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Acta Crystallogr Sect E Struct Rep Online. 2010 August 1; 66(Pt 8): o2008–o2009.
Published online 2010 July 14. doi:  10.1107/S1600536810027091
PMCID: PMC3007307

2-Amino-5-chloro­pyridinium 4-carb­oxy­butano­ate

Abstract

In the title salt, C5H6ClN2 +·C5H7O4 , the 2-amino-5-chloro­pyridinium cation is essentially planar, with a maximum deviation of 0.010 (3) Å. In the crystal structure, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl­ate O atoms of the anion via a pair of N—H(...)O hydrogen bonds, forming an R 2 2(8) ring motif. The ion pairs are further connected via O—H(...)O, N—H(...)O and C—H(...)O hydrogen bonds, forming a layer parallel to the bc plane. In the layer, the hydrogen glutarate anions self-assemble via O—H(...)O hydrogen bonds, forming a supra­molecular chain along the c axis. Furthermore, the cations and anions are stacked down along the a axis, forming a three-dimensional network.

Related literature

For background to the chemistry of substituted pyridines, see: Katritzky et al. (1996 [triangle]); Pozharski et al. (1997 [triangle]). For related structures, see: Hemamalini & Fun (2010a [triangle],b [triangle]). For the conformation of glutaric acid, see: Saraswathi et al. (2001 [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]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2008-scheme1.jpg

Experimental

Crystal data

  • C5H6ClN2 +·C5H7O4
  • M r = 260.67
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2008-efi1.jpg
  • a = 5.1970 (14) Å
  • b = 14.509 (4) Å
  • c = 15.970 (5) Å
  • V = 1204.2 (6) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.32 mm−1
  • T = 296 K
  • 0.31 × 0.13 × 0.07 mm

Data collection

  • Bruker APEXII DUO CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.908, T max = 0.979
  • 8054 measured reflections
  • 3346 independent reflections
  • 2007 reflections with I > 2σ(I)
  • R int = 0.036

Refinement

  • R[F 2 > 2σ(F 2)] = 0.044
  • wR(F 2) = 0.111
  • S = 1.01
  • 3346 reflections
  • 162 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.15 e Å−3
  • Δρmin = −0.20 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1288 Friedel pairs
  • Flack parameter: 0.00 (9)

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/S1600536810027091/is2574sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810027091/is2574Isup2.hkl

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

Acknowledgments

MH and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012. MH also thanks Universiti Sains Malaysia 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). We have recently reported the crystal structures of 2-amino-5-methylpyridinium 4-carboxybutanoate (Hemamalini & Fun, 2010a) and 2-amino-5-bromopyridinium hydrogen glutarate (Hemamalini & Fun, 2010b). In continuation of our studies of pyridinium salts, the crystal structure determination of the title compound has been undertaken.

The asymmetric unit (Fig. 1) contains a 2-amino-5-chloropyridinium cation and a hydrogen glutarate anion. The 2-amino-5-chloropyridinium cation is essentially planar, with a maximum deviation of 0.010 (3) Å for atom C2. The dihedral angle between the pyridine ring and the mean plane formed by the hydrogen glutarate anion is 35.55 (13)°. In the 2-amino-5-chloropyridinium cation, a wide angle [C1—N1—C5= 123.1 (2)°] is subtended at the protonated N1 atom. The backbone conformation of the hydrogen glutarate anion can be described by the two torsion angles C7-C8-C9-C10 of 179.51 (19)° and C6-C7-C8-C9 of 72.4 (3)°. As evident from the torsion angles, the backbone is in a fully extended conformation (Saraswathi et al., 2001) of the two carboxyl groups, one is deprotonated while the other is not.

In the crystal packing, the protonated N1 atom and the 2-amino group (N2) are hydrogen-bonded to the carboxylate oxygen atoms (O1 and O2) via a pair of intermolecular N1—H1···O1 and N2—H1N2···O2 hydrogen bonds, forming a ring motif R22(8) (Bernstein et al., 1995). The ion pairs are further connected via N2—H2N2···O2, O3—H1O3···O1 and C4—H4A···O4 (Table 1) hydrogen bonds, forming a two-dimensional network parallel to the bc plane (Fig. 2). The hydrogen glutarate anions self-assemble through O3—H1O3···O1 hydrogen bonds, forming one-dimensional supramolecular chains along the c axis (Fig. 3). Furthermore, the cations and anions are stacked down along the a axis, forming a 3D-network as shown in Fig. 4. This crystal structure is isomorphous to the crystal structure of 2-amino-5-bromopyridinium hydrogen glutarate (Hemamalini & Fun, 2010b).

Experimental

A hot methanol solution (20 ml) of 2-amino-5-chloropyridine (64 mg, Aldrich) and glutaric acid (66 mg, Merck) were mixed and warmed over a heating magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature and brown crystals of the title compound appeared after a few days.

