organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 12| December 2012| Pages o3319-o3320

2-Amino-5-methyl­pyridinium tri­fluoro­acetate

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[Pozharski, A. F., Soldatenkov, A. T. & Katritzky, A. R. (1997). In Heterocycles in Life and Society. New York: Wiley.]); Katritzky et al. (1996[Katritzky, A. R., Rees, C. W. & Scriven, E. F. V. (1996). In Comprehensive Heterocyclic Chemistry II. Oxford: Pergamon Press.]). For details of hydrogen bonding, see: Jeffrey & Saenger (1991[Jeffrey, G. A. & Saenger, W. (1991). In Hydrogen Bonding in Biological Structures. Berlin: Springer.]); Jeffrey (1997[Jeffrey, G. A. (1997). In An Introduction of Hydrogen Bonding. Oxford University Press.]); Scheiner (1997[Scheiner, S. (1997). In Hydrogen Bonding: A Theoretical Perspective. Oxford University Press.]). For hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]). For standard bond-length data, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]). For a related structure, see: Rodrigues et al. (2001[Rodrigues, V. H., Paixão, J. A., Costa, M. M. R. R. & Matos Beja, A. (2001). Acta Cryst. C57, 417-420.]).

[Scheme 1]

Experimental

Crystal data
  • C6H9N2+·C2F3O2

  • Mr = 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[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.926, Tmax = 0.985

  • 12012 measured reflections

  • 3216 independent reflections

  • 2627 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.23 e Å−3

  • Δρmin = −0.30 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1368 Friedel pairs

  • Flack parameter: −0.1 (7)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


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.

Refinement top

The F atoms of the anion are disordered over two sets of sites, with occupancies of 0.505 (17):0.495 (17). Atoms H1N1, H1N2 and H2N2 were located in a difference Fourier maps and refined freely. The remaining hydrogen atoms were positioned geometrically [C–H= 0.95–0.98 Å] and were refined using a riding model, with Uiso(H)=1.2 Ueq(C) or 1.5Ueq(methyl C). A rotating group model was used for the methyl group.

