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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)°.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536801001982/bt6012sup1.cif
Contains datablocks I, default

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536801001982/bt6012Isup2.hkl
Contains datablock I

CCDC reference: 159840

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




Comment top

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.

Experimental top

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

Refinement top

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 top

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 top
[Figure 1] Fig. 1. The molecular configuration and atom-numbering scheme for (I) showing 50% probability ellipsoids.
4-Chloro-2-methylthio-6-(piperidin-1-yl)pyrimidine top
Crystal data top
C10H14ClN3SDx = 1.417 Mg m3
Mr = 243.75Melting point: 356-358 K K
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
a = 13.189 (3) ÅCell parameters from 15006 reflections
b = 8.577 (2) Åθ = 2.9–30.5°
c = 20.195 (4) ŵ = 0.49 mm1
V = 2284.4 (8) Å3T = 150 K
Z = 8Block, colourless
F(000) = 10240.40 × 0.40 × 0.36 mm
Data collection top
Enraf Nonius KappaCCD area-detector
diffractometer
2580 independent reflections
Radiation source: Enraf Nonius FR591 rotating anode2124 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.070
Detector resolution: 9.091 pixels mm-1θmax = 27.5°, θmin = 3.0°
ϕ and ω scansh = 1717
Absorption correction: multi-scan
(SORTAV; Blessing, 1995)
k = 1110
Tmin = 0.829, Tmax = 0.844l = 2626
11709 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.117H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0691P)2 + 0.3268P]
where P = (Fo2 + 2Fc2)/3
2580 reflections(Δ/σ)max < 0.001
137 parametersΔρmax = 0.29 e Å3
0 restraintsΔρmin = 0.36 e Å3
Crystal data top
C10H14ClN3SV = 2284.4 (8) Å3
Mr = 243.75Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 13.189 (3) ŵ = 0.49 mm1
b = 8.577 (2) ÅT = 150 K
c = 20.195 (4) Å0.40 × 0.40 × 0.36 mm
Data collection top
Enraf Nonius KappaCCD area-detector
diffractometer
2580 independent reflections
Absorption correction: multi-scan
(SORTAV; Blessing, 1995)
2124 reflections with I > 2σ(I)
Tmin = 0.829, Tmax = 0.844Rint = 0.070
11709 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0410 restraints
wR(F2) = 0.117H-atom parameters constrained
S = 1.06Δρmax = 0.29 e Å3
2580 reflectionsΔρmin = 0.36 e Å3
137 parameters
Special details top

