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Foize Ahmad G, Syed Mohammed Mujaheer A, NizamMohideen M, Gulam Mohamed M, Viswanathan V. The crystal structures and Hirshfeld surface analysis of 6-(naphthalen-1-yl)-6a-nitro-6,6a,6b,7,9,11a-hexa-hydro-spiro-[chromeno[3',4':3,4]pyrrolo-[1,2- c]thia-zole-11,11'-indeno-[1,2- b]quinoxaline] and 6'-(naphthalen-1-yl)-6a'-nitro-6',6a',6b',7',8',9',10',12a'-octa-hydro-2 H-spiro-[ace-naphthyl-ene-1,12'-chromeno[3,4- a]indolizin]-2-one. ACTA CRYSTALLOGRAPHICA SECTION E-CRYSTALLOGRAPHIC COMMUNICATIONS 2019; 75:1519-1524. [PMID: 31636986 PMCID: PMC6775748 DOI: 10.1107/s205698901901291x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/18/2019] [Indexed: 12/02/2022]
Abstract
The crystal structures of the title spiro derivatives are described and the analysis of the intermolecular contacts in the crystals using Hirshfeld surface analysis and two-dimensional fingerprint plots is reported. The title compounds, 6-(naphthalen-1-yl)-6a-nitro-6,6a,6 b,7,9,11a-hexahydrospiro[chromeno[3′,4′:3,4]pyrrolo[1,2-c]thiazole-11,11′-indeno[1,2-b]quinoxaline], C37H26N4O3S, (I), and 6′-(naphthalen-1-yl)-6a′-nitro-6′,6a′,6b′,7′,8′,9′,10′,12a′-octahydro-2H-spiro[acenaphthylene-1,12′-chromeno[3,4-a]indolizin]-2-one, C36H28N2O4, (II), are new spiro derivatives, in which both the pyrrolidine rings adopt twisted conformations. In (I), the five-membered thiazole ring adopts an envelope conformation, while the eight-membered pyrrolidine-thiazole ring adopts a boat conformation. An intramolecular C—H⋯N hydrogen bond occurs, involving a C atom of the pyran ring and an N atom of the pyrazine ring. In (II), the six-membered piperidine ring adopts a chair conformation. An intramolecular C—H⋯O hydrogen bond occurs, involving a C atom of the pyrrolidine ring and the keto O atom. For both compounds, the crystal structure is stabilized by intermolecular C—H⋯O hydrogen bonds. In (I), the C—H⋯O hydrogen bonds link adjacent molecules, forming R22(16) loops propagating along the b-axis direction, while in (II) they form zigzag chains along the b-axis direction. In both compounds, C—H⋯π interactions help to consolidate the structure, but no significant π–π interactions with centroid–centroid distances of less than 4 Å are observed.
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Affiliation(s)
- G Foize Ahmad
- PG & Research Department of Physics, The New College (Autonomous), University of Madras, Chennai 600 014, Tamil Nadu, India
| | - A Syed Mohammed Mujaheer
- PG & Research Department of Physics, The New College (Autonomous), University of Madras, Chennai 600 014, Tamil Nadu, India
| | - M NizamMohideen
- PG & Research Department of Physics, The New College (Autonomous), University of Madras, Chennai 600 014, Tamil Nadu, India
| | - M Gulam Mohamed
- PG & Research Department of Physics, The New College (Autonomous), University of Madras, Chennai 600 014, Tamil Nadu, India
| | - V Viswanathan
- Department of Biophysics, All India Institute of Medical Science, New Delhi 110029, India
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NizamMohideen M, Syed Abuthahir S, Viswanathan V, Velmurugan D, Karthik Ananth M. The crystal structures and Hirshfeld surface analyses of four 3,5-diacetyl-2-methyl-2,3-di-hydro-1,3,4-thia-diazol-2-yl derivatives. ACTA CRYSTALLOGRAPHICA SECTION E-CRYSTALLOGRAPHIC COMMUNICATIONS 2019; 75:1436-1444. [PMID: 31636972 PMCID: PMC6775747 DOI: 10.1107/s2056989019011915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/28/2019] [Indexed: 11/10/2022]
Abstract
