4-Chloro-2-methyl­thio-6-(1-piperidyl)­pyrimidine

The structure of the title compound, C₁₀H₁₄ClN₃S, comprises a non-planar mol­ecule with only one intramolecular close-contact association between a piperidinyl C-H group and a pyrimidine N atom. The pyrimidine-methyl­thio torsion angle is 5.7 (2)°.

Key indicators

• Single-crystal X-ray study
• T = 150 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.041
• wR factor = 0.116
• Data-to-parameter ratio = 18.8

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

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S1. Comment

The title compound, (I), was prepared from 4,6-dichloro-2-methylthiopyrimidine. Both Cl atoms can be displaced by nucleophiles before the methylthio group but the reactivity of the second Cl atom is much less than the first. This difference in reaction rate can be used to prepare unsymmetrical 4,6-substituted 2-methylthiopyrimidines because the product of the loss of the first Cl atom can be separated in large yield, e.g. compound (I). An interesting feature of the structure of 4,6-dichloro-2-methylthiopyrimidine is that there are six unique molecules in the asymmetric unit (Lynch & McClenaghan, 2000); differences arising due to the out-of-plane twist the methylthio bond makes with respect to the pyrimidine ring. The structure determination of the title compound was undertaken within a study of the effects that different substituents of 2-methylthiopyrimidines have on the pyrimidine–methylthio torsion angle.

S2. Experimental

The title compound, (I), was prepared by Spa Contract Synthesis. Crystals of (I) were grown from an ethanol solution.

S3. Refinement

All H atoms were included in the refinement, at calculated positions, as riding models with C—H set to 0.95 Å (Ar—H), 0.98 Å (CH₃) and 0.99 Å (CH₂). The methyl group was allowed to rotate about its local threefold axis.

Computing details

Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); cell refinement: DENZO and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); software used to prepare material for publication: SHELXL97.

Figures

Fig. 1. The molecular configuration and atom-numbering scheme for (I) showing 50% probability ellipsoids.

4-Chloro-2-methylthio-6-(piperidin-1-yl)pyrimidine

Crystal data

C10H14ClN3S	Dx = 1.417 Mg m^−3
Mr = 243.75	Melting point: 356-358 K K
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
a = 13.189 (3) Å	Cell parameters from 15006 reflections
b = 8.577 (2) Å	θ = 2.9–30.5°
c = 20.195 (4) Å	µ = 0.49 mm^−1
V = 2284.4 (8) Å^3	T = 150 K
Z = 8	Block, colourless
F(000) = 1024	0.40 × 0.40 × 0.36 mm

Data collection

Enraf Nonius KappaCCD area-detector diffractometer	2580 independent reflections
Radiation source: Enraf Nonius FR591 rotating anode	2124 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.070
Detector resolution: 9.091 pixels mm^-1	θmax = 27.5°, θmin = 3.0°
ϕ and ω scans	h = −17→17
Absorption correction: multi-scan (SORTAV; Blessing, 1995)	k = −11→10
Tmin = 0.829, Tmax = 0.844	l = −26→26
11709 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.117	H-atom parameters constrained
S = 1.06	w = 1/[σ^2(Fo^2) + (0.0691P)^2 + 0.3268P] where P = (Fo^2 + 2Fc^2)/3
2580 reflections	(Δ/σ)max < 0.001
137 parameters	Δρmax = 0.29 e Å^−3
0 restraints	Δρmin = −0.36 e Å^−3

