Pyridine-4-carboximidamidate chloride

Fan, P.; Wang, L.; Zhang, H.

doi:10.1107/S160053680903517X

organic compounds

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Volume 65| Part 10| October 2009| Page o2408

doi:10.1107/S160053680903517X

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Pyridine-4-carboximidamidate chloride

Ping Fan,^a ^* Lei Wang ^a and Huidong Zhang ^b

^aCollege of Chemistry, Liaoning University, Shenyang 110036, People's Republic of China, and ^bLiaoning Fixed Star Chemicals (Group) Co. Ltd, Dandong 118000, People's Republic of China
^*Correspondence e-mail: pingfan@lnu.edu.cn

(Received 27 July 2009; accepted 1 September 2009; online 9 September 2009)

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 ); Kamei et al. (2005 ).

Experimental

Crystal data

C₆H₈N₃⁺·Cl⁻
M_r = 157.60
Orthorhombic, P b c a
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 ) 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[F² > 2σ(F²)] = 0.033
wR(F²) = 0.092
S = 1.04
1435 reflections
124 parameters
All H-atom parameters refined
Δρ_max = 0.23 e Å⁻³
Δρ_min = −0.18 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2A⋯N1ⁱ	0.88 (2)	2.22 (2)	3.058 (2)	160 (2)
N2—H2B⋯Cl1	0.83 (2)	2.79 (2)	3.476 (2)	142 (2)
N3—H3A⋯Cl1	0.93 (2)	2.19 (2)	3.100 (2)	167 (2)
N3—H3B⋯Cl1ⁱⁱ	0.89 (2)	2.41 (2)	3.270 (2)	161 (2)
C5—H5⋯Cl1ⁱⁱⁱ	0.90 (2)	2.68 (2)	3.556 (2)	166 (2)
Symmetry codes: (i) $[-x, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, z]$ ; (iii) $[x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ .

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97.

Supporting information

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

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

checkCIF report

Comment top

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.

Related literature top

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

Experimental top

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.

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	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.

Pyridine-4-carboximidamidate chloride top

Crystal data top

C₆H₈N₃⁺·Cl⁻	F(000) = 656
M_r = 157.60	D_x = 1.432 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 542 reflections
a = 7.3928 (13) Å	θ = 2.3–22.8°
b = 10.4467 (16) Å	µ = 0.44 mm⁻¹
c = 18.925 (3) Å	T = 293 K
V = 1461.6 (4) Å³	Block, colourless
Z = 8	0.37 × 0.32 × 0.21 mm

Data collection top

Bruker SMART CCD area-detector diffractometer	1435 independent reflections
Radiation source: fine-focus sealed tube	1215 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.018
ϕ and ω scans	θ_max = 26.0°, θ_min = 2.2°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −9→1
T_min = 0.853, T_max = 0.911	k = −1→12
1949 measured reflections	l = −23→1

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.033	All H-atom parameters refined
wR(F²) = 0.092	w = 1/[σ²(F_o²) + (0.0416P)² + 0.5489P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max = 0.001
1435 reflections	Δρ_max = 0.23 e Å⁻³
124 parameters	Δρ_min = −0.18 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0056 (15)

Crystal data top

C₆H₈N₃⁺·Cl⁻	V = 1461.6 (4) Å³
M_r = 157.60	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 7.3928 (13) Å	µ = 0.44 mm⁻¹
b = 10.4467 (16) Å	T = 293 K
c = 18.925 (3) Å	0.37 × 0.32 × 0.21 mm

Data collection top

Bruker SMART CCD area-detector diffractometer	1435 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2001)	1215 reflections with I > 2σ(I)
T_min = 0.853, T_max = 0.911	R_int = 0.018
1949 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.033	0 restraints
wR(F²) = 0.092	All H-atom parameters refined
S = 1.04	Δρ_max = 0.23 e Å⁻³
1435 reflections	Δρ_min = −0.18 e Å⁻³
124 parameters

