2-Amino-5-methyl­pyridinium trifluoro­acetate

Thanigaimani, K.; Farhadikoutenaei, A.; Khalib, N.C.; Arshad, S.; Razak, I.A.

doi:10.1107/S1600536812045291

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 68| Part 12| December 2012| Pages o3319-o3320

doi:10.1107/S1600536812045291

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2-Amino-5-methylpyridinium trifluoroacetate

Kaliyaperumal Thanigaimani,^a Abbas Farhadikoutenaei,^a Nuridayanti Che Khalib,^a Suhana Arshad ^a and Ibrahim Abdul Razak ^a ^*‡

^aSchool of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
^*Correspondence e-mail: arazaki@usm.my

(Received 22 October 2012; accepted 2 November 2012; online 10 November 2012)

In the title salt, C₆H₉N₂⁺·C₂F₃O₂⁻, the F atoms of the anion are disordered over two sets of sites, with refined occupancies in a ratio of 0.505 (17):0.495 (17). In the crystal, cations and anions are linked via N—H⋯O hydrogen bonds, forming R₂²(8) ring motifs. The ionic units are linked into a two-dimensional network parallel to (100) by N—H⋯O and weak C—H⋯O hydrogen bonds. The crystal structure is further stabilized by weak C—H⋯F hydrogen bonds, resulting in a three-dimensional network.

Related literature

For background to the chemistry of substituted pyridines, see: Pozharski et al. (1997 ); Katritzky et al. (1996 ). For details of hydrogen bonding, see: Jeffrey & Saenger (1991 ); Jeffrey (1997 ); Scheiner (1997 ). For hydrogen-bond motifs, see: Bernstein et al. (1995 ). For standard bond-length data, see: Allen et al. (1987 ). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 ). For a related structure, see: Rodrigues et al. (2001 ).

Experimental

Crystal data

C₆H₉N₂⁺·C₂F₃O₂⁻
M_r = 222.17
Orthorhombic, P n a 2₁
a = 18.725 (4) Å
b = 4.6256 (10) Å
c = 11.319 (2) Å
V = 980.4 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.15 mm⁻¹
T = 100 K
0.54 × 0.29 × 0.11 mm

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ) T_min = 0.926, T_max = 0.985
12012 measured reflections
3216 independent reflections
2627 reflections with I > 2σ(I)
R_int = 0.041

Refinement

R[F² > 2σ(F²)] = 0.046
wR(F²) = 0.114
S = 1.07
3216 reflections
177 parameters
1 restraint
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.23 e Å⁻³
Δρ_min = −0.30 e Å⁻³
Absolute structure: Flack (1983 ), 1368 Friedel pairs
Flack parameter: −0.1 (7)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N1⋯O2	0.98 (3)	1.75 (3)	2.7281 (19)	177 (2)
N2—H2N2⋯O1	0.95 (3)	1.92 (3)	2.865 (2)	173 (2)
N2—H1N2⋯O2ⁱ	0.86 (3)	1.99 (3)	2.8347 (18)	167 (3)
C3—H3A⋯F2ⁱⁱ	0.95	2.51	3.429 (6)	164
C5—H5A⋯O1ⁱⁱⁱ	0.95	2.27	3.1910 (19)	162
Symmetry codes: (i) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z]$ ; (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/S1600536812045291/lh5549sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812045291/lh5549Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812045291/lh5549Isup3.cml

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). Trifluoroacetic acid is a very strong carboxylic acid, easily volatile, and used for protein purification. An example of a crystal structure of a trifluoroacetate salts has been reported (Rodrigues et al., 2001). In order to study potential hydrogen bonding interactions the crystal structure determination of the title compound (I) was carried out.

The asymmetric unit (Fig. 1) contains one 2-amino-5-methylpyridinium cation and one trifluoroacetate anion. The F atoms of the anion are disordered over two sets of sites, with occupancies of 0.505 (17) and 0.495 (17). In the 2-amino-5-methylpyridinium cation, a wider than normal angle [C1—N1—C5 = 122.77 (14)°] is subtended at the protonated N1 atom. The 2-amino-5-methylpyridinium cation is essentially planar, with a maximum deviation of 0.016 (2) Å for atom N2. The bond lengths (Allen et al., 1987) and angles are normal.

In the crystal (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 (100) by N2—H1N2···O2ⁱ and C5—H5A···O1ⁱⁱⁱ hydrogen bonds (symmetry codes in Table 1). The crystal structure is further stabilized by C3—H3A···F2ⁱⁱ hydrogen bonds, resulting in a three-dimensional network.

