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Acta Crystallogr Sect E Struct Rep Online. 2009 September 1; 65(Pt 9): o2295–o2296.
Published online 2009 August 29. doi:  10.1107/S1600536809033819
PMCID: PMC2970001

(RS)-(2-Bromo-4-fluoro­anilino)[2-(4,6-dimethoxy­pyrimidin-2-yl­oxy)phen­yl]acetonitrile

Abstract

In the title compound, C20H16BrFN4O3, the pyrimidine and 2-bromo-4-fluoro­phenyl rings are twisted away from the central benzene ring, making dihedral angles of 77.7 (1) and 85.5 (1), respectively. A pair of C—H(...)F inter­actions is involved in an R 2 2(8) motif, linking the mol­ecules into dimers. These ring motifs are situated about the crystallographic centres of symmetry. C—H(...)O hydrogen bonds link the dimers into chains running parallel to [1An external file that holds a picture, illustration, etc.
Object name is e-65-o2295-efi1.jpg1]. Additionally, a weak C—F(...)π-electron ring inter­action was observed in the crystal packing [F(...)Cg = 3.459 (4) Å; Cg is the centroid of the pyrimidine ring]. There is also an intra­molecular N—H(...)Br inter­action in the structure.

Related literature

Pyrimidinylbenzoates are highly effective herbicides with acetohydroxy­acid synthase (AHAS) as a target, see: Duggleby & Pang (2000 [triangle]). For related structures, see: Li & Huang (2007 [triangle]); Li & Wang (2007 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]). For graph-set motifs, see: Etter et al. (1990 [triangle]).

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Object name is e-65-o2295-scheme1.jpg

Experimental

Crystal data

  • C20H16BrFN4O3
  • M r = 459.28
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2295-efi3.jpg
  • a = 8.9131 (4) Å
  • b = 10.6646 (4) Å
  • c = 11.7804 (5) Å
  • α = 67.235 (1)°
  • β = 82.088 (1)°
  • γ = 81.277 (2)°
  • V = 1016.77 (7) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 2.06 mm−1
  • T = 299 K
  • 0.25 × 0.20 × 0.20 mm

Data collection

  • Bruker SMART APEX CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.606, T max = 0.662
  • 10737 measured reflections
  • 4588 independent reflections
  • 2636 reflections with I > 2σ(I)
  • R int = 0.027

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.166
  • S = 1.05
  • 4588 reflections
  • 267 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.83 e Å−3
  • Δρmin = −0.47 e Å−3

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SAINT-Plus (Bruker, 2001 [triangle]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: PLATON.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809033819/fb2161sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809033819/fb2161Isup2.hkl

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

Acknowledgments

The author acknowledges financial support by the Opening Fund of the Key Laboratory of Chemical Biology and Trad­itional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University (No. KLCBTCMR2008–05), the Hunan Province Natural Science Foundation of China (No.09 J J6023) and the Scientific Research Foundation of Huaihua University.

supplementary crystallographic information

Comment

Pyrimidine derivatives are rich in various biological properties. In particular, pyrimidinylbenzoates are highly effective herbicides with acetohydroxyacid synthase (AHAS) as a target (Duggleby & Pang, 2000). Here we report the crystal structure of one of such a pyrimidine derivative.

In the title molecule (Fig. 1), the bond lengths and angles are within normal ranges (Allen et al., 1987) being in accordance with the corresponding values in similar compounds (Li & Huang, 2007; Li & Wang, 2007). The pyrimidine (N1//N2//C3—C6) and the benzene rings (C15—C20) are twisted away from the mid-benzene ring (C7—C12) with the dihedral angles equal to 77.7 (1) and 85.4 (1)°, respectively. The interplanar angle between the pyrimidine (N1//N2//C3—C6) and the benzene ring (C15—C20) is only 16.6 (1)°.

Pairs of C—H···F interactions form a graph-set R22(8) (Etter et al., 1990) about the crystallographic centres of symmetry, i. e. the molecules form dimers. C-H···O hydrogen bonds link these dimers into one-dimensional chains running parallel to the [111] direction (Fig. 2). Additionally, a weak C—F···π-electron ring interaction is present in the crystal structure (F···Cg = 3.459 (4) Å, C18···Cg = 3.779 (5) Å, C···F···Cg = 92.9 (3)°. (Cg is the centroid of the pyrimidine ring defined by the atoms N1//N2//C3—C6; symmetry code x-1, y, z)). Moreover, there is an intramolecular N-H···Br interaction in the structure (Tab. 1; Fig. 2)).

