Home The crystal structure of 3,5-difluoroisonicotinic acid, C6H3F2NO2
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The crystal structure of 3,5-difluoroisonicotinic acid, C6H3F2NO2

  • Yan Zeng ORCID logo EMAIL logo and Chao-Jun Du ORCID logo
Published/Copyright: April 29, 2020

Abstract

C6H3F2NO2, monoclinic, P21/n (no. 14), a = 6.8050(10) Å, b = 6.8443(9) Å, c = 12.7196(14) Å, β = 94.562(4)°, V = 590.54(13) Å3, Z = 4, Rgt(F) = 0.0395, wRref(F2) = 0.1038, T = 150(2) K.

CCDC no.: 1995576

The molecular structure is shown in the figure. Hydrogen bonds are shown as dashed lines. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Colorless block
Size:0.25 × 0.20 × 0.15 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.18 mm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω
θmax, completeness:26.0°, >99%
N(hkl)measured, N(hkl)unique, Rint:10438, 1158, 0.062
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 881
N(param)refined:104
Programs:Bruker [1], SHELX [2], Olex2 [3], [4]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

AtomxyzUiso*/Ueq
C10.7052(3)0.2517(3)0.19376(14)0.0182(4)
C20.5748(3)0.2754(3)0.28316(13)0.0165(4)
C30.3854(3)0.3507(3)0.27058(13)0.0176(4)
C40.2684(3)0.3694(3)0.35407(14)0.0188(4)
H40.1387220.4205210.3422310.023*
C50.5192(3)0.2450(3)0.46777(13)0.0195(4)
H50.5672020.2068820.5369100.023*
C60.6397(3)0.2259(3)0.38566(14)0.0181(4)
F10.82217(16)0.15257(17)0.40713(8)0.0279(3)
F20.31187(15)0.41032(17)0.17503(8)0.0257(3)
N10.3367(2)0.3161(2)0.45141(11)0.0188(4)
O10.61250(19)0.1734(2)0.10957(9)0.0232(4)
H10.697(4)0.168(4)0.050(2)0.082(10)*
O20.8764(2)0.3024(2)0.20209(10)0.0273(4)

Source of material

All of the starting materials were used as received. 1.59 g (0.01 mol) 3,5-difluoroisonicotinic acid was added to a solution mixed by 10 mL THF and 1 mL double-destilled water under room temperature. After stirring for 10 min, the solution was filtered and let evaporate automatically. Many colorless block crystals were harvested, which are suitable for single-XRD measurement, yield 67.3% (based on 3,5-difluoroisonicotinic acid).

Experimental details

The structure was solved by direct methods with the SHELXS program. All H-atoms from C atoms were positioned with idealized geometry and refined isotropically (Uiso(H) = 1.2Ueq(C)) using a riding model with C—H = 0.950 Å. The hydrogen atom of the carboxyl group was positioned on the basis of a Q peak and refined freely.

Comment

It’s known that fluorine-substituted isonicotinic acid derivatives have been used as ligands to construct metal-organic frameworks combined with transition metal and lanthanide, including 2-fluoroisonicotinic acid [5], [6] and 3-fluoroisonicotinic acid [7], [8], [9], [10]. The same is true for 3,5-dichloroisonicotinate containing complexes [11], [12]. However crystal structures of mono- or multi-fluorine-substituted have not been reported.

As shown in the figure, the title compound crystallizes with the whole organic molecule as its asymmetric unit. All atoms are nearly co-planar except the two O atoms and one H atom from the carboxyl group. The distances of N1⋯H1 and O1⋯H1 are 1.636 and 0.99 Å, respectively, and the bond length of C1—O1 is much longer (1.313 Å) than the bond length of C1 = O2 (1.212 Å), which indicates that the carboxyl group is protonated. There is an one-dimesional supramolecular structure generated by the O—H⋯N hydrogen bond through a head-to-tail mode (see the figure).

References

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Received: 2020-03-16
Accepted: 2020-04-08
Published Online: 2020-04-29
Published in Print: 2020-06-25

©2020 Yan Zeng et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 Public License.

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  77. Crystal structure of 5-methyl-3-phenyl-1-tosyl-1,2,3,4-tetrahydropyridine, C19H21NO2S
  78. Crystal structure of bis((3-chlorosalicylidene)-ethylenediaminato-κ4N,N′,O,O′)nickel (II), C16H12Cl2NiN2O2
  79. Crystal structure of (E)-N′-(2-chloro-6-hydroxybenzylidene)-4-hydroxybenzohydrazide — dihydrofuran-2(3H)-one (1/1), C18H17ClN2O5
  80. Crystal structure of bis((3-bromosalicylidene)-ethylenediaminato-κ4N,N′,O,O′) nickel (II), C16H12Br2NiN2O2
  81. Crystal structure of trimethylsulfoxonium tetrachloridocobaltate(II) [(CH3)3SO]2CoCl4
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