2. Experimental Crystal data
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1 data reports ISSN Crystal structure of 5-[bis(methylsulfonyl)methyl]-1,3-dimethyl-5-(methylsulfonyl)pyrimidine-2,4,6(1H,3H,5H)-trione Eyad Mallah, a * Ahmed Al-Sheikh, a Kamal Sweidan, b Wael Abu Dayyih a and Manfred Steimann c a Faculty of Pharmacy and Medical Science, University of Petra, Amman, Jordan, b Department of Chemistry, Faculty of Science, University of Jordan, Amman, Jordan, and c Institut für Anorganische Chemie der Universität Tübingen, Auf der Morgenstelle 18, Tübingen, Germany. *Correspondence eyad782002@yahoo.com Received 8 December 2014; accepted 16 December 2014 Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland In the title compound, C 10 H 16 N 2 O 9 S 3, the pyrimidine ring of the 1,3-dimethyl barbituric acid moiety has an envelope conformation with the C atom carrying the methylsulfonyl and bis(methylsulfonyl)methyl substituents as the flap. The dihedral angle between mean plane of the pyrimidine ring and the S/C/S plane is 72.4 (3). In the crystal, molecules are linked via C HO hydrogen bonds, forming a threedimensional structure. Keywords: crystal structure; barbituric acid; pyrimidines; methylsulfonyl; trione; hydrogen bonding. CCDC reference: Experimental 2.1. Crystal data C 10 H 16 N 2 O 9 S 3 M r = Triclinic, P1 a = (16) Å b = (17) Å c = (3) Å = (3) = (3) 2.2. Data collection Stoe IPDS diffractometer measured reflections 3175 independent reflections 2.3. Refinement R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections Table 1 Hydrogen-bond geometry (Å, ). = (3) V = (3) Å 3 Z =2 Mo K radiation = 0.53 mm 1 T = 173 K mm 2582 reflections with I > 2(I) R int = parameters H-atom parameters constrained max = 0.39 e Å 3 min = 0.44 e Å 3 D HA D H HA DA D HA 1. Related literature For examples of the biological activity of pyrimidines, see: Habibi & Tarameshloo (2011); Holtkamp & Meierkord (2007). For aspects of nucleic acid binding, see: Demeunynck et al. (2004). For drug applications of C5-substituted barbituric and 2-thiobarbituric acids, see: Getova & Georgiev (1989); Kratt et al. (1990); Kotha et al. (2005). For the structures of similar compounds, see: Huang & Chen (1986); Ye et al. (1989); Al-Sheikh et al. (2009); Awad et al. (2014); Glidewell et al. (1995). For the synthesis of the starting material, see: Sweidan et al. (2009). C5 H5BO8 i (6) 131 C6 H6AO9 ii (5) 138 C8 H8CO8 iii (5) 133 C10 H10AO5 iv (5) 130 Symmetry codes: (i) x; y þ 1; z; (ii) x þ 1; y þ 2; z; (iii) x; y þ 2; z; (iv) x þ 1; y þ 1; z þ 1. Data collection: X-AREA (Stoe & Cie, 2008); cell refinement: X- AREA; data reduction: X-RED32 (Stoe & Cie, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008; molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009). Acknowledgements We are indebted to the University of Petra, the University of Jordan and the University of Tübingen for their endless help and support. o58 Mallah et al. doi: /s