Experimental

Solution of 2-(4,6-dimethoxypyrimidin-2-yloxy)benzaldehyde (0.26 g, 1 mmol) and 4-bromo-2-fluoroaniline (0.21 g, 1.1 mmol) in 10 ml of methanol was stirred at room temperature for 0.5 h. Then trimethylsilanecarbonitrile (TMSCN) (0.15 g, 1.5 mmol) was added and the reaction mixture was stirred for another 12 h. The resulting mixture was filtered off by suction and the filter cake was washed with little methanol. The crude product was dried under infrared lamp and the title compound was obtained as a white solid (the yield 0.22 g, 74%, melting point: 383–385 K). The product was recrystallized from ethanol at room temperature to give block colourless crystals with average size: 0.20 × 0.15 × 0.10 mm.

Refinement

All the H atoms could have been determined in the difference electron density map. The N4—H4A distance was restrained to 0.86 (1) Å while the displacement parameter of H4A this atom was constrained: Uiso(H4A) = 1.2Ueq(N4). The remaining H atoms were positioned into idealized positions, with C—H = 0.93, 0.98 and 0.96 Å for aryl, methine and methyl groups, respectively. Uiso(Haryl/methine) = 1.2Ueq(Caryl/methine) and Uiso(Hmethyl) = 1.5Ueq(Cmethyl).

Figures

Fig. 1.
The title molecule with the atom-numbering scheme. The displacement ellipsoids are drawn at the 30% probability level.
Fig. 2.
Section of the title structure, showing the a chain of the molecules linked by weak C-H···F and C-H···O interactions represented by dashed lines (Tab. 1). The chain is parallel to [111]. Also the N-H···Br ...

Crystal data

C20H16BrFN4O3Z = 2
Mr = 459.28F(000) = 464
Triclinic, P1Dx = 1.500 Mg m3
Hall symbol: -P 1Melting point = 383–385 K
a = 8.9131 (4) ÅMo Kα radiation, λ = 0.71073 Å
b = 10.6646 (4) ÅCell parameters from 2760 reflections
c = 11.7804 (5) Åθ = 2.3–24.1°
α = 67.235 (1)°µ = 2.06 mm1
β = 82.088 (1)°T = 299 K
γ = 81.277 (2)°Block, colourless
V = 1016.77 (7) Å30.25 × 0.20 × 0.20 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer4588 independent reflections
Radiation source: fine focus sealed Siemens Mo tube2636 reflections with I > 2σ(I)
graphiteRint = 0.027
0.3° wide ω scansθmax = 27.5°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −11→11
Tmin = 0.606, Tmax = 0.662k = −13→13
10737 measured reflectionsl = −15→15

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.055Hydrogen site location: difference Fourier map
wR(F2) = 0.166H atoms treated by a mixture of independent and constrained refinement
S = 1.05w = 1/[σ2(Fo2) + (0.0884P)2 + 0.0427P] where P = (Fo2 + 2Fc2)/3
4588 reflections(Δ/σ)max < 0.001
267 parametersΔρmax = 0.83 e Å3
1 restraintΔρmin = −0.46 e Å3
59 constraints

Special details

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)

