supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers Open access

pv2402 scheme

Acta Cryst. (2011). E67, o1094    [ doi:10.1107/S1600536811012323 ]

1-(4,6-Dimethylpyrimidin-2-yl)-3-(3,5-dinitrobenzoyl)thiourea monohydrate

S. Saeed, N. Rashid, W.-T. Wong and R. Hussain

Abstract top

The organic molecule in the title molecule, C14H12N6O5S·H2O, is roughly planar with a maximum deviation of 0.156 (2) Å. An intramolecular N-H...N hydrogen bond occurs. In the crystal, intermolecular N-H...O and O-H...O hydrogen-bonding interactions connect the molecules into a two-dimensional network that lies parallel to (101).

Comment top

The background to this study has been described in our previous work on the structural chemistry of N,N'-disubstituted thiourea (Saeed et al., 2011). In continuation of our studies, the crystal structure of the title compound, is presented in this paper.

In the title molecule (Fig. 1), the nitro groups N1/O1/O2 and N2/O3/O4 are oriented are 5.05 (11) and 9.40 (15)°, respectively, with rest to the mean-plane of the phenyl ring C1—C6. Moreover, the 4,6-dimethyl-pyrimidinyl ring plane, C9—C14/N5/N6, makes a dihedral angle of 1.31 (5)° with the the plane formed by the atoms C7/O5/N3/C8/S1/N4.

The structure is stabilized by intra-molecular N—H···O and N—H···N hydrogen bonding interactions. The inter-molecular hydrogen bonds O—H···O link the molecules into a two dimensinal network (Tab. 1 and Fig. 2).

Related literature top

For background to this study and our previous work on the structural chemistry of N,N'-disubstituted thiourea, see: Saeed et al. (2011).

Experimental top

A solution of 3,5-dinitrobenzoyl chloride (0.01 mol) in anhydrous acetone (75 ml) and 3% tetrabutylammonium bromide as a phase-transfer catalyst in anhydrous acetone was added dropwise to a suspension of dry potassium thiocyanate (0.01 mol) in acetone (50 ml) and the reaction mixture was refluxed for 50 min. After cooling to room temperature, a solution of 2-amino-4,6-dimethylpyrimidine (0.01 mol) in anhydrous acetone (25 ml) was added dropwise and the resulting mixture refluxed for 3 h. Hydrochloric acid (0.1 N, 300 ml) was added, and the solution was filtered. The solid product was washed with water and purified by re-crystallization from ethanol.

Refinement top

All of the C-bound H atoms were observable from difference Fourier map but were placed at geometrically idealized positions with C—H = 0.93 and 0.96Å for phenyl and methyl H-atoms, respectively. The C-bound H-atoms were refined using riding model with Uiso(H) = 1.2Ueq(C). Both the N– and O-bound H-atoms were located from difference Fourier map and refined isotropically.

Computing details top

Data collection: SMART (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. An ORTEP plot of the title molecule drawn with 50% probability thermal ellipsoids showing the atom numbering scheme.
[Figure 2] Fig. 2. Packing diagram of the title compound viewed down the a axis.
1-(4,6-Dimethylpyrimidin-2-yl)-3-(3,5-dinitrobenzoyl)thiourea monohydrate top
Crystal data top
C14H12N6O5S·H2OF(000) = 816
Mr = 394.37Dx = 1.563 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 11914 reflections
a = 6.7892 (6) Åθ = 2.0–25.0°
b = 10.1823 (9) ŵ = 0.24 mm−1
c = 24.267 (2) ÅT = 297 K
β = 92.901 (1)°Prism, yellow
V = 1675.4 (3) Å30.40 × 0.16 × 0.14 mm
Z = 4
Data collection top
Bruker SMART 1000 CCD
diffractometer		2942 independent reflections
Radiation source: fine-focus sealed tube2499 reflections with I > 2σ(I)
graphiteRint = 0.020
ω scansθmax = 25.0°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)		h = −8→8
Tmin = 0.909, Tmax = 0.967k = −11→12
9067 measured reflectionsl = −23→28
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.038H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.105 w = 1/[σ2(Fo2) + (0.0466P)2 + 0.9069P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.003
2942 reflectionsΔρmax = 0.20 e Å−3
263 parametersΔρmin = −0.23 e Å−3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0044 (6)
Crystal data top
C14H12N6O5S·H2OV = 1675.4 (3) Å3
Mr = 394.37Z = 4
Monoclinic, P21/nMo Kα radiation
a = 6.7892 (6) ŵ = 0.24 mm−1
b = 10.1823 (9) ÅT = 297 K
c = 24.267 (2) Å0.40 × 0.16 × 0.14 mm
β = 92.901 (1)°
Data collection top
Bruker SMART 1000 CCD
diffractometer		2942 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)		2499 reflections with I > 2σ(I)
Tmin = 0.909, Tmax = 0.967Rint = 0.020
9067 measured reflectionsθmax = 25.0°
Refinement top
R[F2 > 2σ(F2)] = 0.038H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.105Δρmax = 0.20 e Å−3
S = 1.06Δρmin = −0.23 e Å−3
2942 reflectionsAbsolute structure: ?
263 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