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

	x	y	z	U_iso*/U_eq
N1	0.0852 (2)	0.38353 (14)	0.75509 (8)	0.0367 (4)
C1	0.0499 (3)	0.36114 (17)	0.82329 (10)	0.0367 (4)
Cl1	0.15740 (8)	0.91636 (4)	1.05546 (2)	0.0432 (2)
N2	0.0353 (2)	0.79417 (15)	0.89141 (9)	0.0369 (4)
C2	0.0593 (3)	0.45387 (17)	0.87518 (9)	0.0341 (4)
N3	0.1766 (3)	0.66264 (17)	0.97084 (9)	0.0428 (4)
C3	0.1026 (2)	0.57807 (15)	0.85578 (9)	0.0285 (4)
C4	0.1401 (3)	0.60305 (17)	0.78520 (9)	0.0337 (4)
C5	0.1315 (3)	0.50297 (18)	0.73774 (9)	0.0376 (4)
C6	0.1052 (2)	0.68338 (16)	0.90895 (9)	0.0310 (4)
H4	0.171 (3)	0.6863 (18)	0.7679 (10)	0.033 (5)*
H1	0.015 (3)	0.275 (2)	0.8348 (11)	0.044 (6)*
H2	0.032 (3)	0.4327 (18)	0.9204 (11)	0.041 (5)*
H5	0.159 (3)	0.519 (2)	0.6925 (12)	0.048 (6)*
H2B	0.037 (3)	0.854 (2)	0.9202 (13)	0.060 (7)*
H2A	−0.016 (3)	0.803 (2)	0.8500 (12)	0.050 (6)*
H3B	0.229 (4)	0.590 (2)	0.9833 (12)	0.056 (7)*
H3A	0.184 (3)	0.732 (2)	1.0012 (14)	0.061 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0452 (9)	0.0312 (8)	0.0338 (8)	0.0019 (7)	0.0001 (7)	−0.0051 (7)
C1	0.0439 (11)	0.0261 (9)	0.0400 (10)	−0.0002 (8)	−0.0007 (9)	0.0007 (7)
Cl1	0.0580 (3)	0.0357 (3)	0.0359 (3)	0.0007 (2)	−0.0055 (2)	−0.00566 (18)
N2	0.0484 (10)	0.0262 (8)	0.0360 (9)	0.0009 (7)	0.0006 (8)	−0.0043 (7)
C2	0.0436 (11)	0.0306 (9)	0.0280 (9)	0.0035 (8)	0.0027 (8)	0.0019 (7)
N3	0.0613 (12)	0.0348 (9)	0.0323 (8)	0.0070 (8)	−0.0090 (8)	−0.0067 (7)
C3	0.0313 (9)	0.0266 (8)	0.0277 (8)	0.0021 (7)	−0.0020 (7)	−0.0021 (7)
C4	0.0421 (10)	0.0280 (9)	0.0310 (9)	−0.0020 (8)	0.0003 (8)	0.0024 (7)
C5	0.0488 (12)	0.0377 (10)	0.0264 (9)	−0.0002 (8)	0.0022 (8)	−0.0012 (8)
C6	0.0348 (9)	0.0280 (9)	0.0300 (9)	−0.0018 (7)	0.0031 (7)	−0.0020 (7)

Geometric parameters (Å, º) top

N1—C5	1.335 (2)	N3—C6	1.303 (2)
N1—C1	1.337 (2)	N3—H3B	0.89 (2)
C1—C2	1.381 (3)	N3—H3A	0.93 (3)
C1—H1	0.96 (2)	C3—C4	1.389 (2)
N2—C6	1.310 (2)	C3—C6	1.491 (2)
N2—H2B	0.83 (3)	C4—C5	1.380 (3)
N2—H2A	0.88 (2)	C4—H4	0.958 (19)
C2—C3	1.386 (2)	C5—H5	0.90 (2)
C2—H2	0.91 (2)

C5—N1—C1	116.80 (15)	C2—C3—C4	118.47 (16)
N1—C1—C2	123.63 (17)	C2—C3—C6	120.99 (15)
N1—C1—H1	115.7 (12)	C4—C3—C6	120.52 (15)
C2—C1—H1	120.6 (12)	C5—C4—C3	118.33 (17)
C6—N2—H2B	119.8 (17)	C5—C4—H4	118.5 (11)
C6—N2—H2A	119.2 (15)	C3—C4—H4	123.2 (11)
H2B—N2—H2A	121 (2)	N1—C5—C4	124.05 (17)
C1—C2—C3	118.68 (16)	N1—C5—H5	118.2 (15)
C1—C2—H2	119.3 (13)	C4—C5—H5	117.7 (15)
C3—C2—H2	122.0 (13)	N3—C6—N2	122.31 (17)
C6—N3—H3B	123.9 (15)	N3—C6—C3	119.28 (16)
C6—N3—H3A	116.9 (16)	N2—C6—C3	118.41 (16)
H3B—N3—H3A	119 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1ⁱ	0.88 (2)	2.22 (2)	3.058 (2)	160 (2)
N3—H3A···Cl1	0.93 (2)	2.19 (2)	3.100 (2)	167 (2)
N2—H2B···Cl1	0.83 (2)	2.79 (2)	3.476 (2)	142 (2)
N3—H3B···Cl1ⁱⁱ	0.89 (2)	2.41 (2)	3.270 (2)	161 (2)
C5—H5···Cl1ⁱⁱⁱ	0.90 (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.

Experimental details

Crystal data
Chemical formula	C₆H₈N₃⁺·Cl⁻
M_r	157.60
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	293
a, b, c (Å)	7.3928 (13), 10.4467 (16), 18.925 (3)
V (Å³)	1461.6 (4)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.44
Crystal size (mm)	0.37 × 0.32 × 0.21

Data collection
Diffractometer	Bruker SMART CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2001)
T_min, T_max	0.853, 0.911
No. of measured, independent and observed [I > 2σ(I)] reflections	1949, 1435, 1215
R_int	0.018
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.033, 0.092, 1.04
No. of reflections	1435
No. of parameters	124
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.18

Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1ⁱ	0.88 (2)	2.22 (2)	3.058 (2)	160 (2)
N3—H3A···Cl1	0.93 (2)	2.19 (2)	3.100 (2)	167 (2)
N2—H2B···Cl1	0.83 (2)	2.79 (2)	3.476 (2)	142 (2)
N3—H3B···Cl1ⁱⁱ	0.89 (2)	2.41 (2)	3.270 (2)	161 (2)
C5—H5···Cl1ⁱⁱⁱ	0.90 (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.

References

Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
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. CrossRef CAS Google Scholar
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. Web of Science CrossRef PubMed CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 10| October 2009| Page o2408

doi:10.1107/S160053680903517X

Open

access