xyzUiso*/Ueq
Br10.87179 (6)0.19137 (4)0.47691 (3)0.1134 (3)
C10.8782 (7)0.4408 (4)0.8262 (5)0.1187 (16)
H1A0.82120.36530.84270.178*
H1B0.80920.52180.81750.178*
H1C0.93920.42120.89350.178*
C21.3827 (9)0.1531 (8)0.4604 (6)0.174 (3)
H2A1.46430.12460.51340.261*
H2B1.42410.17330.37640.261*
H2C1.31830.08100.48430.261*
C31.0640 (5)0.3549 (4)0.7042 (4)0.0895 (11)
C41.1396 (6)0.3699 (5)0.5916 (4)0.1173 (15)
H41.13260.45340.52540.141*
C51.2246 (5)0.2596 (5)0.5801 (4)0.1054 (14)
C61.1638 (4)0.1373 (3)0.7778 (3)0.0650 (8)
C71.2094 (3)−0.1058 (3)0.8622 (2)0.0581 (7)
C81.3569 (4)−0.1646 (4)0.8608 (3)0.0783 (9)
H81.4359−0.11960.86580.094*
C91.3867 (4)−0.2903 (4)0.8520 (4)0.0888 (11)
H91.4867−0.33070.85060.107*
C101.2715 (5)−0.3569 (4)0.8453 (3)0.0848 (11)
H101.2933−0.44220.83910.102*
C111.1221 (4)−0.2986 (3)0.8477 (3)0.0672 (8)
H111.0439−0.34440.84260.081*
C121.0890 (3)−0.1719 (3)0.8578 (2)0.0523 (6)
C130.9288 (3)−0.1037 (3)0.8654 (2)0.0537 (7)
H130.9238−0.05670.92300.064*
C140.8165 (4)−0.2064 (4)0.9153 (3)0.0695 (8)
C150.7744 (3)0.1025 (3)0.7335 (3)0.0580 (7)
C160.7497 (4)0.2024 (3)0.6176 (3)0.0721 (8)
C170.6375 (5)0.3112 (4)0.6020 (4)0.0936 (12)
H170.62290.37710.52370.112*
C180.5498 (5)0.3204 (4)0.7017 (4)0.0931 (12)
C190.5653 (4)0.2244 (4)0.8178 (4)0.0841 (10)
H190.50170.23170.88510.101*
C200.6787 (4)0.1154 (3)0.8330 (3)0.0689 (8)
H200.69080.04960.91170.083*
F10.4432 (4)0.4297 (3)0.6871 (3)0.1400 (11)
N11.0762 (3)0.2366 (3)0.8016 (2)0.0702 (7)
N21.2403 (3)0.1355 (3)0.6752 (3)0.0813 (8)
N30.7278 (4)−0.2815 (4)0.9507 (4)0.1020 (11)
N40.8911 (3)−0.0024 (2)0.7473 (2)0.0667 (7)
H4A0.949 (3)−0.018 (3)0.692 (3)0.080*
O10.9737 (4)0.4619 (3)0.7162 (3)0.1144 (10)
O21.2974 (6)0.2699 (5)0.4710 (3)0.1620 (17)
O31.1745 (2)0.0177 (2)0.88013 (18)0.0660 (5)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Br10.1488 (5)0.1099 (4)0.0510 (3)0.0276 (3)−0.0032 (2)−0.0139 (2)
