Redetermination of 3-(ammonio­meth­yl)pyridinium dichloride

Liang, W.-X.; Wang, G.; Qu, Z.-R.

doi:10.1107/S1600536809025859

organic compounds

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Volume 65| Part 8| August 2009| Page o1814

doi:10.1107/S1600536809025859

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Redetermination of 3-(ammoniomethyl)pyridinium dichloride

Wen-Xian Liang,^a Gang Wang ^a and Zhi-Rong Qu ^a ^*

^aOrdered Matter Science Research Center, College of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
^*Correspondence e-mail: quzr@seu.edu.cn

(Received 28 June 2009; accepted 3 July 2009; online 11 July 2009)

The crystal structure of the title compound, C₆H₁₀N₂²⁺·2Cl⁻, has been reported previously in the non-standard setting P2₁/a [Genet (1965 ). Bull. Soc. Fr. Miner. Crist. 88, 463–470], with an R value of 0.16. The current redetermination improves significantly the precision of the geometric parameters. In the crystal packing, cations and anions are linked by intermolecular N—H⋯Cl and C—H⋯Cl hydrogen bonds into a three-dimensional network.

Related literature

For related structures, see: Genet (1965); Chtioui & Jouini (2004 ); Long et al. (1997 ).

Experimental

Crystal data

C₆H₁₀N₂²⁺·2Cl⁻
M_r = 181.06
Monoclinic, P 2₁ /c
a = 4.5874 (9) Å
b = 12.650 (3) Å
c = 14.814 (3) Å
β = 93.61 (3)°
V = 857.9 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.69 mm⁻¹
T = 293 K
0.50 × 0.45 × 0.15 mm

Data collection

Rigaku SCXmini diffractometer
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ) T_min = 0.720, T_max = 0.909
8831 measured reflections
1961 independent reflections
1684 reflections with I > 2σ(I)
R_int = 0.035

Refinement

R[F² > 2σ(F²)] = 0.033
wR(F²) = 0.076
S = 1.08
1961 reflections
92 parameters
H-atom parameters constrained
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.19 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯Cl2ⁱ	0.89	2.35	3.1914 (16)	157
N1—H1B⋯Cl2ⁱⁱ	0.89	2.27	3.1206 (16)	159
N1—H1C⋯Cl1ⁱⁱⁱ	0.89	2.28	3.1622 (16)	170
N2—H2⋯Cl1^iv	0.86	2.25	3.0520 (16)	154
C3—H3⋯Cl2ⁱ	0.93	2.77	3.606 (2)	150
C6—H6A⋯Cl1^v	0.97	2.74	3.676 (2)	163
C6—H6B⋯Cl2^vi	0.97	2.82	3.700 (2)	152
Symmetry codes: (i) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[x+1, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ ; (iii) -x+1, -y+1, -z; (iv) x+1, y+1, z; (v) -x+2, -y+1, -z; (vi) $[-x+2, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear; data reduction: CrystalClear; 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: PRPKAPPA (Ferguson, 1999 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809025859/rz2346sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809025859/rz2346Isup2.hkl

checkCIF report

Comment top

Pyridin-3-ylmethanamine is a important ligand used in coordination chemistry. Recently, there has been an increased interest in the properties of layer perovskite structures because of their applications in high temperature superconductivity. Two general classes of M(II) halide layer perovskite structures exist, the ammoniummethylprididine series (Chtioui & Jouini, 2004) and the ammoniummethylprididinium series (Long et al., 1997). In the latter series, the asymmetrical dication bridges between layers, with both the NH₃⁺ group and the pyridinium N—H group hydrogen bonding to the halide ions in the layer. The cation-layer interactions involve an ammonium group that hydrogen bonds to the perovskite layer (Long et al., 1997). We report herein the crystal structure of the title compound, which was prepared by the reaction of pyridin-3-ylmethanamine and hydrochloric acid. Its crystal structure has been reported previously in the non standard setting P2₁/a (Genet, 1965), with an R value of 0.16. The current redetermination improves significantly the precision of the geometric parameters.

