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Acta Crystallogr Sect E Struct Rep Online. 2009 April 1; 65(Pt 4): o857.
Published online 2009 March 25. doi:  10.1107/S1600536809009258
PMCID: PMC2968961

2-(4-Amino­pyridinio)acetate

Abstract

In the title compound, C7H8N2O2, the dihedral angle between the pyridinium ring and the carboxyl­atomethyl group is 74.5 (1)°. Strong inter­molecular N—H(...)O hydrogen bonds between the amine and carboxyl­ate groups form a layered hydrogen-bonded network perpendicular to [010]. In addition, there are some weak C—H(...)O hydrogen bonds present in the structure.

Related literature

For the biological activity of pyridinium derivatives, see: Sliwa & Mianowska (1989 [triangle]). For hydrogen-bond definitions, see: Desiraju & Steiner (1999 [triangle]). For the analysis of bond order, see: Ludvík et al. (2007 [triangle]). For the Cambridge Structural Database (Version 5.30 and addenda up to 12th February 2009), see: Allen (2002 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-0o857-scheme1.jpg

Experimental

Crystal data

  • C7H8N2O2
  • M r = 152.15
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o857-efi3.jpg
  • a = 8.9766 (18) Å
  • b = 9.0555 (18) Å
  • c = 8.9886 (18) Å
  • β = 106.57 (3)°
  • V = 700.3 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 293 K
  • 0.16 × 0.14 × 0.12 mm

Data collection

  • Rigaku R-AXIS RAPID-S diffractometer
  • Absorption correction: none
  • 7228 measured reflections
  • 1599 independent reflections
  • 1123 reflections with I > 2σ(I)
  • R int = 0.052

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.117
  • S = 1.11
  • 1599 reflections
  • 106 parameters
  • 2 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.17 e Å−3
  • Δρmin = −0.20 e Å−3

Data collection: RAPID-AUTO (Rigaku, 1998 [triangle]); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]) and Mercury (Macrae et al., 2006 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809009258/fb2140sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809009258/fb2140Isup2.hkl

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

Acknowledgments

The author thanks Chifeng University for supporting this work.

supplementary crystallographic information

Comment

It is known that pyridinium derivatives have antibacterial and fungicidal activities (Sliwa & Mianowska, 1989). As 4-amino-pyridinium-N-acetate contains both amino and carboxylate groups, it may form interesting hydrogen-bonded network. Therefore the crystal structure analysis of the title compound has been undertaken. The molecular structure of the title structure is shown in Fig. 1. The dihedral angle between the planes of pyridinium ring and carboxymethylene fragment is 74.5°. Strong (Desiraju & Steiner, 1999) intermolecular N1—H1A···O2i and N1—H1B···O2ii (i: x + 1, -y + 1/2, z + 1/2; ii: x + 1, y, z) hydrogen bonds form the zig-zagged layer perpendicular to [010] (Fig. 2; Table 1), O2 is the acceptor of both amine hydrogens. In addition, weak hydrogen bonds between the pyridinium ring, methylene and the carboxylate groups, i.e. C4—H4···O1iv and C6—H6A···O1iv (iv: x, -y + 1/2, z + 1/2), are also involved in these layers. C3—H3···O1iii (iii: -x, -y, -z) hydrogen bonds between the pyridinium ring and the carboxylate groups interconnect the neighbouring layers (Table 1).

Experimental

A solution of 4-aminopyridine (5.46 g, 0.058 mol), 1-chloroacetic acid (13.1 g, 0.139 mol) and Na2CO3 (16.6 g, 0.157 mol) in 110 ml of H2O was stirred for 3 h at 373 K. Then the solution was acidified by concentrated HCl to pH = 2. The solution was left overnight in a refrigerator, the precipitation was filtered, affording colourless block shaped (about 0.12 mm - 0.14 mm) crystals of 4-amino-pyridinium-N-acetate.

