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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2755.
Published online 2009 October 17. doi:  10.1107/S160053680904149X
PMCID: PMC2971019

2-Amino-5-chloro­pyridinium nitrate

Abstract

The title structure, C5H6ClN2 +·NO3 , is held together by extensive hydrogen bonding between the NO3 ions and 2-amino-5-chloro­pyridinium H atoms. The cation–anion N—H(...)O hydrogen bonds link the ions into a zigzag- chain which develops parallel to the b axis. The structure may be compared with that of the related 2-amino-5-cyano­pyridinium nitrate.

Related literature

For metal-organic frameworks involving amine derivatives, see: Manzur et al. (2007 [triangle]); Ismayilov et al. (2007 [triangle]); Austria et al. (2007 [triangle]). For related structures, see: Pourayoubi et al. (2007 [triangle]); Rademeyer (2005 [triangle], 2007 [triangle]); Dai (2008 [triangle]).

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Object name is e-65-o2755-scheme1.jpg

Experimental

Crystal data

  • C5H6ClN2 +·NO3
  • M r = 191.58
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2755-efi3.jpg
  • a = 4.788 (4) Å
  • b = 13.029 (3) Å
  • c = 12.779 (2) Å
  • β = 101.445 (18)°
  • V = 781.3 (7) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.46 mm−1
  • T = 299 K
  • 0.40 × 0.40 × 0.20 mm

Data collection

  • Enraf–Nonius CAD-4 diffractometer
  • Absorption correction: ψ scan (North et al., 1968 [triangle]) T min = 0.838, T max = 0.914
  • 2057 measured reflections
  • 1691 independent reflections
  • 1312 reflections with I > 2σ(I)
  • R int = 0.017
  • 2 standard reflections frequency: 120 min intensity decay: none

Refinement

  • R[F 2 > 2σ(F 2)] = 0.037
  • wR(F 2) = 0.106
  • S = 1.02
  • 1691 reflections
  • 109 parameters
  • H-atom parameters constrained
  • Δρmax = 0.19 e Å−3
  • Δρmin = −0.25 e Å−3

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994 [triangle]); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]) and PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680904149X/dn2495sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680904149X/dn2495Isup2.hkl

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

supplementary crystallographic information

Comment

Derivatives of the aminoacid are of considerable interest in biological activities and there has been an increased interest in the chemistry of amine derivatives because of the construction of novel metal-organic frameworks (Manzur et al., 2007; Ismayilov et al., 2007; Austria et al., 2007). The crystal structures of 2-amino-5-chloropyridine (Pourayoubi et al., 2007) and their 2-Amino-5-cyanopyridinium nitrate (Dai, 2008) and 2-Aminopyridinium nitrate (Rademeyer, 2007) have been reported in literature. In this paper, we present the X-ray single-crystal structure of 2- Amino-5-chloropyridinium nitrate (I).

The title compound (I) contains an organic cation and a (NO3)- anion (Fig1). The cation is roughly planar with the largest deviation from the mean plane being 0.0553 (9)Å. The NO3 anion is slightly twisted with respect to the pyridinium ring making a dihedral angle of 17.2 (1)°

The monoprotonated chloropyridinium cation (C5H6ClN2)+ and the nitrate anion (NO3)- are linked by N-H···O which forms a zig-zag like chain parallel to the b axis (Table 1, Fig 2).

The crystal structure of 2-Amino-5-cyanopyridinium nitrate (II) (Dai, 2008) was recently published. The title compound (I) and this related compound (II) are isostructural. In both molecules, the asymmetric unit contains an organic cation 2-Amino-5-Xpyridinium (X: chloride (I), C[equivalent]N nitrile (II)) and a nitrate anion. They have the same space group (P21/c) and they are characterized by two-dimensional hydrogen-bonded networks.

The distances and angles of the present 2-amino-5-chloropyridinium nitrate molecule are consistent with the values reported in the literature of 2-aminopyridinium nitrate and 4-aminopyridinium nitrate molecules (Rademeyer 2005;2007).

Experimental

2-Amino-5-chloropridine was dissolved in the solution of methanol and nitric acid (0.5 ml). Yellow crystals were obtained after a month on slow evaporation.

Refinement

All H atoms attached to C atoms and N atoms were fixed geometrically and treated as riding with C—H = 0.93Å and N—H = 0.86 Å with Uiso(H) = 1.2Ueq(C or N).

Figures

Fig. 1.
Representation of the asymetric unit of 2-amino-5-chloropyridinium nitrate with the atom labeling scheme. Ellipsoids are drawn at the 30% probability level. H atoms are represented as small spheres of arbitrary radii. Hydrogen bonds are shown as dashed ...
Fig. 2.
Partial packing view showing the formation of the zigzag chain parallel to the b axis. H atoms not involved in hydrogen bonding have been omitted for clarity.[Symmetry code: (i) -x-1, y+1/2, -z+3/2].

