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Acta Crystallogr Sect E Struct Rep Online. 2009 October 1; 65(Pt 10): o2408.
Published online 2009 September 9. doi:  10.1107/S160053680903517X
PMCID: PMC2970348

Pyridine-4-carboximidamidate chloride

Abstract

In the title salt, C6H8N3 +·Cl, each pyridine­carbox­imid­amidate cation is linked to two symmetry-related cations through N—H(...)N hydrogen bonds, and to two chloride ions by N—H(...)Cl hydrogen bonds. The N—H(...)N hydrogen bonds involve the pyridine N atom and one NH2 group. In the crystal, N—H(...)N and N—H(...)Cl hydrogen bonds extend the structure into two-dimensional layers. Weak C—H(...)Cl inter­actions further connect these layers into a three-dimensional network.

Related literature

For background, see: Chudinov et al. (2005 [triangle]); Kamei et al. (2005 [triangle]).

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Object name is e-65-o2408-scheme1.jpg

Experimental

Crystal data

  • C6H8N3 +·Cl
  • M r = 157.60
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2408-efi1.jpg
  • a = 7.3928 (13) Å
  • b = 10.4467 (16) Å
  • c = 18.925 (3) Å
  • V = 1461.6 (4) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.44 mm−1
  • T = 293 K
  • 0.37 × 0.32 × 0.21 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.853, T max = 0.911
  • 1949 measured reflections
  • 1435 independent reflections
  • 1215 reflections with I > 2σ(I)
  • R int = 0.018

Refinement

  • R[F 2 > 2σ(F 2)] = 0.033
  • wR(F 2) = 0.092
  • S = 1.04
  • 1435 reflections
  • 124 parameters
  • All H-atom parameters refined
  • Δρmax = 0.23 e Å−3
  • Δρmin = −0.18 e Å−3

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SAINT (Bruker, 2001 [triangle]); data reduction: SAINT; 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]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680903517X/bh2242sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680903517X/bh2242Isup2.hkl

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

supplementary crystallographic information

Comment

The title compound, also known as isonicotinamidine hydrochloride, served as a key intermediate in the synthesis of pharmacologically active compounds. It had attracted a great deal of interest during recent years. A series of new piperidinyl- and 1,2,3,6-tetrahydropyridinylpyrimidine derivatives was synthesized by using isonicotinamidine as an important intermediate. Isonicotinamidine has a unique structure and exists in the form of hydrochloride or acetate (Chudinov et al., 2005; Kamei et al., 2005).

The title compound is an organic salt (Fig. 1). In the cation, dihedral angle between the pyridyl ring and the plane confined by N2, N3 and C6 is 42.1°. Each isonicotinamidine cation is connected to two other cations by N—H···N hydrogen bonds, and to two Cl- anions by N—H···Cl hydrogen bonds (Fig. 2), to form two dimensional layers including one-dimensional zigzag chains (Fig. 3). Weak C—H···Cl interactions [C···Cl = 3.556 (2) Å] link these layers to provide a three-dimensional supramolecular network.

Experimental

The title compound was prepared according to the method of Kamei et al. (2005). Block-shaped crystals suitable for X-ray diffraction were obtained from ethanol/acetone.

Refinement

H atoms were located from difference maps and freely refined.

Figures

Fig. 1.
View of (I), showing atomic labels and displacement ellipsoids drawn at 30% probability level.
Fig. 2.
N—H···N and N—H···Cl hydrogen bonds in the crystal.
Fig. 3.
View of the hydrogen bonded one-dimensional chain along b axis.

Crystal data

C6H8N3+·ClF(000) = 656
Mr = 157.60Dx = 1.432 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 542 reflections
a = 7.3928 (13) Åθ = 2.3–22.8°
b = 10.4467 (16) ŵ = 0.44 mm1
c = 18.925 (3) ÅT = 293 K
V = 1461.6 (4) Å3Block, colourless
Z = 80.37 × 0.32 × 0.21 mm

Data collection

Bruker SMART CCD area-detector diffractometer1435 independent reflections
Radiation source: fine-focus sealed tube1215 reflections with I > 2σ(I)
graphiteRint = 0.018
[var phi] and ω scansθmax = 26.0°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −9→1
Tmin = 0.853, Tmax = 0.911k = −1→12
1949 measured reflectionsl = −23→1

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033All H-atom parameters refined
wR(F2) = 0.092w = 1/[σ2(Fo2) + (0.0416P)2 + 0.5489P] where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max = 0.001
1435 reflectionsΔρmax = 0.23 e Å3
124 parametersΔρmin = −0.17 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0056 (15)

