2-Amino-5-bromo­pyridinium trifluoro­acetate

Hemamalini, M.; Fun, H.-K.

doi:10.1107/S1600536810008184

organic compounds

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Volume 66| Part 4| April 2010| Page o775

doi:10.1107/S1600536810008184

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2-Amino-5-bromopyridinium trifluoroacetate

Madhukar Hemamalini ^a and Hoong-Kun Fun ^a ^*‡

^aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
^*Correspondence e-mail: hkfun@usm.my

(Received 22 February 2010; accepted 3 March 2010; online 6 March 2010)

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 R₂²(8) ring motifs.

Related literature

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

Experimental

Crystal data

C₅H₆BrN₂⁺·C₂F₃O₂⁻
M_r = 287.05
Orthorhombic, P n a 2₁
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 ) 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[F² > 2σ(F²)] = 0.039
wR(F²) = 0.099
S = 0.93
2899 reflections
176 parameters
56 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.46 e Å⁻³
Δρ_min = −0.28 e Å⁻³
Absolute structure: Flack (1983 ), 1254 Friedel pairs
Flack parameter: 0.024 (12)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N1⋯O1ⁱ	0.93 (3)	1.80 (3)	2.720 (5)	171 (3)
N2—H1N2⋯O1ⁱⁱ	0.83 (4)	2.05 (4)	2.870 (4)	176 (5)
N2—H2N2⋯O2ⁱ	0.83 (4)	2.03 (4)	2.849 (5)	170 (4)
C1—H1A⋯O2ⁱⁱⁱ	0.93	2.34	3.245 (4)	164
Symmetry codes: (i) x, y, z+1; (ii) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (iii) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

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

Supporting information

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

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

checkCIF report

Comment top

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).

Related literature top

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

Experimental top

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.

Computing details top

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

Figures top

	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.

2-Amino-5-bromopyridinium trifluoroacetate top

Crystal data top

C₅H₆BrN₂⁺·C₂F₃O₂⁻	F(000) = 560
M_r = 287.05	D_x = 1.871 Mg m⁻³
Orthorhombic, Pna2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2n	Cell parameters from 1994 reflections
a = 17.5852 (13) Å	θ = 2.9–22.5°
b = 11.3010 (9) Å	µ = 4.06 mm⁻¹
c = 5.1264 (4) Å	T = 296 K
V = 1018.77 (14) Å³	Plate, colourless
Z = 4	0.73 × 0.41 × 0.09 mm

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	2899 independent reflections
Radiation source: fine-focus sealed tube	1547 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.056
ϕ and ω scans	θ_max = 30.1°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −24→24
T_min = 0.156, T_max = 0.709	k = −14→15
8343 measured reflections	l = −7→7

Refinement top

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)] = 0.039	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.099	w = 1/[σ²(F_o²) + (0.0247P)²] where P = (F_o² + 2F_c²)/3
S = 0.93	(Δ/σ)_max = 0.001
2899 reflections	Δρ_max = 0.46 e Å⁻³
176 parameters	Δρ_min = −0.28 e Å⁻³
56 restraints	Absolute structure: Flack (1983), 1254 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.024 (12)

Crystal data top

C₅H₆BrN₂⁺·C₂F₃O₂⁻	V = 1018.77 (14) Å³
M_r = 287.05	Z = 4
Orthorhombic, Pna2₁	Mo Kα radiation
a = 17.5852 (13) Å	µ = 4.06 mm⁻¹
b = 11.3010 (9) Å	T = 296 K
c = 5.1264 (4) Å	0.73 × 0.41 × 0.09 mm

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	2899 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2009)	1547 reflections with I > 2σ(I)
T_min = 0.156, T_max = 0.709	R_int = 0.056
8343 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.099	Δρ_max = 0.46 e Å⁻³
S = 0.93	Δρ_min = −0.28 e Å⁻³
2899 reflections	Absolute structure: Flack (1983), 1254 Friedel pairs
176 parameters	Absolute structure parameter: 0.024 (12)
56 restraints

Special details top

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) top

	x	y	z	U_iso*/U_eq	Occ. (<1)
Br1	0.93625 (2)	0.38997 (4)	0.26064 (12)	0.0770 (2)
N1	0.80785 (16)	0.5888 (2)	0.7575 (9)	0.0462 (6)
N2	0.7800 (2)	0.7862 (3)	0.8112 (8)	0.0631 (11)
C1	0.8432 (2)	0.4973 (3)	0.6357 (8)	0.0489 (8)
H1A	0.8355	0.4204	0.6947	0.059*
C2	0.8889 (2)	0.5166 (4)	0.4322 (8)	0.0540 (9)
C3	0.9016 (2)	0.6353 (4)	0.3492 (8)	0.0585 (11)
H3A	0.9342	0.6507	0.2106	0.070*
C4	0.8661 (2)	0.7253 (4)	0.4722 (8)	0.0563 (10)
H4A	0.8743	0.8029	0.4183	0.068*
C5	0.81681 (19)	0.7018 (3)	0.6821 (7)	0.0474 (9)
O1	0.70895 (14)	0.5277 (2)	0.1425 (6)	0.0589 (7)
O2	0.67948 (17)	0.7148 (2)	0.2175 (8)	0.0751 (9)
F1A	0.6204 (5)	0.5331 (17)	0.6225 (16)	0.120 (4)	0.59 (2)
F2A	0.5460 (5)	0.6483 (7)	0.419 (3)	0.104 (3)	0.59 (2)
F3A	0.5673 (5)	0.4758 (8)	0.273 (3)	0.095 (3)	0.59 (2)
F1B	0.5407 (6)	0.6290 (16)	0.294 (4)	0.115 (5)	0.41 (2)
F2B	0.5819 (10)	0.4561 (7)	0.392 (4)	0.105 (5)	0.41 (2)
F3B	0.6028 (10)	0.6030 (19)	0.6312 (19)	0.113 (5)	0.41 (2)
C6	0.5992 (2)	0.5688 (3)	0.3866 (8)	0.0636 (11)
C7	0.66887 (19)	0.6091 (3)	0.2336 (9)	0.0510 (9)
H1N1	0.7730 (19)	0.576 (3)	0.891 (7)	0.041 (9)*
H1N2	0.785 (2)	0.856 (3)	0.767 (11)	0.060 (11)*
H2N2	0.748 (2)	0.773 (4)	0.927 (7)	0.067 (14)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br1	0.0861 (3)	0.0606 (3)	0.0842 (3)	0.0050 (2)	0.0152 (3)	−0.0136 (3)
N1	0.0546 (15)	0.0281 (14)	0.0561 (15)	−0.0047 (11)	0.002 (2)	−0.004 (2)
N2	0.085 (2)	0.0291 (17)	0.075 (3)	0.0045 (18)	0.014 (2)	0.0079 (18)
C1	0.058 (2)	0.0280 (18)	0.061 (2)	−0.0045 (16)	−0.0053 (18)	−0.0018 (17)
C2	0.059 (2)	0.040 (2)	0.063 (2)	0.0022 (17)	−0.0031 (18)	−0.0071 (18)
C3	0.061 (2)	0.054 (3)	0.061 (3)	−0.007 (2)	0.0016 (18)	0.0057 (19)
C4	0.067 (2)	0.037 (2)	0.064 (2)	−0.0068 (19)	−0.004 (2)	0.013 (2)
C5	0.0519 (18)	0.0322 (19)	0.058 (2)	−0.0045 (16)	−0.0059 (16)	0.0088 (16)
O1	0.0679 (15)	0.0319 (14)	0.0768 (16)	0.0077 (12)	0.0135 (14)	0.0109 (13)
O2	0.0987 (19)	0.0303 (14)	0.096 (3)	0.0012 (13)	0.0185 (18)	0.0044 (18)
F1A	0.115 (5)	0.166 (9)	0.078 (4)	−0.013 (5)	0.011 (3)	0.046 (5)
F2A	0.093 (4)	0.080 (4)	0.139 (8)	0.018 (3)	0.040 (4)	−0.019 (4)
F3A	0.083 (3)	0.082 (4)	0.119 (6)	−0.036 (3)	0.008 (4)	−0.011 (5)
F1B	0.069 (5)	0.143 (8)	0.132 (9)	0.030 (5)	0.009 (6)	−0.004 (7)
F2B	0.119 (7)	0.062 (6)	0.133 (9)	−0.011 (5)	0.047 (7)	−0.001 (5)
F3B	0.130 (8)	0.121 (9)	0.088 (6)	−0.024 (6)	0.036 (5)	−0.009 (6)
C6	0.065 (3)	0.045 (2)	0.080 (3)	0.002 (2)	0.005 (2)	−0.007 (2)
C7	0.062 (2)	0.037 (2)	0.054 (2)	0.0022 (16)	−0.005 (2)	0.001 (2)

Geometric parameters (Å, º) top

Br1—C2	1.875 (4)	C4—C5	1.407 (5)
N1—C5	1.344 (4)	C4—H4A	0.93
N1—C1	1.358 (5)	O1—C7	1.250 (4)
N1—H1N1	0.93 (4)	O2—C7	1.212 (4)
N2—C5	1.330 (5)	F1A—C6	1.329 (6)
N2—H1N2	0.82 (3)	F2A—C6	1.307 (6)
N2—H2N2	0.84 (3)	F3A—C6	1.327 (6)
C1—C2	1.334 (5)	F1B—C6	1.321 (7)
C1—H1A	0.93	F2B—C6	1.310 (7)
C2—C3	1.425 (6)	F3B—C6	1.314 (7)
C3—C4	1.349 (6)	C6—C7	1.524 (6)
C3—H3A	0.93

