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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2007 Dec 6;64(Pt 1):o168. doi: 10.1107/S160053680706360X

1,3,5-Tris(6-chloro­pyrazin-2-yl­oxy)benzene

Yan Li a, Jian-Wu Wang a,*
PMCID: PMC2915235  PMID: 21200733

Abstract

In the title compound, C18H9Cl3N6O3, all bond lengths and angles are normal. The dihedral angles between the benzene ring and the three pyrazine rings are 72.67 (2), 60.73 (3) and 77.74 (2)°. The crystal packing is stabilized by van der Waals forces and by a weak π–π stacking inter­action between pyrazine rings, with a centroid–centroid distance of 3.487 (2) Å.

Related literature

For related literatures see: Carter & Boer (1974 ▶); Seitz et al. (2002 ▶); Temple et al. (1970 ▶).graphic file with name e-64-0o168-scheme1.jpg

Experimental

Crystal data

  • C18H9Cl3N6O3

  • M r = 463.66

  • Triclinic, Inline graphic

  • a = 9.680 (2) Å

  • b = 10.658 (2) Å

  • c = 11.039 (3) Å

  • α = 72.768 (3)°

  • β = 68.308 (3)°

  • γ = 69.342 (3)°

  • V = 972.0 (4) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.51 mm−1

  • T = 298 (2) K

  • 0.58 × 0.31 × 0.30 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2004 ▶) T min = 0.758, T max = 0.863

  • 4925 measured reflections

  • 3375 independent reflections

  • 2797 reflections with I > 2σ(I)

  • R int = 0.017

Refinement

  • R[F 2 > 2σ(F 2)] = 0.041

  • wR(F 2) = 0.108

  • S = 1.04

  • 3375 reflections

  • 271 parameters

  • H-atom parameters constrained

  • Δρmax = 0.22 e Å−3

  • Δρmin = −0.39 e Å−3

Data collection: SMART (Bruker, 2001 ▶); cell refinement: SAINT (Bruker, 2001 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2001 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and local programs.

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680706360X/fj2085sup1.cif

e-64-0o168-sup1.cif (19KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S160053680706360X/fj2085Isup2.hkl

e-64-0o168-Isup2.hkl (165.5KB, hkl)

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

supplementary crystallographic information

Comment

Pyrazine derivatives were shown to display antimycobacterial (Seitz et al., 2002) and potential antimalarial (Temple et al., 1970) activities. The title compound was prepared for the screening of these bioactivities. We report here the crystal structure of (I).

In (I) (Fig. 1), all bond lengths and angles are normal and in a good agreement with those reported previously (Carter & Boer, 1974). The dihedral angles between benzene ring (C1—C6) and three Pyrazine rings (C7—C10/N1/N2; C11—C14/N3/N4; C15—C18/N5/N6) are 72.67 (2), 60.73 (3) and 77.74 (2)°, respectively. The crystal packing is stabilized by weak π–π stacking interactions and van der Waals forces, proved by the shorter distance Cg1···Cg1ii of 3.487 (2) Å, where Cg1 is a centroid of Pyrazine ring (C11—C14/N3/N4) [symmetry code:(ii) –X,1-Y,2-Z].

Experimental

A flask was charged with 1.26 g (10 mmol) of 1,3,5-trihydroxybenzene, 4.47 g (30 mmol) of 2,6-dichloropyrazine and 3.18 g (30 mmol) of sodium carbonate, followed by addition of 50 ml of dried MeCN. The resultant mixture was refluxed over night. On cooling, the reaction mixture was filtered and the filtrate was portioned between 150 ml of water and 200 ml of dichloromethane. The organic phase was washed with brine, dried over sodium sulfate and evaporated on a rotary evaporator to furnish the crude product as a residue, which was chromatographed on silica gel to afford the pure product as colorless prisms. Crystals suitable for X-ray diffraction were obtained via slow evaporation of a solution of the title compound in ethyl acetate.

Refinement

All H atoms were placed in calculated positions, with C—H = 0.93 Å, and included in the final cycles of refinement using a riding model, with Uiso(H) = 1.2 times Ueq(C).

Figures

Fig. 1.

Fig. 1.

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View of the title compound (I), with displacement ellipsoids drawn at the 40% probability level.