Refinement

All the hydrogens were discernible in the difference electron density map. All the H atoms except the amine group were placed into the geometrically idealized positions and constrained to ride on their parent atoms with Cmethylene—H = 0.97 Å, Caryl—H = 0.93 Å. Uiso(H) = 1.2Ueq(Cparent). The distances N—H of the amine hydrogens were restrained to 0.86 (2) Å because this group is involved in the hydrogen bond pattern, the bond order of C1—N1 (1.331 (2) Å) is about 1.5 (Ludvík et al., 2007) and the result of the search in the Cambridge Crystallographic Structure Database (Allen, 2002; Version 5.30 and addenda up to 12th February 2009) gave the Namine—H···O about 160° as the most probable result. The displacement parameters of the amine hydrogens were constrained: Uiso(H) = 1.2Ueq(N).

Figures

Fig. 1.
The structure of 4-amino-pyridinium-N-acetate with the displacement ellipsoids shown at the 30% probability level.
Fig. 2.
A depiction of the layer perpendicular to b axis with the N1—H1A···O2 and N1—H1B···O2 hydrogen bonds. Symmetry codes: (i) x + 1, -y + 1/2, z + 1/2; (ii) x + 1, y, z.

Crystal data

C7H8N2O2F(000) = 320
Mr = 152.15Dx = 1.443 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 5894 reflections
a = 8.9766 (18) Åθ = 3.3–27.6°
b = 9.0555 (18) ŵ = 0.11 mm1
c = 8.9886 (18) ÅT = 293 K
β = 106.57 (3)°Prism, colourless
V = 700.3 (2) Å30.16 × 0.14 × 0.12 mm
Z = 4

Data collection

Rigaku R-AXIS RAPID-S diffractometer1123 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.052
graphiteθmax = 27.5°, θmin = 3.3°
ω scansh = −11→11
7228 measured reflectionsk = −11→11
1599 independent reflectionsl = −11→11

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.055Hydrogen site location: difference Fourier map
wR(F2) = 0.117H atoms treated by a mixture of independent and constrained refinement
S = 1.11w = 1/[σ2(Fo2) + (0.0391P)2 + 0.2309P] where P = (Fo2 + 2Fc2)/3
1599 reflections(Δ/σ)max < 0.001
106 parametersΔρmax = 0.17 e Å3
2 restraintsΔρmin = −0.20 e Å3
26 constraints

Special details

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)

xyzUiso*/Ueq
C10.4649 (2)0.1375 (2)0.3639 (2)0.0269 (4)
C20.3811 (2)0.0336 (2)0.2546 (2)0.0281 (5)
H20.4307−0.01740.19240.034*
C30.2291 (2)0.0078 (2)0.2398 (2)0.0296 (5)
H30.1759−0.06100.16720.035*
C40.2291 (2)0.1803 (2)0.4331 (2)0.0338 (5)
H40.17600.23000.49290.041*
C50.3814 (2)0.2103 (2)0.4532 (2)0.0346 (5)
H50.43130.27970.52680.042*
C6−0.0153 (2)0.0564 (2)0.2986 (2)0.0321 (5)
H6A−0.04650.09530.38580.039*
H6B−0.0364−0.04880.29270.039*
C7−0.1133 (2)0.1297 (2)0.1497 (2)0.0269 (4)
N10.6143 (2)0.1661 (2)0.3810 (2)0.0361 (5)
H1A0.662 (2)0.228 (2)0.450 (2)0.043*
H1B0.658 (2)0.131 (2)0.312 (2)0.043*
N20.15247 (17)0.07944 (18)0.32765 (17)0.0273 (4)
O1−0.04740 (16)0.19659 (17)0.06662 (16)0.0407 (4)
O2−0.25727 (15)0.11367 (17)0.12513 (16)0.0393 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0265 (10)0.0294 (10)0.0235 (10)0.0018 (8)0.0052 (8)0.0062 (8)
C20.0303 (11)0.0285 (11)0.0263 (10)0.0032 (8)0.0093 (8)−0.0020 (8)
C30.0312 (11)0.0311 (11)0.0243 (10)−0.0003 (9)0.0045 (8)−0.0023 (9)
C40.0335 (11)0.0383 (12)0.0298 (11)0.0031 (9)0.0093 (9)−0.0080 (10)
C50.0327 (11)0.0377 (12)0.0320 (11)−0.0034 (10)0.0070 (9)−0.0123 (10)
C60.0258 (11)0.0387 (12)0.0316 (11)0.0001 (9)0.0078 (8)0.0063 (10)
C70.0268 (11)0.0277 (10)0.0250 (10)0.0013 (8)0.0053 (8)−0.0013 (8)
N10.0273 (10)0.0454 (12)0.0349 (11)−0.0065 (8)0.0079 (8)−0.0043 (9)
N20.0216 (8)0.0353 (10)0.0233 (8)0.0026 (7)0.0035 (6)0.0012 (7)
O10.0358 (8)0.0505 (10)0.0352 (8)−0.0031 (7)0.0089 (7)0.0149 (7)
O20.0214 (8)0.0584 (10)0.0354 (8)0.0015 (7)0.0038 (6)0.0053 (7)