The crystal structures of four 3,5-diacetyl-2-methyl-2,3-dihydro-1,3,4-thiadiazol-2-yl derivatives, viz. 4-phenyl benzoate, 4-phenyl isobutyrate, 4-phenyl propionate and 4-phenyl cinnamate, are described and the intermolecular contacts in the crystals are analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots. The title compounds, 4-(5-acetamido-3-acetyl-2-methyl-2,3-dihydro-1,3,4-thiadiazol-2-yl)phenyl benzoate, C20H19N3O4S (I), 4-(5-acetamido-3-acetyl-2-methyl-2,3-dihydro-1,3,4-thiadiazol-2-yl)phenyl isobutyrate 0.25-hydrate, C17H21N3O4S·0.25H2O (II), 4-(5-acetamido-3-acetyl-2-methyl-2,3-dihydro-1,3,4-thiadiazol-2-yl)phenyl propionate, C16H19N3O4S (III) and 4-(5-acetamido-3-acetyl-2-methyl-2,3-dihydro-1,3,4-thiadiazol-2-yl)phenyl cinnamate chloroform hemisolvate, C22H21N3O4S·0.5CHCl3 (IV), all crystallize with two independent molecules (A and B) in the asymmetric unit in the triclinic P space group. Compound II crystallizes as a quaterhydrate, while compound IV crystallizes as a chloroform hemisolvate. In compounds I, II, III (molecules A and B) and IV (molecule A) the five-membered thiadiazole ring adopts an envelope conformation, with the tetrasubstituted C atom as the flap. In molecule B of IV this ring is flat (r.m.s. deviation 0.044 Å). The central benzene ring is in general almost normal to the mean plane of the thiadiazole ring in each molecule, with dihedral angles ranging from 75.8 (1) to 85.5 (2)°. In the crystals of all four compounds, the A and B molecules are linked via strong N—H⋯O hydrogen bonds and generate centrosymmetric four-membered R44(28) ring motifs. There are C—H⋯O hydrogen bonds present in the crystals of all four compounds, and in I and II there are also C—H⋯π interactions present. The intermolecular contacts in the crystals of all four compounds were analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots.
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Affiliation(s)
- M NizamMohideen
- PG & Research Department of Physics, The New College (Autonomous), University of Madras, Chennai 600 014, Tamil Nadu, India
| | - S Syed Abuthahir
- PG & Research Department of Physics, The New College (Autonomous), University of Madras, Chennai 600 014, Tamil Nadu, India
| | - V Viswanathan
- Department of Biophysics, All India Institute of Medical Science, New Delhi 110 029, India
| | - D Velmurugan
- CAS in Crystallography and Biophysics, University of Madras, Chennai 600 025, India
| | - M Karthik Ananth
- Department of Food Quality & Safety, Institute for Postharvest and Food Sciences, Volcani Center, ARO, Rishon LeZion 7528809, Israel
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Syed Abuthahir S, NizamMohideen M, Viswanathan V, Abiraman T, Balasubramanian S. The crystal structures and Hirshfeld surface analysis of N', N'''-((1 E,1' E)-{[methyl-enebis(-oxy)]bis-(6-bromo-3,1-phenyl-ene)}bis-(methan-ylyl-idene))bis-(isonicotinohydrazide) dihydrate and N', N'''-((1 E,1' E)-{[butane-1,4-diylbis(-oxy)]bis-(2,1-phenyl-ene)}bis-(methan-ylyl-idene))bis-(isonicotino-hydrazide) [+ solvent]. Acta Crystallogr E Crystallogr Commun 2019; 75:655-661. [PMID: 31110806 PMCID: PMC6505606 DOI: 10.1107/s2056989019005048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 04/12/2019] [Indexed: 11/27/2022]
Abstract
The title compounds, C27H20Br2N6O4·2H2O, (I), and C30H28N6O4·[+ solvent], (II), both crystallize with one half-mol-ecule in the asymmetric unit. The whole mol-ecule of (I) is generated by twofold rotation symmetry, with the twofold rotation axis bis-ecting the C atom of the -O-CH2-O- bridge. This results in a folded or U-shaped conformation of the mol-ecule. The whole mol-ecule of (II) is generated by inversion symmetry, with the central CH2-CH2 bond of the -O-(CH2)4-O- bridge being located about a center of inversion. This results in a step-like conformation of the mol-ecule. The central C(=O)N-N=C regions of the isonicotinohydrazide moieties in both compounds are planar and the configuration about the imine C=N bonds is E. In compound (I), the benzene and pyridine rings are inclined to each other by 37.60 (6)°. The two symmetry-related pyridine rings are inclined to each other by 74.24 (6)°, and the two symmetry-related benzene rings by 7.69 (6)°. In compound (II), the benzene and pyridine rings are