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Acta Crystallogr Sect E Struct Rep Online. 2010 April 1; 66(Pt 4): o775.
Published online 2010 March 6. doi:  10.1107/S1600536810008184
PMCID: PMC2983956

2-Amino-5-bromo­pyridinium trifluoro­acetate

Abstract

In the title compound, C5H6BrN2 +·C2F3O2 , the F atoms of the anion are disordered over two sets of sites, with occupancies of 0.59 (2):0.41 (2). In the crystal structure, the anions and cations are linked into a two-dimensional network parallel to (100) by N—H(...)O and C—H(...)O hydrogen bonds. Within this network, the N—H(...)O hydrogen bonds generate R 2 2(8) ring motifs.

Related literature

For background to the chemistry of substituted pyridines, see: Pozharski et al. (1997 [triangle]); Katritzky et al. (1996 [triangle]). For related structures, see: Goubitz et al. (2001 [triangle]); Vaday & Foxman (1999 [triangle]). For details of hydrogen bonding, see: Jeffrey & Saenger (1991 [triangle]); Jeffrey (1997 [triangle]); Scheiner (1997 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0o775-scheme1.jpg

Experimental

Crystal data

  • C5H6BrN2 +·C2F3O2
  • M r = 287.05
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o775-efi1.jpg
  • a = 17.5852 (13) Å
  • b = 11.3010 (9) Å
  • c = 5.1264 (4) Å
  • V = 1018.77 (14) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 4.06 mm−1
  • T = 296 K
  • 0.73 × 0.41 × 0.09 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.156, T max = 0.709
  • 8343 measured reflections
  • 2899 independent reflections
  • 1547 reflections with I > 2σ(I)
  • R int = 0.056

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.099
  • S = 0.93
  • 2899 reflections
  • 176 parameters
  • 56 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.46 e Å−3
  • Δρmin = −0.28 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1254 Friedel pairs
  • Flack parameter: 0.024 (12)

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810008184/ci5042sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810008184/ci5042Isup2.hkl

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

Acknowledgments

MH and HKF thank the Malaysian Government and Universiti Sains Malaysia (USM) for the Research University Golden Goose grant No. 1001/PFIZIK/811012. MH thanks USM for a post-doctoral research fellowship.

supplementary crystallographic information

Comment

Pyridine and its derivatives play an important role in heterocyclic chemistry (Pozharski et al., 1997; Katritzky et al., 1996). They are often involved in hydrogen-bond interactions (Jeffrey & Saenger, 1991; Jeffrey, 1997; Scheiner, 1997). The crystal structures of 2-amino-5-bromopyridine (Goubitz et al., 2001) and 2-amino-5-bromopyridinium propynoate (Vaday & Foxman, 1999) have been reported. In order to study hydrogen bonding interactions, the title salt was prepared and its crystal structure is reported here.

The asymmetric unit of (I) (Fig. 1) contains one 2-amino-5-bromopyridinium cation and one trifluoroacetate anion, indicating that proton transfer has occurred during the co-crystallisation. The 2-amino-5-methylpyridinium cation is essentially planar, with a maximum deviation of 0.016 (4) Å for atom C1; As a result of protonation, the C1—N1—C5 angle is widened to 122.5 (4)°. The bond lengths and angles are normal (Allen et al., 1987).

In the crystal packing (Fig. 2), the cations and anions are linked via N—H···O hydrogen bonds to form R22(8) ring motifs (Bernstein et al., 1995). The ionic units are linked into a two-dimensional network parallel to the (100) by N—H···O and C—H···O hydrogen bonds (Table 1).

Experimental

To a hot methanol solution (20 ml) of 2-amino-5-bromopyridine (44 mg, Aldrich) was added a few drops of trifluoroacetic acid. The solution was warmed over a water bath for a few minutes. The resulting solution was allowed to cool slowly to room temperature. Crystals of the title compound appeared after a few days.

Refinement

Atoms H1N1, H1N2 and H2N2 were located in a difference Fourier map and refined; the N–H distances of the NH2 group were restrained to be equal. The remaining H atoms were positioned geometrically [C–H = 0.93 Å] and were refined using a riding model, with Uiso(H) = 1.2Ueq(C). The F atoms of the anion are disordered over two positions with occupancies of 0.59 (2):0.41 (2). The C—F distances were restrained to be equal and the Uij components of F atoms were restrained to an approximate isotropic behaviour.

Figures

Fig. 1.
The asymmetric unit of the title compound. Displacement ellipsoids are drawn at the 30% probability level. Both disorder components are shown.
Fig. 2.
The crystal packing of the title compound, showing hydrogen-bonded (dashed lines) networks.