Geometric parameters (Å, °)

C1—N11.331 (2)C5—H50.9300
C1—C51.410 (3)C6—N21.468 (2)
C1—C21.412 (3)C6—C71.528 (3)
C2—C31.353 (3)C6—H6A0.9700
C2—H20.9300C6—H6B0.9700
C3—N21.351 (2)C7—O11.236 (2)
C3—H30.9300C7—O21.256 (2)
C4—C51.354 (3)N1—H1A0.859 (16)
C4—N21.354 (3)N1—H1B0.881 (15)
C4—H40.9300
N1—C1—C5121.68 (19)N2—C6—C7113.54 (16)
N1—C1—C2122.00 (18)N2—C6—H6A108.9
C5—C1—C2116.32 (17)C7—C6—H6A108.9
C3—C2—C1120.36 (18)N2—C6—H6B108.9
C3—C2—H2119.8C7—C6—H6B108.9
C1—C2—H2119.8H6A—C6—H6B107.7
N2—C3—C2121.80 (18)O1—C7—O2126.61 (18)
N2—C3—H3119.1O1—C7—C6119.14 (17)
C2—C3—H3119.1O2—C7—C6114.24 (17)
C5—C4—N2121.39 (19)C1—N1—H1A119.6 (15)
C5—C4—H4119.3C1—N1—H1B118.9 (15)
N2—C4—H4119.3H1A—N1—H1B121 (2)
C4—C5—C1120.72 (19)C3—N2—C4119.40 (17)
C4—C5—H5119.6C3—N2—C6119.69 (17)
C1—C5—H5119.6C4—N2—C6120.71 (16)
N1—C1—C2—C3−179.64 (18)N2—C6—C7—O2−178.50 (17)
C5—C1—C2—C3−0.2 (3)C2—C3—N2—C40.3 (3)
C1—C2—C3—N20.0 (3)C2—C3—N2—C6175.09 (17)
N2—C4—C5—C10.3 (3)C5—C4—N2—C3−0.5 (3)
N1—C1—C5—C4179.46 (19)C5—C4—N2—C6−175.22 (18)
C2—C1—C5—C40.0 (3)C7—C6—N2—C3−72.5 (2)
N2—C6—C7—O11.6 (3)C7—C6—N2—C4102.2 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1A···O2i0.86 (2)2.10 (2)2.946 (2)170 (2)
N1—H1A···O1i0.86 (2)2.61 (2)3.265 (2)135 (2)
N1—H1B···O2ii0.88 (2)2.04 (2)2.891 (2)162 (2)
C3—H3···O1iii0.932.423.334 (3)166
C4—H4···O1iv0.932.383.247 (3)155
C6—H6A···O1iv0.972.493.359 (3)149

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FB2140).

References

  • Allen, F. H. (2002). Acta Cryst. B58, 380–388. [PubMed]
  • Desiraju, G. R. & Steiner, T. (1999). The Weak Hydrogen Bond In Structural Chemistry and Biology, p. 13. New York: Oxford University Press Inc.
  • Ludvík, J., Urban, J., Fábry, J. & Císařová, I. (2007). Acta Cryst. C63, o259–o262. [PubMed]
  • Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst.39, 453–457.
  • Rigaku (1998). RAPID-AUTO Rigaku Corporation, Tokyo, Japan.
  • Rigaku/MSC (2002). CrystalStructure Rigaku/MSC Inc., The Woodlands, Texas, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Sliwa, W. & Mianowska, B. (1989). Heterocycles, 29, 557–595.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography