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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1252.
Published online 2009 May 14. doi:  10.1107/S1600536809016857
PMCID: PMC2969793

4,6-Dimethyl-2-thioxo-1,2-dihydro­pyrimidin-3-ium chloride–thio­urea (1/1)

Abstract

In the title compound, C6H9N2S+·Cl·CH4N2S, the 4,6-di­methyl-2-thioxo-1,2-dihydro­pyrimidin-3-ium cation is proton­ated at one of the pyrimidine N atoms. The cations are bridged by the chloride anions through a pair of N—H(...)Cl hydrogen bonds. The amino groups of each thio­urea adduct inter­act with the chloride anions through a pair of N—H(...)Cl hydrogen bonds and the S atom of another thio­urea adduct through a pair of N—H(...)S hydrogen bonds. These inter­actions result in a layered hydrogen-bonded network propagating parallel to the bc plane. Except for two H atoms, all atoms are on special positions.

Related literature

For related structures, see: Seth & Sur (1995 [triangle]); Jianqiang et al. (2006 [triangle]). For bond-length data, see: Arslan et al. (2004 [triangle]); Hemamalini et al. (2005 [triangle]).

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Object name is e-65-o1252-scheme1.jpg

Experimental

Crystal data

  • C6H9N2S+·Cl·CH4N2S
  • M r = 252.78
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1252-efi1.jpg
  • a = 6.6459 (4) Å
  • b = 21.6144 (14) Å
  • c = 8.3878 (5) Å
  • V = 1204.88 (12) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.63 mm−1
  • T = 293 K
  • 0.10 × 0.10 × 0.10 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: none
  • 1080 measured reflections
  • 636 independent reflections
  • 447 reflections with I > 2σ(I)
  • R int = 0.024

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.175
  • S = 1.05
  • 636 reflections
  • 49 parameters
  • H-atom parameters constrained
  • Δρmax = 0.44 e Å−3
  • Δρmin = −0.51 e Å−3

Data collection: COLLECT (Nonius, 1998 [triangle]); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: PLATON/PLUTON (Spek, 2009 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809016857/er2066sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809016857/er2066Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank the Agence Universitaire de la Francophonie for financial support (AUF-PSCI No. 6314PS804).

supplementary crystallographic information

Comment

The title compound, C6H9N2S.CH4N2SCl, was characterized by 1H and 13C NMR, solid-state IR and X-ray crystallographic techniques. The X-ray structure determination reveals that the compound crystallizes in the orthorhombic space group Cmcm with a protonated molecular moiety, a chloride anion and one thiourea adduct in the asymmetric unit. The molecular geometry is illustrated in Fig. 1. The C—S bond length of 1.649 (7) Å in the molecular adduct and 1.698 (8) Å in the thiourea are double bonds character and are comparable to those observed for 1-(biphenyl-4-carbonyl)-3-p-tolyl-thiourea [1.647 (3) Å for C—S (Arslan et al., 2004)]. The C—N bond lengths are in the range [1.322 (6)-1.371 (6) Å] and are shorter than the double C—N bond length (Hemamalini et al. <i/>, 2005). All atoms, except H5B and H5C, lie on a mirror plane, similar to the observed structure of 4,6-dimethylpyrimidine-2(1H</>)-thione (Seth & Sur, 1995). The molecular adduct forms hydrogen bonds with two chloride anions by N1—H1···Cl1(-x + 1/2, -y + 1/2, -z + 1) (Fig. 2). Each thiourea molecule is linked to two other thioura molecule by hydrogen bonds and one chloride anion respectively by N2—H2B···S2(-x, -y, -z + 1) and N2—H2A···Cl1 (Table. 2).

Experimental

Thiourea (2 g, 26 mmol) was reacted with 2,4-pentadione (2.6 g, 26 mmol) in C3H6O (20 ml) solution, to give the corresponding 1:1 adduct after two hour under refluxing. After cooling to room temperature, 3.4 ml HCl 10M was added dropwise to the solution and the resulting mixture was refluxed for one hour before left standing overnight. The filtrate gave yellowish crystal suitable for X-ray analyses after four days of slow evaporation. Yield: 87.69%. m.p. 190±2 °C. Anal. Calc. for C7H13N4S2Cl (%): C, 33.26; H, 5.18; N, 22.16. Found: C, 33.37; H, 5.15; N, 22.25. Selected IR data (cm-1, KBr pellet): 1599 (ν C═N), 1187 (ν C═S). 1H NMR (200 MHz, D2O, δ, p.p.m.): 2.40 (s, 6H, –CH3); 6.83 (s, 1H, –CH). 13C NMR (200 MHz, D2O, δ, p.p.m.): 19.26 (–CH3); 118.32 (–CH); 168.02 (N═C); 172.90 (N═C—S—H).

Refinement

The H atoms of the NH2 groups were located in the Fourier difference maps and refined by riding motion. Others H atoms were placed geometrically and refined with a riding model. Uiso(H) for H was assigned as 1.2Ueq of the attached C atoms (1.5 for methyl C atoms).

Figures

Fig. 1.
An ORTEP view of the asymmetric unit of the title compound, showing the atom-numbering scheme. Displacement ellipsoids are plotted at the 50% probability level. Symmetry code: (i) -x, y, -z + 1/2
Fig. 2.
Molecular representation of the compound showing hydrogen bonds. The broken lines stand for hydrogen bonds.

