Crystal structure of trimethylammonium 5-(2, 4-dinitrophenyl)-1, 3 ...

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Sep 4, 2014 - 5-(2,4-dinitrophenyl)-1,3-dimethyl-2,6- dioxo-1,2,3,6-tetrahydropyrimidin-4- olate. Sridevi Gunaseelan and Kalaivani Doraisamyraja*. PG and ...

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ISSN 1600-5368

Crystal structure of trimethylammonium 5-(2,4-dinitrophenyl)-1,3-dimethyl-2,6dioxo-1,2,3,6-tetrahydropyrimidin-4olate Sridevi Gunaseelan and Kalaivani Doraisamyraja* PG and Research Department of Chemistry, Seethalakshmi Ramaswami College, Tiruchirappalli 620 002, Tamil Nadu, India. *Correspondence e-mail: [email protected]

2. Experimental

Received 24 July 2014; accepted 4 September 2014

2.1. Crystal data Edited by A. J. Lough, University of Toronto, Canada

The asymmetric unit of the title molecular salt, C3H10N+C12H9N4O7 [alternative name: trimethylammonium 5-(2,4dinitrophenyl)-1,3-dimethyl barbiturate], contains one anion and two half-occupancy cations. The cations are disordered about inversion centres. The tetrahydropyrimidine ring is ˚ ] and essentially planar [maximum deviation = 0.007 (2) A forms a dihedral angle of 41.12 (6) with the plane of the benzene ring. In the crystal, N—H  O hydrogen bonds link the cations to the anions. Keywords: crystal structure; barbiturates; biological activity; trimethylammonium salt; tetrahydropyrimidin-4-olate salt; anionic -complexes. CCDC reference: 1022943

For the biological activity of barbiturates, see: Hueso et al. (2003); Kalaivani et al. (2008); Tripathi (2009); Kalaivani & Buvaneswari (2010). For various types of anionic -complexes, see: Terrier (1982); Gnanadoss & Kalaivani (1985); Al-Kaysi et al. (2005); For barbiturates as carbon-bonded -complexes, see: Kalaivani & Malarvizhi (2009); Buvaneswari & Kalaivani (2011); Kalaivani et al. (2012); Babykala & Kalaivani (2012, 2013); Sridevi & Kalaivani (2012); Rajamani & Kalaivani (2012). For the crystal structure of a related barbiturate, see: Mangaiyarkarasi & Kalaivani (2013)

Gunaseelan and Doraisamyraja

= 100.856 (2) ˚3 V = 915.66 (9) A Z=2 Mo K radiation  = 0.11 mm 1 T = 293 K 0.35  0.35  0.30 mm

2.2. Data collection Bruker Kappa APEXII CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2004) Tmin = 9536, Tmax = 9865

16319 measured reflections 4271 independent reflections 2922 reflections with I > 2(I) Rint = 0.026

2.3. Refinement

1. Related literature

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C3H10N+C12H9N4O7 Mr = 381.35 Triclinic, P1 ˚ a = 9.8417 (5) A ˚ b = 9.9474 (6) A ˚ c = 10.4241 (5) A = 103.454 (2) = 106.479 (2)

R[F 2 > 2(F 2)] = 0.051 wR(F 2) = 0.164 S = 0.99 4271 reflections 341 parameters 76 restraints

H atoms treated by a mixture of independent and constrained refinement ˚ 3 max = 0.23 e A ˚ 3 min = 0.20 e A

Table 1 ˚ ,  ). Hydrogen-bond geometry (A D—H  A

D—H

H  A

D  A

D—H  A

N5—H5A  O7 N6—H6A  O5

0.91 (2) 0.92 (2)

1.80 (2) 1.83 (2)

2.666 (3) 2.737 (3)

156 (2) 171 (2)

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT and XPREP (Bruker, 2004); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97.

doi:10.1107/S1600536814019977

Acta Cryst. (2014). E70, o1102–o1103

data reports Acknowledgements The authors are grateful to SERB–DST, New Delhi, for the financial support and SAIF, IIT Madras, for the data collection. Supporting information for this paper is available from the IUCr electronic archives (Reference: LH5722).

References Al-Kaysi, R. O., Mueller, A. M., Ahn, T. S., Lee, S. & Bardeen, C. J. (2005). Langmuir, 21, 7990–7994. Altomare, A., Cascarano, G., Giacovazzo, C. & Guagliardi, A. (1993). J. Appl. Cryst. 26, 343–350. Babykala, R. & Kalaivani, D. (2012). Acta Cryst. E68, o541. Babykala, R. & Kalaivani, D. (2013). Acta Cryst. E69, o398–o399. Bruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.

