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Crystal structure of fluroxypyr

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aDepartment of Chemistry (BK21 plus) and Research Institute of Natural Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
*Correspondence e-mail: mychoi@gnu.ac.kr, thkim@gnu.ac.kr

Edited by J. Simpson, University of Otago, New Zealand (Received 17 November 2016; accepted 19 November 2016; online 25 November 2016)

In the title pyridine herbicide {systematic name: 2-[(4-amino-3,5-di­chloro-6-fluoro­pyridin-2-yl)­oxy]acetic acid}, C7H5Cl2FN2O3, the mean plane of the carb­oxy­lic acid substituent and the pyridyl ring plane subtend a dihedral angle of 77.5 (1)°. In the crystal, pairs of O—H⋯O hydrogen bonds form inversion dimers with R22(8) ring motifs. These are extended into chains along [011] by N—H⋯F hydrogen bonds. In addition, inter­molecular N—H⋯O hydrogen bonds and weak ππ inter­actions [ring centroid separation = 3.4602 (9) Å] connect these chains into a three-dimensional network.

1. Chemical context

Fluroxypyr belongs to the pyridine family of herbicides. It is widely used on cereal crops, olive trees and fallow croplands to control broad-leaf weeds (Moreno-Castilla et al., 2012[Moreno-Castilla, C., López-Ramón, M. V., Pastrana-Martínez, L. M., Álvarez-Merino, M. A. & Fontecha-Cámara, M. A. (2012). Adsorption, 18, 173-179.]; Wang et al., 2011[Wang, L., Xu, J., Zhao, P. & Pan, C. (2011). Bull. Environ. Contam. Toxicol. 86, 449-453.]). Pyridine herbicides such as fluroxypyr are effective and popular chemicals for post-emergence broad-leaf weed control, particularly in turf during cool seasons. The efficacy of this herbicide may be affected by environmental conditions including the relative humidity, temperature and soil moisture. Because of this, its application often provides inconsistent broad-leaf weed control in winter or early spring (Reed & McCullough, 2012[Reed, T. V. & McCullough, P. E. (2012). Hort. Sci. 47, 1548-1549.]). Until now, its crystal structure had not been reported and we describe it herein.

[Scheme 1]

2. Structural commentary

The structure of fluroxypyr is shown in Fig. 1[link]. The dihedral angle between the mean plane of the carb­oxy­lic acid group (C6/C7/O2/O3) and the pyridyl ring (N1/C1–C5) is 77.5 (1)°. All bond lengths and bond angles are normal and comparable to those observed in the crystal structure of a related pyridine-containing herbicide (Cho et al., 2015[Cho, S., Kim, J., Lee, S. & Kim, T. H. (2015). Acta Cryst. E71, o55.]).

[Figure 1]
Figure 1
The structure of the title compound, with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radius.

3. Supra­molecular features

In the crystal, the solid-state structure is stabilized by pairs of N2—H2B⋯O2 hydrogen bonds, forming inversion dimers with R22(18) ring motifs (Table 1[link] and Fig. 2[link]). These dimers are linked by pairs of O3—H3⋯O2i/O2 hydrogen bonds that form classical carb­oxy­lic-acid-based inversion dimers with R22(8) ring motifs. These contacts form chains propagating along [011] (yellow dashed lines in Fig. 2[link]). In addition, inter­molecular N2—H2A⋯F1 hydrogen bonds connect these chains, yielding sheets extending parallel to the bc plane (red dashed line in Fig. 3[link]). These sheets are further linked by weak inter­molecular ππ inter­actions between the pyridyl rings (N1/C1–C5) [Cg1⋯Cg1iv = 3.4602 (9) Å; symmetry code: (iv) −x, −y + 2, −z], resulting in a three-dimensional network structure (black dashed lines in Fig. 4[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O3—H3⋯O2i 0.84 1.84 2.6801 (15) 174
N2—H2A⋯F1ii 0.88 2.39 2.9950 (15) 126
N2—H2B⋯O2iii 0.88 2.25 3.0201 (16) 146
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) x, y+1, z; (iii) -x+1, -y+2, -z.
[Figure 2]
Figure 2
A view along the b axis of the crystal packing of the title compound. The chains are formed through inter­molecular O—H⋯O and N—H⋯O hydrogen bonds (yellow dashed lines). H atoms not involved in these inter­actions have been omitted for clarity.
[Figure 3]
Figure 3
The two-dimensional network formed through inter­molecular N—H⋯F hydrogen bonds (red dashed lines). Inter­molecular O/N–H⋯O hydrogen bonds within a chain are shown as yellow dashed lines. H atoms not involved in these inter­actions have been omitted for clarity.
[Figure 4]
Figure 4
A packing diagram showing the three-dimensional architecture formed by weak ππ inter­actions (black dashed lines). Inter­molecular O—H⋯O, N—H⋯O and N—H⋯F hydrogen bonds within a sheet are shown as yellow and red dashed lines. H atoms not involved in inter­molecular inter­actions have been omitted for clarity.

