Heterocyclic tautomerism: reassignment of two crystal structures of 2-amino-1,3-thiazolidin-4-one derivatives

2014 ◽  
Vol 70 (8) ◽  
pp. 812-816 ◽  
Author(s):  
Andrzej K. Gzella ◽  
Marcin Kowiel ◽  
Aneta Suseł ◽  
Magdalena N. Wojtyra ◽  
Roman Lesyk

The structures of 5-(2-hydroxyethyl)-2-[(pyridin-2-yl)amino]-1,3-thiazolidin-4-one, C10H11N3O2S, (I), and ethyl 4-[(4-oxo-1,3-thiazolidin-2-yl)amino]benzoate, C12H12N2O3S, (II), which are identical to the entries with refcodes GACXOZ [Váňaet al.(2009).J. Heterocycl. Chem.46, 635–639] and HEGLUC [Behbehani & Ibrahim (2012).Molecules,17, 6362–6385], respectively, in the Cambridge Structural Database [Allen (2002).Acta Cryst.B58, 380–388], have been redetermined at 130 K. This structural study shows that both investigated compounds exist in their crystal structures as the tautomer with the carbonyl–imine group in the five-membered heterocyclic ring and an exocyclic amine N atom, rather than the previously reported tautomer with a secondary amide group and an exocyclic imine N atom. The physicochemical and spectroscopic data of the two investigated compounds are the same as those of GACXOZ and HEGLUC, respectively. In the thiazolidin-4-one system of (I), the S and chiral C atoms, along with the hydroxyethyl group, are disordered. The thiazolidin-4-one fragment takes up two alternative locations in the crystal structure, which allows the molecule to adoptRandSconfigurations. The occupancy factors of the disordered atoms are 0.883 (2) (for theRconfiguration) and 0.117 (2) (for theSconfiguration). In (I), the main factor that determines the crystal packing is a system of hydrogen bonds, involving both strong N—H...N and O—H...O and weak C—H...O hydrogen bonds, linking the molecules into a three-dimensional hydrogen-bond network. On the other hand, in (II), the molecules are linkedviaN—H...O hydrogen bonds into chains.

2014 ◽  
Vol 70 (10) ◽  
pp. 998-1002 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Atekeh Tarahhomi ◽  
Arnold L. Rheingold ◽  
James A. Golen

InN,N,N′,N′-tetraethyl-N′′-(4-fluorobenzoyl)phosphoric triamide, C15H25FN3O2P, (I), andN-(2,6-difluorobenzoyl)-N′,N′′-bis(4-methylpiperidin-1-yl)phosphoric triamide, C19H28F2N3O2P, (II), the C—N—C angle at each tertiary N atom is significantly smaller than the two P—N—C angles. For the other new structure,N,N′-dicyclohexyl-N′′-(2-fluorobenzoyl)-N,N′-dimethylphosphoric triamide, C21H33FN3O2P, (III), one C—N—C angle [117.08 (12)°] has a greater value than the related P—N—C angle [115.59 (9)°] at the same N atom. Furthermore, for most of the analogous structures with a [C(=O)NH]P(=O)[N(C)(C)]2skeleton deposited in the Cambridge Structural Database [CSD; Allen (2002).Acta Cryst.B58, 380–388], the C—N—C angle is significantly smaller than the two P—N—C angles; exceptions were found for four structures with theN-methylcyclohexylamide substituent, similar to (III), one structure with the seven-membered cyclic amide azepan-1-yl substituent and one structure with anN-methylbenzylamide substituent. The asymmetric units of (I), (II) and (III) contain one molecule, and in the crystal structures, adjacent molecules are linkedviapairs of N—H...O=P hydrogen bonds to form dimers.