Acta Cryst. (2014). E70, o1102–o1103

Buvaneswari, M. & Kalaivani, D. (2011). Acta Cryst. E67, o1433–o1434. Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Gnanadoss, L. M. & Kalaivani, D. (1985). J. Org. Chem. 50, 1174–1178. Hueso, F., Moreno, M. N., Martinez, J. M. & Ramirez, M. J. (2003). J. Inorg. Biochem. 94, 326–334. Kalaivani, D. & Buvaneswari, M. (2010). Recent Advances in Clinical Medicine, pp. 255–260. Cambridge: WSEAS Publications. Kalaivani, D., Buvaneswari, M. & Rajeswari, S. (2012). Acta Cryst. E68, o29– o30. Kalaivani, D. & Malarvizhi, R. (2009). Acta Cryst. E65, o2548. Kalaivani, D., Malarvizhi, R. & Subbalakshmi, R. (2008). Med. Chem. Res. 17, 369–373. Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470. Mangaiyarkarasi, G. & Kalaivani, D. (2013). Acta Cryst. E69, o592–o593. Rajamani, K. & Kalaivani, D. (2012). Acta Cryst. E68, o2395. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Sridevi, G. & Kalaivani, D. (2012). Acta Cryst. E68, o1044. Terrier, F. (1982). Chem. Rev. 82, 77–152. Tripathi, K. D. (2009). In Essentials of Medical Pharmacology, 6th ed. Chennai: Jaypee Brothers.

Gunaseelan and Doraisamyraja



C3H10N+C12H9N4O7

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supporting information

supporting information Acta Cryst. (2014). E70, o1102–o1103

[doi:10.1107/S1600536814019977]

Crystal structure of trimethylammonium 5-(2,4-dinitrophenyl)-1,3-dimethyl-2,6dioxo-1,2,3,6-tetrahydropyrimidin-4-olate Sridevi Gunaseelan and Kalaivani Doraisamyraja S1. Comment Barbiturates are pyrimidine derivatives and most of them have anticonvulsant activity (Hueso et al., 2003; Kalaivani et al., 2008; Tripathi, 2009; Kalaivani & Buvaneswari, 2010). Various different types of anionic sigma complexes such as carbon-bonded, nitrogen-bonded, oxygen-bonded and Spiro-Meisenheimer complexes have been reported by different groups of scientists (Terrier, 1982; Gnanadoss & Kalaivani, 1985; Al-Kaysi et al., 2005). A number of crystalline barbiturates in the form of carbon-bonded sigma complexes have been prepared and reported by our group (Kalaivani & Malarvizhi, 2009; Buvaneswari & Kalaivani, 2011; Kalaivani et al., 2012; Babykala & Kalaivani, 2012; Sridevi & Kalaivani, 2012; Rajamani & Kalaivani, 2012; Babykala & Kalaivani, 2013). The asymmetric unit of a related barbiturate prepared from 1-chloro-2,4-dinitrobenzene (DNCB) and barbituric acid in the presence of trimethylamine (Mangaiyarkarasi & Kalaivani, 2013) comprises of two cations and two anions. However, in the present investigation, the asymmetric unit of the molecular salt is comprised of one 5-(2,4-dinitrophenyl)-1,3-dimethylbarbiturate anion and two half occupancy trimethylammonium cations. The molecular structure of the title compound is shown in Fig. 1. The cations lie on inversion centres and hence are disordered. In the crystal, N—H···O hydrogen bonds exist between the protonated nitrogen atoms of the cations and oxygen atoms of the carbonyl groups of anions. The tetrahydropyrimidine ring is essentially planar (maximum deviation = 0.007 (2) Å for N3) and forms a dihedral angle of 41.12 (6)Å with the benzene ring. The nitro group which para with respect to the junction of two rings forms a dihedral of -5.7 (2)° with the benzene ring and may be involved to a greater extent in electron delocalization with the benzene than the nitro group ortho to the junction of the two rings which forms a dihedral angle of 38.8 (2)° with the benzene ring. S2. Experimental Analytical grade 1-chloro-2,4-dinitrobenzene (2.02 g,0.01 mol) was dissolved in 20 ml of absolute alcohol. 1,3-Dimethylbarbituric acid (1.56 g,0.01 mol) was also dissolved in 30 ml of absolute alcohol separately. These two solutions were then mixed. To this mixture, 4 ml of trimethylamine (0.03 mol) was added and shaken well for 5–6 hrs. The slightly turbid solution obtained was filtered and kept as such at 298K. After a period of three weeks, dark shiny maroon red coloured crystals of the title salt crystallized out from the solution. The crystals were filtered, powdered well using agate mortar and washed with 30 ml of dry ether. The dry solid of the title compound obtained was quickly washed with 1 ml of absolute alcohol to remove unreacted reactants and finally with 25 ml of dry ether. The pure powder was recrystllized from hot etanol (Yield: 80%; m.pt; 513 K). Good quality single crystals, suitable for X-ray diffraction studies, were obtained by slow evaporation of a solution of the title compound in ethanol at room temperature. The crystals obtained were non-hygroscopic and extraordinarily stable at room temperature. Solubility at 298 K: 2.78 g/100 mL(water); 4.58 g/100 mL(Ethanol); 17.78 g/100 mL(DMSO).

