organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

4-Chloro-2-{3-chloro-2-[(3,5-di­methyl­piperidin-1-yl)meth­yl]phenyl­sulfan­yl}-6-meth­oxy­pyrimidine

aSchool of Chemistry and Environmental Science, Guizhou University for Nationalities, Guiyang 550025, People's Republic of China, and bCollege of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471022, People's Republic of China
*Correspondence e-mail: zhumei@iccas.ac.cn

(Received 1 January 2010; accepted 5 February 2010; online 17 February 2010)

In the title compound, C19H23Cl2N3OS, 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[Joffe, A. M., Farley, J. D., Linden, D. & Goldsand, G. (1989). Am. J. Med., 87, 332-338.]); Petersen & Schmidt (2003[Petersen, E. & Schmidt, D. R. (2003). Expert Rev. Anti-Infect. Ther. 1, 175-182.]); Blum (2001[Blum, J. L. (2001). Oncologist, 6, 56-64.]); Gompper et al. (2004[Gompper, R., Mair, H.-J. & Polborn, K. (2004). Synthesis, pp. 696-708.]); Michael (2005[Michael, J. P. (2005). Nat. Prod. Rep., 22, 627-646.]); Nadal & Olavarria (2004[Nadal, E. & Olavarria, E. (2004). Int. J. Clin. Pract., 58, 511-516.]).

[Scheme 1]

Experimental

Crystal data
  • C19H23Cl2N3OS

  • Mr = 412.36

  • Triclinic, [P \overline 1]

  • 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[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.852, Tmax = 0.901

  • 7861 measured reflections

  • 3848 independent reflections

  • 2553 reflections with I > 2σ(I)

  • Rint = 0.019

Refinement
  • R[F2 > 2σ(F2)] = 0.041

  • wR(F2) = 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[Bruker (2004). APEX2, and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2004[Bruker (2004). APEX2, and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Pyrimidine derivatives are widespread in medicinal and natural products chemistry. A number of natural products, pharmaceuticals, and functional materials incorporate this heterocycle (Michael, 2005. Several examples of pharmaceutically important compounds include trimethoprim (Joffe et al., 1989), sulfadiazine (Petersen & Schmidt, 2003),Gleevec (imatinib mesilate) (Nadal & Olavarria, 2004), and Xeloda (capecitabine) (Blum, 2001). Natural and unnatural polymers also contain pyrimidine derivatives (Gompper et al., 2004). The potent physiological properties of these pyrimidine derivatives led to vast research of their use as medicines in the field of pharmaceutical chemistry. So in the recent decades, many chemists have been attracted by the synthesis of pyrimidines. In this context, we report the synthesis ofthe title compound.

The molecular structure is shown in Fig. 1. The bond lengths and angles are within normal ranges. The pyrimidine ring makes dihedral angles of 86.6 (9)° with the benzene ring. In the crystal structure,The cyclohexyl groups display chair-type conformation.

Related literature top

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 top

To a solution of 2,4-dichloro-6-methoxypyrimidine (0.5 mmol) and 3-chloro-2-((3,5-dimethylpiperidin-1-yl)methyl)benzenethiol (0.5 mmol) in dry methylbenzene was added NaH (0.6 mmol). The mixture was stirred for 12 h at room temperature. After evaporation of the solvent, the residue was purified by column chromatography on silica gel to afford the title compound as a colorless solid (yield 78%). The title compound was recrystallized from CH2Cl2 at room temperature to give the desired crystals suitable for single-crystal X-ray diffraction.

Refinement top

All H atoms were positioned geometrically and treated as riding, with C—H bond lengths constrained to 0.93 Å (aromatic CH) or 0.97 Å (methylene CH2), and with Uĩso~(H) = 1.2Ueq(C) or 1.5Ueq(methylene C).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); 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 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. View of the molecular structure of (I) with atom numbering scheme and 30% probability displacement ellipsoids.
4-Chloro-2-{3-chloro-2-[(3,5-dimethylpiperidin-1-yl)methyl]phenylsulfanyl}- 6-methoxypyrimidine top
Crystal data top
C19H23Cl2N3OSZ = 2
Mr = 412.36F(000) = 432
Triclinic, P1Dx = 1.313 Mg m3
a = 8.000 (4) ÅMo Kα radiation, λ = 0.71073 Å
b = 11.454 (6) ÅCell parameters from 2557 reflections
c = 12.001 (7) Åθ = 2.5–25.9°
α = 87.820 (7)°µ = 0.42 mm1
β = 76.084 (6)°T = 296 K
γ = 77.700 (6)°Block, colourless
V = 1042.9 (10) Å30.39 × 0.37 × 0.25 mm
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
3848 independent reflections
Radiation source: fine-focus sealed tube2553 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
phi and ω scansθmax = 25.5°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 99
Tmin = 0.852, Tmax = 0.901k = 1313
7861 measured reflectionsl = 1414
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) = 0.119H-atom parameters constrained
S = 1.03 w = 1/[σ2(Fo2) + (0.0498P)2 + 0.3748P]
where P = (Fo2 + 2Fc2)/3
3848 reflections(Δ/σ)max < 0.001
238 parametersΔρmax = 0.30 e Å3
0 restraintsΔρmin = 0.31 e Å3
Crystal data top
C19H23Cl2N3OSγ = 77.700 (6)°
Mr = 412.36V = 1042.9 (10) Å3
Triclinic, P1Z = 2
a = 8.000 (4) ÅMo Kα radiation
b = 11.454 (6) ŵ = 0.42 mm1
c = 12.001 (7) ÅT = 296 K
α = 87.820 (7)°0.39 × 0.37 × 0.25 mm
β = 76.084 (6)°
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
3848 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
2553 reflections with I > 2σ(I)
Tmin = 0.852, Tmax = 0.901Rint = 0.019
7861 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0410 restraints
wR(F2) = 0.119H-atom parameters constrained
S = 1.03Δρmax = 0.30 e Å3
3848 reflectionsΔρmin = 0.31 e Å3
238 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.8993 (3)0.4679 (2)0.3790 (2)0.0511 (6)
C20.7914 (4)0.5783 (3)0.4072 (2)0.0639 (7)
H20.80310.64170.35720.077*
C30.6657 (4)0.5951 (3)0.5096 (3)0.0772 (10)
H30.59130.66950.52810.093*
C40.6503 (4)0.5026 (4)0.5841 (3)0.0765 (10)
H40.56570.51360.65330.092*
C50.7618 (4)0.3926 (3)0.5555 (2)0.0649 (8)
C60.8897 (3)0.3706 (2)0.4527 (2)0.0517 (6)