2013 ◽  
Vol 69 (12) ◽  
pp. 1549-1552 ◽  
Author(s):  
Vladimir V. Chernyshev ◽  
Sergey Y. Efimov ◽  
Ksenia A. Paseshnichenko ◽  
Andrey A. Shiryaev

The title salt, C8H12NO+·C7H10NO5−, crystallizes in two polymorphic modifications,viz.monoclinic (M) and orthorhombic (O). The crystal structures of both polymorphic modifications have been established from laboratory powder diffraction data. The crystal packing motifs in the two polymorphs are different, but the conformations of the anions are generally similar. InM, the anions are linked by pairs of hydrogen bonds of the N—H...O and O—H...O types into chains along theb-axis direction, and neighbouring molecules within the chain are related by the 21screw axis. The cations link these chainsviaO—H...O and N—H...O hydrogen bonds into layers parallel to (001). InO, the anions are linked by O—H...O hydrogen bonds into helices along [001], and neighbouring molecules within the helix are related by the 21screw axis. The neighbouring helical turns are linked by N—H...O hydrogen bonds. The cations link the helicesviaO—H...O and N—H...O hydrogen bonds, thus forming a three-dimensional network.


2018 ◽  
Vol 74 (8) ◽  
pp. 1111-1116 ◽  
Author(s):  
Shet M. Prakash ◽  
S. Naveen ◽  
N. K. Lokanath ◽  
P. A. Suchetan ◽  
Ismail Warad

2-Aminopyridine and citric acid mixed in 1:1 and 3:1 ratios in ethanol yielded crystals of two 2-aminopyridinium citrate salts, viz. C5H7N2 +·C6H7O7 − (I) (systematic name: 2-aminopyridin-1-ium 3-carboxy-2-carboxymethyl-2-hydroxypropanoate), and 3C5H7N2 +·C6H5O7 3− (II) [systematic name: tris(2-aminopyridin-1-ium) 2-hydroxypropane-1,2,3-tricarboxylate]. The supramolecular synthons present are analysed and their effect upon the crystal packing is presented in the context of crystal engineering. Salt I is formed by the protonation of the pyridine N atom and deprotonation of the central carboxylic group of citric acid, while in II all three carboxylic groups of the acid are deprotonated and the charges are compensated for by three 2-aminopyridinium cations. In both structures, a complex supramolecular three-dimensional architecture is formed. In I, the supramolecular aggregation results from Namino—H...Oacid, Oacid...H—Oacid, Oalcohol—H...Oacid, Namino—H...Oalcohol, Npy—H...Oalcohol and Car—H...Oacid interactions. The molecular conformation of the citrate ion (CA3−) in II is stabilized by an intramolecular Oalcohol—H...Oacid hydrogen bond that encloses an S(6) ring motif. The complex three-dimensional structure of II features Namino—H...Oacid, Npy—H...Oacid and several Car—H...Oacid hydrogen bonds. In the crystal of I, the common charge-assisted 2-aminopyridinium–carboxylate heterosynthon exhibited in many 2-aminopyridinium carboxylates is not observed, instead chains of N—H...O hydrogen bonds and hetero O—H...O dimers are formed. In the crystal of II, the 2-aminopyridinium–carboxylate heterosynthon is sustained, while hetero O—H...O dimers are not observed. The crystal structures of both salts display a variety of hydrogen bonds as almost all of the hydrogen-bond donors and acceptors present are involved in hydrogen bonding.


Author(s):  
Jecika Maciel Velasques ◽  
Vanessa Carratu Gervini ◽  
Lisliane Kickofel ◽  
Renan Lira de Farias ◽  
Adriano Bof de Oliveira