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.

The structure was solved by direct methods (SHELXS97) and expanded using Fourier techniques. All non-H atoms were refined anisotropically.

All of the C-bound H atoms are observable from difference Fourier map but are all placed at geometrical positions with C—H = 0.93 and 0.96Å for phenyl and methyl H-atoms. All C-bound H-atoms are refined using riding model with Uiso(H) = 1.2Ueq(Carrier). Both the N– and O-bound H-atoms were located from difference Fourier map and refined isotropically.

Highest peak is 0.20 at (0.0792, 0.5848, 0.1447) [0.83Å from Hl4C] Deepest hole is -0.23 at (0.0397, 0.8302, 0.0937) [0.74Å from Sl]

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.64692 (10)0.68130 (5)0.59394 (2)0.05020 (19)
O10.9131 (3)0.89155 (18)0.30790 (8)0.0777 (6)
O21.0041 (4)0.7610 (2)0.24468 (8)0.0851 (7)
O30.9757 (3)0.29505 (18)0.27197 (7)0.0759 (6)
O40.8719 (4)0.21594 (17)0.34703 (7)0.0802 (6)
O50.7636 (3)0.73999 (15)0.48300 (6)0.0608 (5)
O60.5934 (4)0.4521 (2)0.70525 (8)0.0692 (6)
H6A0.561 (5)0.395 (4)0.7269 (16)0.108 (14)*
H6B0.569 (6)0.512 (4)0.7202 (16)0.108 (15)*
N10.9439 (3)0.7823 (2)0.29029 (8)0.0563 (5)
N20.9151 (3)0.30735 (18)0.31844 (8)0.0519 (5)
N30.7393 (2)0.52460 (16)0.50834 (6)0.0338 (4)
H3N0.753 (3)0.447 (2)0.4988 (8)0.035 (6)*
N40.6648 (2)0.42786 (15)0.59103 (7)0.0354 (4)
H4N0.632 (3)0.440 (2)0.6254 (10)0.037 (5)*
N50.6445 (3)0.21615 (16)0.61919 (7)0.0405 (4)
N60.7339 (2)0.26275 (15)0.52709 (6)0.0346 (4)
C10.8532 (3)0.6919 (2)0.37878 (8)0.0395 (5)
H10.83830.77750.39130.047*
C20.9061 (3)0.6685 (2)0.32582 (8)0.0416 (5)
C30.9278 (3)0.5444 (2)0.30505 (8)0.0437 (5)
H30.96450.53050.26910.052*
C40.8928 (3)0.4414 (2)0.33990 (8)0.0399 (5)
C50.8407 (3)0.45841 (19)0.39404 (8)0.0363 (4)
H50.81880.38650.41660.044*
C60.8221 (3)0.58592 (19)0.41368 (8)0.0341 (4)
C70.7720 (3)0.62534 (18)0.47127 (8)0.0362 (4)
C80.6868 (3)0.54090 (18)0.56219 (8)0.0330 (4)
C90.6830 (3)0.29543 (18)0.57718 (8)0.0331 (4)
C100.6548 (3)0.0876 (2)0.60875 (8)0.0417 (5)
C110.7017 (3)0.04196 (19)0.55717 (8)0.0429 (5)
H110.7055−0.04770.54990.051*
C120.7424 (3)0.13190 (19)0.51685 (8)0.0371 (4)
C130.7985 (4)0.0930 (2)0.46069 (8)0.0496 (6)
H13A0.92620.12810.45390.060*
H13B0.70320.12690.43380.060*
H13C0.8021−0.00100.45810.060*
C140.6125 (4)−0.0021 (2)0.65554 (9)0.0600 (7)
H14A0.62080.04620.68950.072*
H14B0.7073−0.07220.65730.072*
H14C0.4824−0.03810.64980.072*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0823 (4)0.0302 (3)0.0389 (3)0.0073 (2)0.0114 (3)−0.0046 (2)