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
[Figure 1] Fig. 1. The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme. Both disorder components are shown.
[Figure 2] 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+·C2F3O2F(000) = 456
Mr = 222.17Dx = 1.505 Mg m3
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2nCell parameters from 4200 reflections
a = 18.725 (4) Åθ = 2.8–32.5°
b = 4.6256 (10) ŵ = 0.15 mm1
c = 11.319 (2) ÅT = 100 K
V = 980.4 (3) Å3Plate, colourless
Z = 40.54 × 0.29 × 0.11 mm
Data collection top
Bruker SMART APEXII DUO CCD area-detector
diffractometer
3216 independent reflections
Radiation source: fine-focus sealed tube2627 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.041
ϕ and ω scansθmax = 32.7°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 2828
Tmin = 0.926, Tmax = 0.985k = 66
12012 measured reflectionsl = 1617
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.046H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.114 w = 1/[σ2(Fo2) + (0.0538P)2 + 0.1405P]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
3216 reflectionsΔρmax = 0.23 e Å3
177 parametersΔρmin = 0.30 e Å3
1 restraintAbsolute structure: Flack (1983), 1368 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.1 (7)
Crystal data top
C6H9N2+·C2F3O2V = 980.4 (3) Å3
Mr = 222.17Z = 4
Orthorhombic, Pna21Mo Kα radiation
a = 18.725 (4) ŵ = 0.15 mm1
b = 4.6256 (10) ÅT = 100 K
c = 11.319 (2) Å0.54 × 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)
Tmin = 0.926, Tmax = 0.985Rint = 0.041
12012 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.046H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.114Δρmax = 0.23 e Å3
S = 1.07Δρmin = 0.30 e Å3
3216 reflectionsAbsolute structure: Flack (1983), 1368 Friedel pairs
177 parametersAbsolute 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
xyzUiso*/UeqOcc. (<1)
F10.5951 (6)0.360 (3)0.6163 (9)0.0636 (17)0.505 (17)
F20.5409 (3)0.0250 (13)0.6382 (9)0.075 (2)0.505 (17)
F30.5859 (5)0.076 (4)0.4723 (7)0.104 (4)0.505 (17)
F1X0.6094 (7)0.352 (2)0.5755 (15)0.097 (4)0.495 (17)
F2X0.5478 (4)0.032 (2)0.6626 (5)0.080 (2)0.495 (17)
F3X0.5752 (3)0.0168 (15)0.4869 (6)0.0479 (14)0.495 (17)
O10.67666 (7)0.0887 (3)0.73348 (10)0.0384 (3)
O20.70767 (6)0.1522 (3)0.54434 (9)0.0312 (3)
N10.80834 (7)0.5530 (3)0.60374 (10)0.0248 (3)
N20.78211 (9)0.5050 (4)0.80182 (12)0.0320 (3)
C10.81952 (8)0.6336 (4)0.71687 (12)0.0257 (3)
C20.87136 (9)0.8495 (4)0.73742 (14)0.0307 (3)
H2A0.88060.91410.81560.037*
C30.90806 (9)0.9649 (4)0.64496 (15)0.0316 (3)
H3A0.94321.10840.65990.038*
C40.89527 (8)0.8768 (4)0.52703 (13)0.0279 (3)
C50.84486 (8)0.6703 (4)0.51114 (12)0.0257 (3)
H5A0.83470.60540.43330.031*
C60.93586 (10)1.0012 (4)0.42471 (17)0.0364 (4)
H6A0.91860.91470.35100.055*
H6B0.98680.95940.43420.055*
H6C0.92861.21100.42210.055*
C70.59832 (9)0.0794 (4)0.58757 (15)0.0312 (3)
C80.66781 (9)0.0707 (4)0.62616 (13)0.0268 (3)
H2N20.7456 (13)0.369 (6)0.785 (2)0.040 (6)*
H1N20.7919 (14)0.558 (6)0.873 (3)0.050 (7)*
H1N10.7723 (13)0.405 (6)0.585 (2)0.043 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.075 (3)0.027 (2)0.089 (4)0.0046 (19)0.017 (2)0.007 (2)
F20.0328 (17)0.044 (2)0.148 (6)0.0071 (15)0.004 (3)0.043 (3)
F30.093 (4)0.194 (10)0.0252 (15)0.097 (5)0.010 (2)0.014 (4)
F1X0.092 (6)0.021 (2)0.177 (11)0.005 (3)0.069 (7)0.017 (5)
F2X0.041 (3)0.154 (6)0.044 (2)0.038 (3)0.0180 (16)0.011 (3)
F3X0.0410 (16)0.060 (3)0.042 (3)0.0108 (16)0.0251 (16)0.0201 (19)
O10.0462 (7)0.0534 (9)0.0156 (5)0.0029 (6)0.0001 (4)0.0020 (5)
O20.0337 (5)0.0450 (7)0.0149 (4)0.0038 (5)0.0021 (4)0.0058 (5)
N10.0316 (6)0.0292 (7)0.0136 (5)0.0038 (5)0.0025 (4)0.0004 (5)