Crystal data

C5H6BrN2+·C2F3O2F(000) = 560
Mr = 287.05Dx = 1.871 Mg m3
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2nCell parameters from 1994 reflections
a = 17.5852 (13) Åθ = 2.9–22.5°
b = 11.3010 (9) ŵ = 4.06 mm1
c = 5.1264 (4) ÅT = 296 K
V = 1018.77 (14) Å3Plate, colourless
Z = 40.73 × 0.41 × 0.09 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer2899 independent reflections
Radiation source: fine-focus sealed tube1547 reflections with I > 2σ(I)
graphiteRint = 0.056
[var phi] and ω scansθmax = 30.1°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −24→24
Tmin = 0.156, Tmax = 0.709k = −14→15
8343 measured reflectionsl = −7→7

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.039H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.099w = 1/[σ2(Fo2) + (0.0247P)2] where P = (Fo2 + 2Fc2)/3
S = 0.93(Δ/σ)max = 0.001
2899 reflectionsΔρmax = 0.46 e Å3
176 parametersΔρmin = −0.28 e Å3
56 restraintsAbsolute structure: Flack (1983), 1254 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.024 (12)

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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*/UeqOcc. (<1)
Br10.93625 (2)0.38997 (4)0.26064 (12)0.0770 (2)
N10.80785 (16)0.5888 (2)0.7575 (9)0.0462 (6)
N20.7800 (2)0.7862 (3)0.8112 (8)0.0631 (11)
C10.8432 (2)0.4973 (3)0.6357 (8)0.0489 (8)
H1A0.83550.42040.69470.059*
C20.8889 (2)0.5166 (4)0.4322 (8)0.0540 (9)
C30.9016 (2)0.6353 (4)0.3492 (8)0.0585 (11)
H3A0.93420.65070.21060.070*
C40.8661 (2)0.7253 (4)0.4722 (8)0.0563 (10)
H4A0.87430.80290.41830.068*
C50.81681 (19)0.7018 (3)0.6821 (7)0.0474 (9)
O10.70895 (14)0.5277 (2)0.1425 (6)0.0589 (7)
O20.67948 (17)0.7148 (2)0.2175 (8)0.0751 (9)
F1A0.6204 (5)0.5331 (17)0.6225 (16)0.120 (4)0.59 (2)
F2A0.5460 (5)0.6483 (7)0.419 (3)0.104 (3)0.59 (2)
F3A0.5673 (5)0.4758 (8)0.273 (3)0.095 (3)0.59 (2)
F1B0.5407 (6)0.6290 (16)0.294 (4)0.115 (5)0.41 (2)
F2B0.5819 (10)0.4561 (7)0.392 (4)0.105 (5)0.41 (2)
F3B0.6028 (10)0.6030 (19)0.6312 (19)0.113 (5)0.41 (2)
C60.5992 (2)0.5688 (3)0.3866 (8)0.0636 (11)
C70.66887 (19)0.6091 (3)0.2336 (9)0.0510 (9)
H1N10.7730 (19)0.576 (3)0.891 (7)0.041 (9)*
H1N20.785 (2)0.856 (3)0.767 (11)0.060 (11)*
H2N20.748 (2)0.773 (4)0.927 (7)0.067 (14)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Br10.0861 (3)0.0606 (3)0.0842 (3)0.0050 (2)0.0152 (3)−0.0136 (3)
N10.0546 (15)0.0281 (14)0.0561 (15)−0.0047 (11)0.002 (2)−0.004 (2)
N20.085 (2)0.0291 (17)0.075 (3)0.0045 (18)0.014 (2)0.0079 (18)
C10.058 (2)0.0280 (18)0.061 (2)−0.0045 (16)−0.0053 (18)−0.0018 (17)
C20.059 (2)0.040 (2)0.063 (2)0.0022 (17)−0.0031 (18)−0.0071 (18)
C30.061 (2)0.054 (3)0.061 (3)−0.007 (2)0.0016 (18)0.0057 (19)
C40.067 (2)0.037 (2)0.064 (2)−0.0068 (19)−0.004 (2)0.013 (2)
C50.0519 (18)0.0322 (19)0.058 (2)−0.0045 (16)−0.0059 (16)0.0088 (16)
O10.0679 (15)0.0319 (14)0.0768 (16)0.0077 (12)0.0135 (14)0.0109 (13)
O20.0987 (19)0.0303 (14)0.096 (3)0.0012 (13)0.0185 (18)0.0044 (18)
F1A0.115 (5)0.166 (9)0.078 (4)−0.013 (5)0.011 (3)0.046 (5)
F2A0.093 (4)0.080 (4)0.139 (8)0.018 (3)0.040 (4)−0.019 (4)
F3A0.083 (3)0.082 (4)0.119 (6)−0.036 (3)0.008 (4)−0.011 (5)
F1B0.069 (5)0.143 (8)0.132 (9)0.030 (5)0.009 (6)−0.004 (7)
F2B0.119 (7)0.062 (6)0.133 (9)−0.011 (5)0.047 (7)−0.001 (5)
F3B0.130 (8)0.121 (9)0.088 (6)−0.024 (6)0.036 (5)−0.009 (6)
C60.065 (3)0.045 (2)0.080 (3)0.002 (2)0.005 (2)−0.007 (2)
C70.062 (2)0.037 (2)0.054 (2)0.0022 (16)−0.005 (2)0.001 (2)