Refinement

Atoms H1N2 and H2N2 were located from a difference Fourier map and were refined freely. The remaining hydrogen atoms were positioned geometrically (N—H = 0.86, O—H = 0.81 and C—H = 0.93 or 0.97 Å) and were refined using a riding model, with Uiso(H) = 1.2Ueq(C, N) or 1.5Ueq(O). 1288 Friedel pairs were used to determine the absolute configuration.

Figures

Fig. 1.
The asymmetric unit of the title compound. Displacement ellipsoids are drawn at the 30% probability level.
Fig. 2.
The crystal packing of (I), showing hydrogen-bonded (dashed lines) 2D networks parallel to the bc-plane. H atoms not involved in the intermolecular interactions have been omitted for clarity.
Fig. 3.
Carboxyl–carboxylate interactions made up of hydrogen glutarate anion.
Fig. 4.
The crystal packing of the title compound (I), showing the stacking of the molecules down the a-axis.

Crystal data

C5H6ClN2+·C5H7O4F(000) = 544
Mr = 260.67Dx = 1.438 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1567 reflections
a = 5.1970 (14) Åθ = 2.8–25.9°
b = 14.509 (4) ŵ = 0.32 mm1
c = 15.970 (5) ÅT = 296 K
V = 1204.2 (6) Å3Plate, brown
Z = 40.31 × 0.13 × 0.07 mm

Data collection

Bruker APEXII DUO CCD area-detector diffractometer3346 independent reflections
Radiation source: fine-focus sealed tube2007 reflections with I > 2σ(I)
graphiteRint = 0.036
[var phi] and ω scansθmax = 30.2°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −7→7
Tmin = 0.908, Tmax = 0.979k = −20→17
8054 measured reflectionsl = −22→22

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.044H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.111w = 1/[σ2(Fo2) + (0.0443P)2] where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max = 0.001
3346 reflectionsΔρmax = 0.15 e Å3
162 parametersΔρmin = −0.20 e Å3
0 restraintsAbsolute structure: Flack (1983), 1288 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.00 (9)

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*/Ueq
Cl10.34184 (19)0.28909 (5)0.39845 (5)0.0846 (3)
N1−0.1438 (4)0.22907 (12)0.21798 (11)0.0464 (5)
H1−0.26370.18900.21060.056*
N2−0.2316 (5)0.28468 (18)0.08678 (14)0.0633 (6)
C1−0.0138 (5)0.22829 (16)0.29108 (14)0.0493 (6)
H1A−0.05320.18440.33150.059*
C20.1721 (5)0.29045 (15)0.30579 (15)0.0533 (6)
C30.2266 (6)0.35662 (17)0.24403 (18)0.0628 (7)
H3A0.35200.40110.25360.075*
C40.0971 (5)0.35565 (17)0.17106 (17)0.0590 (7)
H4A0.13520.39920.13020.071*
C5−0.0947 (5)0.28969 (15)0.15589 (14)0.0480 (6)
O10.5116 (3)0.09526 (11)0.19901 (9)0.0523 (4)
O20.4048 (4)0.14235 (12)0.07274 (9)0.0606 (5)
O30.1889 (4)−0.04241 (12)−0.15991 (10)0.0631 (5)
H1O30.1253−0.0541−0.20500.095*
O4−0.1908 (4)−0.06355 (14)−0.10194 (11)0.0672 (5)
C60.3720 (4)0.09123 (14)0.13352 (12)0.0401 (5)
C70.1567 (5)0.02110 (16)0.13408 (13)0.0465 (5)
H7A0.03460.03810.17730.056*
H7B0.2281−0.03840.14910.056*
C80.0127 (5)0.01093 (16)0.05204 (13)0.0476 (6)
H8A−0.1445−0.02360.06170.057*
H8B−0.03480.07150.03150.057*
C90.1709 (5)−0.03760 (16)−0.01336 (13)0.0501 (6)
H9A0.3275−0.0027−0.02290.060*
H9B0.2198−0.09780.00780.060*
C100.0341 (5)−0.04956 (14)−0.09493 (14)0.0442 (5)
H1N2−0.187 (7)0.3179 (19)0.0435 (19)0.076 (9)*
H2N2−0.353 (7)0.242 (2)0.0786 (17)0.082 (10)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0957 (6)0.0674 (4)0.0908 (5)−0.0065 (5)−0.0402 (5)−0.0032 (4)
N10.0463 (11)0.0449 (9)0.0481 (10)−0.0088 (10)0.0025 (9)0.0045 (8)
N20.0720 (16)0.0697 (15)0.0482 (13)−0.0195 (14)0.0022 (11)0.0144 (13)
C10.0560 (15)0.0430 (12)0.0488 (13)−0.0006 (12)−0.0008 (12)0.0034 (11)
C20.0518 (14)0.0437 (12)0.0642 (14)0.0028 (13)−0.0088 (13)−0.0028 (11)
C30.0545 (17)0.0447 (14)0.089 (2)−0.0090 (13)−0.0021 (15)0.0035 (14)
C40.0580 (17)0.0483 (13)0.0706 (17)−0.0088 (13)0.0105 (14)0.0126 (13)
C50.0526 (15)0.0433 (12)0.0481 (13)−0.0006 (12)0.0097 (11)0.0044 (11)
O10.0570 (10)0.0671 (10)0.0327 (7)−0.0186 (9)−0.0060 (7)0.0075 (7)
O20.0792 (13)0.0617 (10)0.0409 (8)−0.0187 (10)−0.0131 (8)0.0155 (8)
O30.0598 (11)0.0885 (12)0.0409 (9)−0.0110 (11)−0.0013 (9)−0.0122 (8)
O40.0462 (10)0.1013 (14)0.0540 (10)−0.0025 (11)−0.0084 (9)−0.0141 (10)
C60.0429 (13)0.0446 (11)0.0328 (10)0.0016 (11)0.0009 (10)−0.0014 (9)
C70.0513 (13)0.0518 (12)0.0364 (10)−0.0062 (12)0.0032 (10)−0.0012 (9)
C80.0453 (13)0.0537 (13)0.0438 (12)−0.0013 (12)−0.0018 (10)−0.0068 (10)
C90.0490 (13)0.0598 (15)0.0417 (12)0.0065 (13)−0.0080 (11)−0.0099 (10)
C100.0479 (15)0.0412 (11)0.0437 (12)0.0040 (10)−0.0075 (11)−0.0037 (10)