C71.0146 (4)0.2522 (3)0.4215 (2)0.0613 (7)
H7A1.13420.26480.39770.074*
H7B1.00710.20190.48860.074*
C81.1282 (4)0.1048 (3)0.2685 (3)0.0722 (8)
H8A1.16010.04190.32060.087*
H8B1.22690.14390.24320.087*
C91.0929 (4)0.0498 (3)0.1644 (3)0.0773 (9)
H91.06120.11450.11260.093*
C100.9343 (4)0.0090 (3)0.2069 (3)0.0838 (10)
H10A0.90480.04030.14180.101*
H10B0.96470.07530.25620.101*
C110.7761 (4)0.0801 (3)0.2730 (3)0.0867 (10)
H110.74380.14360.22020.104*
C120.8245 (4)0.1367 (3)0.3699 (3)0.0757 (9)
H12A0.72470.19720.40830.091*
H12B0.85030.07610.42560.091*
C131.2537 (5)0.0357 (3)0.1000 (3)0.1102 (13)
H13A1.34850.00550.07490.165*
H13B1.22840.06760.03450.165*
H13C1.28710.09980.14940.165*
C140.6166 (5)0.0238 (4)0.3187 (5)0.151 (2)
H14A0.64280.03600.37380.226*
H14B0.58940.01240.25620.226*
H14C0.51740.08440.35470.226*
C150.9754 (3)0.4023 (2)0.14901 (19)0.0466 (6)
C161.0372 (3)0.3253 (2)0.0292 (2)0.0483 (6)
C170.8596 (3)0.3280 (2)0.0188 (2)0.0528 (6)
H170.81790.30300.07780.063*
C180.7513 (3)0.3697 (2)0.0833 (2)0.0500 (6)
C191.3329 (4)0.2760 (3)0.1362 (3)0.0729 (8)
H19A1.35250.35540.13170.109*
H19B1.39980.23980.20850.109*
H19C1.36950.22920.07490.109*
Cl10.73889 (14)0.27940 (11)0.65587 (8)0.1117 (4)
Cl20.52759 (9)0.37327 (8)0.10766 (6)0.0780 (3)
N10.9758 (3)0.19101 (19)0.32894 (19)0.0585 (6)
N20.8031 (3)0.40866 (18)0.16994 (16)0.0497 (5)
N31.0978 (3)0.36245 (17)0.05379 (16)0.0480 (5)
O11.1505 (2)0.28158 (17)0.12653 (14)0.0651 (5)
S11.06955 (9)0.45367 (7)0.25092 (6)0.0613 (2)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0428 (14)0.0719 (18)0.0443 (13)0.0167 (13)0.0152 (11)0.0130 (13)
C20.0580 (18)0.0735 (19)0.0658 (18)0.0100 (15)0.0263 (15)0.0174 (15)
C30.0500 (18)0.095 (2)0.088 (2)0.0002 (16)0.0258 (17)0.043 (2)
C40.0440 (17)0.127 (3)0.0581 (18)0.0211 (19)0.0025 (13)0.0381 (19)
C50.0497 (16)0.102 (2)0.0489 (15)0.0256 (16)0.0123 (12)0.0129 (15)
C60.0387 (14)0.0765 (18)0.0458 (14)0.0172 (13)0.0144 (11)0.0118 (13)
C70.0502 (16)0.0762 (19)0.0630 (17)0.0127 (14)0.0235 (13)0.0044 (14)
C80.0544 (18)0.075 (2)0.086 (2)0.0077 (15)0.0158 (15)0.0109 (16)
C90.088 (2)0.0613 (19)0.084 (2)0.0076 (17)0.0285 (18)0.0092 (16)
C100.090 (2)0.063 (2)0.104 (3)0.0093 (18)0.038 (2)0.0161 (18)
C110.069 (2)0.078 (2)0.126 (3)0.0152 (17)0.044 (2)0.019 (2)
C120.0523 (18)0.080 (2)0.096 (2)0.0149 (15)0.0165 (16)0.0183 (17)
C130.120 (3)0.099 (3)0.097 (3)0.015 (2)0.003 (2)0.023 (2)
C140.081 (3)0.149 (4)0.234 (6)0.048 (3)0.028 (3)0.070 (4)
C150.0469 (15)0.0525 (15)0.0424 (13)0.0118 (12)0.0128 (11)0.0016 (11)
C160.0533 (16)0.0477 (14)0.0413 (13)0.0097 (11)0.0065 (11)0.0045 (11)
C170.0575 (16)0.0600 (16)0.0461 (14)0.0163 (13)0.0179 (12)0.0061 (12)
C180.0462 (15)0.0567 (15)0.0498 (14)0.0110 (12)0.0159 (12)0.0012 (12)
C190.0481 (17)0.087 (2)0.0704 (19)0.0035 (15)0.0056 (14)0.0227 (16)
Cl10.1161 (8)0.1555 (10)0.0669 (5)0.0582 (7)0.0048 (5)0.0201 (6)
Cl20.0450 (4)0.1197 (7)0.0740 (5)0.0198 (4)0.0189 (3)0.0135 (4)
N10.0447 (13)0.0622 (14)0.0712 (14)0.0079 (11)0.0197 (11)0.0128 (11)
N20.0428 (12)0.0640 (13)0.0436 (11)0.0108 (10)0.0120 (9)0.0063 (9)
N30.0459 (12)0.0536 (12)0.0436 (11)0.0111 (9)0.0076 (9)0.0041 (9)
O10.0607 (12)0.0770 (13)0.0517 (11)0.0109 (10)0.0021 (9)0.0198 (9)
S10.0499 (4)0.0947 (6)0.0468 (4)0.0301 (4)0.0108 (3)0.0118 (3)
Geometric parameters (Å, º) top
C1—C21.374 (4)C11—C141.527 (5)
C1—C61.400 (4)C11—H110.9800
C1—S11.778 (3)C12—N11.451 (3)
C2—C31.378 (4)C12—H12A0.9700
C2—H20.9300C12—H12B0.9700
C3—C41.367 (5)C13—H13A0.9600
C3—H30.9300C13—H13B0.9600
C4—C51.381 (4)C13—H13C0.9600
C4—H40.9300C14—H14A0.9600
C5—C61.392 (4)C14—H14B0.9600
C5—Cl11.744 (3)C14—H14C0.9600
C6—C71.504 (4)C15—N21.327 (3)
C7—N11.462 (3)C15—N31.336 (3)
C7—H7A0.9700C15—S11.759 (2)
C7—H7B0.9700C16—N31.327 (3)
C8—N11.450 (3)C16—O11.334 (3)
C8—C91.531 (4)C16—C171.390 (3)
C8—H8A0.9700C17—C181.356 (3)
C8—H8B0.9700C17—H170.9300
C9—C131.501 (5)C18—N21.331 (3)
C9—C101.533 (4)C18—Cl21.735 (3)
C9—H90.9800C19—O11.423 (3)
C10—C111.517 (4)C19—H19A0.9600
C10—H10A0.9700C19—H19B0.9600
C10—H10B0.9700C19—H19C0.9600
C11—C121.518 (4)
C2—C1—C6122.1 (2)C10—C11—H11107.8
C2—C1—S1118.1 (2)C14—C11—H11107.8
C6—C1—S1119.5 (2)N1—C12—C11112.1 (3)
C1—C2—C3120.0 (3)N1—C12—H12A109.2
C1—C2—H2120.0C11—C12—H12A109.2
C3—C2—H2120.0N1—C12—H12B109.2
C4—C3—C2120.1 (3)C11—C12—H12B109.2
C4—C3—H3119.9H12A—C12—H12B107.9
C2—C3—H3119.9C9—C13—H13A109.5
C3—C4—C5119.2 (3)C9—C13—H13B109.5
C3—C4—H4120.4H13A—C13—H13B109.5
C5—C4—H4120.4C9—C13—H13C109.5
C4—C5—C6122.9 (3)H13A—C13—H13C109.5
C4—C5—Cl1116.9 (2)H13B—C13—H13C109.5
C6—C5—Cl1120.1 (2)C11—C14—H14A109.5
C5—C6—C1115.7 (3)C11—C14—H14B109.5
C5—C6—C7123.5 (3)H14A—C14—H14B109.5
C1—C6—C7120.8 (2)C11—C14—H14C109.5
N1—C7—C6112.1 (2)H14A—C14—H14C109.5
N1—C7—H7A109.2H14B—C14—H14C109.5
C6—C7—H7A109.2N2—C15—N3127.9 (2)
N1—C7—H7B109.2N2—C15—S1120.94 (18)
C6—C7—H7B109.2N3—C15—S1111.10 (18)
H7A—C7—H7B107.9N3—C16—O1119.2 (2)
N1—C8—C9111.9 (2)N3—C16—C17122.8 (2)
N1—C8—H8A109.2O1—C16—C17118.0 (2)
C9—C8—H8A109.2C18—C17—C16115.4 (2)
N1—C8—H8B109.2C18—C17—H17122.3
C9—C8—H8B109.2C16—C17—H17122.3
H8A—C8—H8B107.9N2—C18—C17124.9 (2)
