4-Chloro-2-{3-chloro-2-[(3,5-dimethyl-piperidin-1-yl)meth-yl]phenyl-sulfan-yl}-6-methoxy-pyrimidine.

In the title compound, C(19)H(23)Cl(2)N(3)OS, the dihedral angle between the benzene ring and the pyrimidine ring is 86.6 (9)°. The piperidine ring adopts a chair conformation.

Related literature

For the biological activity of pyrimidine derivatives, see: Joffe et al. (1989 ▶); Petersen & Schmidt (2003 ▶); Blum (2001 ▶); Gompper et al. (2004 ▶); Michael (2005 ▶); Nadal & Olavarria (2004 ▶).

Experimental

Crystal data

C19H23Cl2N3OS

M = 412.36

Triclinic,

a = 8.000 (4) Å

b = 11.454 (6) Å

c = 12.001 (7) Å

α = 87.820 (7)°

β = 76.084 (6)°

γ = 77.700 (6)°

V = 1042.9 (10) Å3

Z = 2

Mo Kα radiation

μ = 0.42 mm−1

T = 296 K

0.39 × 0.37 × 0.25 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer

Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ▶) T min = 0.852, T max = 0.901

7861 measured reflections

3848 independent reflections

2553 reflections with I > 2σ(I)

R int = 0.019

Refinement

R[F 2 > 2σ(F 2)] = 0.041

wR(F 2) = 0.119

S = 1.03

3848 reflections

238 parameters

H-atom parameters constrained

Δρmax = 0.30 e Å−3

Δρmin = −0.31 e Å−3

Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810004599/pb2021sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810004599/pb2021Isup2.hkl

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

C19H23Cl2N3OS	Z = 2
Mr = 412.36	F(000) = 432
Triclinic, P1	Dx = 1.313 Mg m−3
a = 8.000 (4) Å	Mo Kα radiation, λ = 0.71073 Å
b = 11.454 (6) Å	Cell parameters from 2557 reflections
c = 12.001 (7) Å	θ = 2.5–25.9°
α = 87.820 (7)°	µ = 0.42 mm−1
β = 76.084 (6)°	T = 296 K
γ = 77.700 (6)°	Block, colourless
V = 1042.9 (10) Å3	0.39 × 0.37 × 0.25 mm

Bruker SMART APEXII CCD area-detector diffractometer	3848 independent reflections
Radiation source: fine-focus sealed tube	2553 reflections with I > 2σ(I)
graphite	Rint = 0.019
phi and ω scans	θmax = 25.5°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −9→9
Tmin = 0.852, Tmax = 0.901	k = −13→13
7861 measured reflections	l = −14→14

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)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.119	H-atom parameters constrained
S = 1.02	w = 1/[σ2(Fo2) + (0.0498P)2 + 0.3748P] where P = (Fo2 + 2Fc2)/3
3848 reflections	(Δ/σ)max < 0.001
238 parameters	Δρmax = 0.30 e Å−3
0 restraints	Δρmin = −0.30 e Å−3

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2sigma(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

	x	y	z	Uiso*/Ueq
C1	0.8993 (3)	0.4679 (2)	0.3790 (2)	0.0511 (6)
C2	0.7914 (4)	0.5783 (3)	0.4072 (2)	0.0639 (7)
H2	0.8031	0.6417	0.3572	0.077*
C3	0.6657 (4)	0.5951 (3)	0.5096 (3)	0.0772 (10)
H3	0.5913	0.6695	0.5281	0.093*
C4	0.6503 (4)	0.5026 (4)	0.5841 (3)	0.0765 (10)
H4	0.5657	0.5136	0.6533	0.092*
C5	0.7618 (4)	0.3926 (3)	0.5555 (2)	0.0649 (8)
C6	0.8897 (3)	0.3706 (2)	0.4527 (2)	0.0517 (6)
C7	1.0146 (4)	0.2522 (3)	0.4215 (2)	0.0613 (7)
H7A	1.1342	0.2648	0.3977	0.074*
H7B	1.0071	0.2019	0.4886	0.074*
C8	1.1282 (4)	0.1048 (3)	0.2685 (3)	0.0722 (8)
H8A	1.1601	0.0419	0.3206	0.087*
H8B	1.2269	0.1439	0.2432	0.087*
C9	1.0929 (4)	0.0498 (3)	0.1644 (3)	0.0773 (9)
H9	1.0612	0.1145	0.1126	0.093*
C10	0.9343 (4)	−0.0090 (3)	0.2069 (3)	0.0838 (10)
H10A	0.9048	−0.0403	0.1418	0.101*
H10B	0.9647	−0.0753	0.2562	0.101*
C11	0.7761 (4)	0.0801 (3)	0.2730 (3)	0.0867 (10)
H11	0.7438	0.1436	0.2202	0.104*
C12	0.8245 (4)	0.1367 (3)	0.3699 (3)	0.0757 (9)
H12A	0.7247	0.1972	0.4083	0.091*
H12B	0.8503	0.0761	0.4256	0.091*
C13	1.2537 (5)	−0.0357 (3)	0.1000 (3)	0.1102 (13)
H13A	1.3485	0.0055	0.0749	0.165*
H13B	1.2284	−0.0676	0.0345	0.165*
H13C	1.2871	−0.0998	0.1494	0.165*
C14	0.6166 (5)	0.0238 (4)	0.3187 (5)	0.151 (2)
H14A	0.6428	−0.0360	0.3738	0.226*
H14B	0.5894	−0.0124	0.2562	0.226*
H14C	0.5174	0.0844	0.3547	0.226*
C15	0.9754 (3)	0.4023 (2)	0.14901 (19)	0.0466 (6)
C16	1.0372 (3)	0.3253 (2)	−0.0292 (2)	0.0483 (6)
C17	0.8596 (3)	0.3280 (2)	−0.0188 (2)	0.0528 (6)
H17	0.8179	0.3030	−0.0778	0.063*
C18	0.7513 (3)	0.3697 (2)	0.0833 (2)	0.0500 (6)
C19	1.3329 (4)	0.2760 (3)	−0.1362 (3)	0.0729 (8)
H19A	1.3525	0.3554	−0.1317	0.109*
H19B	1.3998	0.2398	−0.2085	0.109*
H19C	1.3695	0.2292	−0.0749	0.109*
Cl1	0.73889 (14)	0.27940 (11)	0.65587 (8)	0.1117 (4)
Cl2	0.52759 (9)	0.37327 (8)	0.10766 (6)	0.0780 (3)
N1	0.9758 (3)	0.19101 (19)	0.32894 (19)	0.0585 (6)
N2	0.8031 (3)	0.40866 (18)	0.16994 (16)	0.0497 (5)
N3	1.0978 (3)	0.36245 (17)	0.05379 (16)	0.0480 (5)
O1	1.1505 (2)	0.28158 (17)	−0.12653 (14)	0.0651 (5)
