ = 2 in the space groupP-1, has been described variously as occurring as the keto–amine tautomer [Maciejewskaet al.(1999).J. Phys. Org. Chem.12, 875–880] and as the phenol–imine tautomer [Tunçet al.(2009).J. Chem. Crystallogr.39, 672–676]. Rerefinement of this structure using one of the original data sets shows that both of the independent molecules exist in the keto–amine form. In the structures of compounds (I), (VI), (VII) and (VIII), hydrogen bonds generate simple chains, while a chain of rings is formed in (V). Sheets are formed by hydrogen bonds in both (II) and (III), while in (IV), the sheet structure is built from aromatic π–π stacking interactions.

Author(s):  
Zouaoui Setifi ◽  
Fatima Setifi ◽  
Necmi Dege ◽  
Rafika El Ati ◽  
Christopher Glidewell

The redetermination of the structure of the title compound, [Fe(C15H12N4)2](ClO4)2, (I), confirms the structure previously reported [Kucharski et al. (1978a). Aust. J. Chem. 31, 53–56], but models the perchlorate over four sets of atomic sites, rather than using just one set of sites as in the original report. The supramolecular assembly, not reported previously, takes the form of a complex three-dimensional framework built from C—H...O hydrogen bonds. The isotypic nickel(II) analogue, [Ni(C15H12N4)2](ClO4)2, (III), has been refined using the original data set [Wang et al. (2011). Acta Cryst. E67, m78], again using a four-component disorder model for the anion, rather than a two-component model as in the original report, leading to more satisfactory Cl—O distances and O—Cl—O angles.


2012 ◽  
Vol 68 (5) ◽  
pp. o199-o203 ◽  
Author(s):  
Andrés F. Yépes ◽  
Alirio Palma ◽  
Antonio Marchal ◽  
Justo Cobo ◽  
Christopher Glidewell

In both 2-amino-6-methoxy-4-(4-methylanilino)-5-nitrosopyrimidine, C12H13N5O2, (I), and ethylN-[4-(1-adamantylamino)-2-amino-5-nitrosopyrimidin-6-yl]-3-aminopropionate, C19H28N6O3, (II), the nitrosopyrimidine unit is planar and the bond distances provide evidence for significant polarization of the electronic structures. In (II), the ethoxycarbonyl fragment of the molecule is disordered over two sets of sites with occupancies of 0.910 (4) and 0.090 (4). In the molecules of both compounds, there is an intramolecular N—H...O hydrogen bond. The molecules of (I) are linked into a chain of rings by a combination of N—H...O and C—H...O hydrogen bonds, while the molecules of (II) are linked by a two-centre N—H...N hydrogen bond and a three-centre N—H...(N,O) hydrogen bond to form sheets containing four distinct types of ring.


2012 ◽  
Vol 68 (3) ◽  
pp. o131-o140 ◽  
Author(s):  
Maria C. Blanco ◽  
Alirio Palma ◽  
Justo Cobo ◽  
Christopher Glidewell

The structures are reported of nine closely related tetrahydro-1,4-epoxy-1-benzazepines carrying pendant heterocyclic substituents, namely: 2-exo-(5-nitrofuran-2-yl)-2,3,4,5-tetrahydro-1,4-epoxy-1H-1-benzazepine, C14H12N2O4, (I), 7-fluoro-2-exo-(1-methyl-1H-pyrrol-2-yl)-2,3,4,5-tetrahydro-1,4-epoxy-1H-1-benzazepine, C15H15FN2O, (II), 7-fluoro-2-exo-(5-methylfuran-2-yl)-2,3,4,5-tetrahydro-1,4-epoxy-1H-1-benzazepine, C15H14FNO2, (III), 7-fluoro-2-exo-(3-methylthiophen-2-yl)-2,3,4,5-tetrahydro-1,4-epoxy-1H-1-benzazepine, C15H14FNOS, (IV), 7-fluoro-2-exo-(5-methylthiophen-2-yl)-2,3,4,5-tetrahydro-1,4-epoxy-1H-1-benzazepine, C15H14FNOS, (V), 7-chloro-2-exo-(5-methylfuran-2-yl)-2,3,4,5-tetrahydro-1,4-epoxy-1H-1-benzazepine, C15H14ClNO2, (VI), 2-exo-(5-methylfuran-2-yl)-7-trifluoromethoxy-2,3,4,5-tetrahydro-1,4-epoxy-1H-1-benzazepine, C16H14F3NO3, (VII), 2-exo-(3-methylthiophen-2-yl)-7-trifluoromethoxy-2,3,4,5-tetrahydro-1,4-epoxy-1H-1-benzazepine, C16H14F3NO2S, (VIII), and 2-exo-(5-nitrofuran-2-yl)-7-trifluoromethoxy-2,3,4,5-tetrahydro-1,4-epoxy-1H-1-benzazepine, C15H11F3N2O5, (IX). All nine compounds crystallize in centrosymmetric space groups as racemic mixtures with configuration (2RS,4SR). There are no direction-specific interactions between the molecules in (V). The molecules in (III), (IV), (VI) and (VII) are linked into simple chains, by means of a single C—H...O hydrogen bond in each of (III), (VI) and (VII), and by means of a single C—H...π(arene) hydrogen bond in (IV), while the molecules in (VIII) are linked into a chain of rings. In each of (I) and (II), a combination of one C—H...O hydrogen bond and one C—H...π(arene) hydrogen bond links the molecules into sheets, albeit of completely different construction in the two compounds. In (IX), the sheet structure is built from a combination of four independent C—H...O hydrogen bonds and one C—H...π(arene) hydrogen bond. Comparisons are made with some related compounds.


2018 ◽  
Vol 74 (1) ◽  
pp. 45-53
Author(s):  
Belakavadi K. Sagar ◽  
Hemmige S. Yathirajan ◽  
Ravindranath S. Rathore ◽  
Christopher Glidewell

Four closely related N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)benzamides, bearing different substituents on the benzamide ring, have been synthesized and structurally characterized. In each of N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-3-fluorobenzamide, C22H18FNO2S, (I), N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-4-chlorobenzamide, C22H18ClNO2S, (II), N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-2,6-difluorobenzamide, C22H17F2NO2S, (III), and N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-2-methoxybenzamide, C23H21NO3S, (IV), the last of which crystallizes with Z′ = 2 in the space group P\overline{1}, the fused six-membered ring adopts a half-chair conformation. In each of (I)–(III), this ring is disordered over two sets of atomic sites having occupancies of 0.811 (6) and 0.189 (6) in (I), 0.645 (7) and 0.355 (7) in (II), and 0.784 (6) and 0.216 (6) in (III), such that the two disorder components of the ring are almost enantiomeric. Molecules of (I) are linked into chains by π–π stacking interactions, and those of (II) are linked into chains by a C—H...π hydrogen bond. A combination of two C—H...O hydrogen bonds and two C—H...π hydrogen bonds links the molecules of (III) into complex sheets, but the molecules of (IV) are linked by a combination of two hydrogen bonds, one each of the C—H...O and C—H...π types, to form centrosymmetric tetramers. The structures of (I)–(IV) are compared with that of the unsubstituted analogue N-(3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)benzamide and a new refinement of the parent amine 2-amino-3-benzoyl-4,5,6,7-tetrahydrobenzo[b]thiophene, using the original data set, has found that here too the fused six-membered ring exhibits conformational disorder, with occupancies of 0.887 (9) and 0.113 (9). Comparisons are made with some related compounds.