inclined to each other by 25.56 (11)°. The symmetry-related pyridine rings are parallel, as are the two symmetry-related benzene rings. In the crystal of (I), a pair of water mol-ecules link the organic mol-ecules via Owater-H⋯O and Owater-H⋯N hydrogen bonds, forming chains along [001], and enclosing an R 4 2(8) and two R 1 2(5) ring motifs. The chains are linked by N-H⋯Npyridine hydrogen bonds, forming a supra-molecular framework. There are also a number of C-H⋯O hydrogen bonds, and C-H⋯π and offset π-π inter-actions [inter-planar distance = 3.294 (1) Å] present reinforcing the framework. In the crystal of (II), mol-ecules are linked by N-H⋯Npyridine hydrogen bonds, forming a supra-molecular framework. Here too there are also a number of C-H⋯O hydrogen bonds present, and a C-H⋯π inter-action, reinforcing the framework. For compound (II), a region of disordered electron density was corrected for using the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9-18] routine in PLATON. Their formula mass and unit-cell characteristics were not taken into account during refinement.
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Affiliation(s)
- S. Syed Abuthahir
- PG & Research Department of Physics, The New College (Autonomous), Chennai 600 014, Tamil Nadu, India
| | - M. NizamMohideen
- PG & Research Department of Physics, The New College (Autonomous), Chennai 600 014, Tamil Nadu, India
| | - V. Viswanathan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
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Abstract
The asymmetric unit of the title molecular salt, C7H10N+·C2Cl3O2−, consists of two cations and two anions. In the crystal, N—H...O hydrogen bonds link the components into [100] chains incorporatingR23(10) loops and weak π–π stacking [centroid-to-centroid distance = 3.865 (2) Å] is also observed.
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Sathya K, Dhamodharan P, Dhandapani M. Computational, spectral and structural studies of a new non linear optical crystal: 2-hydroxy pyridinium 3,5-dinitrobenzoate. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sivakumar P, Sudhahar S, Israel S, Chakkaravarthi G. 2-Amino-4-methylpyridinium 2-(4-nitrophenyl)acetate. IUCRDATA 2016. [DOI: 10.1107/s2414314616012037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In the title molecular salt, C6H9N2+·C8H6NO4−, the cation is protonated at its pyridine N atom. In the crystal, the anions are connected by a pair of C—H...O contacts into [100] chains, which generateR22(11) loops and these chains are linkedviaanother C—H...O contact which encloses anR24(10) loop. Adjacent anions and cations are connected through N—H... O hydrogen bonds, generating anR22(8) loop. Two pairs of anions and cations are linked by N—H...O hydrogen bonds, forming a tetramer with anR22(8) loop motif. The packing also features weak C—H...π and π–π [centroid-to-centroid distances = 3.8972 (11) and 3.9549 (10) Å] interactions, which result in a three-dimensional network.
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Sivakumar P, Devi RN, Israel S, Chakkaravarthi G. 2-Amino-3-methylpyridinium 4-methoxybenzoate. IUCRDATA 2016. [DOI: 10.1107/s2414314616011263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In the title molecular salt, C6H9N2+·C8H7O3−, the cation is protonated at its pyridine N atom and is inclined by 3.39 (9)° to the benzene ring of the anion, which is deprotonated at the carboxyl group. The methoxy group is twisted with respect to the benzene ring to which it is attached, the methyl C atom deviating from the ring plane by 0.023 (2) Å. In the crystal, the anions and cations are linked by two N—H...O hydrogen bonds, forming anR22(8) ring motif. They are also linked by a weak offset π–π interaction [centroid-to-centroid distance = 3.890 (1) Å]. The anions and cations are further connected through N—H...O and C—H...O hydrogen bonds, forming slabs parallel to (001).
