6-Chloro-4-(dimethyl­amino­methyl­eneamino)-2-(methyl­sulfan­yl)pyrimidine

Torre, J.M. de la; Cobo, J.; Nogueras, M.; Low, J.N.

doi:10.1107/S1600536806032004

organic compounds

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ISSN: 2056-9890

Volume 62| Part 9| September 2006| Pages o3910-o3911

https://doi.org/10.1107/S1600536806032004

6-Chloro-4-(dimethylaminomethyleneamino)-2-(methylsulfanyl)pyrimidine

José M. de la Torre,^a Justo Cobo,^a Manuel Nogueras ^a and John Nicolson Low ^b ^*

^aDepartamento de Química Inorgánica y Orgánica, Universidad de Jaén, 23071 Jaén, Spain, and ^bDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen, AB24 3UE, Scotland.
^*Correspondence e-mail: che562@abdn.ac.uk

(Received 24 July 2006; accepted 14 August 2006; online 16 August 2006)

The molecules in the title compound, C₈H₁₁ClN₄S, are linked in pairs by a π–π stacking interaction. There are, however, no other direction-specific interactions.

Comment

In our search for good candidates for intermediates in the synthesis of new pyrimidine fused ring systems, we have prepared the title compound, (I), (Fig. 1), a formyl derivative of 4-amino-6-chloro-2-(methylsulfanyl)pyrimidine, using the Vilsmeier formylation reaction (Vilsmeier & Haack, 1927 ).

The bond lengths and angles show no unusual features. The essentially planar group consisting of atoms N4, C41, N42, C43 and C44 forms a dihedral angle of 31.49 (8)° with that of the planar pyrimidine ring. The leading torsion angles are given in Table 1. The molecules are linked into pairs by a π–π stacking interaction (Fig. 2). The molecules at (x, y, z) and (1 − x, 1 − y, 1 − z) are parallel, with an interplanar spacing of 3.4661 (2) Å. The ring-centroid separation is 3.359 (2) Å corresponding to a ring offset of 0.857 Å.

Figure 1
A view of (I) with our numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.

Figure 2
A view of the π–π stacking viewed perpendicular to the plane of the pyrimidine ring. Atoms labelled with an asterisk (*) are in the molecule at (1 − x, 1 − y, 1 − z). For the sake of clarity, all H atoms have been omitted.

Experimental

The Vilsmeier reagent was prepared in an ice-bath by adding phosphorus oxychloride (1.8 mmol) to N,N-dimethylformamide (38 mmol) and stirring for 15 min. 4-Amino-6-chloro-2-(methylsulfanyl)pyrimidine (0.2 g, 1.14 mmol) was then added and the reaction temperature raised to 323–333 K, and the mixture stirred for 2 h. The reaction mixture was then poured on to crushed ice and neutralized with NaOH (10% in water) until the pH was raised to 8–9. The resulting white solid was filtered off and recrystallized from DMSO-d₆ producing white crystalline blocks suitable for single-crystal X-ray diffraction (yield 60%; m.p. 374–376 K). MS (70 eV): 232/230 (38:100, M+2/M⁺), 217/215 (17/18, [(M+2/M) − CH₃]⁺), 186/184 (17/18, [(M+2/M) − SCH₂]⁺), 149 (31, [M − SCH₃ − Cl]⁺), 71 (4, [N=CH—N(CH₃)₂]⁺).

Crystal data

C₈H₁₁ClN₄S
M_r = 230.72
Triclinic, $[P \overline 1]$
a = 7.4817 (2) Å
b = 8.5739 (2) Å
c = 9.818 (3) Å
α = 111.973 (2)°
β = 91.661 (2)°
γ = 114.566 (2)°
V = 518.31 (15) Å³
Z = 2
D_x = 1.478 Mg m⁻³
Mo Kα radiation
μ = 0.54 mm⁻¹
T = 120 (2) K
Block, colourless
0.30 × 0.30 × 0.20 mm

Data collection

Nonius KappaCCD diffractometer
φ and ω scans
Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ) T_min = 0.856, T_max = 0.901
12192 measured reflections
2378 independent reflections
2015 reflections with I > 2σ(I)
R_int = 0.032
θ_max = 27.5°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.040
wR(F²) = 0.106
S = 1.13
2378 reflections
130 parameters
H-atom parameters constrained
w = 1/[σ²(F_o²) + (0.0456P)² + 0.5109P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.43 e Å⁻³
Δρ_min = −0.36 e Å⁻³

Table 1
Selected torsion angles (°)

N3—C2—S2—C21	0.17 (18)
N1—C2—S2—C21	−179.75 (14)
N3—C4—N4—C41	−25.4 (3)
C5—C4—N4—C41	156.38 (18)
C4—N4—C41—N41	174.23 (17)
N4—C41—N41—C43	−3.4 (3)
N4—C41—N41—C44	175.22 (18)
C2—N1—C6—Cl6	−177.26 (13)
C4—C5—C6—Cl6	175.75 (14)

H atoms were treated as riding atoms, with aromatic C—H = 0.95 Å and U_iso(H) = 1.2U_eq(C), and C—H = 0.98 Å and U_iso(H) = 1.5U_eq(C). The positions of all methyl H atoms were checked in a difference map.

Data collection: COLLECT (Bruker–Nonius, 2004 ); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000 ); data reduction: EVALCCD (Duisenberg et al., 2003 ); program(s) used to solve structure: SIR2004 (Burla et al., 2005 ); program(s) used to refine structure: OSCAIL (McArdle, 2003 ) and SHELXL97 (Sheldrick, 1997 ); molecular graphics: PLATON (Spek, 2003 ); software used to prepare material for publication: SHELXL97 and WORDPERFECT macro PRPKAPPA (Ferguson, 1999 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536806032004/om2046sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806032004/om2046Isup2.hkl

Computing details top

Data collection: COLLECT (Bruker–Nonius, 2004); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: OSCAIL (McArdle, 2003) and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and WORDPERFECT macro PRPKAPPA (Ferguson, 1999).

6-Chloro-4-(dimethylaminomethyleneamino)-2-(methylsulfanyl)pyrimidine top

Crystal data top

C₈H₁₁ClN₄S	Z = 2
M_r = 230.72	F(000) = 240
Triclinic, P1	D_x = 1.478 Mg m⁻³
a = 7.4817 (2) Å	Mo Kα radiation, λ = 0.71069 Å
b = 8.5739 (2) Å	Cell parameters from 2378 reflections
c = 9.818 (3) Å	θ = 4.2–27.5°
α = 111.973 (2)°	µ = 0.54 mm⁻¹
β = 91.661 (2)°	T = 120 K
γ = 114.566 (2)°	Block, colourless
V = 518.31 (15) Å³	0.30 × 0.30 × 0.20 mm

Data collection top

Nonius KappaCCD diffractometer	2015 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.032
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	θ_max = 27.5°, θ_min = 4.2°
T_min = 0.856, T_max = 0.901	h = −9→9
12192 measured reflections	k = −11→11
2378 independent reflections	l = −12→12

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)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.106	H-atom parameters constrained
S = 1.13	w = 1/[σ²(F_o²) + (0.0456P)² + 0.5109P] where P = (F_o² + 2F_c²)/3
2378 reflections	(Δ/σ)_max < 0.001
130 parameters	Δρ_max = 0.43 e Å⁻³
0 restraints	Δρ_min = −0.36 e Å⁻³

Special details top

Experimental. The scale factors in the experimental table are calculated from the 'size' command in the SHELXL97 input file.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.7202 (2)	0.4345 (2)	0.35311 (18)	0.0187 (3)
C2	0.7336 (3)	0.4427 (3)	0.4933 (2)	0.0171 (4)
S2	0.71334 (8)	0.23243 (7)	0.49580 (5)	0.02132 (15)
C21	0.7347 (3)	0.2824 (3)	0.6919 (2)	0.0255 (4)
N3	0.7589 (2)	0.5869 (2)	0.62132 (18)	0.0176 (3)
C4	0.7747 (3)	0.7458 (3)	0.6112 (2)	0.0172 (4)
N4	0.8032 (2)	0.9024 (2)	0.73831 (18)	0.0192 (3)
C41	0.7393 (3)	0.8703 (3)	0.8511 (2)	0.0183 (4)
N41	0.7704 (2)	1.0073 (2)	0.98542 (18)	0.0195 (3)
C43	0.8898 (3)	1.2062 (3)	1.0181 (2)	0.0241 (4)
C44	0.6831 (3)	0.9661 (3)	1.1064 (2)	0.0234 (4)
C5	0.7678 (3)	0.7549 (3)	0.4712 (2)	0.0191 (4)
C6	0.7360 (3)	0.5939 (3)	0.3494 (2)	0.0185 (4)
Cl6	0.70810 (8)	0.58526 (7)	0.16889 (5)	0.02420 (15)
H21A	0.7244	0.1718	0.7059	0.038*
H21B	0.6262	0.3111	0.7275	0.038*
H21C	0.8652	0.3914	0.7495	0.038*
H41	0.6665	0.7426	0.8370	0.022*
H43A	0.9684	1.2170	0.9409	0.036*
H43B	0.9814	1.2724	1.1170	0.036*
H43C	0.8002	1.2632	1.0183	0.036*
H44A	0.5920	0.8302	1.0680	0.035*
H44B	0.6078	1.0377	1.1441	0.035*
H44C	0.7910	1.0027	1.1885	0.035*
H5	0.7842	0.8662	0.4618	0.023*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0197 (8)	0.0177 (8)	0.0186 (8)	0.0086 (7)	0.0043 (6)	0.0077 (6)
C2	0.0159 (9)	0.0168 (9)	0.0173 (9)	0.0072 (7)	0.0030 (7)	0.0064 (7)
S2	0.0301 (3)	0.0171 (2)	0.0182 (3)	0.0133 (2)	0.00435 (19)	0.00624 (19)
C21	0.0362 (12)	0.0228 (10)	0.0195 (10)	0.0149 (9)	0.0050 (8)	0.0094 (8)
N3	0.0191 (8)	0.0167 (8)	0.0170 (8)	0.0088 (6)	0.0024 (6)	0.0065 (6)
C4	0.0153 (8)	0.0160 (9)	0.0185 (9)	0.0069 (7)	0.0023 (7)	0.0062 (7)
N4	0.0217 (8)	0.0176 (8)	0.0172 (8)	0.0098 (7)	0.0023 (6)	0.0055 (6)
C41	0.0179 (9)	0.0154 (9)	0.0188 (9)	0.0087 (7)	0.0017 (7)	0.0036 (7)
N41	0.0220 (8)	0.0178 (8)	0.0184 (8)	0.0100 (7)	0.0032 (6)	0.0064 (7)
C43	0.0299 (11)	0.0174 (9)	0.0222 (10)	0.0112 (8)	0.0031 (8)	0.0054 (8)
C44	0.0266 (10)	0.0270 (10)	0.0187 (9)	0.0146 (9)	0.0064 (8)	0.0091 (8)
C5	0.0203 (9)	0.0163 (9)	0.0210 (9)	0.0084 (8)	0.0040 (7)	0.0084 (8)
C6	0.0174 (9)	0.0222 (9)	0.0174 (9)	0.0097 (8)	0.0040 (7)	0.0093 (8)
Cl6	0.0333 (3)	0.0244 (3)	0.0183 (2)	0.0146 (2)	0.00694 (19)	0.0109 (2)

Geometric parameters (Å, º) top

N1—C6	1.337 (2)	C41—H41	0.95
N1—C2	1.350 (2)	N41—C43	1.455 (3)
C2—N3	1.331 (2)	N41—C44	1.460 (3)
C2—S2	1.7553 (19)	C43—H43A	0.98
S2—C21	1.796 (2)	C43—H43B	0.98
C21—H21A	0.98	C43—H43C	0.98
C21—H21B	0.98	C44—H44A	0.98
C21—H21C	0.98	C44—H44B	0.98
N3—C4	1.360 (2)	C44—H44C	0.98
C4—N4	1.378 (2)	C5—C6	1.367 (3)
C4—C5	1.406 (3)	C5—H5	0.95
N4—C41	1.296 (3)	C6—Cl6	1.748 (2)
C41—N41	1.330 (2)

C6—N1—C2	113.18 (16)	C41—N41—C44	121.80 (17)
N3—C2—N1	127.66 (17)	C43—N41—C44	116.60 (16)
N3—C2—S2	119.89 (14)	N41—C43—H43A	109.5
N1—C2—S2	112.44 (14)	N41—C43—H43B	109.5
C2—S2—C21	102.86 (9)	H43A—C43—H43B	109.5
S2—C21—H21A	109.5	N41—C43—H43C	109.5
S2—C21—H21B	109.5	H43A—C43—H43C	109.5
H21A—C21—H21B	109.5	H43B—C43—H43C	109.5
S2—C21—H21C	109.5	N41—C44—H44A	109.5
H21A—C21—H21C	109.5	N41—C44—H44B	109.5
H21B—C21—H21C	109.5	H44A—C44—H44B	109.5
C2—N3—C4	116.74 (16)	N41—C44—H44C	109.5
N3—C4—N4	120.58 (17)	H44A—C44—H44C	109.5
N3—C4—C5	120.53 (17)	H44B—C44—H44C	109.5
N4—C4—C5	118.87 (17)	C6—C5—C4	115.92 (17)
C41—N4—C4	116.07 (17)	C6—C5—H5	122.0
N4—C41—N41	123.31 (18)	C4—C5—H5	122.0
N4—C41—H41	118.3	N1—C6—C5	125.91 (18)
N41—C41—H41	118.3	N1—C6—Cl6	114.60 (14)
C41—N41—C43	121.59 (17)	C5—C6—Cl6	119.48 (15)

C6—N1—C2—N3	0.3 (3)	C4—N4—C41—N41	174.23 (17)
C6—N1—C2—S2	−179.79 (13)	N4—C41—N41—C43	−3.4 (3)
N3—C2—S2—C21	0.17 (18)	N4—C41—N41—C44	175.22 (18)
N1—C2—S2—C21	−179.75 (14)	N3—C4—C5—C6	2.7 (3)
N1—C2—N3—C4	−0.5 (3)	N4—C4—C5—C6	−179.04 (17)
S2—C2—N3—C4	179.60 (13)	C2—N1—C6—C5	1.6 (3)
C2—N3—C4—N4	−179.32 (17)	C2—N1—C6—Cl6	−177.26 (13)
C2—N3—C4—C5	−1.1 (3)	C4—C5—C6—N1	−3.1 (3)
N3—C4—N4—C41	−25.4 (3)	C4—C5—C6—Cl6	175.75 (14)
C5—C4—N4—C41	156.38 (18)

Acknowledgements

JT, MN and JC thank the Consejería de Innovacíon, Ciencia y Empresa (Junta de Andalucía, Spain) and the Universidad de Jaén, Spain, for financial support. JT thanks also the Universidad de Jaén for a research scholarship.

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