Geometric parameters (Å, °)

Cl1—C21.723 (3)O2—C61.233 (2)
N1—C11.349 (3)O3—C101.317 (3)
N1—C51.350 (3)O3—H1O30.8102
N1—H10.8600O4—C101.192 (3)
N2—C51.315 (3)C6—C71.513 (3)
N2—H1N20.87 (3)C7—C81.516 (3)
N2—H2N20.89 (3)C7—H7A0.9700
C1—C21.342 (3)C7—H7B0.9700
C1—H1A0.9300C8—C91.504 (3)
C2—C31.405 (4)C8—H8A0.9700
C3—C41.346 (4)C8—H8B0.9700
C3—H3A0.9300C9—C101.494 (3)
C4—C51.403 (3)C9—H9A0.9700
C4—H4A0.9300C9—H9B0.9700
O1—C61.274 (2)
C1—N1—C5123.1 (2)O2—C6—C7120.75 (19)
C1—N1—H1118.4O1—C6—C7116.57 (18)
C5—N1—H1118.4C6—C7—C8115.19 (18)
C5—N2—H1N2119 (2)C6—C7—H7A108.5
C5—N2—H2N2123.0 (19)C8—C7—H7A108.5
H1N2—N2—H2N2117 (3)C6—C7—H7B108.5
C2—C1—N1120.4 (2)C8—C7—H7B108.5
C2—C1—H1A119.8H7A—C7—H7B107.5
N1—C1—H1A119.8C9—C8—C7112.1 (2)
C1—C2—C3118.8 (2)C9—C8—H8A109.2
C1—C2—Cl1120.74 (19)C7—C8—H8A109.2
C3—C2—Cl1120.5 (2)C9—C8—H8B109.2
C4—C3—C2120.0 (2)C7—C8—H8B109.2
C4—C3—H3A120.0H8A—C8—H8B107.9
C2—C3—H3A120.0C10—C9—C8113.5 (2)
C3—C4—C5120.8 (2)C10—C9—H9A108.9
C3—C4—H4A119.6C8—C9—H9A108.9
C5—C4—H4A119.6C10—C9—H9B108.9
N2—C5—N1118.6 (2)C8—C9—H9B108.9
N2—C5—C4124.5 (2)H9A—C9—H9B107.7
N1—C5—C4116.9 (2)O4—C10—O3122.6 (2)
C10—O3—H1O3115.7O4—C10—C9124.6 (2)
O2—C6—O1122.7 (2)O3—C10—C9112.8 (2)
C5—N1—C1—C21.1 (4)C3—C4—C5—N2179.2 (3)
N1—C1—C2—C30.6 (4)C3—C4—C5—N10.9 (4)
N1—C1—C2—Cl1−179.20 (18)O2—C6—C7—C87.5 (3)
C1—C2—C3—C4−1.4 (4)O1—C6—C7—C8−173.7 (2)
Cl1—C2—C3—C4178.4 (2)C6—C7—C8—C972.4 (3)
C2—C3—C4—C50.7 (4)C7—C8—C9—C10179.51 (19)
C1—N1—C5—N2179.8 (2)C8—C9—C10—O4−34.9 (3)
C1—N1—C5—C4−1.8 (3)C8—C9—C10—O3144.7 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.861.802.659 (3)173
O3—H1O3···O1ii0.811.792.598 (2)173
N2—H1N2···O2iii0.87 (3)2.00 (3)2.848 (3)163 (3)
N2—H2N2···O2i0.89 (3)1.92 (3)2.808 (3)173 (2)
C1—H1A···O4iv0.932.443.315 (3)156
C4—H4A···O4v0.932.593.396 (3)145

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS2574).

References

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