2011 ◽  
Vol 34 (5-6) ◽  
pp. 127-130 ◽  
Author(s):  
Yaya Sow ◽  
Libasse Diop ◽  
Kieran C. Molloy ◽  
Gabrielle Kociok-Köhn

Abstract The title compounds [R2NH2][C2O4SnMe3](R=i-Bu, Cy), in which tin atoms adopt a distorted trigonal bipyramidal configuration, have been prepared and submitted to an X-ray diffraction study. These compounds have been obtained from the reaction of (Cy2NH2)2C2O4·H2O or (i-Bu2NH2)2C2O4 with SnMe3Cl. In both [R2NH2][C2O4SnMe3] compounds, the trans complex has an almost regular trigonal bipyramidal geometry around the tin atom. The SnMe3 residues are connected as a chain with bridging oxalate anions in a trans-SnC3O2 framework, the oxygen atoms being in axial positions. The cations connect linear adjacent chains through NH…O hydrogen bonds giving layered structures.


1998 ◽  
Vol 54 (4) ◽  
pp. 399-416 ◽  
Author(s):  
S. C. Abrahams ◽  
H. W. Schmalle ◽  
T. Williams ◽  
A. Reller ◽  
F. Lichtenberg ◽  
...  

The possibility that the structure of the novel semiconducting perovskite-related material strontium niobium oxide, Sr5Nb5O17, refined by Schmalle et al. [Acta Cryst. (1995), C51, 1243–1246] in space group Pnn2, might instead belong to space group Pnnm has been investigated following an analysis of the atomic coordinates that indicated the latter space group to be more likely. All I obs were carefully remeasured, first those within a hemisphere containing c *, then all that lay within the full sphere of reflection. Refinement was undertaken, with each of two different sets of weights, in each space group. Each data set was used under three limiting intensity conditions: I obs > 4σ(I obs), I obs > 2σ(I obs) and finally with all reflections, but setting magnitudes with I obs ≤ 0 equal to 0. Fourteen separate tests based only upon the X-ray diffraction data may be used to distinguish between Pnn2 and Pnnm. Nine tests favored the latter choice, four were indeterminate and one was not used. Seven further tests may be made on the basis of physical measurement; of these, three strongly indicated Pnnm, one was indeterminate and three could not be used. The evidence clearly suggests the space group is Pnnm. The use of all reflections, including those with negative magnitude set equal to zero, is essential to avoid ambiguity in the X-ray diffraction tests and achieve the highest reliability. Refinement with weights based on variances of Type A and Type B [Schwarzenbach et al. (1995). Acta Cryst. A51, 565–569] resulted in improved reliability compared with that obtained from a popular empirical weighting scheme. The revised structure differs in several respects from that published previously.


2000 ◽  
Vol 56 (2) ◽  
pp. 273-286 ◽  
Author(s):  
Brian O'Leary ◽  
Trevor R. Spalding ◽  
George Ferguson ◽  
Christopher Glidewell