N20.0454 (8)0.0368 (9)0.0138 (5)0.0023 (7)0.0001 (5)0.0032 (5)
C10.0341 (7)0.0277 (8)0.0154 (6)0.0089 (6)0.0027 (5)0.0032 (6)
C20.0412 (8)0.0290 (9)0.0220 (6)0.0061 (7)0.0067 (6)0.0064 (6)
C30.0351 (8)0.0299 (9)0.0298 (7)0.0036 (6)0.0051 (6)0.0059 (7)
C40.0305 (7)0.0298 (9)0.0235 (7)0.0075 (6)0.0013 (5)0.0003 (6)
C50.0321 (6)0.0302 (8)0.0147 (5)0.0069 (6)0.0025 (5)0.0014 (5)
C60.0394 (8)0.0377 (10)0.0320 (7)0.0008 (7)0.0038 (7)0.0033 (8)
C70.0380 (7)0.0299 (9)0.0255 (6)0.0003 (6)0.0007 (6)0.0037 (6)
C80.0318 (7)0.0305 (8)0.0181 (6)0.0052 (6)0.0001 (5)0.0008 (6)
Geometric parameters (Å, º) top
F1—C71.341 (11)N2—H1N20.86 (3)
F2—C71.311 (6)C1—C21.412 (2)
F3—C71.325 (8)C2—C31.361 (3)
F1X—C71.287 (11)C2—H2A0.9500
F2X—C71.290 (5)C3—C41.416 (2)
F3X—C71.297 (6)C3—H3A0.9500
O1—C81.2289 (18)C4—C51.355 (2)
O2—C81.2478 (19)C4—C61.500 (2)
N1—C11.3500 (18)C5—H5A0.9500
N1—C51.3640 (19)C6—H6A0.9800
N1—H1N10.98 (3)C6—H6B0.9800
N2—C11.330 (2)C6—H6C0.9800
N2—H2N20.95 (3)C7—C81.538 (2)
C1—N1—C5122.78 (14)C4—C6—H6A109.5
C1—N1—H1N1119.9 (15)C4—C6—H6B109.5
C5—N1—H1N1117.3 (15)H6A—C6—H6B109.5
C1—N2—H2N2121.8 (14)C4—C6—H6C109.5
C1—N2—H1N2116.0 (19)H6A—C6—H6C109.5
H2N2—N2—H1N2122 (2)H6B—C6—H6C109.5
N2—C1—N1118.73 (15)F1X—C7—F2X110.9 (7)
N2—C1—C2124.01 (14)F1X—C7—F3X107.3 (7)
N1—C1—C2117.26 (14)F2X—C7—F3X106.0 (5)
C3—C2—C1119.86 (14)F2—C7—F1102.4 (6)
C3—C2—H2A120.1F3—C7—F1104.0 (8)
C1—C2—H2A120.1F1X—C7—C8109.7 (5)
C2—C3—C4121.77 (16)F2X—C7—C8110.8 (3)
C2—C3—H3A119.1F3X—C7—C8112.1 (3)
C4—C3—H3A119.1F2—C7—C8113.8 (3)
C5—C4—C3116.49 (14)F3—C7—C8115.0 (4)
C5—C4—C6121.40 (14)F1—C7—C8114.0 (5)
C3—C4—C6122.10 (16)O1—C8—O2129.24 (16)
C4—C5—N1121.84 (13)O1—C8—C7115.18 (15)
C4—C5—H5A119.1O2—C8—C7115.57 (13)
N1—C5—H5A119.1
C5—N1—C1—N2179.15 (15)F2X—C7—C8—O132.3 (6)
C5—N1—C1—C20.2 (2)F3X—C7—C8—O1150.5 (4)
N2—C1—C2—C3178.70 (16)F2—C7—C8—O151.3 (5)
N1—C1—C2—C30.6 (2)F3—C7—C8—O1174.4 (9)
C1—C2—C3—C40.7 (2)F1—C7—C8—O165.7 (5)
C2—C3—C4—C50.4 (2)F1X—C7—C8—O288.4 (9)
C2—C3—C4—C6179.53 (17)F2X—C7—C8—O2148.9 (5)
C3—C4—C5—N10.1 (2)F3X—C7—C8—O230.7 (4)
C6—C4—C5—N1179.11 (15)F2—C7—C8—O2129.9 (5)
C1—N1—C5—C40.1 (2)F3—C7—C8—O26.8 (9)
F1X—C7—C8—O190.5 (9)F1—C7—C8—O2113.2 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O20.98 (3)1.75 (3)2.7281 (19)177 (2)
N2—H2N2···O10.95 (3)1.92 (3)2.865 (2)173 (2)
N2—H1N2···O2i0.86 (3)1.99 (3)2.8347 (18)167 (3)
C3—H3A···F2ii0.952.513.429 (6)164
C5—H5A···O1iii0.952.273.1910 (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, z1/2.

Experimental details

Crystal data
Chemical formulaC6H9N2+·C2F3O2
Mr222.17
Crystal system, space groupOrthorhombic, Pna21
Temperature (K)100
a, b, c (Å)18.725 (4), 4.6256 (10), 11.319 (2)
V3)980.4 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.15
Crystal size (mm)0.54 × 0.29 × 0.11
Data collection
DiffractometerBruker SMART APEXII DUO CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.926, 0.985
No. of measured, independent and
observed [I > 2σ(I)] reflections
12012, 3216, 2627
Rint0.041
(sin θ/λ)max1)0.761
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.046, 0.114, 1.07
No. of reflections3216
No. of parameters177
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.23, 0.30
Absolute structureFlack (1983), 1368 Friedel pairs
Absolute structure parameter0.1 (7)

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

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O20.98 (3)1.75 (3)2.7281 (19)177 (2)
N2—H2N2···O10.95 (3)1.92 (3)2.865 (2)173 (2)
N2—H1N2···O2i0.86 (3)1.99 (3)2.8347 (18)167 (3)
C3—H3A···F2ii0.95002.51003.429 (6)164.00
C5—H5A···O1iii0.95002.27003.1910 (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, z1/2.
 

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