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Rajkumar MA, NizamMohideen M, Xavier SSJ, Anbarasu S, Devarajan DPA. Crystal structure of 2-amino-5-nitro-pyridinium sulfamate. ACTA CRYSTALLOGRAPHICA SECTION E-CRYSTALLOGRAPHIC COMMUNICATIONS 2015; 71:231-3. [PMID: 25878827 PMCID: PMC4384627 DOI: 10.1107/s2056989015000365] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/08/2015] [Indexed: 11/23/2022]
Abstract
The title molecular salt, obtained by the reaction of sulfamic acid with 2-amino-5-nitropyridine, is the result of a proton transfer from sulfamic acid to the N atom of the pyridine ring. In the crystal, the cations and anions are linked by a number of N—H⋯O and N—H⋯N hydrogen bonds, forming sheets lying parallel to (100). The title molecular salt, C5H6N3O2+ ·H2NO3S−, was obtained from the reaction of sulfamic acid with 2-amino-5-nitropyridine. A proton transfer from sulfamic acid to the pyridine N atom occurred, resulting in the formation of a salt. As expected, this protonation leads to the widening of the C—N—C angle of the pyridine ring, to 122.9 (3)°, with the pyridinium ring being essentially planar (r.m.s. deviation = 0.025 Å). In the crystal, the ion pairs are joined by three N—H⋯O and one N—H⋯N hydrogen bonds in which the pyridinium N atom and the amino N atom act as donors, and are hydrogen bonded to the carboxylate O atoms and the N atom of the sulfamate anion, thus generating an R33(22) ring motif. These motifs are linked by further N—H⋯O hydrogen bonds enclosing R33(8) loops, forming sheets parallel to (100). The sheets are linked via weak C—H⋯O hydrogen bonds, forming a three-dimensional structure. The O atoms of the nitro group are disordered over two sets of sites with a refined occupancy ratio of 0.737 (19):0.263 (19).
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Affiliation(s)
- M Ambrose Rajkumar
- Physics Research Centre, Department of Physics, St. Xavier's College (Autonomous), Palayamkottai 627 002, Tamil Nadu, India
| | - M NizamMohideen
- Department of Physics, The New College (Autonomous), Chennai 600 014, Tamil Nadu, India
| | - S Stanly John Xavier
- Department of Chemistry, St. Xavier's College (Autonomous), Palayamkottai 627 002, Tamil Nadu, India
| | - S Anbarasu
- Physics Research Centre, Department of Physics, St. Xavier's College (Autonomous), Palayamkottai 627 002, Tamil Nadu, India
| | - Dr Prem Anand Devarajan
- Physics Research Centre, Department of Physics, St. Xavier's College (Autonomous), Palayamkottai 627 002, Tamil Nadu, India
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Sivakumar N, Muralidharan S, Chakkaravarthi G, Velmurugan D, Anbalagan G. Crystal structure of bis[4-(dimethylamino)pyridinium] bis(2-nitrobenzoate) trihydrate. Acta Crystallogr Sect E Struct Rep Online 2014; 70:221-3. [PMID: 25484657 PMCID: PMC4257197 DOI: 10.1107/s1600536814020583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 09/14/2014] [Indexed: 11/10/2022]
Abstract
The title salt, 2C7H11N2+·2C7H4NO4−·3H2O, crystallized with two anions and two cations in the asymmetric unit, together with three water molecules. Both 4-dimethylaminopyridinium cations are protonated at their pyridine N atoms with the plane of the N(CH3)2hetero atoms inclined to the pyridine ring by 4.5 (2) and 1.4 (2)°. In the 2-nitrobenzoate anions, the carboxyl and nitro groups are inclined to their respective benzene rings by 77.1 (3) and 20.0 (3)°, and 75.8 (2) and 20.9 (3)°. In the crystal, the anions are linkedviaO—H...O hydrogen bonds involving the water molecules, forming chains along [100]. The cations are linked to these chains by N—H...O hydrogen bonds. The chains are linkedviaC—H...O hydrogen bonds and C—H...π and π–π interactions [inter-centroid distances range from 3.617 (1) to 3.851 (1) Å], forming a three-dimensional structure.