Crystal data

C5H6ClN2+·NO3F(000) = 392.0
Mr = 191.58Dx = 1.620 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 25 reflections
a = 4.788 (4) Åθ = 10–15°
b = 13.029 (3) ŵ = 0.46 mm1
c = 12.779 (2) ÅT = 299 K
β = 101.445 (18)°Prism, yellow
V = 781.3 (7) Å30.40 × 0.40 × 0.20 mm
Z = 4

Data collection

Enraf–Nonius CAD-4 diffractometer1312 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.017
graphiteθmax = 27.0°, θmin = 2.3°
Nonprofiled ω/2θ scansh = −1→6
Absorption correction: ψ scan (North et al., 1968)k = −16→1
Tmin = 0.838, Tmax = 0.914l = −16→15
2057 measured reflections2 standard reflections every 120 min
1691 independent reflections intensity decay: none

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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.106H-atom parameters constrained
S = 1.02w = 1/[σ2(Fo2) + (0.0566P)2 + 0.1965P] where P = (Fo2 + 2Fc2)/3
1691 reflections(Δ/σ)max < 0.001
109 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = −0.25 e Å3

Special details

Experimental. Number of psi-scan sets used was 3 Theta correction was applied. Averaged transmission function was used. No Fourier smoothing was applied (North et al., 1968).
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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
Cl10.35469 (12)0.37026 (4)0.42068 (4)0.0558 (2)
N1−0.4403 (4)−0.03452 (11)0.63887 (12)0.0404 (4)
N2−0.2955 (4)0.22776 (13)0.73365 (13)0.0484 (4)
H2A−0.34870.16460.73010.058*
H2B−0.34400.26790.78040.058*
N3−0.0639 (3)0.19881 (11)0.59367 (12)0.0373 (3)
H3−0.11530.13560.59430.045*
C1−0.1377 (4)0.26344 (13)0.66666 (13)0.0349 (4)
C2−0.0428 (4)0.36615 (14)0.66731 (15)0.0399 (4)
H2−0.08540.41220.71750.048*
C30.1112 (4)0.39778 (15)0.59430 (15)0.0411 (4)
H3A0.17510.46520.59500.049*
C40.1737 (4)0.32811 (14)0.51762 (14)0.0373 (4)
C50.0878 (4)0.22883 (14)0.51921 (14)0.0383 (4)
H50.13180.18190.47010.046*
O1−0.5381 (3)−0.12309 (10)0.62043 (12)0.0545 (4)
O2−0.2376 (3)−0.00614 (11)0.59683 (13)0.0523 (4)
O3−0.5384 (4)0.02366 (12)0.70018 (14)0.0635 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0681 (4)0.0477 (3)0.0615 (3)−0.0101 (2)0.0366 (3)−0.0017 (2)
N10.0517 (9)0.0326 (8)0.0380 (8)−0.0009 (7)0.0115 (7)0.0026 (6)
N20.0649 (10)0.0414 (9)0.0454 (9)−0.0019 (8)0.0269 (8)−0.0030 (7)
N30.0455 (8)0.0264 (7)0.0427 (8)−0.0034 (6)0.0156 (7)−0.0047 (6)
C10.0387 (9)0.0339 (8)0.0324 (8)0.0019 (7)0.0081 (7)−0.0013 (7)
C20.0495 (10)0.0318 (9)0.0389 (9)0.0003 (7)0.0098 (8)−0.0077 (7)
C30.0495 (10)0.0290 (8)0.0445 (10)−0.0039 (7)0.0088 (8)−0.0051 (7)
C40.0384 (9)0.0362 (9)0.0396 (9)−0.0013 (7)0.0136 (7)−0.0006 (7)
C50.0444 (9)0.0333 (9)0.0406 (9)−0.0005 (7)0.0171 (8)−0.0082 (7)
O10.0784 (10)0.0347 (7)0.0552 (8)−0.0152 (7)0.0251 (8)−0.0006 (6)
O20.0590 (9)0.0369 (7)0.0685 (9)−0.0069 (6)0.0308 (8)−0.0010 (6)
O30.0788 (11)0.0513 (9)0.0708 (10)−0.0089 (8)0.0403 (9)−0.0158 (8)

Geometric parameters (Å, °)

Cl1—C41.7358 (19)N3—H30.8600
N1—O31.247 (2)C1—C21.413 (3)
N1—O11.250 (2)C2—C31.363 (3)
N1—O21.255 (2)C2—H20.9300
N2—C11.333 (2)C3—C41.411 (3)
N2—H2A0.8600C3—H3A0.9300
N2—H2B0.8600C4—C51.359 (3)
N3—C11.355 (2)C5—H50.9300
N3—C51.364 (2)
O3—N1—O1120.41 (17)C3—C2—C1119.96 (16)
O3—N1—O2120.64 (16)C3—C2—H2120.0
O1—N1—O2118.93 (16)C1—C2—H2120.0
C1—N2—H2A120.0C2—C3—C4119.95 (17)
C1—N2—H2B120.0C2—C3—H3A120.0
H2A—N2—H2B120.0C4—C3—H3A120.0
C1—N3—C5123.36 (15)C5—C4—C3119.70 (17)
C1—N3—H3118.3C5—C4—Cl1120.49 (14)
C5—N3—H3118.3C3—C4—Cl1119.80 (14)
N2—C1—N3118.95 (16)C4—C5—N3119.23 (16)
N2—C1—C2123.31 (16)C4—C5—H5120.4
N3—C1—C2117.74 (15)N3—C5—H5120.4

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2A···O30.862.052.900 (2)169
N2—H2B···O1i0.862.062.912 (2)174
N3—H3···O20.861.942.800 (2)179

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2495).

References

  • Austria, C., Zhang, J. & Valle, H. (2007). Inorg. Chem.46, 6283–6290. [PubMed]
  • Dai, J. (2008). Acta Cryst. E64, o1899. [PMC free article] [PubMed]
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  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Harms, K. & Wocadlo, S. (1995). XCAD4 Université de Marburg, Germany.
  • Ismayilov, R. H., Wang, W. Z. & Lee, G. H. (2007). Dalton Trans pp. 2898–2907. [PubMed]
  • Manzur, J., Vega, A. & Garcia, A. M. (2007). Eur. J. Inorg. Chem.35, 5500–5510.
  • North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.
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  • Rademeyer, M. (2005). Acta Cryst. E61, o2496–o2498.
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