Special details

Experimental. PLEASE NOTE cell_measurement_ fields are not relevant to area detector data, the entire data set is used to refine the cell, which is indexed from all observed reflections in a 10 degree phi range.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
N1	0.40565 (10)	−0.13958 (15)	0.41858 (7)	0.0247 (3)
C2	0.36235 (12)	−0.08692 (18)	0.47313 (8)	0.0242 (3)
S2	0.25591 (3)	0.03635 (5)	0.46554 (2)	0.02906 (16)
C21	0.23515 (14)	0.0312 (2)	0.37775 (9)	0.0352 (5)
H21	0.2952	0.0714	0.3549	0.044*
H22	0.1763	0.0958	0.3666	0.044*
H23	0.2226	−0.0766	0.3638	0.044*
N3	0.38882 (11)	−0.11320 (16)	0.53622 (7)	0.0269 (3)
C4	0.46762 (14)	−0.20955 (19)	0.54096 (8)	0.0254 (4)
Cl4	0.50641 (4)	−0.25289 (5)	0.62175 (2)	0.03458 (17)
C5	0.52051 (13)	−0.27526 (18)	0.48988 (9)	0.0263 (4)
H5	0.5758	−0.3443	0.4970	0.033*
C6	0.48734 (13)	−0.23358 (19)	0.42617 (9)	0.0245 (4)
N61	0.53176 (13)	−0.28667 (19)	0.36979 (7)	0.0322 (4)
C62	0.62913 (15)	−0.3687 (2)	0.36993 (9)	0.0361 (4)
H621	0.6263	−0.4571	0.3384	0.045*
H622	0.6423	−0.4113	0.4147	0.045*
C63	0.71465 (15)	−0.2595 (2)	0.35043 (10)	0.0382 (5)
H631	0.7217	−0.1764	0.3841	0.048*
H632	0.7792	−0.3181	0.3486	0.048*
C64	0.69324 (15)	−0.1868 (2)	0.28338 (9)	0.0368 (4)
H641	0.6953	−0.2686	0.2488	0.046*
H642	0.7463	−0.1089	0.2731	0.046*
C65	0.58996 (15)	−0.1084 (2)	0.28281 (9)	0.0335 (4)
H651	0.5912	−0.0169	0.3127	0.042*
H652	0.5748	−0.0710	0.2375	0.042*
C66	0.50718 (14)	−0.2200 (2)	0.30501 (9)	0.0326 (4)
H661	0.4418	−0.1636	0.3077	0.041*
H662	0.4999	−0.3047	0.2721	0.041*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0219 (7)	0.0245 (6)	0.0276 (7)	−0.0012 (5)	−0.0001 (5)	0.0001 (5)
C2	0.0221 (8)	0.0206 (7)	0.0299 (8)	−0.0014 (6)	−0.0010 (6)	−0.0008 (6)
S2	0.0269 (3)	0.0295 (3)	0.0308 (3)	0.00478 (17)	−0.00029 (16)	−0.00190 (17)
C21	0.0332 (11)	0.0412 (11)	0.0313 (10)	0.0100 (8)	−0.0053 (7)	0.0003 (7)
N3	0.0275 (8)	0.0266 (7)	0.0267 (7)	−0.0008 (6)	0.0003 (5)	−0.0004 (5)
C4	0.0272 (9)	0.0257 (8)	0.0233 (8)	−0.0045 (7)	−0.0013 (7)	0.0024 (6)
Cl4	0.0401 (3)	0.0392 (3)	0.0245 (3)	0.00439 (19)	−0.00355 (17)	0.00434 (17)
C5	0.0258 (9)	0.0243 (8)	0.0288 (9)	0.0006 (6)	−0.0001 (7)	0.0028 (7)
C6	0.0235 (9)	0.0227 (8)	0.0273 (9)	−0.0037 (6)	0.0024 (6)	−0.0012 (6)
N61	0.0301 (9)	0.0389 (9)	0.0277 (8)	0.0078 (7)	0.0033 (6)	0.0019 (6)
C62	0.0378 (11)	0.0374 (10)	0.0331 (9)	0.0143 (8)	0.0062 (7)	0.0011 (7)
C63	0.0303 (10)	0.0520 (11)	0.0324 (10)	0.0071 (9)	−0.0017 (8)	−0.0063 (8)
C64	0.0338 (10)	0.0444 (10)	0.0321 (9)	−0.0048 (9)	0.0039 (8)	−0.0038 (8)
C65	0.0436 (11)	0.0320 (9)	0.0249 (8)	0.0019 (8)	−0.0006 (7)	−0.0025 (7)
C66	0.0307 (10)	0.0444 (11)	0.0227 (9)	0.0036 (7)	−0.0005 (7)	−0.0030 (7)

Geometric parameters (Å, º)