2 data reports Supporting information for this paper is available from the IUCr electronic archives (Reference: SU5040). References Al-Sheikh, A., Sweidan, K., Kuhn, N., Maichle-Mössmer, C. & Steimann, M. (2009). Z. Naturforsch. Teil B, 64, Awad, R., Mallah, E., Abu Dayyih, W., Sweidan, K. & Steimann, M. (2014). Acta Cryst. E70, o877. Demeunynck, M., Bailly, C. & David Wilson, W. (2004). In Small Molecule DNA and RNA Binders: From Synthesis to Nucleic Acid Complexes. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA. Getova, D. & Georgiev, V. (1989). Acta Physiol. Pharmacol. Bulg. 15, Glidewell, C., Lightfoot, P. & Patterson, I. L. J. (1995). Acta Cryst. C51, Habibi, A. & Tarameshloo, Z. (2011). J. Iran. Chem. Soc. 8, Holtkamp, M. & Meierkord, H. (2007). Cell. Mol. Life Sci. 64, Huang, X. & Chen, B. (1986). Synthesis, pp Kotha, S., Deb, A. C. & Kumar, R. (2005). Bioorg. Med. Chem. Lett. 15, Kratt, G., Salbeck, G., Bonin, W. & Duewel, D. (1990). Ger. Offen. DE 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, Sheldrick, G. M. (2008). Acta Cryst. A64, Spek, A. L. (2009). Acta Cryst. D65, Stoe & Cie (2008). X-AREA and X-RED32. Stoe & Cie, Darmstadt, Germany. Sweidan, K., Abu-Rayyan, A., Al-Sheikh, A., Maichle-Mösmer, C., Steimann, M. & Kuhn, N. (2009). Z. Naturforsch. Teil B, 64, Ye, F., Chen, B. & Huang, X. (1989). Synthesis, pp Mallah et al. C 10 H 16 N 2 O 9 S 3 o59
3 [doi: /s ] Crystal structure of 5-[bis(methylsulfonyl)methyl]-1,3-dimethyl-5-(methylsulfonyl)pyrimidine-2,4,6(1H,3H,5H)-trione Eyad Mallah, Ahmed Al-Sheikh, Kamal Sweidan, Wael Abu Dayyih and Manfred Steimann S1. Comment Compounds containing pyrimidine play a vital role in biological activity (Habibi & Tarameshloo, 2011; Holtkamp & Meierkord, 2007). This activity differs from molecule to molecule depending on the tautomery and the nature of the substituents (Demeunynck et al., 2004). In view of the pharmaceutical significance of pyrimidines we became interested in obtaining new barbituric acid derivatives. C5-substituted barbituric and 2-thiobarbituric acids have been used for sedative, hypnotics and anticonvulsant drug applications (Getova & Georgiev 1989; Kratt et al., 1990; Kotha et al., 2005). 1,3-dimethyl barbituric acid has a tendency to accept negative charges by delocalization of π electrons and can exhibit zwitterionic nature. The title compound, which was synthesized via the reaction of 1,3-dimethyl-5-bis-(thiomethyl)methylenebarbituric acid and m-chloroperbenzoic acid, may find applications in bio-organic chemistry. Several noteworthy features are evident in the crystal structure of the title compound, Fig. 1. The three central sulfonyl groups utilize one methyl group which have almost identical S C bond lengths [S1 C (4) Å, S2 C (4) Å, S3 C (4) Å] and they are slightly shorter than those reported for (PhSO 2 ) 2 CH 2 (1.786 Å; Glidewell et al. 1995) and for bis(methylsulfonyl)methane (1.781 Å; Awad et al. 2014). Interestingly, significant elongation of the (C4 C7) bond length [1.547 (5) Å] may be attributed to interactions between the sulfonyl groups located at position C7. As a result of crystal packing the geometry of one of the sulfonyl groups is as expected; having one sulfur-oxygen bond slightly shorter than the other [S2 O1 = (3) Å, and S1 O3 = (3) Å]. The carbonyl groups that are located on the barbituric acid ring have approximately the same bond lengths, varying from (4) to (4) Å. The pyrimidine ring in barbituric acid moiety is significantly distorted from