Acta Cryst. (2014). E70, o1102–o1103

sup-1

supporting information S3. Refinement The hydrogen atoms boned to the N atoms of the cation were located in a difference Fourier map and refined isotropically with Uiso(H) = 1.2Ueq(N) and restrained to N—H = 0.91 (2)Å. Hydrogen atoms on methyl groups of the trimethyl ammonium cation were located in a difference Fourier map and refined with fixed isotropic displacement parameters with Uiso(H) = 1.5Ueq(C). The C—H and H···H distances were restrained to 0.96 (2)Å and 1.568 (2)Å respectively. All the other hydrogen atoms were geometrically constrained and allowed to ride on their parent atoms. The cations are disordered across inversion centres. There are two cation moieties in the asymmetric unit each with 0.5 site occupancy. The anisotropic displacement parameters of the disordered atoms were restrained with an effective standard deviation of 0.02. The N—C and C···C distances were restrained to 1.45 (2) Å and 2.36 (2) Å respectively.

Figure 1 The asymmetric unit of title compound showing 30% probability displacement ellipsoids. The cations are half occupancy. Trimethylammonium 5-(2,4-dinitrophenyl)-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate Crystal data C3H10N+·C12H9N4O7− Mr = 381.35 Triclinic, P1 a = 9.8417 (5) Å b = 9.9474 (6) Å c = 10.4241 (5) Å α = 103.454 (2)° β = 106.479 (2)° γ = 100.856 (2)° V = 915.66 (9) Å3

Z=2 F(000) = 400 Dx = 1.383 Mg m−3 Mo Kα radiation, λ = 0.71073 Å Cell parameters from 5386 reflections θ = 2.1–27.5° µ = 0.11 mm−1 T = 293 K Block, red 0.35 × 0.35 × 0.30 mm

Data collection Bruker Kappa APEXII CCD diffractometer Radiation source: fine-focus sealed tube ω and φ scan

Acta Cryst. (2014). E70, o1102–o1103

Absorption correction: multi-scan (SADABS; Bruker, 2004) Tmin = 9536, Tmax = 9865 16319 measured reflections 4271 independent reflections

sup-2

supporting information h = −12→12 k = −12→12 l = −13→13

2922 reflections with I > 2σ(I) Rint = 0.026 θmax = 27.7°, θmin = 2.1° Refinement Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.051 wR(F2) = 0.164 S = 0.99 4271 reflections 341 parameters 76 restraints Hydrogen site location: mixed

H atoms treated by a mixture of independent and constrained refinement w = 1/[σ2(Fo2) + (0.0891P)2 + 0.1912P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max < 0.001 Δρmax = 0.23 e Å−3 Δρmin = −0.20 e Å−3 Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 Extinction coefficient: 0.020 (4)

Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

C1 C2 H2 C3 C4 C5 H5 C6 H6 C7 C8 C9 C10 C11 H11A H11B H11C C12 H12A H12B H12C N1 N2 N3 N4

x

y

z

Uiso*/Ueq

0.3976 (2) 0.2837 (2) 0.2434 0.22965 (18) 0.29063 (16) 0.40705 (19) 0.4508 0.4590 (2) 0.5347 0.24320 (16) 0.21150 (17) 0.1589 (2) 0.23385 (19) 0.1303 (3) 0.1415 0.0301 0.1944 0.1746 (3) 0.1987 0.2405 0.0752 0.4546 (2) 0.09232 (17) 0.18912 (16) 0.16852 (17)

0.7207 (3) 0.6256 (2) 0.5342 0.66915 (18) 0.80221 (18) 0.8947 (2) 0.9853 0.8561 (3) 0.9208 0.84301 (17) 0.74090 (18) 0.9213 (2) 0.98455 (19) 0.6789 (3) 0.5884 0.6674 0.7116 1.1619 (2) 1.2185 1.2061 1.1559 0.6754 (3) 0.56946 (15) 1.01709 (16) 0.78490 (17)

0.07803 (19) 0.08545 (17) 0.0208 0.19261 (16) 0.29787 (16) 0.28249 (19) 0.3481 0.1734 (2) 0.1644 0.41888 (15) 0.48671 (16) 0.65492 (18) 0.46730 (18) 0.6741 (3) 0.6277 0.6704 0.7704 0.6375 (2) 0.5799 0.7326 0.6342 −0.0364 (2) 0.18014 (14) 0.58517 (15) 0.60370 (15)

0.0655 (6) 0.0548 (5) 0.066* 0.0440 (4) 0.0424 (4) 0.0584 (5) 0.070* 0.0712 (6) 0.085* 0.0415 (4) 0.0435 (4) 0.0560 (5) 0.0507 (4) 0.0840 (7) 0.126* 0.126* 0.126* 0.0740 (6) 0.111* 0.111* 0.111* 0.0970 (8) 0.0511 (4) 0.0531 (4) 0.0529 (4)

Acta Cryst. (2014). E70, o1102–o1103

Occ. (