Crystal structure of 5-[bis-(methyl-sulfon-yl)meth-yl]-1,3-dimethyl-5-(methyl-sulfon-yl)pyrimidine-2,4,6(1H,3H,5H)-trione.

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 methyl-sulfonyl and bis-(methyl-sulfon-yl)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, mol-ecules are linked via C-H⋯O hydrogen bonds, forming a three-dimensional structure.

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 ▸).

Experimental

Crystal data

C10H16N2O9S3

M = 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

Δρmax = 0.39 e Å−3

Δρmin = −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 ▸).

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

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

Click here for additional data file.

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

Click here for additional data file.

. 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.

. 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

C10H16N2O9S3	Z = 2
Mr = 404.43	F(000) = 420
Triclinic, P1	Dx = 1.722 Mg m−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.9415 (16) Å	Cell parameters from 30 reflections
b = 8.5796 (17) Å	θ = 10.3–20.1°
c = 12.756 (3) Å	µ = 0.53 mm−1
α = 77.08 (3)°	T = 173 K
β = 79.50 (3)°	Plate, colourless
γ = 67.83 (3)°	0.15 × 0.10 × 0.05 mm
V = 779.9 (3) Å3

Stoe IPDS diffractometer	2582 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.069
Graphite monochromator	θmax = 26.4°, θmin = 3.1°
phi scans	h = −9→9
11105 measured reflections	k = −10→10
3175 independent reflections	l = −15→15

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.060	H-atom parameters constrained
wR(F2) = 0.105	w = 1/[σ2(Fo2) + (0.P)2 + 1.8882P] where P = (Fo2 + 2Fc2)/3
S = 1.24	(Δ/σ)max < 0.001
3175 reflections	Δρmax = 0.39 e Å−3
223 parameters	Δρmin = −0.44 e Å−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0053 (11)

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 F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

	x	y	z	Uiso*/Ueq
S1	0.26932 (13)	0.98015 (13)	0.40183 (7)	0.0206 (2)
S2	0.04979 (12)	1.12489 (12)	0.20775 (7)	0.0203 (2)
S3	0.36913 (12)	0.56897 (12)	0.32733 (8)	0.0203 (2)
N1	0.0632 (4)	0.6845 (4)	0.1414 (3)	0.0199 (7)
N2	0.3363 (4)	0.7382 (4)	0.0629 (2)	0.0194 (7)
O1	0.1593 (4)	1.2283 (4)	0.1838 (3)	0.0357 (7)
O2	0.1389 (4)	1.1372 (4)	0.4315 (2)	0.0322 (7)
O3	0.3197 (4)	0.8360 (4)	0.4871 (2)	0.0312 (7)
O4	0.0233 (4)	1.0569 (4)	0.1216 (2)	0.0308 (7)
O5	0.5284 (4)	0.5940 (4)	0.3464 (2)	0.0289 (7)
O6	0.3920 (4)	0.4469 (4)	0.2607 (2)	0.0287 (6)
O7	−0.0780 (4)	0.7631 (4)	0.3019 (2)	0.0267 (6)
O8	0.2123 (4)	0.6024 (4)	−0.0170 (2)	0.0255 (6)
O9	0.4500 (3)	0.8776 (3)	0.1470 (2)	0.0222 (6)
C1	0.0528 (5)	0.7430 (5)	0.2337 (3)	0.0186 (7)
C2	0.2063 (5)	0.6684 (5)	0.0579 (3)	0.0177 (7)
C3	0.3452 (5)	0.8054 (5)	0.1483 (3)	0.0164 (7)
C4	0.2215 (5)	0.7758 (5)	0.2529 (3)	0.0171 (7)
C5	−0.0927 (5)	0.6445 (6)	0.1232 (3)	0.0275 (9)
H5A	−0.1683	0.6306	0.1920	0.041*
H5B	−0.0473	0.5383	0.0935	0.041*
H5C	−0.1662	0.7378	0.0721	0.041*
C6	0.4587 (5)	0.7625 (5)	−0.0362 (3)	0.0257 (9)
H6A	0.4152	0.8825	−0.0712	0.039*
H6B	0.4591	0.6901	−0.0859	0.039*
H6C	0.5830	0.7309	−0.0175	0.039*
C7	0.1493 (5)	0.9322 (5)	0.3113 (3)	0.0169 (7)
H7	0.0390	0.9184	0.3587	0.020*
C8	−0.1646 (5)	1.2318 (5)	0.2710 (3)	0.0272 (9)
H8A	−0.1492	1.2715	0.3338	0.041*
H8B	−0.2333	1.1540	0.2949	0.041*
H8C	−0.2316	1.3301	0.2199	0.041*
C9	0.4678 (5)	1.0156 (5)	0.3342 (3)	0.0241 (8)
H9A	0.5235	1.0504	0.3833	0.036*
H9B	0.4363	1.1060	0.2711	0.036*
H9C	0.5546	0.9102	0.3105	0.036*
C10	0.2393 (6)	0.5223 (5)	0.4497 (3)	0.0280 (9)
H10A	0.3164	0.4225	0.4954	0.042*
H10B	0.1361	0.4979	0.4342	0.042*
H10C	0.1930	0.6206	0.4874	0.042*