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
N10.0852 (2)0.38353 (14)0.75509 (8)0.0367 (4)
C10.0499 (3)0.36114 (17)0.82329 (10)0.0367 (4)
Cl10.15740 (8)0.91636 (4)1.05546 (2)0.0432 (2)
N20.0353 (2)0.79417 (15)0.89141 (9)0.0369 (4)
C20.0593 (3)0.45387 (17)0.87518 (9)0.0341 (4)
N30.1766 (3)0.66264 (17)0.97084 (9)0.0428 (4)
C30.1026 (2)0.57807 (15)0.85578 (9)0.0285 (4)
C40.1401 (3)0.60305 (17)0.78520 (9)0.0337 (4)
C50.1315 (3)0.50297 (18)0.73774 (9)0.0376 (4)
C60.1052 (2)0.68338 (16)0.90895 (9)0.0310 (4)
H40.171 (3)0.6863 (18)0.7679 (10)0.033 (5)*
H10.015 (3)0.275 (2)0.8348 (11)0.044 (6)*
H20.032 (3)0.4327 (18)0.9204 (11)0.041 (5)*
H50.159 (3)0.519 (2)0.6925 (12)0.048 (6)*
H2B0.037 (3)0.854 (2)0.9202 (13)0.060 (7)*
H2A−0.016 (3)0.803 (2)0.8500 (12)0.050 (6)*
H3B0.229 (4)0.590 (2)0.9833 (12)0.056 (7)*
H3A0.184 (3)0.732 (2)1.0012 (14)0.061 (7)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0452 (9)0.0312 (8)0.0338 (8)0.0019 (7)0.0001 (7)−0.0051 (7)
C10.0439 (11)0.0261 (9)0.0400 (10)−0.0002 (8)−0.0007 (9)0.0007 (7)
Cl10.0580 (3)0.0357 (3)0.0359 (3)0.0007 (2)−0.0055 (2)−0.00566 (18)
N20.0484 (10)0.0262 (8)0.0360 (9)0.0009 (7)0.0006 (8)−0.0043 (7)
C20.0436 (11)0.0306 (9)0.0280 (9)0.0035 (8)0.0027 (8)0.0019 (7)
N30.0613 (12)0.0348 (9)0.0323 (8)0.0070 (8)−0.0090 (8)−0.0067 (7)
C30.0313 (9)0.0266 (8)0.0277 (8)0.0021 (7)−0.0020 (7)−0.0021 (7)
C40.0421 (10)0.0280 (9)0.0310 (9)−0.0020 (8)0.0003 (8)0.0024 (7)
C50.0488 (12)0.0377 (10)0.0264 (9)−0.0002 (8)0.0022 (8)−0.0012 (8)
C60.0348 (9)0.0280 (9)0.0300 (9)−0.0018 (7)0.0031 (7)−0.0020 (7)

Geometric parameters (Å, °)

N1—C51.335 (2)N3—C61.303 (2)
N1—C11.337 (2)N3—H3B0.89 (2)
C1—C21.381 (3)N3—H3A0.93 (3)
C1—H10.96 (2)C3—C41.389 (2)
N2—C61.310 (2)C3—C61.491 (2)
N2—H2B0.83 (3)C4—C51.380 (3)
N2—H2A0.88 (2)C4—H40.958 (19)
C2—C31.386 (2)C5—H50.90 (2)
C2—H20.91 (2)
C5—N1—C1116.80 (15)C2—C3—C4118.47 (16)
N1—C1—C2123.63 (17)C2—C3—C6120.99 (15)
N1—C1—H1115.7 (12)C4—C3—C6120.52 (15)
C2—C1—H1120.6 (12)C5—C4—C3118.33 (17)
C6—N2—H2B119.8 (17)C5—C4—H4118.5 (11)
C6—N2—H2A119.2 (15)C3—C4—H4123.2 (11)
H2B—N2—H2A121 (2)N1—C5—C4124.05 (17)
C1—C2—C3118.68 (16)N1—C5—H5118.2 (15)
C1—C2—H2119.3 (13)C4—C5—H5117.7 (15)
C3—C2—H2122.0 (13)N3—C6—N2122.31 (17)
C6—N3—H3B123.9 (15)N3—C6—C3119.28 (16)
C6—N3—H3A116.9 (16)N2—C6—C3118.41 (16)
H3B—N3—H3A119 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2A···N1i0.88 (2)2.22 (2)3.058 (2)160 (2)
N3—H3A···Cl10.93 (2)2.19 (2)3.100 (2)167 (2)
N2—H2B···Cl10.83 (2)2.79 (2)3.476 (2)142 (2)
N3—H3B···Cl1ii0.89 (2)2.41 (2)3.270 (2)161 (2)
C5—H5···Cl1iii0.90 (2)2.68 (2)3.556 (2)166 (2)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BH2242).

References

  • Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Chudinov, M. V., Konstantinova, I. D., Ryzhova, O. I., Esipov, R. S., Yurkevich, A. M., Shvets, V. I. & Miroshnikov, A. I. (2005). Pharm. Chem. J.39, 212–215.
  • Kamei, K., Maeda, N., Katsuragi-Ogino, R., Koyama, M., Nakajima, M., Tatsuoka, T., Ohno, T. & Inoue, T. (2005). Bioorg. Med. Chem. Lett.15, 2990–2993. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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