The acetic acid-catalyzed reaction between 5-chloroisatin and 4-methylthiosemicarbazide yields the title compound, C10H9ClN4OS (I) (common name: 5-chloroisatin-4-methylthiosemicarbazone). The molecule is nearly planar (r.m.s. deviation = 0.047 Å for all non-H atoms), with a maximum deviation of 0.089 (1) Å for the O atom. AnS(6) ring motif formed by an intramolecular N—H...O hydrogen bond is observed. In the crystal, molecules are linked by N—H...O hydrogen bonds, forming chains propagating along thea-axis direction. The chains are linked by N—H...S hydrogen bonds, forming a three-dimensional supramolecular structure. The three-dimensional framework is reinforced by C—H...π interactions. The absolute structure of the molecule in the crystal was determined by resonant scattering [Flack parameter = 0.006 (9)]. The crystal structure of the same compound, measured at 100 K, has been reported on previously [Qasem Aliet al.(2012).Acta Cryst.E68, o964–o965]. The Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are the H...H (23.1%), H...C (18.4%), H...Cl (13.7%), H...S (12.0%) and H...O (11.3%) interactions. A molecular docking evaluation of the title compound with the ribonucleoside diphosphate reductase (RDR) enzyme was carried out. The title compound (I) and the active site of the selected enzyme show Cl...H—C(LYS140),Cg(aromatic ring)...H—C(SER71), H...O—C(GLU200)and FeIII...O...FeIIIintermolecular interactions, which suggests a solid theoretical structure–activity relationship.


2014 ◽  
Vol 70 (7) ◽  
pp. o816-o817
Author(s):  
R. A. Nagalakshmi ◽  
J. Suresh ◽  
S. Sivakumar ◽  
R. Ranjith Kumar ◽  
P. L. Nilantha Lakshman

In the title compound, C22H18BrN5O4, the central six-membered ring, derived from 1,4-dihydropyridine, adopts a distorted boat conformation with a puckering amplitude of 0.197 (3) Å, the imidazole ring adopts a twisted conformation with a puckering amplitude of 0.113 (3) Å, and the oxindole moiety is planar with an r.m.s. deviation of 0.0125 Å. Two intramolecular N—H...O hydrogen bonds are formed, each closing anS(6) loop. In the crystal, strong N—H...O hydrogen bonds lead to the formation of zigzag chains along thecaxis. These are consolidated in the three-dimensional crystal packing by weak N—H...O hydrogen bonding, as well as by C—H...O, C—H...Br and C—H...π interactions. A small region of electron density well removed from the main molecule was removed with the SQUEEZE procedure inPLATON[Spek (2009).Acta Cryst. D65, 148–155] following unsuccessful attempts to model it as a plausible solvent molecule. The unit-cell characteristics do not take into account this feature of the structure.


Author(s):  
Zeliha Atioğlu ◽  
Mehmet Akkurt ◽  
Namiq Q. Shikhaliyev ◽  
Ulviyya F. Askerova ◽  
Aytan A. Niyazova ◽  
...  

In the title compound, C16H12F5N3O, the dihedral angle between the aromatic rings is 31.84 (8)°. In the crystal, the molecules are linked into dimers possessing crystallographic twofold symmetry by pairwise N—H...O hydrogen bonds and weak C—H...O hydrogen bonds and aromatic π–π stacking interactions link the dimers into a three-dimensional network. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from F...H/H...F (41.1%), H...H (21.8%), C...H/H...C (9.7%) C...C (7.1%) and O...H/H...O (7.1%) contacts. The contribution of some disordered solvent to the scattering was removed using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18] in PLATON. The solvent contribution was not included in the reported molecular weight and density.


Author(s):  
Eliza de L. Chazin ◽  
Paola de S. Sanches ◽  
Thatyana R. A. Vasconcelos ◽  
Claudia R. B. Gomes ◽  
James L. Wardell ◽  
...  

The crystal structures of 6-methoxy-1,3-benzoxathiol-2-one, C9H8O3S, (I), and 2-oxo-1,3-benzoxathiol-6-yl acetate, C9H6O4S, (II), are described. Compound (I) is almost planar (r.m.s. deviation for the non-H atoms = 0.011 Å), whereas (II) shows a substantial twist between the fused-ring system and the acetate substituent [dihedral angle = 74.42 (3)°]. For both structures, the bond distances in the heterocyclic ring suggest that little if any conjugation occurs. In the crystal of (I), C—H...O hydrogen bonds link the molecules into [1-11] chains incorporating alternatingR22(8) andR22(12) inversion dimers. The extended structure of (II) featuresC(7) [201] chains linked by C—H...O hydrogen bonds, with further C—H...O bonds and weak π–π stacking interactions connecting the chains into a three-dimensional network. Hirshfeld fingerprint analyses for (I) and (II) are presented and discussed.