	U11	U22	U33	U12	U13	U23
S1	0.0214 (5)	0.0306 (5)	0.0163 (4)	−0.0142 (4)	0.0000 (3)	−0.0093 (4)
S2	0.0178 (4)	0.0206 (5)	0.0194 (5)	−0.0040 (4)	0.0005 (3)	−0.0038 (4)
S3	0.0173 (4)	0.0210 (5)	0.0207 (5)	−0.0057 (4)	−0.0023 (4)	−0.0016 (4)
N1	0.0153 (15)	0.0221 (17)	0.0245 (17)	−0.0071 (13)	−0.0042 (12)	−0.0058 (13)
N2	0.0209 (16)	0.0235 (17)	0.0146 (15)	−0.0078 (13)	0.0004 (12)	−0.0070 (13)
O1	0.0328 (17)	0.0331 (18)	0.0394 (18)	−0.0133 (14)	−0.0022 (14)	−0.0010 (14)
O2	0.0262 (15)	0.0404 (18)	0.0368 (17)	−0.0127 (13)	0.0034 (12)	−0.0236 (14)
O3	0.0381 (17)	0.0426 (18)	0.0188 (14)	−0.0216 (14)	−0.0056 (12)	−0.0014 (12)
O4	0.0357 (16)	0.0259 (16)	0.0254 (15)	−0.0020 (13)	−0.0083 (12)	−0.0056 (12)
O5	0.0196 (14)	0.0361 (17)	0.0314 (16)	−0.0106 (12)	−0.0068 (12)	−0.0019 (13)
O6	0.0330 (16)	0.0234 (15)	0.0272 (15)	−0.0053 (12)	−0.0050 (12)	−0.0059 (12)
O7	0.0186 (13)	0.0409 (18)	0.0274 (15)	−0.0162 (12)	0.0049 (11)	−0.0151 (13)
O8	0.0302 (15)	0.0265 (15)	0.0230 (14)	−0.0091 (12)	−0.0045 (12)	−0.0105 (12)
O9	0.0220 (13)	0.0283 (15)	0.0216 (14)	−0.0147 (12)	0.0020 (11)	−0.0083 (11)
C1	0.0161 (17)	0.0206 (19)	0.0201 (18)	−0.0068 (15)	−0.0023 (14)	−0.0043 (15)
C2	0.0185 (17)	0.0152 (18)	0.0179 (18)	−0.0024 (14)	−0.0067 (14)	−0.0025 (14)
C3	0.0127 (16)	0.0166 (18)	0.0185 (18)	−0.0033 (14)	−0.0016 (13)	−0.0035 (14)
C4	0.0150 (16)	0.0226 (19)	0.0150 (17)	−0.0081 (14)	−0.0004 (13)	−0.0040 (14)
C5	0.025 (2)	0.033 (2)	0.033 (2)	−0.0163 (18)	−0.0071 (17)	−0.0088 (18)
C6	0.029 (2)	0.032 (2)	0.0184 (19)	−0.0129 (18)	0.0041 (16)	−0.0089 (17)
C7	0.0159 (17)	0.023 (2)	0.0136 (17)	−0.0085 (15)	0.0010 (13)	−0.0051 (14)
C8	0.0178 (18)	0.031 (2)	0.026 (2)	−0.0027 (17)	0.0022 (16)	−0.0050 (17)
C9	0.0219 (19)	0.035 (2)	0.023 (2)	−0.0167 (17)	−0.0028 (15)	−0.0069 (17)
C10	0.032 (2)	0.031 (2)	0.022 (2)	−0.0180 (19)	0.0004 (17)	0.0011 (17)