C5—N1—C1	122.5 (4)	N2—C5—N1	118.8 (3)
C5—N1—H1N1	116 (2)	N2—C5—C4	123.0 (4)
C1—N1—H1N1	121 (2)	N1—C5—C4	118.1 (4)
C5—N2—H1N2	120 (4)	F2B—C6—F3B	106.2 (8)
C5—N2—H2N2	124 (3)	F2B—C6—F1B	109.0 (10)
H1N2—N2—H2N2	116 (5)	F3B—C6—F1B	103.2 (9)
C2—C1—N1	120.7 (4)	F2A—C6—F3A	107.3 (7)
C2—C1—H1A	119.6	F2A—C6—F1A	107.2 (6)
N1—C1—H1A	119.6	F3A—C6—F1A	106.1 (6)
C1—C2—C3	118.8 (4)	F2A—C6—C7	115.8 (6)
C1—C2—Br1	120.6 (3)	F2B—C6—C7	119.1 (7)
C3—C2—Br1	120.6 (3)	F3B—C6—C7	111.4 (7)
C4—C3—C2	119.8 (4)	F1B—C6—C7	106.8 (8)
C4—C3—H3A	120.1	F3A—C6—C7	110.4 (6)
C2—C3—H3A	120.1	F1A—C6—C7	109.5 (5)
C3—C4—C5	120.0 (4)	O2—C7—O1	127.8 (4)
C3—C4—H4A	120.0	O2—C7—C6	116.9 (4)
C5—C4—H4A	120.0	O1—C7—C6	115.2 (3)

C5—N1—C1—C2	−0.2 (6)	F2B—C6—C7—O2	174.5 (14)
N1—C1—C2—C3	1.7 (5)	F3B—C6—C7—O2	−61.4 (13)
N1—C1—C2—Br1	−178.9 (3)	F1B—C6—C7—O2	50.6 (12)
C1—C2—C3—C4	−1.6 (6)	F3A—C6—C7—O2	142.0 (8)
Br1—C2—C3—C4	179.0 (3)	F1A—C6—C7—O2	−101.5 (10)
C2—C3—C4—C5	0.1 (6)	F2A—C6—C7—O1	−161.2 (9)
C1—N1—C5—N2	179.8 (3)	F2B—C6—C7—O1	−6.5 (14)
C1—N1—C5—C4	−1.4 (6)	F3B—C6—C7—O1	117.6 (12)
C3—C4—C5—N2	−179.8 (4)	F1B—C6—C7—O1	−130.4 (12)
C3—C4—C5—N1	1.4 (5)	F3A—C6—C7—O1	−39.0 (8)
F2A—C6—C7—O2	19.8 (10)	F1A—C6—C7—O1	77.5 (10)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N1···O1ⁱ	0.93 (3)	1.80 (3)	2.720 (5)	171 (3)
N2—H1N2···O1ⁱⁱ	0.83 (4)	2.05 (4)	2.870 (4)	176 (5)
N2—H2N2···O2ⁱ	0.83 (4)	2.03 (4)	2.849 (5)	170 (4)
C1—H1A···O2ⁱⁱⁱ	0.93	2.34	3.245 (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.

Experimental details

Crystal data
Chemical formula	C₅H₆BrN₂⁺·C₂F₃O₂⁻
M_r	287.05
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	296
a, b, c (Å)	17.5852 (13), 11.3010 (9), 5.1264 (4)
V (Å³)	1018.77 (14)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	4.06
Crystal size (mm)	0.73 × 0.41 × 0.09

Data collection
Diffractometer	Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2009)
T_min, T_max	0.156, 0.709
No. of measured, independent and observed [I > 2σ(I)] reflections	8343, 2899, 1547
R_int	0.056
(sin θ/λ)_max (Å⁻¹)	0.705

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.099, 0.93
No. of reflections	2899
No. of parameters	176
No. of restraints	56
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.46, −0.28
Absolute structure	Flack (1983), 1254 Friedel pairs
Absolute structure parameter	0.024 (12)

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N1···O1ⁱ	0.93 (3)	1.80 (3)	2.720 (5)	171 (3)
N2—H1N2···O1ⁱⁱ	0.83 (4)	2.05 (4)	2.870 (4)	176 (5)
N2—H2N2···O2ⁱ	0.83 (4)	2.03 (4)	2.849 (5)	170 (4)
C1—H1A···O2ⁱⁱⁱ	0.93	2.34	3.245 (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

‡Thomson Reuters ResearcherID: A-3561-2009.

Acknowledgements

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.

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