Related literature top

For background to the chemistry of substituted pyridines, see: Pozharski et al. (1997); Katritzky et al. (1996). For details of hydrogen bonding, see: Jeffrey & Saenger (1991); Jeffrey (1997); Scheiner (1997). For hydrogen-bond motifs, see: Bernstein et al. (1995). For standard bond-length data, see: Allen et al. (1987). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986). For a related structure, see: Rodrigues et al. (2001).

Experimental top

To a hot methanol solution (20 ml) of 2-amino-5-methylpyridine (54 mg, Aldrich) was added a few drops of trifluoroacetic acid. The solution was warmed over a heating magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature and crystals of the title compound (I) 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 molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme. Both disorder components are shown.
	Fig. 2. The crystal packing diagram of the title compound. Only major disorder component is shown. Hydrogen bonds are shown as dashed lines.

2-Amino-5-methylpyridinium trifluoroacetate top

Crystal data top

C₆H₉N₂⁺·C₂F₃O₂⁻	F(000) = 456
M_r = 222.17	D_x = 1.505 Mg m⁻³
Orthorhombic, Pna2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2n	Cell parameters from 4200 reflections
a = 18.725 (4) Å	θ = 2.8–32.5°
b = 4.6256 (10) Å	µ = 0.15 mm⁻¹
c = 11.319 (2) Å	T = 100 K
V = 980.4 (3) Å³	Plate, colourless
Z = 4	0.54 × 0.29 × 0.11 mm

Data collection top

Bruker SMART APEXII DUO CCD area-detector diffractometer	3216 independent reflections
Radiation source: fine-focus sealed tube	2627 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.041
ϕ and ω scans	θ_max = 32.7°, θ_min = 2.2°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −28→28
T_min = 0.926, T_max = 0.985	k = −6→6
12012 measured reflections	l = −16→17

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)] = 0.046	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.114	w = 1/[σ²(F_o²) + (0.0538P)² + 0.1405P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max < 0.001
3216 reflections	Δρ_max = 0.23 e Å⁻³
177 parameters	Δρ_min = −0.30 e Å⁻³
1 restraint	Absolute structure: Flack (1983), 1368 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.1 (7)

Crystal data top

C₆H₉N₂⁺·C₂F₃O₂⁻	V = 980.4 (3) Å³
M_r = 222.17	Z = 4
Orthorhombic, Pna2₁	Mo Kα radiation
a = 18.725 (4) Å	µ = 0.15 mm⁻¹
b = 4.6256 (10) Å	T = 100 K
c = 11.319 (2) Å	0.54 × 0.29 × 0.11 mm

Data collection top

Bruker SMART APEXII DUO CCD area-detector diffractometer	3216 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2009)	2627 reflections with I > 2σ(I)
T_min = 0.926, T_max = 0.985	R_int = 0.041
12012 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.046	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.114	Δρ_max = 0.23 e Å⁻³
S = 1.07	Δρ_min = −0.30 e Å⁻³
3216 reflections	Absolute structure: Flack (1983), 1368 Friedel pairs
177 parameters	Absolute structure parameter: −0.1 (7)
1 restraint

Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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 > σ(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)
F1	0.5951 (6)	−0.360 (3)	0.6163 (9)	0.0636 (17)	0.505 (17)
F2	0.5409 (3)	0.0250 (13)	0.6382 (9)	0.075 (2)	0.505 (17)
F3	0.5859 (5)	−0.076 (4)	0.4723 (7)	0.104 (4)	0.505 (17)
F1X	0.6094 (7)	−0.352 (2)	0.5755 (15)	0.097 (4)	0.495 (17)
F2X	0.5478 (4)	−0.032 (2)	0.6626 (5)	0.080 (2)	0.495 (17)
F3X	0.5752 (3)	0.0168 (15)	0.4869 (6)	0.0479 (14)	0.495 (17)
O1	0.67666 (7)	0.0887 (3)	0.73348 (10)	0.0384 (3)
O2	0.70767 (6)	0.1522 (3)	0.54434 (9)	0.0312 (3)
N1	0.80834 (7)	0.5530 (3)	0.60374 (10)	0.0248 (3)
N2	0.78211 (9)	0.5050 (4)	0.80182 (12)	0.0320 (3)
C1	0.81952 (8)	0.6336 (4)	0.71687 (12)	0.0257 (3)
C2	0.87136 (9)	0.8495 (4)	0.73742 (14)	0.0307 (3)
H2A	0.8806	0.9141	0.8156	0.037*
C3	0.90806 (9)	0.9649 (4)	0.64496 (15)	0.0316 (3)
H3A	0.9432	1.1084	0.6599	0.038*
C4	0.89527 (8)	0.8768 (4)	0.52703 (13)	0.0279 (3)
C5	0.84486 (8)	0.6703 (4)	0.51114 (12)	0.0257 (3)
H5A	0.8347	0.6054	0.4333	0.031*
C6	0.93586 (10)	1.0012 (4)	0.42471 (17)	0.0364 (4)
H6A	0.9186	0.9147	0.3510	0.055*
H6B	0.9868	0.9594	0.4342	0.055*
H6C	0.9286	1.2110	0.4221	0.055*
C7	0.59832 (9)	−0.0794 (4)	0.58757 (15)	0.0312 (3)
C8	0.66781 (9)	0.0707 (4)	0.62616 (13)	0.0268 (3)
H2N2	0.7456 (13)	0.369 (6)	0.785 (2)	0.040 (6)*
H1N2	0.7919 (14)	0.558 (6)	0.873 (3)	0.050 (7)*
H1N1	0.7723 (13)	0.405 (6)	0.585 (2)	0.043 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.075 (3)	0.027 (2)	0.089 (4)	−0.0046 (19)	−0.017 (2)	0.007 (2)
F2	0.0328 (17)	0.044 (2)	0.148 (6)	0.0071 (15)	0.004 (3)	−0.043 (3)
F3	0.093 (4)	0.194 (10)	0.0252 (15)	−0.097 (5)	−0.010 (2)	0.014 (4)
F1X	0.092 (6)	0.021 (2)	0.177 (11)	0.005 (3)	−0.069 (7)	−0.017 (5)
F2X	0.041 (3)	0.154 (6)	0.044 (2)	−0.038 (3)	0.0180 (16)	−0.011 (3)
F3X	0.0410 (16)	0.060 (3)	0.042 (3)	−0.0108 (16)	−0.0251 (16)	0.0201 (19)
O1	0.0462 (7)	0.0534 (9)	0.0156 (5)	−0.0029 (6)	0.0001 (4)	0.0020 (5)
O2	0.0337 (5)	0.0450 (7)	0.0149 (4)	−0.0038 (5)	0.0021 (4)	−0.0058 (5)
N1	0.0316 (6)	0.0292 (7)	0.0136 (5)	0.0038 (5)	−0.0025 (4)	−0.0004 (5)
N2	0.0454 (8)	0.0368 (9)	0.0138 (5)	0.0023 (7)	0.0001 (5)	−0.0032 (5)
C1	0.0341 (7)	0.0277 (8)	0.0154 (6)	0.0089 (6)	−0.0027 (5)	−0.0032 (6)
C2	0.0412 (8)	0.0290 (9)	0.0220 (6)	0.0061 (7)	−0.0067 (6)	−0.0064 (6)
C3	0.0351 (8)	0.0299 (9)	0.0298 (7)	0.0036 (6)	−0.0051 (6)	−0.0059 (7)
C4	0.0305 (7)	0.0298 (9)	0.0235 (7)	0.0075 (6)	−0.0013 (5)	0.0003 (6)
C5	0.0321 (6)	0.0302 (8)	0.0147 (5)	0.0069 (6)	−0.0025 (5)	−0.0014 (5)
C6	0.0394 (8)	0.0377 (10)	0.0320 (7)	0.0008 (7)	0.0038 (7)	0.0033 (8)
C7	0.0380 (7)	0.0299 (9)	0.0255 (6)	−0.0003 (6)	−0.0007 (6)	0.0037 (6)
C8	0.0318 (7)	0.0305 (8)	0.0181 (6)	0.0052 (6)	−0.0001 (5)	−0.0008 (6)

Geometric parameters (Å, º) top

F1—C7	1.341 (11)	N2—H1N2	0.86 (3)
F2—C7	1.311 (6)	C1—C2	1.412 (2)
F3—C7	1.325 (8)	C2—C3	1.361 (3)
F1X—C7	1.287 (11)	C2—H2A	0.9500
F2X—C7	1.290 (5)	C3—C4	1.416 (2)
F3X—C7	1.297 (6)	C3—H3A	0.9500
O1—C8	1.2289 (18)	C4—C5	1.355 (2)
O2—C8	1.2478 (19)	C4—C6	1.500 (2)
N1—C1	1.3500 (18)	C5—H5A	0.9500
N1—C5	1.3640 (19)	C6—H6A	0.9800
N1—H1N1	0.98 (3)	C6—H6B	0.9800
N2—C1	1.330 (2)	C6—H6C	0.9800
N2—H2N2	0.95 (3)	C7—C8	1.538 (2)