The structure of 1,1,3,3,5,5-hexaphenyltrisiloxane-1,5-diol–pyrazine (4/1), (C36H32O4Si3)4·C4H4N2 (1), contains finite centrosymmetric aggregates; the diol units form dimers, by means of O—H...O hydrogen bonds, and pairs of such dimers are linked to the pyrazine by means of O—H...N hydrogen bonds. In 1,1,3,3,5,5-hexaphenyltrisiloxane-1,5-diol–pyridine (2/3), (C36H32O4Si3)2·(C5H5N)3 (2), the diol units are linked into centrosymmetric pairs by means of disordered O—H...O hydrogen bonds: two of the three pyridine molecules are linked to the diol dimer by means of ordered O—H...N hydrogen bonds, while the third pyridine unit, which is disordered across a centre of inversion, links the diol dimers into a C 3 3(9) chain by means of O—H...N and C—H...O hydrogen bonds. In 1,1,3,3-tetraphenyldisiloxane-1,3-diol–hexamethylenetetramine (1/1), (C24H22O3Si2)·C6H12N4 (3), the diol acts as a double donor and the hexamethylenetetramine acts as a double acceptor in ordered O—H...N hydrogen bonds and the structure consists of C 2 2(10) chains of alternating diol and amine units. In 1,1,3,3-tetraphenyldisiloxane-1,3-diol–2,2′-bipyridyl (1/1), C24H22O3Si2·C10H8N2 (4), there are two independent diol molecules, both lying across centres of inversion and therefore both containing linear Si—O—Si groups: each diol acts as a double donor of hydrogen bonds and the unique 2,2′-bipyridyl molecule acts as a double acceptor, thus forming C 2 2(11) chains of alternating diol and amine units. The structural motif in 1,1,3,3-tetraphenyldisiloxane-1,3-diol–pyrazine (2/1), (C24H22O3Si2)2·C4H4N2 (5), is a chain-of-rings: pairs of diol molecules are linked by O—H...O hydrogen bonds into centrosymmetric R 2 2(12) dimers and these dimers are linked into C 2 2(13) chains by means of O—H...N hydrogen bonds to the pyrazine units. 1,1,3,3-Tetraphenyldisiloxane-1,3-diol–pyridine (1/1), C24H22O3Si2·C5H5N (6), and 1,1,3,3-tetraphenyldisiloxane-1,3-diol–pyrimidine (1/1), C24H22O3Si2·C4H4N2 (7), are isomorphous: in each compound the amine unit is disordered across a centre of inversion. The diol molecules form C(6) chains, by means of disordered O—H...O hydrogen bonds, and these chains are linked into two-dimensional nets built from R 6 6(26) rings, by a combination of O—H...N and C—H...O hydrogen bonds.


2010 ◽  
Vol 66 (6) ◽  
pp. 733-740 ◽  
Author(s):  
Kay Diederichs

An indicator which is calculated after the data reduction of a test data set may be used to estimate the (systematic) instrument error at a macromolecular X-ray source. The numerical value of the indicator is the highest signal-to-noise [I/σ(I)] value that the experimental setup can produce and its reciprocal is related to the lower limit of the mergingRfactor. In the context of this study, the stability of the experimental setup is influenced and characterized by the properties of the X-ray beam, shutter, goniometer, cryostream and detector, and also by the exposure time and spindle speed. Typical values of the indicator are given for data sets from the JCSG archive. Some sources of error are explored with the help of test calculations usingSIM_MX[Diederichs (2009),Acta Cryst.D65, 535–542]. One conclusion is that the accuracy of data at low resolution is usually limited by the experimental setup rather than by the crystal. It is also shown that the influence of vibrations and fluctuations may be mitigated by a reduction in spindle speed accompanied by stronger attenuation.


2007 ◽  
Vol 63 (11) ◽  
pp. o4354-o4354
Author(s):  
Hong-Yan Ma ◽  
Ji Shi ◽  
Chang-Hong Wang ◽  
Zheng-Tao Wang

The title compound, C14H10O5, was isolated from Senecio cannabifolius Less var. integrifolius aqueous extract. The structure was elucidated on the basis of spectroscopic data, including MS, 1H NMR and 13C NMR, and the relative configuration was confirmed by X-ray crystallographic analysis. The benzofuran ring is almost coplanar with the furan ring [dihedral angle = 10.47 (15)°]. A chain is formed through supramolecular R 2 2(10) synthons and three-centre hydrogen bonds.


Author(s):  
Alagappa Rammohan ◽  
James A. Kaduk

The crystal structure of dirubidium hydrogen citrate, 2Rb+·HC6H5O72−, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The un-ionized carboxylic acid group forms helical chains of very strong hydrogen bonds (O...O ∼ 2.42 Å) along thebaxis. The hydroxy group participates in a chain of intra- and intermolecular hydrogen bonds along thecaxis. These hydrogen bonds result in corrugated hydrogen-bonded layers in thebcplane. The Rb+cations are six-coordinate, and share edges and corners to form layers in theabplane. The interlayer contacts are composed of the hydrophobic methylene groups.


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