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; Manfred Steimann

doi:10.1107/S2056989014027455

. 2015 Jan 1;71(Pt 1):o58–o59. doi: 10.1107/S2056989014027455

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, Manfred Steimann ^c

PMCID: PMC4331903 PMID: 25705508

Abstract

In the title compound, C₁₀H₁₆N₂O₉S₃, 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—H⋯O hydrogen bonds, forming a three-dimensional structure.

Keywords: crystal structure, barbituric acid, pyrimidines, methylsulfonyl, trione, hydrogen bonding

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 ▸). graphic file with name e-71-00o58-scheme1.jpg

Experimental

Crystal data

C₁₀H₁₆N₂O₉S₃
M _r = 404.43
Triclinic,
a = 7.9415 (16) Å
b = 8.5796 (17) Å
c = 12.756 (3) Å
α = 77.08 (3)°
β = 79.50 (3)°
γ = 67.83 (3)°
V = 779.9 (3) Å³
Z = 2
Mo Kα radiation
μ = 0.53 mm⁻¹
T = 173 K
0.15 × 0.10 × 0.05 mm

Data collection

Stoe IPDS diffractometer
11105 measured reflections
3175 independent reflections
2582 reflections with I > 2σ(I)
R _int = 0.069

Refinement

R[F ² > 2σ(F ²)] = 0.060
wR(F ²) = 0.105
S = 1.24
3175 reflections
223 parameters
H-atom parameters constrained
Δρ_max = 0.39 e Å⁻³
Δρ_min = −0.44 e Å⁻³

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 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I, New_Global_Publ_Block. DOI: 10.1107/S2056989014027455/su5040sup1.cif

e-71-00o58-sup1.cif^{(19.7KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989014027455/su5040Isup2.hkl

e-71-00o58-Isup2.hkl^{(155.7KB, hkl)}

Click here for additional data file.^{(6.4KB, cml)}

Supporting information file. DOI: 10.1107/S2056989014027455/su5040Isup3.cml

Click here for additional data file.^{(1.9MB, tif)}

. DOI: 10.1107/S2056989014027455/su5040fig1.tif

The molecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 20% probability level.

Click here for additional data file.^{(2.9MB, tif)}

. DOI: 10.1107/S2056989014027455/su5040fig2.tif

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).

CCDC reference: 1039815

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
C5H5BO8ⁱ	0.98	2.51	3.240(6)	131
C6H6AO9ⁱⁱ	0.98	2.59	3.380(5)	138
C8H8CO8ⁱⁱⁱ	0.98	2.51	3.263(5)	133
C10H10AO5^iv	0.98	2.50	3.219(5)	130

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) .

Acknowledgments

We are indebted to the University of Petra, the University of Jordan and the University of Tübingen for their endless help and support.

supplementary crystallographic information

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—C9 1.752 (4) Å, S2—C8 1.744 (4) Å, S3—C10 1.762 (4) Å] and they are slightly shorter than those reported for (PhSO₂)₂CH₂ (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 = 1.415 (3) Å, and S1—O3 = 1.434 (3) Å]. The carbonyl groups that are located on the barbituric acid ring have approximately the same bond lengths, varying from 1.200 (4) to 1.211 (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 CH₂Cl₂/Et₂O to give colourless crystals (yield: 1.0 g, 51%).