Crystal data

C18H9Cl3N6O3 Z = 2
Mr = 463.66 F000 = 468
Triclinic, P1 Dx = 1.584 Mg m−3
Hall symbol: -P 1 Mo Kα radiation λ = 0.71073 Å
a = 9.680 (2) Å Cell parameters from 1699 reflections
b = 10.658 (2) Å θ = 2.8–23.1º
c = 11.039 (3) Å µ = 0.51 mm−1
α = 72.768 (3)º T = 298 (2) K
β = 68.308 (3)º Prism, colorless
γ = 69.342 (3)º 0.58 × 0.31 × 0.30 mm
V = 972.0 (4) Å3
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Data collection

Bruker SMART CCD area-detector diffractometer 3375 independent reflections
Radiation source: fine-focus sealed tube 2797 reflections with I > 2σ(I)
Monochromator: graphite Rint = 0.017
T = 298(2) K θmax = 25.0º
φ and ω scans θmin = 2.0º
Absorption correction: multi-scan(SADABS; Sheldrick, 2004) h = −9→11
Tmin = 0.758, Tmax = 0.863 k = −12→12
4925 measured reflections l = −13→12
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Refinement

Refinement on F2 Secondary atom site location: difference Fourier map
Least-squares matrix: full Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.041 H-atom parameters constrained
wR(F2) = 0.108   w = 1/[σ2(Fo2) + (0.0537P)2 + 0.2339P] where P = (Fo2 + 2Fc2)/3
S = 1.04 (Δ/σ)max = 0.001
3375 reflections Δρmax = 0.22 e Å−3
271 parameters Δρmin = −0.39 e Å−3
Primary atom site location: structure-invariant direct methods Extinction correction: none
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Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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 > σ(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.
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Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
Cl1 0.04661 (7) 0.67966 (7) 0.44208 (6) 0.0642 (2)
Cl2 0.43548 (9) 1.27994 (7) −0.59901 (7) 0.0772 (2)
Cl3 0.32169 (10) 1.47146 (8) 0.07383 (9) 0.0893 (3)
O1 0.43622 (16) 0.85408 (15) 0.05573 (15) 0.0530 (4)
O2 0.1867 (2) 0.93858 (16) −0.27062 (15) 0.0616 (4)
O3 −0.01216 (16) 1.23869 (14) 0.03280 (16) 0.0513 (4)
N1 −0.1102 (3) 1.4653 (2) 0.2505 (2) 0.0743 (6)
N2 0.4938 (2) 0.6220 (2) 0.3517 (2) 0.0701 (6)
N3 0.2331 (3) 1.0283 (2) −0.6181 (2) 0.0672 (6)
N4 0.1437 (2) 1.34503 (17) 0.05891 (17) 0.0469 (4)
N5 0.3057 (2) 1.09657 (17) −0.42807 (17) 0.0459 (4)
N6 0.25692 (18) 0.76867 (16) 0.23874 (16) 0.0409 (4)
C1 0.0239 (4) 1.4929 (3) 0.2147 (3) 0.0718 (8)
H1B 0.0338 1.5541 0.2539 0.086*
C2 0.3070 (3) 1.1226 (3) −0.6499 (2) 0.0600 (6)
H2B 0.3358 1.1674 −0.7377 0.072*
C3 −0.1181 (3) 1.3782 (3) 0.1916 (2) 0.0610 (6)
H3B −0.2104 1.3560 0.2147 0.073*
C4 0.5191 (3) 0.7021 (3) 0.2337 (2) 0.0626 (7)
H4B 0.6188 0.7094 0.1867 0.075*
C5 0.1484 (3) 1.4320 (2) 0.1203 (2) 0.0542 (6)
C6 0.1940 (3) 0.9688 (3) −0.4911 (2) 0.0602 (6)
H6B 0.1415 0.9025 −0.4643 0.072*
C7 0.3414 (2) 1.1549 (2) −0.5553 (2) 0.0488 (5)
C8 0.2308 (3) 1.0047 (2) −0.3975 (2) 0.0470 (5)
C9 0.3493 (3) 0.6156 (2) 0.4159 (2) 0.0540 (6)
H9A 0.3264 0.5614 0.5000 0.065*
C10 0.2025 (3) 0.9832 (2) −0.1693 (2) 0.0467 (5)