S1	1.06955 (9)	0.45367 (7)	0.25092 (6)	0.0613 (2)

	U11	U22	U33	U12	U13	U23
C1	0.0428 (14)	0.0719 (18)	0.0443 (13)	−0.0167 (13)	−0.0152 (11)	−0.0130 (13)
C2	0.0580 (18)	0.0735 (19)	0.0658 (18)	−0.0100 (15)	−0.0263 (15)	−0.0174 (15)
C3	0.0500 (18)	0.095 (2)	0.088 (2)	−0.0002 (16)	−0.0258 (17)	−0.043 (2)
C4	0.0440 (17)	0.127 (3)	0.0581 (18)	−0.0211 (19)	−0.0025 (13)	−0.0381 (19)
C5	0.0497 (16)	0.102 (2)	0.0489 (15)	−0.0256 (16)	−0.0123 (12)	−0.0129 (15)
C6	0.0387 (14)	0.0765 (18)	0.0458 (14)	−0.0172 (13)	−0.0144 (11)	−0.0118 (13)
C7	0.0502 (16)	0.0762 (19)	0.0630 (17)	−0.0127 (14)	−0.0235 (13)	−0.0044 (14)
C8	0.0544 (18)	0.075 (2)	0.086 (2)	−0.0077 (15)	−0.0158 (15)	−0.0109 (16)
C9	0.088 (2)	0.0613 (19)	0.084 (2)	−0.0076 (17)	−0.0285 (18)	−0.0092 (16)
C10	0.090 (2)	0.063 (2)	0.104 (3)	−0.0093 (18)	−0.038 (2)	−0.0161 (18)
C11	0.069 (2)	0.078 (2)	0.126 (3)	−0.0152 (17)	−0.044 (2)	−0.019 (2)
C12	0.0523 (18)	0.080 (2)	0.096 (2)	−0.0149 (15)	−0.0165 (16)	−0.0183 (17)
C13	0.120 (3)	0.099 (3)	0.097 (3)	−0.015 (2)	−0.003 (2)	−0.023 (2)
C14	0.081 (3)	0.149 (4)	0.234 (6)	−0.048 (3)	−0.028 (3)	−0.070 (4)
C15	0.0469 (15)	0.0525 (15)	0.0424 (13)	−0.0118 (12)	−0.0128 (11)	−0.0016 (11)
C16	0.0533 (16)	0.0477 (14)	0.0413 (13)	−0.0097 (11)	−0.0065 (11)	−0.0045 (11)
C17	0.0575 (16)	0.0600 (16)	0.0461 (14)	−0.0163 (13)	−0.0179 (12)	−0.0061 (12)
C18	0.0462 (15)	0.0567 (15)	0.0498 (14)	−0.0110 (12)	−0.0159 (12)	−0.0012 (12)
C19	0.0481 (17)	0.087 (2)	0.0704 (19)	−0.0035 (15)	0.0056 (14)	−0.0227 (16)
Cl1	0.1161 (8)	0.1555 (10)	0.0669 (5)	−0.0582 (7)	−0.0048 (5)	0.0201 (6)
Cl2	0.0450 (4)	0.1197 (7)	0.0740 (5)	−0.0198 (4)	−0.0189 (3)	−0.0135 (4)
N1	0.0447 (13)	0.0622 (14)	0.0712 (14)	−0.0079 (11)	−0.0197 (11)	−0.0128 (11)
N2	0.0428 (12)	0.0640 (13)	0.0436 (11)	−0.0108 (10)	−0.0120 (9)	−0.0063 (9)
N3	0.0459 (12)	0.0536 (12)	0.0436 (11)	−0.0111 (9)	−0.0076 (9)	−0.0041 (9)
O1	0.0607 (12)	0.0770 (13)	0.0517 (11)	−0.0109 (10)	−0.0021 (9)	−0.0198 (9)
S1	0.0499 (4)	0.0947 (6)	0.0468 (4)	−0.0301 (4)	−0.0108 (3)	−0.0118 (3)

