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

Gaye, P.A.; Barry, A.H.; Gaye, M.; Sarr, A.D.; Sall, A.S.

doi:10.1107/S1600536809016857

organic compounds

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ISSN: 2056-9890

Volume 65| Part 6| June 2009| Page o1252

doi:10.1107/S1600536809016857

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

Papa Aly Gaye,^a ^* Aliou Hamady Barry,^b Mohamed Gaye,^a Aminata Diasse Sarr ^a and Abdou Salam Sall ^a

^aDépartement de Chimie, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal, and ^bDépartement de Chimie, Faculté des Sciences, Université de Nouakchott, Nouakchott, Mauritania
^*Correspondence e-mail: mlgayeastou@yahoo.fr

(Received 2 April 2009; accepted 5 May 2009; online 14 May 2009)

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 ); Jianqiang et al. (2006 ). For bond-length data, see: Arslan et al. (2004 ); Hemamalini et al. (2005 ).

Experimental

Crystal data

C₆H₉N₂S⁺·Cl⁻·CH₄N₂S
M_r = 252.78
Orthorhombic, C m c m
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[F² > 2σ(F²)] = 0.055
wR(F²) = 0.175
S = 1.05
636 reflections
49 parameters
H-atom parameters constrained
Δρ_max = 0.44 e Å⁻³
Δρ_min = −0.51 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯Cl1ⁱ	0.86	2.46	3.310 (4)	171
N2—H2A⋯Cl1	0.86	2.50	3.297 (5)	154
N2—H2B⋯S2ⁱⁱ	0.86	2.49	3.347 (5)	173
Symmetry codes: (i) $[-x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ ; (ii) -x, -y, -z+1.

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

Supporting information

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

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

checkCIF report

Comment top

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).

Related literature top

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

Experimental top

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).

Computing details top

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

Figures top

	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.

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

Crystal data top

C₆H₉N₂S⁺·Cl⁻·CH₄N₂S	F(000) = 528
M_r = 252.78	D_x = 1.393 Mg m⁻³
Orthorhombic, Cmcm	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2c 2	Cell parameters from 653 reflections
a = 6.6459 (4) Å	θ = 1.0–25.4°
b = 21.6144 (14) Å	µ = 0.63 mm⁻¹
c = 8.3878 (5) Å	T = 293 K
V = 1204.88 (12) Å³	Prism, yellow
Z = 4	0.10 × 0.10 × 0.10 mm

Data collection top

Nonius KappaCCD diffractometer	447 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.024
Graphite monochromator	θ_max = 25.3°, θ_min = 3.1°
ϕ scans	h = −7→7
1080 measured reflections	k = −25→25
636 independent reflections	l = −10→10

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.055	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.175	H-atom parameters constrained
S = 1.05	w = 1/[σ²(F_o²) + (0.1002P)² + 1.9948P] where P = (F_o² + 2F_c²)/3
636 reflections	(Δ/σ)_max = 0.004
49 parameters	Δρ_max = 0.44 e Å⁻³
0 restraints	Δρ_min = −0.51 e Å⁻³

Crystal data top

C₆H₉N₂S⁺·Cl⁻·CH₄N₂S	V = 1204.88 (12) Å³
M_r = 252.78	Z = 4
Orthorhombic, Cmcm	Mo Kα radiation
a = 6.6459 (4) Å	µ = 0.63 mm⁻¹
b = 21.6144 (14) Å	T = 293 K
c = 8.3878 (5) Å	0.10 × 0.10 × 0.10 mm

Data collection top

Nonius KappaCCD diffractometer	447 reflections with I > 2σ(I)
1080 measured reflections	R_int = 0.024
636 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.055	0 restraints
wR(F²) = 0.175	H-atom parameters constrained
S = 1.05	Δρ_max = 0.44 e Å⁻³
636 reflections	Δρ_min = −0.51 e Å⁻³
49 parameters

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 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) top

	x	y	z	U_iso*/U_eq	Occ. (<1)
Cl1	0.0000	0.22960 (8)	0.7500	0.0492 (6)
S1	0.5000	0.32187 (9)	0.7500	0.0582 (7)
S2	0.0000	−0.02324 (10)	0.7500	0.1135 (15)
N1	0.5000	0.21069 (18)	0.6134 (5)	0.0424 (10)
H1	0.5000	0.2302	0.5240	0.051*
N2	0.0000	0.0864 (2)	0.6144 (5)	0.0558 (12)
H2A	0.0000	0.1262	0.6154	0.067*
H2B	0.0000	0.0669	0.5251	0.067*
C1	0.5000	0.1485 (2)	0.6079 (6)	0.0423 (11)
C2	0.0000	0.0553 (4)	0.7500	0.0526 (19)
C3	0.5000	0.1172 (3)	0.7500	0.0448 (17)
H3	0.5000	0.0741	0.7500	0.054*
C4	0.5000	0.2456 (3)	0.7500	0.0431 (16)
C5	0.5000	0.1187 (3)	0.4493 (6)	0.0589 (15)
H5A	0.5000	0.1499	0.3679	0.088*
H5B	0.3821	0.0934	0.4385	0.088*	0.50
H5C	0.6179	0.0934	0.4385	0.088*	0.50