C13—C9—C8111.4 (3)N2—C18—Cl2115.60 (19)
C13—C9—C10112.8 (3)C17—C18—Cl2119.48 (19)
C8—C9—C10107.9 (3)O1—C19—H19A109.5
C13—C9—H9108.2O1—C19—H19B109.5
C8—C9—H9108.2H19A—C19—H19B109.5
C10—C9—H9108.2O1—C19—H19C109.5
C11—C10—C9111.0 (3)H19A—C19—H19C109.5
C11—C10—H10A109.4H19B—C19—H19C109.5
C9—C10—H10A109.4C8—N1—C12111.5 (2)
C11—C10—H10B109.4C8—N1—C7111.9 (2)
C9—C10—H10B109.4C12—N1—C7111.8 (2)
H10A—C10—H10B108.0C15—N2—C18113.9 (2)
C12—C11—C10110.0 (3)C16—N3—C15115.1 (2)
C12—C11—C14110.9 (3)C16—O1—C19118.0 (2)
C10—C11—C14112.3 (3)C15—S1—C1103.40 (12)
C12—C11—H11107.8
C6—C1—C2—C31.7 (4)N3—C16—C17—C181.0 (4)
S1—C1—C2—C3175.51 (19)O1—C16—C17—C18178.0 (2)
C1—C2—C3—C41.2 (4)C16—C17—C18—N21.2 (4)
C2—C3—C4—C50.0 (4)C16—C17—C18—Cl2178.17 (19)
C3—C4—C5—C60.7 (4)C9—C8—N1—C1259.6 (3)
C3—C4—C5—Cl1178.5 (2)C9—C8—N1—C7174.4 (2)
C4—C5—C6—C10.1 (4)C11—C12—N1—C857.7 (3)
Cl1—C5—C6—C1178.95 (17)C11—C12—N1—C7176.2 (2)
C4—C5—C6—C7178.6 (2)C6—C7—N1—C8157.2 (2)
Cl1—C5—C6—C70.5 (3)C6—C7—N1—C1276.9 (3)
C2—C1—C6—C51.0 (3)N3—C15—N2—C180.1 (4)
S1—C1—C6—C5174.74 (17)S1—C15—N2—C18178.03 (18)
C2—C1—C6—C7177.5 (2)C17—C18—N2—C150.7 (4)
S1—C1—C6—C73.8 (3)Cl2—C18—N2—C15178.70 (18)
C5—C6—C7—N1109.8 (3)O1—C16—N3—C15178.6 (2)
C1—C6—C7—N171.8 (3)C17—C16—N3—C150.4 (3)
N1—C8—C9—C13177.8 (3)N2—C15—N3—C160.2 (4)
N1—C8—C9—C1057.8 (3)S1—C15—N3—C16178.04 (17)
C13—C9—C10—C11179.1 (3)N3—C16—O1—C190.5 (3)
C8—C9—C10—C1155.6 (4)C17—C16—O1—C19178.5 (2)
C9—C10—C11—C1254.9 (4)N2—C15—S1—C115.0 (2)
C9—C10—C11—C14178.9 (3)N3—C15—S1—C1166.64 (18)
C10—C11—C12—N155.2 (4)C2—C1—S1—C1595.9 (2)
C14—C11—C12—N1180.0 (3)C6—C1—S1—C1590.2 (2)

Experimental details

Crystal data
Chemical formulaC19H23Cl2N3OS
Mr412.36
Crystal system, space groupTriclinic, P1
Temperature (K)296
a, b, c (Å)8.000 (4), 11.454 (6), 12.001 (7)
α, β, γ (°)87.820 (7), 76.084 (6), 77.700 (6)
V3)1042.9 (10)
Z2
Radiation typeMo Kα
µ (mm1)0.42
Crystal size (mm)0.39 × 0.37 × 0.25
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.852, 0.901
No. of measured, independent and
observed [I > 2σ(I)] reflections
7861, 3848, 2553
Rint0.019
(sin θ/λ)max1)0.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.119, 1.03
No. of reflections3848
No. of parameters238
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.30, 0.31

Computer programs: APEX2 (Bruker, 2004), SAINT (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

 

Acknowledgements

This work was supported by the Doctoral Foundation of Luoyang Normal University.

References

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