C1—N1—C5	122.78 (14)	C4—C6—H6A	109.5
C1—N1—H1N1	119.9 (15)	C4—C6—H6B	109.5
C5—N1—H1N1	117.3 (15)	H6A—C6—H6B	109.5
C1—N2—H2N2	121.8 (14)	C4—C6—H6C	109.5
C1—N2—H1N2	116.0 (19)	H6A—C6—H6C	109.5
H2N2—N2—H1N2	122 (2)	H6B—C6—H6C	109.5
N2—C1—N1	118.73 (15)	F1X—C7—F2X	110.9 (7)
N2—C1—C2	124.01 (14)	F1X—C7—F3X	107.3 (7)
N1—C1—C2	117.26 (14)	F2X—C7—F3X	106.0 (5)
C3—C2—C1	119.86 (14)	F2—C7—F1	102.4 (6)
C3—C2—H2A	120.1	F3—C7—F1	104.0 (8)
C1—C2—H2A	120.1	F1X—C7—C8	109.7 (5)
C2—C3—C4	121.77 (16)	F2X—C7—C8	110.8 (3)
C2—C3—H3A	119.1	F3X—C7—C8	112.1 (3)
C4—C3—H3A	119.1	F2—C7—C8	113.8 (3)
C5—C4—C3	116.49 (14)	F3—C7—C8	115.0 (4)
C5—C4—C6	121.40 (14)	F1—C7—C8	114.0 (5)
C3—C4—C6	122.10 (16)	O1—C8—O2	129.24 (16)
C4—C5—N1	121.84 (13)	O1—C8—C7	115.18 (15)
C4—C5—H5A	119.1	O2—C8—C7	115.57 (13)
N1—C5—H5A	119.1

C5—N1—C1—N2	−179.15 (15)	F2X—C7—C8—O1	32.3 (6)
C5—N1—C1—C2	0.2 (2)	F3X—C7—C8—O1	150.5 (4)
N2—C1—C2—C3	178.70 (16)	F2—C7—C8—O1	51.3 (5)
N1—C1—C2—C3	−0.6 (2)	F3—C7—C8—O1	174.4 (9)
C1—C2—C3—C4	0.7 (2)	F1—C7—C8—O1	−65.7 (5)
C2—C3—C4—C5	−0.4 (2)	F1X—C7—C8—O2	88.4 (9)
C2—C3—C4—C6	−179.53 (17)	F2X—C7—C8—O2	−148.9 (5)
C3—C4—C5—N1	−0.1 (2)	F3X—C7—C8—O2	−30.7 (4)
C6—C4—C5—N1	179.11 (15)	F2—C7—C8—O2	−129.9 (5)
C1—N1—C5—C4	0.1 (2)	F3—C7—C8—O2	−6.8 (9)
F1X—C7—C8—O1	−90.5 (9)	F1—C7—C8—O2	113.2 (5)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N1···O2	0.98 (3)	1.75 (3)	2.7281 (19)	177 (2)
N2—H2N2···O1	0.95 (3)	1.92 (3)	2.865 (2)	173 (2)
N2—H1N2···O2ⁱ	0.86 (3)	1.99 (3)	2.8347 (18)	167 (3)
C3—H3A···F2ⁱⁱ	0.95	2.51	3.429 (6)	164
C5—H5A···O1ⁱⁱⁱ	0.95	2.27	3.1910 (19)	162

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

Experimental details

Crystal data
Chemical formula	C₆H₉N₂⁺·C₂F₃O₂⁻
M_r	222.17
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	100
a, b, c (Å)	18.725 (4), 4.6256 (10), 11.319 (2)
V (Å³)	980.4 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.15
Crystal size (mm)	0.54 × 0.29 × 0.11

Data collection
Diffractometer	Bruker SMART APEXII DUO CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2009)
T_min, T_max	0.926, 0.985
No. of measured, independent and observed [I > 2σ(I)] reflections	12012, 3216, 2627
R_int	0.041
(sin θ/λ)_max (Å⁻¹)	0.761

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.046, 0.114, 1.07
No. of reflections	3216
No. of parameters	177
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.30
Absolute structure	Flack (1983), 1368 Friedel pairs
Absolute structure parameter	−0.1 (7)

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···O2	0.98 (3)	1.75 (3)	2.7281 (19)	177 (2)
N2—H2N2···O1	0.95 (3)	1.92 (3)	2.865 (2)	173 (2)
N2—H1N2···O2ⁱ	0.86 (3)	1.99 (3)	2.8347 (18)	167 (3)
C3—H3A···F2ⁱⁱ	0.9500	2.5100	3.429 (6)	164.00
C5—H5A···O1ⁱⁱⁱ	0.9500	2.2700	3.1910 (19)	162.00

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

Footnotes

‡Thomson Reuters ResearcherID: A-5599-2009.

Acknowledgements

The authors thank the Malaysian Government and Universiti Sains Malaysia (USM) for the research facilities and Fundamental Research Grant Scheme (FRGS) No. 203/PFIZIK/6711171 to conduct this work. KT thanks The Academy of Sciences for the Developing World and USM for a TWAS–USM fellowship.

References

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