C1—C2	1.374 (4)	C11—C14	1.527 (5)
C1—C6	1.400 (4)	C11—H11	0.9800
C1—S1	1.778 (3)	C12—N1	1.451 (3)
C2—C3	1.378 (4)	C12—H12A	0.9700
C2—H2	0.9300	C12—H12B	0.9700
C3—C4	1.367 (5)	C13—H13A	0.9600
C3—H3	0.9300	C13—H13B	0.9600
C4—C5	1.381 (4)	C13—H13C	0.9600
C4—H4	0.9300	C14—H14A	0.9600
C5—C6	1.392 (4)	C14—H14B	0.9600
C5—Cl1	1.744 (3)	C14—H14C	0.9600
C6—C7	1.504 (4)	C15—N2	1.327 (3)
C7—N1	1.462 (3)	C15—N3	1.336 (3)
C7—H7A	0.9700	C15—S1	1.759 (2)
C7—H7B	0.9700	C16—N3	1.327 (3)
C8—N1	1.450 (3)	C16—O1	1.334 (3)
C8—C9	1.531 (4)	C16—C17	1.390 (3)
C8—H8A	0.9700	C17—C18	1.356 (3)
C8—H8B	0.9700	C17—H17	0.9300
C9—C13	1.501 (5)	C18—N2	1.331 (3)
C9—C10	1.533 (4)	C18—Cl2	1.735 (3)
C9—H9	0.9800	C19—O1	1.423 (3)
C10—C11	1.517 (4)	C19—H19A	0.9600
C10—H10A	0.9700	C19—H19B	0.9600
C10—H10B	0.9700	C19—H19C	0.9600
C11—C12	1.518 (4)
C2—C1—C6	122.1 (2)	C10—C11—H11	107.8
C2—C1—S1	118.1 (2)	C14—C11—H11	107.8
C6—C1—S1	119.5 (2)	N1—C12—C11	112.1 (3)
C1—C2—C3	120.0 (3)	N1—C12—H12A	109.2
C1—C2—H2	120.0	C11—C12—H12A	109.2
C3—C2—H2	120.0	N1—C12—H12B	109.2
C4—C3—C2	120.1 (3)	C11—C12—H12B	109.2
C4—C3—H3	119.9	H12A—C12—H12B	107.9
C2—C3—H3	119.9	C9—C13—H13A	109.5
C3—C4—C5	119.2 (3)	C9—C13—H13B	109.5
C3—C4—H4	120.4	H13A—C13—H13B	109.5
C5—C4—H4	120.4	C9—C13—H13C	109.5
C4—C5—C6	122.9 (3)	H13A—C13—H13C	109.5
C4—C5—Cl1	116.9 (2)	H13B—C13—H13C	109.5
C6—C5—Cl1	120.1 (2)	C11—C14—H14A	109.5
C5—C6—C1	115.7 (3)	C11—C14—H14B	109.5
C5—C6—C7	123.5 (3)	H14A—C14—H14B	109.5
C1—C6—C7	120.8 (2)	C11—C14—H14C	109.5
N1—C7—C6	112.1 (2)	H14A—C14—H14C	109.5
N1—C7—H7A	109.2	H14B—C14—H14C	109.5
C6—C7—H7A	109.2	N2—C15—N3	127.9 (2)
N1—C7—H7B	109.2	N2—C15—S1	120.94 (18)
C6—C7—H7B	109.2	N3—C15—S1	111.10 (18)
H7A—C7—H7B	107.9	N3—C16—O1	119.2 (2)
N1—C8—C9	111.9 (2)	N3—C16—C17	122.8 (2)
N1—C8—H8A	109.2	O1—C16—C17	118.0 (2)
C9—C8—H8A	109.2	C18—C17—C16	115.4 (2)
N1—C8—H8B	109.2	C18—C17—H17	122.3
C9—C8—H8B	109.2	C16—C17—H17	122.3
H8A—C8—H8B	107.9	N2—C18—C17	124.9 (2)
C13—C9—C8	111.4 (3)	N2—C18—Cl2	115.60 (19)
C13—C9—C10	112.8 (3)	C17—C18—Cl2	119.48 (19)
C8—C9—C10	107.9 (3)	O1—C19—H19A	109.5
C13—C9—H9	108.2	O1—C19—H19B	109.5
C8—C9—H9	108.2	H19A—C19—H19B	109.5
C10—C9—H9	108.2	O1—C19—H19C	109.5
C11—C10—C9	111.0 (3)	H19A—C19—H19C	109.5
C11—C10—H10A	109.4	H19B—C19—H19C	109.5
C9—C10—H10A	109.4	C8—N1—C12	111.5 (2)
C11—C10—H10B	109.4	C8—N1—C7	111.9 (2)
C9—C10—H10B	109.4	C12—N1—C7	111.8 (2)
H10A—C10—H10B	108.0	C15—N2—C18	113.9 (2)
C12—C11—C10	110.0 (3)	C16—N3—C15	115.1 (2)
C12—C11—C14	110.9 (3)	C16—O1—C19	118.0 (2)
C10—C11—C14	112.3 (3)	C15—S1—C1	103.40 (12)
C12—C11—H11	107.8
C6—C1—C2—C3	−1.7 (4)	N3—C16—C17—C18	−1.0 (4)
S1—C1—C2—C3	−175.51 (19)	O1—C16—C17—C18	178.0 (2)
C1—C2—C3—C4	1.2 (4)	C16—C17—C18—N2	1.2 (4)
C2—C3—C4—C5	0.0 (4)	C16—C17—C18—Cl2	−178.17 (19)
C3—C4—C5—C6	−0.7 (4)	C9—C8—N1—C12	59.6 (3)
C3—C4—C5—Cl1	178.5 (2)	C9—C8—N1—C7	−174.4 (2)
C4—C5—C6—C1	0.1 (4)	C11—C12—N1—C8	−57.7 (3)
Cl1—C5—C6—C1	−178.95 (17)	C11—C12—N1—C7	176.2 (2)
C4—C5—C6—C7	178.6 (2)	C6—C7—N1—C8	157.2 (2)
Cl1—C5—C6—C7	−0.5 (3)	C6—C7—N1—C12	−76.9 (3)
C2—C1—C6—C5	1.0 (3)	N3—C15—N2—C18	−0.1 (4)
S1—C1—C6—C5	174.74 (17)	S1—C15—N2—C18	178.03 (18)
C2—C1—C6—C7	−177.5 (2)	C17—C18—N2—C15	−0.7 (4)
S1—C1—C6—C7	−3.8 (3)	Cl2—C18—N2—C15	178.70 (18)
C5—C6—C7—N1	109.8 (3)	O1—C16—N3—C15	−178.6 (2)
C1—C6—C7—N1	−71.8 (3)	C17—C16—N3—C15	0.4 (3)
N1—C8—C9—C13	177.8 (3)	N2—C15—N3—C16	0.2 (4)
N1—C8—C9—C10	−57.8 (3)	S1—C15—N3—C16	−178.04 (17)
C13—C9—C10—C11	179.1 (3)	N3—C16—O1—C19	0.5 (3)
C8—C9—C10—C11	55.6 (4)	C17—C16—O1—C19	−178.5 (2)
C9—C10—C11—C12	−54.9 (4)	N2—C15—S1—C1	15.0 (2)
C9—C10—C11—C14	−178.9 (3)	N3—C15—S1—C1	−166.64 (18)
C10—C11—C12—N1	55.2 (4)	C2—C1—S1—C15	−95.9 (2)
C14—C11—C12—N1	180.0 (3)	C6—C1—S1—C15	90.2 (2)