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Babu KSS, Dhavamurthy M, NizamMohideen M, Peramaiyan G, Mohan R. 2-Amino-6-methyl-pyridinium 4-methyl-benzene-sulfonate. Acta Crystallogr Sect E Struct Rep Online 2014; 70:o600-1. [PMID: 24860395 PMCID: PMC4011207 DOI: 10.1107/s1600536814008587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 04/15/2014] [Indexed: 11/10/2022]
Abstract
In the asymmetric unit of the title salt, C6H9N2+·C7H7O3S−, there are two independent 2-amino-6-methylpyridinium cations and two independent 4-methylbenzenesulfonate anions. Both cations are protonated at their pyridine N atoms and their geometries reveal amine–imine tautomerism. In the 4-methylbenzenesulfonate anions, the carboxylate groups are twisted out of the benzene ring planes by 88.4 (1) and 86.2 (2)°. In the crystal, the sulfonate O atoms of an anion interact with the protonated N atoms and the 2-amino groups of a cation via a pair of N—H⋯O hydrogen bonds, forming an R22(8) ring motif. These motifs are connected via N—H⋯O hydrogen bonds, forming chains running along the a-axis direction. Within the chains there are weak C—H⋯O hydrogen bonds present. In addition, aromatic π–π stacking interactions [centroid–centroid distances = 3.771 (2), 3.599 (2), 3.599 (2) and 3.497 (2) Å] involving neighbouring chains are also observed.
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Affiliation(s)
- K Syed Suresh Babu
- Department of Physics, Presidency College (Autonomous), Chennai 600 005, Tamil Nadu, India ; Department of Physics, The New College (Autonomous), Chennai 600 014, Tamil Nadu, India
| | - M Dhavamurthy
- Department of Physics, Presidency College (Autonomous), Chennai 600 005, Tamil Nadu, India
| | - M NizamMohideen
- Department of Physics, The New College (Autonomous), Chennai 600 014, Tamil Nadu, India
| | - G Peramaiyan
- Department of Physics, Presidency College (Autonomous), Chennai 600 005, Tamil Nadu, India
| | - R Mohan
- Department of Physics, Presidency College (Autonomous), Chennai 600 005, Tamil Nadu, India
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Rajkumar MA, Xavier SSJ, Anbarasu S, Devarajan PA, NizamMohideen M. 2-Amino-5-nitro-pyridinium hydrogen oxalate. Acta Crystallogr Sect E Struct Rep Online 2014; 70:o473-4. [PMID: 24826170 PMCID: PMC3998560 DOI: 10.1107/s160053681400525x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/07/2014] [Indexed: 11/18/2022]
Abstract
In the cation of the title molecular salt, C5H6N3O2+·C2HO4−, the dihedral angle between the aromatic ring and the nitro group is 3.5 (3)°; in the anion, the dihedral angle between the CO2 and CO2H planes is 10.5 (2)°. In the crystal, the anions are linked into [100] chains by O—H⋯O hydrogen bonds. The cations cross-link the chains by way of N—H⋯O hydrogen bonds and the structure is consolidated by C—H⋯O interactions.
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Affiliation(s)
- M Ambrose Rajkumar
- Physics Research Centre, Department of Physics, St Xavier's College (Autonomous), Palayamkottai 627 002, Tamil Nadu, India
| | - S Stanly John Xavier
- Department of Chemistry, St Xavier's College (Autonomous), Palayamkottai 627 002, Tamil Nadu, India
| | - S Anbarasu
- Physics Research Centre, Department of Physics, St Xavier's College (Autonomous), Palayamkottai 627 002, Tamil Nadu, India
| | - Prem Anand Devarajan
- Physics Research Centre, Department of Physics, St Xavier's College (Autonomous), Palayamkottai 627 002, Tamil Nadu, India
| | - M NizamMohideen
- Department of Physics, The New College (Autonomous), Chennai 600 014, Tamil Nadu, India
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