planarity and has an envelope conformation with atom C as the flap. In the crystal, molecules are linked via C H O hydrogen bonds forming a three-dimensional structure (Table 1 and Fig. 2) S2. Experimental The title compound was synthesized by adding m-chloroperbenzoic acid (4.5 g, 20 mmol) to a solution containing 1,3-dimethyl-5-bis-(thiomethyl)methylenebarbituric acid (1.3 g, 5 mmol; Sweidan et al., 2009), in dichloromethane (20 ml) at 213 K. After stirring overnight, the solvent was removed in vacuo. Diethylether (20 ml) was added and the precipitated solid was collected and recrystallized from CH 2 Cl 2 /Et 2 O to give colourless crystals (yield: 1.0 g, 51%). S3. Refinement The C-bound H atoms were included in calculated positions and treated as riding atoms: C H = Å with U iso (H) = 1.5U eq (C) for methyl H atoms and = 1.2U eq (C) for other H atoms. sup-1
4 Figure 1 The molecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 20% probability level. sup-2
5 Figure 2 A view along the a axis of the crystal packing of the title compound. The hydrogen bonds are shown as dashed lines (see Table 1 for details). 5-[Bis(methylsulfonyl)methyl]-1,3-dimethyl-5-(methylsulfonyl)pyrimidine-2,4,6(1H,3H,5H)-trione Crystal data C 10 H 16 N 2 O 9 S 3 M r = Triclinic, P1 Hall symbol: -P 1 a = (16) Å b = (17) Å c = (3) Å α = (3) β = (3) γ = (3) V = (3) Å 3 Data collection Stoe IPDS diffractometer Radiation source: fine-focus sealed tube Graphite monochromator phi scans measured reflections 3175 independent reflections Z = 2 F(000) = 420 D x = Mg m 3 Mo Kα radiation, λ = Å Cell parameters from 30 reflections θ = µ = 0.53 mm 1 T = 173 K Plate, colourless mm 2582 reflections with I > 2σ(I) R int = θ max = 26.4, θ min = 3.1 h = 9 9 k = l = sup-3
6 Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = wr(f 2 ) = S = reflections 223 parameters 0 restraints Primary atom site location: structure-invariant direct methods Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ 2 (F o2 ) + (0.P) P] where P = (F o 2 + 2F c2 )/3 (Δ/σ) max < Δρ max = 0.39 e Å 3 Δρ min = 0.44 e Å 3 Extinction correction: SHELXL97 (Sheldrick, 2008, Fc * =kfc[ xfc 2 λ 3 /sin(2θ)] -1/4 Extinction coefficient: (11) Special details Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wr and goodness of fit S are based on F 2, conventional R-factors R are based on F, with F set to zero for negative F 2. The threshold expression of F 2 > σ(f 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 ) x y z U iso */U eq S (13) (13) (7) (2) S (12) (12) (7) (2) S (12) (12) (8) (2) N (4) (4) (3) (7) N (4) (4) (2) (7) O (4) (4) (3) (7) O (4) (4) (2) (7) O (4) (4) (2) (7) O (4) (4) (2) (7) O (4) (4) (2) (7) O (4) (4) (2) (6) O (4) (4) (2) (6) O (4) (4) (2) (6) O (3) (3) (2) (6) C (5) (5) (3) (7) C (5) (5) (3) (7) C (5) (5) (3) (7) C (5) (5) (3) (7) C (5) (6) (3) (9) H5A * H5B * H5C * C (5) (5) (3) (9) sup-4