N1—C2	1.320 (2)	N61—C66	1.464 (2)
N1—C6	1.354 (2)	C62—C63	1.518 (3)
C2—N3	1.340 (2)	C62—H621	0.99
C2—S2	1.7641 (17)	C62—H622	0.99
S2—C21	1.7944 (18)	C63—C64	1.517 (3)
C21—H21	0.98	C63—H631	0.99
C21—H22	0.98	C63—H632	0.99
C21—H23	0.98	C64—C65	1.519 (3)
N3—C4	1.331 (2)	C64—H641	0.99
C4—C5	1.367 (2)	C64—H642	0.99
C4—Cl4	1.7499 (17)	C65—C66	1.519 (3)
C5—C6	1.405 (2)	C65—H651	0.99
C5—H5	0.95	C65—H652	0.99
C6—N61	1.359 (2)	C66—H661	0.99
N61—C62	1.464 (2)	C66—H662	0.99
C2—N1—C6	116.95 (14)	N61—C62—H622	109.5
N1—C2—N3	128.54 (15)	C63—C62—H622	109.5
N1—C2—S2	118.47 (12)	H621—C62—H622	108.1
N3—C2—S2	112.99 (12)	C64—C63—C62	110.28 (16)
C2—S2—C21	101.09 (8)	C64—C63—H631	109.6
S2—C21—H21	109.5	C62—C63—H631	109.6
S2—C21—H22	109.5	C64—C63—H632	109.6
H21—C21—H22	109.5	C62—C63—H632	109.6
S2—C21—H23	109.5	H631—C63—H632	108.1
H21—C21—H23	109.5	C63—C64—C65	110.83 (15)
H22—C21—H23	109.5	C63—C64—H641	109.5
C4—N3—C2	112.08 (14)	C65—C64—H641	109.5
N3—C4—C5	126.88 (15)	C63—C64—H642	109.5
N3—C4—Cl4	115.28 (12)	C65—C64—H642	109.5
C5—C4—Cl4	117.83 (14)	H641—C64—H642	108.1
C4—C5—C6	115.29 (16)	C66—C65—C64	111.30 (15)
C4—C5—H5	122.4	C66—C65—H651	109.4
C6—C5—H5	122.4	C64—C65—H651	109.4
N1—C6—N61	116.59 (15)	C66—C65—H652	109.4
N1—C6—C5	120.18 (15)	C64—C65—H652	109.4
N61—C6—C5	123.21 (16)	H651—C65—H652	108.0
C6—N61—C62	122.50 (14)	N61—C66—C65	110.52 (15)
C6—N61—C66	121.48 (16)	N61—C66—H661	109.5
C62—N61—C66	112.57 (14)	C65—C66—H661	109.5
N61—C62—C63	110.75 (16)	N61—C66—H662	109.5
N61—C62—H621	109.5	C65—C66—H662	109.5
C63—C62—H621	109.5	H661—C66—H662	108.1
C6—N1—C2—N3	0.5 (3)	C4—C5—C6—N61	179.32 (16)
C6—N1—C2—S2	179.83 (11)	N1—C6—N61—C62	170.32 (16)
N1—C2—S2—C21	5.7 (2)	C5—C6—N61—C62	−11.5 (3)
N3—C2—S2—C21	−174.86 (13)	N1—C6—N61—C66	12.8 (3)
N1—C2—N3—C4	−2.2 (2)	C5—C6—N61—C66	−168.99 (16)
S2—C2—N3—C4	178.40 (11)	C6—N61—C62—C63	−100.3 (2)
C2—N3—C4—C5	1.5 (2)	C66—N61—C62—C63	59.0 (2)
C2—N3—C4—Cl4	−179.11 (11)	N61—C62—C63—C64	−56.4 (2)
N3—C4—C5—C6	0.7 (3)	C62—C63—C64—C65	54.1 (2)
Cl4—C4—C5—C6	−178.66 (12)	C63—C64—C65—C66	−53.5 (2)
C2—N1—C6—N61	−179.69 (14)	C6—N61—C66—C65	101.77 (19)
C2—N1—C6—C5	2.1 (2)	C62—N61—C66—C65	−57.7 (2)
C4—C5—C6—N1	−2.6 (2)	C64—C65—C66—N61	54.58 (19)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C66—H661···N1	0.99	2.30	2.744 (2)	106