C11 0.3125 (2) 0.8988 (2) −0.1081 (2) 0.0467 (5)
H11A 0.3812 0.8202 −0.1386 0.056*
C12 0.2348 (2) 0.68880 (19) 0.3581 (2) 0.0407 (5)
C13 0.3169 (2) 0.9348 (2) −0.0002 (2) 0.0421 (5)
C14 0.0097 (2) 1.3191 (2) 0.0952 (2) 0.0440 (5)
C15 0.1076 (2) 1.12977 (19) −0.0168 (2) 0.0403 (5)
C16 0.2156 (2) 1.0492 (2) 0.0488 (2) 0.0409 (4)
H16A 0.2196 1.0713 0.1226 0.049*
C17 0.0996 (2) 1.0992 (2) −0.1265 (2) 0.0444 (5)
H17A 0.0268 1.1553 −0.1699 0.053*
C18 0.3995 (2) 0.77556 (19) 0.1787 (2) 0.0419 (5)
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Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
Cl1 0.0539 (3) 0.0787 (4) 0.0503 (4) −0.0223 (3) −0.0150 (3) 0.0057 (3)
Cl2 0.1024 (5) 0.0756 (4) 0.0561 (4) −0.0460 (4) −0.0100 (4) −0.0072 (3)
Cl3 0.0920 (5) 0.0802 (5) 0.1186 (7) −0.0405 (4) −0.0433 (5) −0.0155 (4)
O1 0.0408 (8) 0.0582 (9) 0.0452 (9) −0.0084 (7) −0.0133 (7) 0.0055 (7)
O2 0.0966 (13) 0.0628 (10) 0.0390 (9) −0.0401 (9) −0.0227 (8) −0.0036 (7)
O3 0.0463 (8) 0.0467 (8) 0.0619 (10) −0.0073 (6) −0.0212 (7) −0.0118 (7)
N1 0.0842 (17) 0.0791 (15) 0.0478 (13) −0.0113 (13) −0.0091 (11) −0.0225 (11)
N2 0.0501 (12) 0.0856 (15) 0.0539 (13) −0.0002 (10) −0.0244 (10) 0.0053 (11)
N3 0.0846 (15) 0.0855 (15) 0.0436 (12) −0.0288 (12) −0.0243 (11) −0.0158 (11)
N4 0.0521 (10) 0.0416 (9) 0.0439 (10) −0.0120 (8) −0.0150 (8) −0.0040 (8)
N5 0.0531 (10) 0.0477 (10) 0.0367 (10) −0.0103 (8) −0.0156 (8) −0.0090 (8)
N6 0.0451 (10) 0.0397 (9) 0.0361 (9) −0.0061 (7) −0.0174 (8) −0.0044 (7)
C1 0.105 (2) 0.0596 (15) 0.0553 (16) −0.0137 (15) −0.0331 (16) −0.0168 (13)
C2 0.0684 (15) 0.0727 (16) 0.0363 (12) −0.0164 (13) −0.0167 (11) −0.0086 (11)
C3 0.0580 (14) 0.0666 (15) 0.0427 (13) −0.0117 (12) −0.0069 (11) −0.0049 (12)
C4 0.0421 (12) 0.0782 (16) 0.0521 (15) −0.0057 (11) −0.0173 (11) 0.0003 (12)
C5 0.0693 (15) 0.0441 (12) 0.0515 (14) −0.0153 (11) −0.0271 (12) −0.0008 (10)
C6 0.0758 (16) 0.0650 (14) 0.0508 (15) −0.0256 (13) −0.0228 (12) −0.0137 (12)
C7 0.0502 (12) 0.0509 (12) 0.0394 (12) −0.0091 (10) −0.0103 (9) −0.0097 (10)
C8 0.0562 (12) 0.0474 (12) 0.0385 (12) −0.0122 (10) −0.0172 (10) −0.0080 (9)
C9 0.0569 (14) 0.0536 (12) 0.0395 (12) −0.0016 (10) −0.0201 (10) −0.0010 (10)
C10 0.0627 (13) 0.0500 (12) 0.0312 (11) −0.0271 (10) −0.0145 (10) 0.0016 (9)
C11 0.0499 (12) 0.0434 (11) 0.0393 (12) −0.0156 (9) −0.0046 (9) −0.0049 (9)
C12 0.0454 (11) 0.0378 (10) 0.0363 (11) −0.0049 (8) −0.0156 (9) −0.0067 (8)
C13 0.0395 (10) 0.0442 (11) 0.0357 (11) −0.0132 (8) −0.0114 (9) 0.0045 (9)
C14 0.0487 (12) 0.0385 (10) 0.0361 (11) −0.0070 (9) −0.0142 (9) 0.0012 (8)
C15 0.0423 (11) 0.0369 (10) 0.0390 (11) −0.0141 (8) −0.0114 (9) −0.0004 (8)
C16 0.0450 (11) 0.0460 (11) 0.0325 (10) −0.0157 (9) −0.0140 (9) −0.0017 (8)
C17 0.0537 (12) 0.0446 (11) 0.0379 (11) −0.0208 (10) −0.0214 (10) 0.0070 (9)
C18 0.0429 (11) 0.0400 (10) 0.0395 (11) −0.0049 (8) −0.0158 (9) −0.0060 (9)
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Geometric parameters (Å, °)