O10.1246 (17)0.0442 (10)0.0658 (12)−0.0034 (10)0.0201 (11)0.0142 (9)
O20.1375 (18)0.0706 (13)0.0507 (11)−0.0010 (12)0.0386 (11)0.0165 (9)
O30.1253 (16)0.0596 (11)0.0457 (10)0.0000 (10)0.0324 (10)−0.0116 (8)
O40.1496 (19)0.0412 (9)0.0524 (11)−0.0108 (11)0.0316 (11)−0.0044 (8)
O50.1047 (13)0.0309 (8)0.0490 (9)−0.0032 (8)0.0266 (9)−0.0014 (7)
O60.1083 (16)0.0545 (11)0.0466 (10)0.0065 (11)0.0221 (10)−0.0072 (9)
N10.0725 (14)0.0516 (12)0.0452 (11)−0.0031 (10)0.0085 (10)0.0142 (9)
N20.0741 (13)0.0450 (11)0.0374 (10)−0.0029 (9)0.0101 (9)−0.0037 (8)
N30.0430 (9)0.0269 (8)0.0320 (8)0.0018 (7)0.0057 (7)−0.0014 (7)
N40.0495 (10)0.0294 (8)0.0278 (8)0.0022 (7)0.0070 (7)−0.0019 (6)
N50.0561 (10)0.0331 (9)0.0327 (9)−0.0012 (7)0.0063 (7)0.0004 (7)
N60.0429 (9)0.0296 (8)0.0315 (8)0.0024 (7)0.0038 (7)−0.0008 (7)
C10.0421 (11)0.0363 (11)0.0403 (11)−0.0004 (8)0.0036 (9)0.0033 (8)
C20.0458 (11)0.0443 (12)0.0349 (11)−0.0030 (9)0.0042 (9)0.0102 (9)
C30.0495 (12)0.0506 (12)0.0316 (10)−0.0043 (10)0.0071 (9)0.0013 (9)
C40.0459 (11)0.0409 (11)0.0330 (10)−0.0012 (9)0.0036 (8)−0.0025 (8)
C50.0390 (10)0.0375 (10)0.0325 (10)−0.0035 (8)0.0033 (8)0.0020 (8)
C60.0337 (10)0.0364 (10)0.0323 (10)−0.0009 (8)0.0025 (7)0.0020 (8)
C70.0409 (11)0.0305 (10)0.0374 (10)−0.0013 (8)0.0041 (8)−0.0001 (8)
C80.0351 (10)0.0317 (9)0.0321 (10)0.0014 (8)0.0013 (8)−0.0011 (8)
C90.0369 (10)0.0304 (9)0.0320 (10)0.0008 (8)0.0023 (8)0.0002 (8)
C100.0557 (12)0.0342 (10)0.0353 (10)−0.0034 (9)0.0044 (9)0.0017 (8)
C110.0602 (13)0.0287 (10)0.0403 (11)0.0009 (9)0.0073 (9)−0.0020 (8)
C120.0438 (11)0.0326 (10)0.0350 (10)0.0028 (8)0.0031 (8)−0.0024 (8)
C130.0744 (15)0.0351 (11)0.0403 (12)0.0044 (10)0.0132 (11)−0.0043 (9)
C140.105 (2)0.0363 (12)0.0400 (12)−0.0073 (12)0.0160 (12)0.0025 (10)
Geometric parameters (Å, °) top
S1—C81.6528 (19)C1—C61.395 (3)
O1—N11.213 (3)C1—H10.9300
O2—N11.218 (3)C2—C31.372 (3)
O3—N21.226 (2)C3—C41.375 (3)
O4—N21.206 (2)C3—H30.9300
O5—C71.204 (2)C4—C51.389 (3)
O6—H6A0.82 (4)C5—C61.391 (3)
O6—H6B0.73 (4)C5—H50.9300
N1—C21.475 (3)C6—C71.509 (3)
N2—C41.472 (3)C10—C111.387 (3)
N3—C81.382 (2)C10—C141.496 (3)
N3—C71.390 (2)C11—C121.379 (3)
N3—H3N0.83 (2)C11—H110.9300
N4—C81.359 (2)C12—C131.487 (3)
N4—C91.397 (2)C13—H13A0.9600
N4—H4N0.88 (2)C13—H13B0.9600
N5—C91.337 (2)C13—H13C0.9600
N5—C101.336 (3)C14—H14A0.9600
N6—C91.323 (2)C14—H14B0.9600
N6—C121.357 (2)C14—H14C0.9600
C1—C21.373 (3)
H6A—O6—H6B101 (4)C1—C6—C7113.88 (17)