4. Database survey

We have reported the crystal structure of several pesticides including compounds with pyridine rings (Cho et al., 2015[Cho, S., Kim, J., Lee, S. & Kim, T. H. (2015). Acta Cryst. E71, o55.]; Kang et al., 2015[Kang, G., Kim, J., Park, H. & Kim, T. H. (2015). Acta Cryst. E71, o588.]; Kwon et al., 2016[Kwon, E., Kim, J., Park, H. & Kim, T. H. (2016). Acta Cryst. E72, 1468-1470.]; Park et al., 2016[Park, H., Kwon, E., Yoon, I. & Kim, J. (2016). Acta Cryst. E72, 1610-1613.]). In addition, a database search (CSD; Groom et al., 2006[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) yielded two other comparable structures, 2-[(3,5,6-tri­chloro­pyridin-2-yl)­oxy]acetic acid (Cho et al., 2014[Cho, S., Kim, J., Jeon, Y. & Kim, T. H. (2014). Acta Cryst. E70, o940.]) and 2,4,5-tri­chloro­phen­oxy­acetic acid (Smith et al., 1976[Smith, G., Kennard, C. H. L. & White, A. H. (1976). Aust. J. Chem. 29, 2727-2730.]).

5. Synthesis and crystallization

The title compound was purchased from Dr. Ehrenstorfer GmbH. Colorless single crystals suitable for X-ray diffraction were obtained from a CH3CN solution by slow evaporation at room temperature.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. All H atoms were positioned geometrically and refined using a riding model with d(O—H) = 0.84 Å, Uiso = 1.5Ueq(C) for the O—H group, d(N—H) = 0.88 Å, Uiso = 1.2Ueq(C) for the amine group, and d(C—H) = 0.99 Å, Uiso = 1.2Ueq(C) for the CH2 group.

Table 2
Experimental details

Crystal data
Chemical formula C7H5Cl2FN2O3
Mr 255.03
Crystal system, space group Triclinic, P[\overline{1}]
Temperature (K) 173
a, b, c (Å) 7.1116 (9), 7.6131 (9), 8.9414 (11)
α, β, γ (°) 86.927 (6), 80.354 (6), 72.587 (5)
V3) 455.38 (10)
Z 2
Radiation type Mo Kα
μ (mm−1) 0.72
Crystal size (mm) 0.23 × 0.22 × 0.04
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction Multi-scan (SADABS; Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.690, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections 8052, 2092, 1972
Rint 0.023
(sin θ/λ)max−1) 0.650
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.028, 0.076, 1.12
No. of reflections 2092
No. of parameters 137
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.29, −0.38
Computer programs: APEX2 and SAINT (Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS97 and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and DIAMOND (Brandenburg, 2010[Brandenburg, K. (2010). DIAMOND. Crystal Impact GbR, Bonn, Germany.]).