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0583 (11)	0.0481 (11)	0.0412 (10)	0.000	0.000	0.000
S1	0.0680 (13)	0.0463 (11)	0.0602 (14)	0.000	0.000	0.000
S2	0.267 (5)	0.0420 (14)	0.0316 (11)	0.000	0.000	0.000
N1	0.048 (2)	0.052 (3)	0.0276 (19)	0.000	0.000	0.0029 (18)
N2	0.084 (3)	0.053 (3)	0.030 (2)	0.000	0.000	0.0004 (19)
C1	0.048 (3)	0.046 (3)	0.033 (3)	0.000	0.000	0.000 (2)
C2	0.078 (5)	0.053 (4)	0.027 (4)	0.000	0.000	0.000
C3	0.059 (4)	0.041 (4)	0.035 (4)	0.000	0.000	0.000
C4	0.036 (3)	0.053 (4)	0.040 (4)	0.000	0.000	0.000
C5	0.086 (4)	0.063 (3)	0.028 (3)	0.000	0.000	−0.007 (2)

Geometric parameters (Å, º) top

S1—C4	1.649 (7)	C1—C5	1.479 (7)
S2—C2	1.698 (8)	C2—N2ⁱ	1.322 (6)
N1—C1	1.345 (6)	C3—C1ⁱ	1.371 (6)
N1—C4	1.371 (5)	C3—H3	0.9300
N1—H1	0.8600	C4—N1ⁱ	1.371 (5)
N2—C2	1.322 (6)	C5—H5A	0.9600
N2—H2A	0.8600	C5—H5B	0.9600
N2—H2B	0.8600	C5—H5C	0.9600
C1—C3	1.371 (6)

C1—N1—C4	125.3 (4)	C1ⁱ—C3—C1	120.8 (6)
C1—N1—H1	117.4	C1ⁱ—C3—H3	119.6
C4—N1—H1	117.4	C1—C3—H3	119.6
C2—N2—H2A	120.0	N1ⁱ—C4—N1	113.3 (6)
C2—N2—H2B	120.0	N1ⁱ—C4—S1	123.3 (3)
H2A—N2—H2B	120.0	N1—C4—S1	123.3 (3)
N1—C1—C3	117.7 (5)	C1—C5—H5A	109.5
N1—C1—C5	117.8 (4)	C1—C5—H5B	109.5
C3—C1—C5	124.5 (5)	H5A—C5—H5B	109.5
N2ⁱ—C2—N2	118.8 (7)	C1—C5—H5C	109.5
N2ⁱ—C2—S2	120.6 (3)	H5A—C5—H5C	109.5
N2—C2—S2	120.6 (3)	H5B—C5—H5C	109.5

C4—N1—C1—C3	0.000 (1)	C5—C1—C3—C1ⁱ	180.0
C4—N1—C1—C5	180.000 (1)	C1—N1—C4—N1ⁱ	0.000 (2)
N1—C1—C3—C1ⁱ	0.000 (2)	C1—N1—C4—S1	180.0

Symmetry code: (i) x, y, −z+3/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···Cl1ⁱⁱ	0.86	2.46	3.310 (4)	171
N2—H2A···Cl1	0.86	2.50	3.297 (5)	154
N2—H2B···S2ⁱⁱⁱ	0.86	2.49	3.347 (5)	173

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

Experimental details

Crystal data
Chemical formula	C₆H₉N₂S⁺·Cl⁻·CH₄N₂S
M_r	252.78
Crystal system, space group	Orthorhombic, Cmcm
Temperature (K)	293
a, b, c (Å)	6.6459 (4), 21.6144 (14), 8.3878 (5)
V (Å³)	1204.88 (12)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.63
Crystal size (mm)	0.10 × 0.10 × 0.10

Data collection
Diffractometer	Nonius KappaCCD diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	1080, 636, 447
R_int	0.024
(sin θ/λ)_max (Å⁻¹)	0.601

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.055, 0.175, 1.05
No. of reflections	636
No. of parameters	49
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.44, −0.51

Computer programs: COLLECT (Nonius, 1998), DENZO/SCALEPACK (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), PLATON/PLUTON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···Cl1ⁱ	0.86	2.46	3.310 (4)	171.4
N2—H2A···Cl1	0.86	2.50	3.297 (5)	153.8
N2—H2B···S2ⁱⁱ	0.86	2.49	3.347 (5)	172.8

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

Acknowledgements

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

References

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