Cl1—C12 1.735 (2) C1—C5 1.371 (4)
Cl2—C7 1.728 (2) C1—H1B 0.9300
Cl3—C5 1.729 (3) C2—C7 1.367 (3)
O1—C18 1.360 (2) C2—H2B 0.9300
O1—C13 1.402 (2) C3—C14 1.390 (3)
O2—C8 1.351 (3) C3—H3B 0.9300
O2—C10 1.411 (3) C4—C18 1.386 (3)
O3—C14 1.357 (3) C4—H4B 0.9300
O3—C15 1.396 (2) C6—C8 1.394 (3)
N1—C3 1.317 (3) C6—H6B 0.9300
N1—C1 1.323 (4) C9—C12 1.364 (3)
N2—C4 1.319 (3) C9—H9A 0.9300
N2—C9 1.330 (3) C10—C17 1.369 (3)
N3—C2 1.326 (3) C10—C11 1.377 (3)
N3—C6 1.326 (3) C11—C13 1.374 (3)
N4—C14 1.312 (3) C11—H11A 0.9300
N4—C5 1.320 (3) C13—C16 1.377 (3)
N5—C8 1.312 (3) C15—C17 1.379 (3)
N5—C7 1.325 (3) C15—C16 1.382 (3)
N6—C18 1.310 (3) C16—H16A 0.9300
N6—C12 1.328 (2) C17—H17A 0.9300
C18—O1—C13 118.64 (15) O2—C8—C6 116.6 (2)
C8—O2—C10 118.93 (16) N2—C9—C12 119.8 (2)
C14—O3—C15 121.38 (16) N2—C9—H9A 120.1
C3—N1—C1 117.2 (2) C12—C9—H9A 120.1
C4—N2—C9 117.46 (19) C17—C10—C11 122.6 (2)
C2—N3—C6 116.8 (2) C17—C10—O2 119.58 (19)
C14—N4—C5 115.09 (19) C11—C10—O2 117.48 (19)
C8—N5—C7 114.59 (18) C13—C11—C10 117.54 (19)
C18—N6—C12 114.85 (16) C13—C11—H11A 121.2
N1—C1—C5 120.6 (2) C10—C11—H11A 121.2
N1—C1—H1B 119.7 N6—C12—C9 124.2 (2)
C5—C1—H1B 119.7 N6—C12—Cl1 116.16 (14)
N3—C2—C7 120.9 (2) C9—C12—Cl1 119.64 (17)
N3—C2—H2B 119.6 C11—C13—C16 122.78 (18)
C7—C2—H2B 119.6 C11—C13—O1 117.27 (18)
N1—C3—C14 120.9 (2) C16—C13—O1 119.85 (19)
N1—C3—H3B 119.6 N4—C14—O3 120.43 (19)
C14—C3—H3B 119.6 N4—C14—C3 122.7 (2)
N2—C4—C18 121.0 (2) O3—C14—C3 116.8 (2)
N2—C4—H4B 119.5 C17—C15—C16 122.55 (19)
C18—C4—H4B 119.5 C17—C15—O3 115.06 (17)
N4—C5—C1 123.6 (2) C16—C15—O3 121.97 (19)
N4—C5—Cl3 116.79 (18) C13—C16—C15 116.97 (19)
C1—C5—Cl3 119.6 (2) C13—C16—H16A 121.5
N3—C6—C8 120.7 (2) C15—C16—H16A 121.5
N3—C6—H6B 119.6 C10—C17—C15 117.57 (19)
C8—C6—H6B 119.6 C10—C17—H17A 121.2
N5—C7—C2 124.0 (2) C15—C17—H17A 121.2
N5—C7—Cl2 116.06 (17) N6—C18—O1 120.19 (17)
C2—C7—Cl2 119.97 (18) N6—C18—C4 122.7 (2)
N5—C8—O2 120.29 (18) O1—C18—C4 117.13 (19)
N5—C8—C6 123.1 (2)
C3—N1—C1—C5 −0.2 (4) N2—C9—C12—Cl1 179.78 (19)
C6—N3—C2—C7 0.5 (4) C10—C11—C13—C16 1.0 (3)
C1—N1—C3—C14 −0.4 (4) C10—C11—C13—O1 −175.44 (17)
C9—N2—C4—C18 −0.6 (4) C18—O1—C13—C11 −111.4 (2)