Supporting information


Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: DIAMOND (Brandenburg, 2010); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

2-[(4-Amino-3,5-dichloro-6-fluoropyridin-2-yl)oxy]acetic acid top
Crystal data top
C7H5Cl2FN2O3Z = 2
Mr = 255.03F(000) = 256
Triclinic, P1Dx = 1.860 Mg m3
a = 7.1116 (9) ÅMo Kα radiation, λ = 0.71073 Å
b = 7.6131 (9) ÅCell parameters from 6070 reflections
c = 8.9414 (11) Åθ = 2.8–27.5°
α = 86.927 (6)°µ = 0.72 mm1
β = 80.354 (6)°T = 173 K
γ = 72.587 (5)°Plate, colourless
V = 455.38 (10) Å30.23 × 0.22 × 0.04 mm
Data collection top
Bruker APEXII CCD
diffractometer
1972 reflections with I > 2σ(I)
φ and ω scansRint = 0.023
Absorption correction: multi-scan
(SADABS; Bruker, 2014)
θmax = 27.5°, θmin = 2.3°
Tmin = 0.690, Tmax = 0.746h = 98
8052 measured reflectionsk = 99
2092 independent reflectionsl = 1011
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.028H-atom parameters constrained
wR(F2) = 0.076 w = 1/[σ2(Fo2) + (0.0371P)2 + 0.2062P]
where P = (Fo2 + 2Fc2)/3
S = 1.12(Δ/σ)max < 0.001
2092 reflectionsΔρmax = 0.29 e Å3
137 parametersΔρmin = 0.38 e Å3
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.43701 (6)0.90760 (5)0.32138 (4)0.02990 (12)
Cl20.09018 (6)1.29195 (5)0.19394 (4)0.02692 (11)
F10.37852 (14)0.60390 (12)0.12163 (11)0.0298 (2)
O10.08333 (16)0.93076 (14)0.31061 (11)0.0234 (2)
O20.41952 (15)0.68493 (14)0.39455 (11)0.0225 (2)
O30.24193 (16)0.50096 (15)0.50373 (13)0.0278 (2)
H30.35150.44080.52950.042*
N10.23296 (18)0.76320 (16)0.09169 (14)0.0202 (2)
N20.2865 (2)1.24580 (17)0.12976 (14)0.0244 (3)
H2A0.24141.35150.08130.029*
H2B0.34291.24170.22550.029*
C10.3133 (2)0.76709 (19)0.05118 (17)0.0202 (3)
C20.3356 (2)0.91926 (19)0.13244 (15)0.0192 (3)
C30.26931 (19)1.08983 (18)0.05718 (15)0.0177 (3)
C40.1811 (2)1.08826 (18)0.09480 (15)0.0176 (3)
C50.16793 (19)0.92352 (19)0.16331 (15)0.0178 (3)
C60.0683 (2)0.7624 (2)0.38160 (17)0.0242 (3)
H6A0.02480.69170.31140.029*
H6B0.03450.79000.47360.029*
C70.2634 (2)0.64680 (19)0.42518 (15)0.0197 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0345 (2)0.0351 (2)0.01671 (18)0.00767 (16)0.00124 (14)0.00224 (14)
Cl20.0359 (2)0.01784 (17)0.02395 (19)0.00397 (14)0.00232 (14)0.00355 (13)
F10.0372 (5)0.0182 (4)0.0318 (5)0.0048 (4)0.0035 (4)0.0076 (4)
O10.0270 (5)0.0214 (5)0.0177 (5)0.0044 (4)0.0008 (4)0.0058 (4)
O20.0245 (5)0.0241 (5)0.0208 (5)0.0101 (4)0.0048 (4)0.0060 (4)