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 (Å2) top
xyzUiso*/Ueq
N10.40565 (10)0.13958 (15)0.41858 (7)0.0247 (3)
C20.36235 (12)0.08692 (18)0.47313 (8)0.0242 (3)
S20.25591 (3)0.03635 (5)0.46554 (2)0.02906 (16)
C210.23515 (14)0.0312 (2)0.37775 (9)0.0352 (5)
H210.29520.07140.35490.044*
H220.17630.09580.36660.044*
H230.22260.07660.36380.044*
N30.38882 (11)0.11320 (16)0.53622 (7)0.0269 (3)
C40.46762 (14)0.20955 (19)0.54096 (8)0.0254 (4)
Cl40.50641 (4)0.25289 (5)0.62175 (2)0.03458 (17)
C50.52051 (13)0.27526 (18)0.48988 (9)0.0263 (4)
H50.57580.34430.49700.033*
C60.48734 (13)0.23358 (19)0.42617 (9)0.0245 (4)
N610.53176 (13)0.28667 (19)0.36979 (7)0.0322 (4)
C620.62913 (15)0.3687 (2)0.36993 (9)0.0361 (4)
H6210.62630.45710.33840.045*
H6220.64230.41130.41470.045*
C630.71465 (15)0.2595 (2)0.35043 (10)0.0382 (5)
H6310.72170.17640.38410.048*
H6320.77920.31810.34860.048*
C640.69324 (15)0.1868 (2)0.28338 (9)0.0368 (4)
H6410.69530.26860.24880.046*
H6420.74630.10890.27310.046*
C650.58996 (15)0.1084 (2)0.28281 (9)0.0335 (4)
H6510.59120.01690.31270.042*
H6520.57480.07100.23750.042*
C660.50718 (14)0.2200 (2)0.30501 (9)0.0326 (4)
H6610.44180.16360.30770.041*
H6620.49990.30470.27210.041*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0219 (7)0.0245 (6)0.0276 (7)0.0012 (5)0.0001 (5)0.0001 (5)
C20.0221 (8)0.0206 (7)0.0299 (8)0.0014 (6)0.0010 (6)0.0008 (6)
S20.0269 (3)0.0295 (3)0.0308 (3)0.00478 (17)0.00029 (16)0.00190 (17)
C210.0332 (11)0.0412 (11)0.0313 (10)0.0100 (8)0.0053 (7)0.0003 (7)
N30.0275 (8)0.0266 (7)0.0267 (7)0.0008 (6)0.0003 (5)0.0004 (5)
C40.0272 (9)0.0257 (8)0.0233 (8)0.0045 (7)0.0013 (7)0.0024 (6)
Cl40.0401 (3)0.0392 (3)0.0245 (3)0.00439 (19)0.00355 (17)0.00434 (17)
C50.0258 (9)0.0243 (8)0.0288 (9)0.0006 (6)0.0001 (7)0.0028 (7)
C60.0235 (9)0.0227 (8)0.0273 (9)0.0037 (6)0.0024 (6)0.0012 (6)
N610.0301 (9)0.0389 (9)0.0277 (8)0.0078 (7)0.0033 (6)0.0019 (6)
C620.0378 (11)0.0374 (10)0.0331 (9)0.0143 (8)0.0062 (7)0.0011 (7)
C630.0303 (10)0.0520 (11)0.0324 (10)0.0071 (9)0.0017 (8)0.0063 (8)
C640.0338 (10)0.0444 (10)0.0321 (9)0.0048 (9)0.0039 (8)0.0038 (8)
C650.0436 (11)0.0320 (9)0.0249 (8)0.0019 (8)0.0006 (7)0.0025 (7)
C660.0307 (10)0.0444 (11)0.0227 (9)0.0036 (7)0.0005 (7)0.0030 (7)
Geometric parameters (Å, º) top
N1—C21.320 (2)N61—C661.464 (2)
N1—C61.354 (2)C62—C631.518 (3)
C2—N31.340 (2)C62—H6210.99
C2—S21.7641 (17)C62—H6220.99
S2—C211.7944 (18)C63—C641.517 (3)
C21—H210.98C63—H6310.99
C21—H220.98C63—H6320.99
C21—H230.98C64—C651.519 (3)
N3—C41.331 (2)C64—H6410.99
C4—C51.367 (2)C64—H6420.99
C4—Cl41.7499 (17)C65—C661.519 (3)
C5—C61.405 (2)C65—H6510.99
C5—H50.95C65—H6520.99
C6—N611.359 (2)C66—H6610.99
N61—C621.464 (2)C66—H6620.99
C2—N1—C6116.95 (14)N61—C62—H622109.5
N1—C2—N3128.54 (15)C63—C62—H622109.5
N1—C2—S2118.47 (12)H621—C62—H622108.1
N3—C2—S2112.99 (12)C64—C63—C62110.28 (16)
C2—S2—C21101.09 (8)C64—C63—H631109.6
S2—C21—H21109.5C62—C63—H631109.6
S2—C21—H22109.5C64—C63—H632109.6
H21—C21—H22109.5C62—C63—H632109.6
S2—C21—H23109.5H631—C63—H632108.1
H21—C21—H23109.5C63—C64—C65110.83 (15)
H22—C21—H23109.5C63—C64—H641109.5
C4—N3—C2112.08 (14)C65—C64—H641109.5
N3—C4—C5126.88 (15)C63—C64—H642109.5
N3—C4—Cl4115.28 (12)C65—C64—H642109.5
C5—C4—Cl4117.83 (14)H641—C64—H642108.1
C4—C5—C6115.29 (16)C66—C65—C64111.30 (15)
C4—C5—H5122.4C66—C65—H651109.4
C6—C5—H5122.4C64—C65—H651109.4
N1—C6—N61116.59 (15)C66—C65—H652109.4
N1—C6—C5120.18 (15)C64—C65—H652109.4
N61—C6—C5123.21 (16)H651—C65—H652108.0
C6—N61—C62122.50 (14)N61—C66—C65110.52 (15)
C6—N61—C66121.48 (16)N61—C66—H661109.5
C62—N61—C66112.57 (14)C65—C66—H661109.5
N61—C62—C63110.75 (16)N61—C66—H662109.5
N61—C62—H621109.5C65—C66—H662109.5
C63—C62—H621109.5H661—C66—H662108.1
C6—N1—C2—N30.5 (3)C4—C5—C6—N61179.32 (16)
C6—N1—C2—S2179.83 (11)N1—C6—N61—C62170.32 (16)
N1—C2—S2—C215.7 (2)C5—C6—N61—C6211.5 (3)
N3—C2—S2—C21174.86 (13)N1—C6—N61—C6612.8 (3)
N1—C2—N3—C42.2 (2)C5—C6—N61—C66168.99 (16)
S2—C2—N3—C4178.40 (11)C6—N61—C62—C63100.3 (2)
C2—N3—C4—C51.5 (2)C66—N61—C62—C6359.0 (2)
C2—N3—C4—Cl4179.11 (11)N61—C62—C63—C6456.4 (2)
N3—C4—C5—C60.7 (3)C62—C63—C64—C6554.1 (2)
Cl4—C4—C5—C6178.66 (12)C63—C64—C65—C6653.5 (2)
C2—N1—C6—N61179.69 (14)C6—N61—C66—C65101.77 (19)
C2—N1—C6—C52.1 (2)C62—N61—C66—C6557.7 (2)
C4—C5—C6—N12.6 (2)C64—C65—C66—N6154.58 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C66—H661···N10.992.302.744 (2)106

Experimental details

Crystal data
Chemical formulaC10H14ClN3S
Mr243.75
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)150
a, b, c (Å)13.189 (3), 8.577 (2), 20.195 (4)
V3)2284.4 (8)
Z8
Radiation typeMo Kα
µ (mm1)0.49
Crystal size (mm)0.40 × 0.40 × 0.36
Data collection
DiffractometerEnraf Nonius KappaCCD area-detector
diffractometer
Absorption correctionMulti-scan
(SORTAV; Blessing, 1995)
Tmin, Tmax0.829, 0.844
No. of measured, independent and
observed [I > 2σ(I)] reflections
11709, 2580, 2124
Rint0.070
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.117, 1.06
No. of reflections2580
No. of parameters137
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.29, 0.36

Computer programs: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998), DENZO and COLLECT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXL97.

Selected torsion angles (º) top
N1—C2—S2—C215.7 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C66—H661···N10.992.302.744 (2)106.1
 

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