2015 ◽  
Vol 71 (11) ◽  
pp. 1388-1391
Author(s):  
Vinola Z. Rodrigues ◽  
C. P. Preema ◽  
S. Naveen ◽  
N. K. Lokanath ◽  
P. A. Suchetan

Crystal structures of twoN-(aryl)arylsulfonamides, namely, 4-methoxy-N-(4-methylphenyl)benzenesulfonamide, C14H15NO3S, (I), andN-(4-fluorophenyl)-4-methoxybenzenesulfonamide, C13H12FNO3S, (II), were determined and analyzed. In (I), the benzenesulfonamide ring is disordered over two orientations, in a 0.516 (7):0.484 (7) ratio, which are inclined to each other at 28.0 (1)°. In (I), the major component of the sulfonyl benzene ring and the aniline ring form a dihedral angle of 63.36 (19)°, while in (II), the planes of the two benzene rings form a dihedral angle of 44.26 (13)°. In the crystal structure of (I), N—H...O hydrogen bonds form infiniteC(4) chains extended in [010], and intermolecular C—H...πarylinteractions link these chains into layers parallel to theabplane. The crystal structure of (II) features N—H...O hydrogen bonds forming infinite one dimensionalC(4) chains along [001]. Further, a pair of C—H...O intermolecular interactions consolidate the crystal packing of (II) into a three-dimensional supramolecular architecture.


2015 ◽  
Vol 71 (10) ◽  
pp. 1159-1164 ◽  
Author(s):  
Chien Ing Yeo ◽  
Yee Seng Tan ◽  
Edward R. T. Tiekink

The crystal and molecular structures of the title salt, C8H8N3S2+·Cl−, (I), and salt hydrate, C8H7ClN3S2+·Cl−·H2O, (II), are described. The heterocyclic ring in (I) is statistically planar and forms a dihedral angle of 9.05 (12)° with the pendant phenyl ring. The comparable angle in (II) is 15.60 (12)°, indicating a greater twist in this cation. An evaluation of the bond lengths in the H2N—C—N—C—N sequence of each cation indicates significant delocalization of π-electron density over these atoms. The common feature of the crystal packing in (I) and (II) is the formation of charge-assisted amino-N—H...Cl−hydrogen bonds, leading to helical chains in (I) and zigzag chains in (II). In (I), these are linked by chains mediated by charge-assisted iminium-N+—H...Cl−hydrogen bonds into a three-dimensional architecture. In (II), the chains are linked into a layer by charge-assisted water-O—H...Cl−and water-O—H...O(water) hydrogen bonds with charge-assisted iminium-N+—H...O(water) hydrogen bonds providing the connections between the layers to generate the three-dimensional packing. In (II), the chloride anion and water molecules are resolved into two proximate sites with the major component being present with a site occupancy factor of 0.9327 (18).


Author(s):  
Charmaine Arderne

The crystal structure of the title salt, C5H16N22+·2Br−, withZ= 12 and more unusuallyZ′ = 3, forms part of a small group of crystal structures in the Cambridge Structural Database that are ammonium bromide salts. One of the diaminium cation chains in the asymmetric unit exhibits positional disorder, which was modelled using a suitable disorder model. This compound also exhibits organic–inorganic layering in its packing arrangement that is typical of this class of compound. An extensive complex three-dimensional hydrogen-bonding network is also identified. The hydrogen bonds evident in this crystal structure were identified as being most likely strong charge-assisted hydrogen bonds.


Sign in / Sign up

Export Citation Format

Share Document