O30.0243 (5)0.0232 (5)0.0355 (6)0.0081 (4)0.0051 (5)0.0130 (4)
N10.0209 (6)0.0169 (5)0.0232 (6)0.0058 (4)0.0055 (5)0.0035 (4)
N20.0318 (7)0.0200 (6)0.0216 (6)0.0103 (5)0.0013 (5)0.0055 (5)
C10.0195 (6)0.0167 (6)0.0242 (7)0.0035 (5)0.0058 (5)0.0025 (5)
C20.0190 (6)0.0226 (7)0.0158 (6)0.0060 (5)0.0025 (5)0.0002 (5)
C30.0170 (6)0.0189 (6)0.0183 (6)0.0065 (5)0.0053 (5)0.0037 (5)
C40.0186 (6)0.0155 (6)0.0181 (6)0.0038 (5)0.0035 (5)0.0002 (5)
C50.0150 (6)0.0200 (6)0.0173 (6)0.0036 (5)0.0037 (5)0.0033 (5)
C60.0236 (7)0.0258 (7)0.0218 (7)0.0081 (6)0.0014 (5)0.0090 (6)
C70.0252 (7)0.0202 (6)0.0132 (6)0.0073 (5)0.0005 (5)0.0007 (5)
Geometric parameters (Å, º) top
Cl1—C21.7181 (14)N2—C31.3506 (17)
Cl2—C41.7216 (14)N2—H2A0.8800
F1—C11.3403 (16)N2—H2B0.8800
O1—C51.3499 (17)C1—C21.370 (2)
O1—C61.4243 (17)C2—C31.4080 (19)
O2—C71.2143 (17)C3—C41.3990 (19)
O3—C71.3158 (17)C4—C51.3877 (19)
O3—H30.8400C6—C71.505 (2)
N1—C11.3117 (19)C6—H6A0.9900
N1—C51.3268 (18)C6—H6B0.9900
C5—O1—C6117.32 (11)C5—C4—C3119.78 (12)
C7—O3—H3109.5C5—C4—Cl2121.01 (11)
C1—N1—C5116.03 (12)C3—C4—Cl2119.20 (10)
C3—N2—H2A120.0N1—C5—O1119.54 (12)
C3—N2—H2B120.0N1—C5—C4123.51 (13)
H2A—N2—H2B120.0O1—C5—C4116.96 (12)
N1—C1—F1115.22 (12)O1—C6—C7112.12 (12)
N1—C1—C2126.49 (13)O1—C6—H6A109.2
F1—C1—C2118.29 (13)C7—C6—H6A109.2
C1—C2—C3118.00 (13)O1—C6—H6B109.2
C1—C2—Cl1122.11 (11)C7—C6—H6B109.2
C3—C2—Cl1119.88 (10)H6A—C6—H6B107.9
N2—C3—C4122.43 (12)O2—C7—O3124.35 (13)
N2—C3—C2121.39 (12)O2—C7—C6124.46 (13)
C4—C3—C2116.17 (12)O3—C7—C6111.18 (12)
C5—N1—C1—F1179.85 (11)C2—C3—C4—Cl2178.35 (10)
C5—N1—C1—C20.2 (2)C1—N1—C5—O1179.97 (12)
N1—C1—C2—C30.9 (2)C1—N1—C5—C40.1 (2)
F1—C1—C2—C3179.10 (12)C6—O1—C5—N10.13 (18)
N1—C1—C2—Cl1178.05 (11)C6—O1—C5—C4179.71 (12)
F1—C1—C2—Cl11.94 (19)C3—C4—C5—N10.9 (2)
C1—C2—C3—N2179.92 (13)Cl2—C4—C5—N1179.01 (10)
Cl1—C2—C3—N21.09 (18)C3—C4—C5—O1179.27 (11)
C1—C2—C3—C41.55 (19)Cl2—C4—C5—O10.82 (17)
Cl1—C2—C3—C4177.43 (10)C5—O1—C6—C778.48 (15)
N2—C3—C4—C5179.93 (12)O1—C6—C7—O24.9 (2)
C2—C3—C4—C51.56 (19)O1—C6—C7—O3173.75 (12)
N2—C3—C4—Cl20.16 (18)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3···O2i0.841.842.6801 (15)174
N2—H2A···F1ii0.882.392.9950 (15)126
N2—H2B···O2iii0.882.253.0201 (16)146
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z; (iii) x+1, y+2, z.
 

Acknowledgements

This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (Nos. 2014R1A1A4A01009105 and 2016R1D1A1B03934376).

References

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