C10.169 (5)0.078 (3)0.107 (4)−0.005 (3)−0.004 (3)−0.037 (3)
C20.200 (7)0.172 (6)0.102 (4)−0.011 (5)0.069 (5)−0.030 (4)
C30.111 (3)0.070 (2)0.075 (2)−0.019 (2)−0.012 (2)−0.0079 (18)
C40.142 (4)0.082 (3)0.087 (3)−0.011 (3)−0.001 (3)0.010 (2)
C50.107 (3)0.117 (3)0.061 (2)−0.026 (3)0.021 (2)−0.004 (2)
C60.071 (2)0.0700 (19)0.0497 (16)−0.0244 (16)−0.0043 (14)−0.0116 (14)
C70.0611 (19)0.0630 (17)0.0426 (14)−0.0014 (14)−0.0020 (12)−0.0140 (12)
C80.059 (2)0.101 (3)0.069 (2)0.0008 (18)−0.0023 (15)−0.0300 (19)
C90.065 (2)0.107 (3)0.077 (2)0.026 (2)−0.0007 (17)−0.030 (2)
C100.102 (3)0.0647 (19)0.075 (2)0.022 (2)0.003 (2)−0.0269 (17)
C110.077 (2)0.0568 (16)0.0649 (19)0.0034 (15)0.0013 (15)−0.0256 (14)
C120.0566 (16)0.0501 (14)0.0428 (13)0.0045 (12)−0.0038 (11)−0.0132 (11)
C130.0570 (16)0.0505 (14)0.0485 (14)0.0048 (12)−0.0048 (12)−0.0170 (12)
C140.061 (2)0.0687 (19)0.072 (2)0.0060 (17)−0.0083 (16)−0.0233 (16)
C150.0625 (17)0.0557 (15)0.0544 (16)0.0062 (13)−0.0135 (13)−0.0209 (13)
C160.087 (2)0.0671 (18)0.0529 (17)0.0105 (16)−0.0157 (15)−0.0164 (14)
C170.117 (3)0.072 (2)0.075 (2)0.033 (2)−0.036 (2)−0.0161 (18)
C180.100 (3)0.080 (2)0.095 (3)0.043 (2)−0.034 (2)−0.038 (2)
C190.076 (2)0.094 (2)0.080 (2)0.0272 (18)−0.0168 (18)−0.041 (2)
C200.0686 (19)0.0682 (18)0.0601 (18)0.0153 (15)−0.0097 (14)−0.0203 (15)
F10.155 (2)0.1206 (19)0.129 (2)0.0875 (17)−0.0487 (17)−0.0542 (16)
N10.0928 (19)0.0533 (14)0.0608 (15)−0.0158 (14)−0.0069 (13)−0.0143 (12)
N20.0848 (19)0.0860 (19)0.0580 (16)−0.0188 (15)0.0059 (14)−0.0110 (14)
N30.070 (2)0.094 (2)0.132 (3)−0.0117 (18)−0.0006 (19)−0.033 (2)
N40.0713 (16)0.0654 (14)0.0482 (14)0.0183 (12)−0.0040 (11)−0.0146 (11)
O10.158 (3)0.0604 (15)0.103 (2)−0.0037 (16)−0.018 (2)−0.0078 (14)
O20.190 (4)0.146 (3)0.082 (2)−0.004 (3)0.054 (2)0.004 (2)
O30.0870 (14)0.0585 (12)0.0492 (11)−0.0112 (10)−0.0040 (10)−0.0159 (9)