C14—N4—C5—C1 −0.4 (3) C18—O1—C13—C16 72.1 (2)
C14—N4—C5—Cl3 −178.98 (14) C5—N4—C14—O3 175.50 (17)
N1—C1—C5—N4 0.7 (4) C5—N4—C14—C3 −0.2 (3)
N1—C1—C5—Cl3 179.2 (2) C15—O3—C14—N4 33.3 (3)
C2—N3—C6—C8 −0.4 (4) C15—O3—C14—C3 −150.69 (19)
C8—N5—C7—C2 −1.0 (3) N1—C3—C14—N4 0.7 (3)
C8—N5—C7—Cl2 178.31 (15) N1—C3—C14—O3 −175.2 (2)
N3—C2—C7—N5 0.2 (4) C14—O3—C15—C17 −150.15 (18)
N3—C2—C7—Cl2 −179.10 (19) C14—O3—C15—C16 37.0 (3)
C7—N5—C8—O2 −179.47 (19) C11—C13—C16—C15 −0.8 (3)
C7—N5—C8—C6 1.1 (3) O1—C13—C16—C15 175.49 (16)
C10—O2—C8—N5 8.9 (3) C17—C15—C16—C13 −0.1 (3)
C10—O2—C8—C6 −171.7 (2) O3—C15—C16—C13 172.23 (17)
N3—C6—C8—N5 −0.5 (4) C11—C10—C17—C15 −0.6 (3)
N3—C6—C8—O2 −179.9 (2) O2—C10—C17—C15 172.20 (17)
C4—N2—C9—C12 1.0 (4) C16—C15—C17—C10 0.8 (3)
C8—O2—C10—C17 76.1 (3) O3—C15—C17—C10 −172.01 (17)
C8—O2—C10—C11 −110.8 (2) C12—N6—C18—O1 179.91 (17)
C17—C10—C11—C13 −0.2 (3) C12—N6—C18—C4 1.8 (3)
O2—C10—C11—C13 −173.20 (17) C13—O1—C18—N6 4.8 (3)
C18—N6—C12—C9 −1.4 (3) C13—O1—C18—C4 −177.0 (2)
C18—N6—C12—Cl1 178.83 (14) N2—C4—C18—N6 −0.9 (4)
N2—C9—C12—N6 0.0 (3) N2—C4—C18—O1 −179.0 (2)
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Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FJ2085).

References

  1. Bruker (2001). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  2. Carter, D. R. & Boer, F. P. (1974). J. Chem. Soc. Perkin Trans. 2, pp. 1841–1844.
  3. Seitz, L. E., Suling, W. J. & Reynolds, R. C. (2002). J. Med. Chem.45, 5604–5606. [DOI] [PubMed]
  4. Sheldrick, G. M. (2001). SHELXTL Version 5.0. Bruker AXS Inc., Madison, Wisconsin, USA.
  5. Sheldrick, G. M. (2004). SADABS University of Göttingen, Germany.
  6. Temple, C. Jr, Rose, J. D. & Montgomery, J. A. (1970). J. Med. Chem.13, 1234–1235. [DOI] [PubMed]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680706360X/fj2085sup1.cif

e-64-0o168-sup1.cif (19KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S160053680706360X/fj2085Isup2.hkl

e-64-0o168-Isup2.hkl (165.5KB, hkl)

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

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography

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