Geometric parameters (Å, °)

Br1—C21.875 (4)C4—C51.407 (5)
N1—C51.344 (4)C4—H4A0.93
N1—C11.358 (5)O1—C71.250 (4)
N1—H1N10.93 (4)O2—C71.212 (4)
N2—C51.330 (5)F1A—C61.329 (6)
N2—H1N20.82 (3)F2A—C61.307 (6)
N2—H2N20.84 (3)F3A—C61.327 (6)
C1—C21.334 (5)F1B—C61.321 (7)
C1—H1A0.93F2B—C61.310 (7)
C2—C31.425 (6)F3B—C61.314 (7)
C3—C41.349 (6)C6—C71.524 (6)
C3—H3A0.93
C5—N1—C1122.5 (4)N2—C5—N1118.8 (3)
C5—N1—H1N1116 (2)N2—C5—C4123.0 (4)
C1—N1—H1N1121 (2)N1—C5—C4118.1 (4)
C5—N2—H1N2120 (4)F2B—C6—F3B106.2 (8)
C5—N2—H2N2124 (3)F2B—C6—F1B109.0 (10)
H1N2—N2—H2N2116 (5)F3B—C6—F1B103.2 (9)
C2—C1—N1120.7 (4)F2A—C6—F3A107.3 (7)
C2—C1—H1A119.6F2A—C6—F1A107.2 (6)
N1—C1—H1A119.6F3A—C6—F1A106.1 (6)
C1—C2—C3118.8 (4)F2A—C6—C7115.8 (6)
C1—C2—Br1120.6 (3)F2B—C6—C7119.1 (7)
C3—C2—Br1120.6 (3)F3B—C6—C7111.4 (7)
C4—C3—C2119.8 (4)F1B—C6—C7106.8 (8)
C4—C3—H3A120.1F3A—C6—C7110.4 (6)
C2—C3—H3A120.1F1A—C6—C7109.5 (5)
C3—C4—C5120.0 (4)O2—C7—O1127.8 (4)
C3—C4—H4A120.0O2—C7—C6116.9 (4)
C5—C4—H4A120.0O1—C7—C6115.2 (3)
C5—N1—C1—C2−0.2 (6)F2B—C6—C7—O2174.5 (14)
N1—C1—C2—C31.7 (5)F3B—C6—C7—O2−61.4 (13)
N1—C1—C2—Br1−178.9 (3)F1B—C6—C7—O250.6 (12)
C1—C2—C3—C4−1.6 (6)F3A—C6—C7—O2142.0 (8)
Br1—C2—C3—C4179.0 (3)F1A—C6—C7—O2−101.5 (10)
C2—C3—C4—C50.1 (6)F2A—C6—C7—O1−161.2 (9)
C1—N1—C5—N2179.8 (3)F2B—C6—C7—O1−6.5 (14)
C1—N1—C5—C4−1.4 (6)F3B—C6—C7—O1117.6 (12)
C3—C4—C5—N2−179.8 (4)F1B—C6—C7—O1−130.4 (12)
C3—C4—C5—N11.4 (5)F3A—C6—C7—O1−39.0 (8)
F2A—C6—C7—O219.8 (10)F1A—C6—C7—O177.5 (10)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N1···O1i0.93 (3)1.80 (3)2.720 (5)171 (3)
N2—H1N2···O1ii0.83 (4)2.05 (4)2.870 (4)176 (5)
N2—H2N2···O2i0.83 (4)2.03 (4)2.849 (5)170 (4)
C1—H1A···O2iii0.932.343.245 (4)164

Symmetry codes: (i) x, y, z+1; (ii) −x+3/2, y+1/2, z+1/2; (iii) −x+3/2, y−1/2, z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI5042).

References

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  • Jeffrey, G. A. (1997). An Introduction to Hydrogen Bonding. Oxford University Press.
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