O1—N1—O2123.7 (2)O5—C7—N3123.49 (18)
O1—N1—C2118.43 (19)O5—C7—C6119.51 (17)
O2—N1—C2117.9 (2)N3—C7—C6117.00 (16)
O4—N2—O3123.56 (19)N4—C8—N3115.18 (16)
O4—N2—C4118.69 (17)N4—C8—S1117.87 (14)
O3—N2—C4117.75 (18)N3—C8—S1126.94 (14)
C8—N3—C7125.51 (17)N6—C9—N5128.26 (17)
C8—N3—H3N114.5 (14)N6—C9—N4119.63 (16)
C7—N3—H3N119.9 (14)N5—C9—N4112.11 (16)
C8—N4—C9132.86 (16)N5—C10—C11121.06 (18)
C8—N4—H4N114.2 (14)N5—C10—C14116.15 (18)
C9—N4—H4N112.9 (14)C11—C10—C14122.79 (19)
C9—N5—C10115.67 (17)C12—C11—C10118.78 (18)
C9—N6—C12115.51 (16)C12—C11—H11120.6
C2—C1—C6119.31 (19)C10—C11—H11120.6
C2—C1—H1120.3N6—C12—C11120.68 (17)
C6—C1—H1120.3N6—C12—C13116.40 (17)
C1—C2—C3122.81 (18)C11—C12—C13122.92 (18)
C1—C2—N1118.21 (19)C12—C13—H13A109.5
C3—C2—N1118.97 (18)C12—C13—H13B109.5
C2—C3—C4116.83 (18)H13A—C13—H13B109.5
C2—C3—H3121.6C12—C13—H13C109.5
C4—C3—H3121.6H13A—C13—H13C109.5
C3—C4—C5123.19 (19)H13B—C13—H13C109.5
C3—C4—N2117.74 (17)C10—C14—H14A109.5
C5—C4—N2119.06 (17)C10—C14—H14B109.5
C4—C5—C6118.16 (17)H14A—C14—H14B109.5
C4—C5—H5120.9C10—C14—H14C109.5
C6—C5—H5120.9H14A—C14—H14C109.5
C5—C6—C1119.68 (17)H14B—C14—H14C109.5
C5—C6—C7126.44 (17)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N4—H4N···O60.88 (2)1.97 (2)2.849 (2)171.9 (19)
N3—H3N···N60.83 (2)2.00 (2)2.705 (2)141.8 (19)
O6—H6A···O3i0.82 (4)2.32 (4)3.119 (3)168 (4)
O6—H6B···O2ii0.73 (4)2.44 (4)3.143 (3)164 (4)
O6—H6B···O1ii0.73 (4)2.62 (4)3.248 (3)146 (4)
Symmetry codes: (i) x−1/2, −y+1/2, z+1/2; (ii) x−1/2, −y+3/2, z+1/2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N4—H4N···O60.88 (2)1.97 (2)2.849 (2)171.9 (19)
N3—H3N···N60.83 (2)2.00 (2)2.705 (2)141.8 (19)
O6—H6A···O3i0.82 (4)2.32 (4)3.119 (3)168 (4)
O6—H6B···O2ii0.73 (4)2.44 (4)3.143 (3)164 (4)
O6—H6B···O1ii0.73 (4)2.62 (4)3.248 (3)146 (4)
Symmetry codes: (i) x−1/2, −y+1/2, z+1/2; (ii) x−1/2, −y+3/2, z+1/2.
Acknowledgements top

The authors are grateful to Allama Iqbal Open University, Islamabad, Pakistan, for the allocation of research and analytical laboratory facilities.

references
References top

Altomare, A., Cascarano, G., Giacovazzo, G., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.

Bruker (2007). SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.

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.

Saeed, S., Rashid, N., Jones, P. G. & Tahir, A. (2011). J. Heterocycl. Chem. 48, 74–84.

Sheldrick, G. M. (2004). SADABS. University of Göttingen, Germany.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.