7 H6A * H6B * H6C * C (5) (5) (3) (7) H * C (5) (5) (3) (9) H8A * H8B * H8C * C (5) (5) (3) (8) H9A * H9B * H9C * C (6) (5) (3) (9) H10A * H10B * H10C * Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 S (5) (5) (4) (4) (3) (4) S (4) (5) (5) (4) (3) (4) S (4) (5) (5) (4) (4) (4) N (15) (17) (17) (13) (12) (13) N (16) (17) (15) (13) (12) (13) O (17) (18) (18) (14) (14) (14) O (15) (18) (17) (13) (12) (14) O (17) (18) (14) (14) (12) (12) O (16) (16) (15) (13) (12) (12) O (14) (17) (16) (12) (12) (13) O (16) (15) (15) (12) (12) (12) O (13) (18) (15) (12) (11) (13) O (15) (15) (14) (12) (12) (12) O (13) (15) (14) (12) (11) (11) C (17) (19) (18) (15) (14) (15) C (17) (18) (18) (14) (14) (14) C (16) (18) (18) (14) (13) (14) C (16) (19) (17) (14) (13) (14) C (2) (2) (2) (18) (17) (18) C (2) (2) (19) (18) (16) (17) C (17) (2) (17) (15) (13) (14) C (18) (2) (2) (17) (16) (17) C (19) (2) (2) (17) (15) (17) C (2) (2) (2) (19) (17) (17) sup-5
8 Geometric parameters (Å, º) S1 O (3) O9 C (4) S1 O (3) C1 C (5) S1 C (4) C3 C (5) S1 C (4) C4 C (5) S2 O (3) C5 H5A S2 O (3) C5 H5B S2 C (4) C5 H5C S2 C (4) C6 H6A S3 O (3) C6 H6B S3 O (3) C6 H6C S3 C (4) C7 H S3 C (4) C8 H8A N1 C (5) C8 H8B N1 C (5) C8 H8C N1 C (5) C9 H9A N2 C (5) C9 H9B N2 C (5) C9 H9C N2 C (5) C10 H10A O7 C (4) C10 H10B O8 C (4) C10 H10C O3 S1 O (19) C7 C4 S (2) O3 S1 C (19) N1 C5 H5A O2 S1 C (19) N1 C5 H5B O3 S1 C (17) H5A C5 H5B O2 S1 C (17) N1 C5 H5C C9 S1 C (17) H5A C5 H5C O1 S2 O (19) H5B C5 H5C O1 S2 C (2) N2 C6 H6A O4 S2 C (2) N2 C6 H6B O1 S2 C (17) H6A C6 H6B O4 S2 C (17) N2 C6 H6C C8 S2 C (18) H6A C6 H6C O5 S3 O (18) H6B C6 H6C O5 S3 C (19) C4 C7 S (3) O6 S3 C (19) C4 C7 S (2) O5 S3 C (17) S1 C7 S (19) O6 S3 C (17) C4 C7 H C10 S3 C (18) S1 C7 H C1 N1 C (3) S2 C7 H C1 N1 C (3) S2 C8 H8A C2 N1 C (3) S2 C8 H8B C3 N2 C (3) H8A C8 H8B C3 N2 C (3) S2 C8 H8C C2 N2 C (3) H8A C8 H8C O7 C1 N (3) H8B C8 H8C sup-6
9 O7 C1 C (3) S1 C9 H9A N1 C1 C (3) S1 C9 H9B O8 C2 N (3) H9A C9 H9B O8 C2 N (3) S1 C9 H9C N2 C2 N (3) H9A C9 H9C O9 C3 N (3) H9B C9 H9C O9 C3 C (3) S3 C10 H10A N2 C3 C (3) S3 C10 H10B C1 C4 C (3) H10A C10 H10B C1 C4 C (3) S3 C10 H10C C3 C4 C (3) H10A C10 H10C C1 C4 S (2) H10B C10 H10C C3 C4 S (2) C2 N1 C1 O (4) O5 S3 C4 C (2) C5 N1 C1 O7 0.3 (6) O6 S3 C4 C (3) C2 N1 C1 C4 6.8 (5) C10 S3 C4 C (3) C5 N1 C1 C (3) O5 S3 C4 C (3) C3 N2 C2 O (4) O6 S3 C4 C (3) C6 N2 C2 O (5) C10 S3 C4 C (2) C3 N2 C2 N1 7.1 (5) O5 S3 C4 C (3) C6 N2 C2 N (3) O6 S3 C4 C (3) C1 N1 C2 O (4) C10 S3 C4 C (3) C5 N1 C2 O (5) C1 C4 C7 S (3) C1 N1 C2 N2 8.9 (5) C3 C4 C7 S (4) C5 N1 C2 N (3) S3 C4 C7 S (4) C2 N2 C3 O (3) C1 C4 C7 S (3) C6 N2 C3 O9 2.2 (5) C3 C4 C7 S (3) C2 N2 C3 C (5) S3 C4 C7 S (17) C6 N2 C3 C (3) O3 S1 C7 C (3) O7 C1 C4 C (3) O2 S1 C7 C (3) N1 C1 C4 C (5) C9 S1 C7 C (4) O7 C1 C4 C (5) O3 S1 C7 S (18) N1 C1 C4 C (3) O2 S1 C7 S (2) O7 C1 C4 S (4) C9 S1 C7 S (2) N1 C1 C4 S (3) O1 S2 C7 C (3) O9 C3 C4 C (3) O4 S2 C7 C (3) N2 C3 C4 C (5) C8 S2 C7 C (3) O9 C3 C4 C (4) O1 S2 C7 S (2) N2 C3 C4 C (3) O4 S2 C7 S (19) O9 C3 C4 S (4) C8 S2 C7 S (2) N2 C3 C4 S (3) Hydrogen-bond geometry (Å, º) D H A D H H A D A D H A C5 H5B O8 i (6) 131 C6 H6A O9 ii (5) 138 sup-7
10 C8 H8C O8 iii (5) 133 C10 H10A O5 iv (5) 130 Symmetry codes: (i) x, y+1, z; (ii) x+1, y+2, z; (iii) x, y+2, z; (iv) x+1, y+1, z+1. sup-8
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metal-organic compounds Acta Crystallographica Section E Structure Reports Online ISSN 1600-5368 b = 8.2387 (7) Å c = 14.7510 (13) Å = 106.1050 (10) V = 1987.5 (3) Å 3 Z =4 Mo K radiation = 2.78 mm 1 T
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