S1—O3	1.434 (3)	O9—C3	1.207 (4)
S1—O2	1.436 (3)	C1—C4	1.539 (5)
S1—C9	1.752 (4)	C3—C4	1.539 (5)
S1—C7	1.823 (4)	C4—C7	1.547 (5)
S2—O1	1.415 (3)	C5—H5A	0.9800
S2—O4	1.434 (3)	C5—H5B	0.9800
S2—C8	1.744 (4)	C5—H5C	0.9800
S2—C7	1.876 (4)	C6—H6A	0.9800
S3—O5	1.430 (3)	C6—H6B	0.9800
S3—O6	1.432 (3)	C6—H6C	0.9800
S3—C10	1.762 (4)	C7—H7	1.0000
S3—C4	1.873 (4)	C8—H8A	0.9800
N1—C1	1.358 (5)	C8—H8B	0.9800
N1—C2	1.396 (5)	C8—H8C	0.9800
N1—C5	1.471 (5)	C9—H9A	0.9800
N2—C3	1.365 (5)	C9—H9B	0.9800
N2—C2	1.392 (5)	C9—H9C	0.9800
N2—C6	1.474 (5)	C10—H10A	0.9800
O7—C1	1.211 (4)	C10—H10B	0.9800
O8—C2	1.200 (4)	C10—H10C	0.9800
O3—S1—O2	117.09 (19)	C7—C4—S3	117.1 (2)
O3—S1—C9	108.84 (19)	N1—C5—H5A	109.5
O2—S1—C9	109.23 (19)	N1—C5—H5B	109.5
O3—S1—C7	107.80 (17)	H5A—C5—H5B	109.5
O2—S1—C7	102.30 (17)	N1—C5—H5C	109.5
C9—S1—C7	111.45 (17)	H5A—C5—H5C	109.5
O1—S2—O4	118.50 (19)	H5B—C5—H5C	109.5
O1—S2—C8	110.4 (2)	N2—C6—H6A	109.5
O4—S2—C8	108.3 (2)	N2—C6—H6B	109.5
O1—S2—C7	110.32 (17)	H6A—C6—H6B	109.5
O4—S2—C7	104.43 (17)	N2—C6—H6C	109.5
C8—S2—C7	103.80 (18)	H6A—C6—H6C	109.5
O5—S3—O6	118.38 (18)	H6B—C6—H6C	109.5
O5—S3—C10	111.37 (19)	C4—C7—S1	126.6 (3)
O6—S3—C10	108.29 (19)	C4—C7—S2	106.8 (2)
O5—S3—C4	107.38 (17)	S1—C7—S2	110.83 (19)
O6—S3—C4	103.90 (17)	C4—C7—H7	103.3
C10—S3—C4	106.69 (18)	S1—C7—H7	103.3
C1—N1—C2	125.2 (3)	S2—C7—H7	103.3
C1—N1—C5	118.2 (3)	S2—C8—H8A	109.5
C2—N1—C5	116.4 (3)	S2—C8—H8B	109.5
C3—N2—C2	124.9 (3)	H8A—C8—H8B	109.5
C3—N2—C6	116.8 (3)	S2—C8—H8C	109.5
C2—N2—C6	117.7 (3)	H8A—C8—H8C	109.5
O7—C1—N1	123.2 (3)	H8B—C8—H8C	109.5
O7—C1—C4	119.7 (3)	S1—C9—H9A	109.5
N1—C1—C4	117.0 (3)	S1—C9—H9B	109.5
O8—C2—N2	121.6 (3)	H9A—C9—H9B	109.5
O8—C2—N1	120.9 (3)	S1—C9—H9C	109.5
N2—C2—N1	117.4 (3)	H9A—C9—H9C	109.5
O9—C3—N2	123.5 (3)	H9B—C9—H9C	109.5