Crystal data

C6H9N2S+·Cl·CH4N2SF(000) = 528
Mr = 252.78Dx = 1.393 Mg m3
Orthorhombic, CmcmMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2c 2Cell parameters from 653 reflections
a = 6.6459 (4) Åθ = 1.0–25.4°
b = 21.6144 (14) ŵ = 0.63 mm1
c = 8.3878 (5) ÅT = 293 K
V = 1204.88 (12) Å3Prism, yellow
Z = 40.10 × 0.10 × 0.10 mm

Data collection

Nonius KappaCCD diffractometer447 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.024
graphiteθmax = 25.3°, θmin = 3.1°
[var phi] scansh = −7→7
1080 measured reflectionsk = −25→25
636 independent reflectionsl = −10→10

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.055Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.175H-atom parameters constrained
S = 1.05w = 1/[σ2(Fo2) + (0.1002P)2 + 1.9948P] where P = (Fo2 + 2Fc2)/3
636 reflections(Δ/σ)max = 0.004
49 parametersΔρmax = 0.44 e Å3
0 restraintsΔρmin = −0.51 e Å3

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 (Å2)

xyzUiso*/UeqOcc. (<1)
Cl10.00000.22960 (8)0.75000.0492 (6)
S10.50000.32187 (9)0.75000.0582 (7)
S20.0000−0.02324 (10)0.75000.1135 (15)
N10.50000.21069 (18)0.6134 (5)0.0424 (10)
H10.50000.23020.52400.051*
N20.00000.0864 (2)0.6144 (5)0.0558 (12)
H2A0.00000.12620.61540.067*
H2B0.00000.06690.52510.067*
C10.50000.1485 (2)0.6079 (6)0.0423 (11)
C20.00000.0553 (4)0.75000.0526 (19)
C30.50000.1172 (3)0.75000.0448 (17)
H30.50000.07410.75000.054*
C40.50000.2456 (3)0.75000.0431 (16)
C50.50000.1187 (3)0.4493 (6)0.0589 (15)
H5A0.50000.14990.36790.088*
H5B0.38210.09340.43850.088*0.50
H5C0.61790.09340.43850.088*0.50

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0583 (11)0.0481 (11)0.0412 (10)0.0000.0000.000
S10.0680 (13)0.0463 (11)0.0602 (14)0.0000.0000.000
S20.267 (5)0.0420 (14)0.0316 (11)0.0000.0000.000
N10.048 (2)0.052 (3)0.0276 (19)0.0000.0000.0029 (18)
N20.084 (3)0.053 (3)0.030 (2)0.0000.0000.0004 (19)
C10.048 (3)0.046 (3)0.033 (3)0.0000.0000.000 (2)
C20.078 (5)0.053 (4)0.027 (4)0.0000.0000.000
C30.059 (4)0.041 (4)0.035 (4)0.0000.0000.000
C40.036 (3)0.053 (4)0.040 (4)0.0000.0000.000
C50.086 (4)0.063 (3)0.028 (3)0.0000.000−0.007 (2)

Geometric parameters (Å, °)

S1—C41.649 (7)C1—C51.479 (7)
S2—C21.698 (8)C2—N2i1.322 (6)
N1—C11.345 (6)C3—C1i1.371 (6)
N1—C41.371 (5)C3—H30.9300
N1—H10.8600C4—N1i1.371 (5)
N2—C21.322 (6)C5—H5A0.9600
N2—H2A0.8600C5—H5B0.9600
N2—H2B0.8600C5—H5C0.9600
C1—C31.371 (6)
C1—N1—C4125.3 (4)C1i—C3—C1120.8 (6)
C1—N1—H1117.4C1i—C3—H3119.6
C4—N1—H1117.4C1—C3—H3119.6
C2—N2—H2A120.0N1i—C4—N1113.3 (6)
C2—N2—H2B120.0N1i—C4—S1123.3 (3)
H2A—N2—H2B120.0N1—C4—S1123.3 (3)
N1—C1—C3117.7 (5)C1—C5—H5A109.5
N1—C1—C5117.8 (4)C1—C5—H5B109.5
C3—C1—C5124.5 (5)H5A—C5—H5B109.5
N2i—C2—N2118.8 (7)C1—C5—H5C109.5
N2i—C2—S2120.6 (3)H5A—C5—H5C109.5
N2—C2—S2120.6 (3)H5B—C5—H5C109.5
C4—N1—C1—C30.000 (1)C5—C1—C3—C1i180.0
C4—N1—C1—C5180.000 (1)C1—N1—C4—N1i0.000 (2)
N1—C1—C3—C1i0.000 (2)C1—N1—C4—S1180.0

Symmetry codes: (i) x, y, −z+3/2.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···Cl1ii0.862.463.310 (4)171
N2—H2A···Cl10.862.503.297 (5)154
N2—H2B···S2iii0.862.493.347 (5)173

Symmetry codes: (ii) −x+1/2, −y+1/2, −z+1; (iii) −x, −y, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: ER2066).

References

  • Arslan, H., Flörke, U. & Külcü, N. (2004). Acta Chim. Slov.51, 787–792.
  • Hemamalini, M., Muthiah, P. T. & Lynch, D. E. (2005). Acta Cryst. E61, o4107–o4109.
  • Jianqiang, Q., Liufang, W., Yingqi, L., Yumin, S., Yinyue, W. & Xiaofei, J. (2006). J. Rare Earths, 24, 15–19.
  • Nonius (1998). COLLECT Nonius BV, Delft, The Nederlands.
  • Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Seth, S. & Sur, H. (1995). Acta Cryst.C51, 487–489.
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

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