Geometric parameters (Å, °)

Br1—C161.887 (3)C9—C101.361 (6)
C1—O11.409 (5)C9—H90.9300
C1—H1A0.9600C10—C111.383 (5)
C1—H1B0.9600C10—H100.9300
C1—H1C0.9600C11—C121.386 (4)
C2—O21.397 (8)C11—H110.9300
C2—H2A0.9600C12—C131.508 (4)
C2—H2B0.9600C13—N41.439 (3)
C2—H2C0.9600C13—C141.491 (5)
C3—O11.335 (5)C13—H130.9800
C3—N11.339 (4)C14—N31.132 (4)
C3—C41.364 (6)C15—N41.383 (4)
C4—C51.342 (7)C15—C161.390 (4)
C4—H40.9300C15—C201.391 (4)
C5—O21.330 (5)C16—C171.383 (5)
C5—N21.365 (5)C17—C181.347 (5)
C6—N21.310 (4)C17—H170.9300
C6—N11.314 (4)C18—F11.358 (4)
C6—O31.376 (3)C18—C191.365 (5)
C7—C81.369 (4)C19—C201.392 (5)
C7—C121.387 (4)C19—H190.9300
C7—O31.396 (3)C20—H200.9300
C8—C91.367 (5)N4—H4A0.830 (18)
C8—H80.9300
O1—C1—H1A109.5C12—C11—H11120.0
O1—C1—H1B109.5C11—C12—C7118.1 (3)
H1A—C1—H1B109.5C11—C12—C13123.2 (3)
O1—C1—H1C109.5C7—C12—C13118.8 (2)
H1A—C1—H1C109.5N4—C13—C14111.1 (2)
H1B—C1—H1C109.5N4—C13—C12111.2 (2)
O2—C2—H2A109.5C14—C13—C12111.2 (2)
O2—C2—H2B109.5N4—C13—H13107.7
H2A—C2—H2B109.5C14—C13—H13107.7
O2—C2—H2C109.5C12—C13—H13107.7
H2A—C2—H2C109.5N3—C14—C13177.8 (4)
H2B—C2—H2C109.5N4—C15—C16120.6 (3)
O1—C3—N1119.5 (4)N4—C15—C20122.5 (3)
O1—C3—C4118.4 (4)C16—C15—C20116.8 (3)
N1—C3—C4122.1 (4)C17—C16—C15121.7 (3)
C5—C4—C3117.5 (4)C17—C16—Br1118.5 (3)
C5—C4—H4121.3C15—C16—Br1119.8 (2)
C3—C4—H4121.3C18—C17—C16119.1 (3)
O2—C5—C4119.0 (4)C18—C17—H17120.5
O2—C5—N2117.6 (5)C16—C17—H17120.5
C4—C5—N2123.4 (4)C17—C18—F1119.1 (4)
N2—C6—N1130.7 (3)C17—C18—C19122.3 (3)
N2—C6—O3116.9 (3)F1—C18—C19118.5 (4)
N1—C6—O3112.5 (3)C18—C19—C20118.3 (3)
C8—C7—C12121.7 (3)C18—C19—H19120.9
C8—C7—O3120.4 (3)C20—C19—H19120.9
C12—C7—O3117.7 (2)C15—C20—C19121.7 (3)
C9—C8—C7119.2 (3)C15—C20—H20119.2
C9—C8—H8120.4C19—C20—H20119.2
C7—C8—H8120.4C6—N1—C3114.1 (3)
C10—C9—C8120.7 (3)C6—N2—C5112.2 (3)
C10—C9—H9119.7C15—N4—C13123.3 (2)
C8—C9—H9119.7C15—N4—H4A127 (3)
C9—C10—C11120.5 (3)C13—N4—H4A110 (3)
C9—C10—H10119.8C3—O1—C1118.3 (3)
C11—C10—H10119.8C5—O2—C2118.1 (4)
C10—C11—C12119.9 (3)C6—O3—C7118.4 (2)
C10—C11—H11120.0
O1—C3—C4—C5−177.2 (5)C16—C17—C18—C19−1.4 (7)
N1—C3—C4—C52.0 (7)C17—C18—C19—C201.7 (7)
C3—C4—C5—O2178.7 (4)F1—C18—C19—C20−177.5 (4)
C3—C4—C5—N2−1.0 (8)N4—C15—C20—C19177.7 (3)
C12—C7—C8—C91.6 (5)C16—C15—C20—C19−1.1 (5)
O3—C7—C8—C9175.3 (3)C18—C19—C20—C15−0.3 (6)
C7—C8—C9—C10−0.3 (5)N2—C6—N1—C30.0 (5)
C8—C9—C10—C11−0.2 (6)O3—C6—N1—C3179.6 (3)
C9—C10—C11—C12−0.4 (5)O1—C3—N1—C6177.7 (3)
C10—C11—C12—C71.6 (4)C4—C3—N1—C6−1.4 (6)
C10—C11—C12—C13−177.9 (3)N1—C6—N2—C50.9 (5)
C8—C7—C12—C11−2.2 (4)O3—C6—N2—C5−178.8 (3)
O3—C7—C12—C11−176.1 (2)O2—C5—N2—C6−180.0 (4)
C8—C7—C12—C13177.3 (3)C4—C5—N2—C6−0.3 (7)
O3—C7—C12—C133.4 (4)C16—C15—N4—C13175.8 (3)
C11—C12—C13—N4−99.4 (3)C20—C15—N4—C13−2.9 (5)
C7—C12—C13—N481.2 (3)C14—C13—N4—C1575.8 (4)
C11—C12—C13—C1425.0 (4)C12—C13—N4—C15−159.8 (3)
C7—C12—C13—C14−154.5 (3)N1—C3—O1—C1−8.6 (6)
N4—C15—C16—C17−177.5 (3)C4—C3—O1—C1170.5 (4)
C20—C15—C16—C171.3 (5)C4—C5—O2—C2−178.7 (6)
N4—C15—C16—Br12.3 (4)N2—C5—O2—C21.0 (9)
C20—C15—C16—Br1−178.9 (2)N2—C6—O3—C7−25.3 (4)
C15—C16—C17—C18−0.1 (6)N1—C6—O3—C7155.0 (3)
Br1—C16—C17—C18−179.9 (3)C8—C7—O3—C694.9 (3)
C16—C17—C18—F1177.8 (4)C12—C7—O3—C6−91.1 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N4—H4A···Br10.83 (2)2.74 (3)3.065 (2)105 (3)
C13—H13···O30.982.412.763 (3)101
C17—H17···F1i0.932.613.541 (4)175
C20—H20···O3ii0.932.683.477 (4)145
C13—H13···O3ii0.982.533.433 (3)153

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+2, −y, −z+2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FB2161).

References

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