O9—C3—C4	119.5 (3)	S3—C10—H10A	109.5
N2—C3—C4	116.9 (3)	S3—C10—H10B	109.5
C1—C4—C3	113.4 (3)	H10A—C10—H10B	109.5
C1—C4—C7	106.7 (3)	S3—C10—H10C	109.5
C3—C4—C7	111.2 (3)	H10A—C10—H10C	109.5
C1—C4—S3	105.6 (2)	H10B—C10—H10C	109.5
C3—C4—S3	102.9 (2)
C2—N1—C1—O7	176.2 (4)	O5—S3—C4—C1	179.8 (2)
C5—N1—C1—O7	0.3 (6)	O6—S3—C4—C1	53.6 (3)
C2—N1—C1—C4	−6.8 (5)	C10—S3—C4—C1	−60.7 (3)
C5—N1—C1—C4	177.2 (3)	O5—S3—C4—C3	60.6 (3)
C3—N2—C2—O8	−175.6 (4)	O6—S3—C4—C3	−65.6 (3)
C6—N2—C2—O8	12.9 (5)	C10—S3—C4—C3	−179.9 (2)
C3—N2—C2—N1	7.1 (5)	O5—S3—C4—C7	−61.6 (3)
C6—N2—C2—N1	−164.4 (3)	O6—S3—C4—C7	172.2 (3)
C1—N1—C2—O8	173.7 (4)	C10—S3—C4—C7	57.9 (3)
C5—N1—C2—O8	−10.2 (5)	C1—C4—C7—S1	153.1 (3)
C1—N1—C2—N2	−8.9 (5)	C3—C4—C7—S1	−82.7 (4)
C5—N1—C2—N2	167.1 (3)	S3—C4—C7—S1	35.1 (4)
C2—N2—C3—O9	−173.7 (3)	C1—C4—C7—S2	−73.5 (3)
C6—N2—C3—O9	−2.2 (5)	C3—C4—C7—S2	50.7 (3)
C2—N2—C3—C4	10.1 (5)	S3—C4—C7—S2	168.54 (17)
C6—N2—C3—C4	−178.3 (3)	O3—S1—C7—C4	−55.8 (3)
O7—C1—C4—C3	−160.3 (3)	O2—S1—C7—C4	−179.8 (3)
N1—C1—C4—C3	22.6 (5)	C9—S1—C7—C4	63.5 (4)
O7—C1—C4—C7	−37.5 (5)	O3—S1—C7—S2	172.24 (18)
N1—C1—C4—C7	145.4 (3)	O2—S1—C7—S2	48.2 (2)
O7—C1—C4—S3	87.7 (4)	C9—S1—C7—S2	−68.4 (2)
N1—C1—C4—S3	−89.3 (3)	O1—S2—C7—C4	−110.8 (3)
O9—C3—C4—C1	159.5 (3)	O4—S2—C7—C4	17.5 (3)
N2—C3—C4—C1	−24.2 (5)	C8—S2—C7—C4	130.9 (3)
O9—C3—C4—C7	39.3 (4)	O1—S2—C7—S1	30.6 (2)
N2—C3—C4—C7	−144.4 (3)	O4—S2—C7—S1	158.95 (19)
O9—C3—C4—S3	−86.9 (4)	C8—S2—C7—S1	−87.7 (2)
N2—C3—C4—S3	89.4 (3)

D—H···A	D—H	H···A	D···A	D—H···A
C5—H5B···O8i	0.98	2.51	3.240 (6)	131
C6—H6A···O9ii	0.98	2.59	3.380 (5)	138
C8—H8C···O8iii	0.98	2.51	3.263 (5)	133
C10—H10A···O5iv	0.98	2.50	3.219 (5)	130

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
C10H10AO5iv	0.98	2.50	3.219(5)	130

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