The asymmetric unit of the title compound (Fig. 1) consists of a two independent chloride anions and a 3-(ammoniomethyl)pyridinium dication. In the cation, the plane through the C2/C6/N2 atoms is tilted by 68.13 (14)° with respect to the pyridine ring. In the crystal packing (Fig. 2), intermolecular N—H···Cl and C—H···Cl hydrogen bonds (Table 1) connect neighbouring cations and anions into a three-dimensional network.

Related literature top

For related structures, see: Genet (1965); Chtioui & Jouini (2004); Long et al. (1997).

Experimental top

A mixture of (pyridin-3-yl)methanamine (0.1 mol, 0.108 g) and HCl (0.2 mol, 0.73 g) were dissolved in water (10 ml). Colourless single crystals of the title compound suitable for X-ray analysis were obtained on slow evaporation of the solvent over a period of 48 h.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); 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: PRPKAPPA (Ferguson, 1999).

Figures top

	Fig. 1. The molecular structure of the title compound, with displacement ellipsoids drawn at the 30% probability level.
	Fig. 2. Packing diagram of the title compound viewed along the a axis>. Hydrogen bonds are shown as dashed lines.

3-(ammoniomethyl)pyridinium dichloride top

Crystal data top

C₆H₁₀N₂²⁺·2Cl⁻	F(000) = 376
M_r = 181.06	D_x = 1.402 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 8048 reflections
a = 4.5874 (9) Å	θ = 3.1–27.5°
b = 12.650 (3) Å	µ = 0.69 mm⁻¹
c = 14.814 (3) Å	T = 293 K
β = 93.61 (3)°	Prism, colourless
V = 857.9 (3) Å³	0.50 × 0.45 × 0.15 mm
Z = 4

Data collection top

Rigaku SCXmini diffractometer	1961 independent reflections
Radiation source: fine-focus sealed tube	1684 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.035
Detector resolution: 13.662 pixels mm^-1	θ_max = 27.5°, θ_min = 3.2°
CCD_Profile_fitting scans	h = −5→5
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −16→16
T_min = 0.720, T_max = 0.909	l = −19→19
8831 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.033	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.076	H-atom parameters constrained
S = 1.08	w = 1/[σ²(F_o²) + (0.0293P)² + 0.274P] where P = (F_o² + 2F_c²)/3
1961 reflections	(Δ/σ)_max = 0.001
92 parameters	Δρ_max = 0.21 e Å⁻³
0 restraints	Δρ_min = −0.19 e Å⁻³

Crystal data top

C₆H₁₀N₂²⁺·2Cl⁻	V = 857.9 (3) Å³
M_r = 181.06	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 4.5874 (9) Å	µ = 0.69 mm⁻¹
b = 12.650 (3) Å	T = 293 K
c = 14.814 (3) Å	0.50 × 0.45 × 0.15 mm
β = 93.61 (3)°

Data collection top

Rigaku SCXmini diffractometer	1961 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	1684 reflections with I > 2σ(I)
T_min = 0.720, T_max = 0.909	R_int = 0.035
8831 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.033	0 restraints
wR(F²) = 0.076	H-atom parameters constrained
S = 1.08	Δρ_max = 0.21 e Å⁻³
1961 reflections	Δρ_min = −0.19 e Å⁻³
92 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
Cl2	0.34023 (9)	0.98847 (3)	0.37672 (3)	0.03348 (13)
N1	0.9075 (3)	0.64924 (10)	−0.01920 (10)	0.0333 (3)
H1A	0.7885	0.6098	0.0120	0.050*
H1B	0.9905	0.6091	−0.0598	0.050*
H1C	0.8058	0.7007	−0.0474	0.050*
C6	1.1364 (4)	0.69588 (14)	0.04332 (13)	0.0365 (4)
H6A	1.2888	0.7253	0.0084	0.044*
H6B	1.2231	0.6405	0.0815	0.044*
C1	1.1087 (4)	0.88417 (13)	0.08977 (12)	0.0337 (4)
H1	1.2349	0.9000	0.0449	0.040*
C5	0.8274 (4)	0.94441 (14)	0.20641 (12)	0.0370 (4)
H5	0.7619	1.0005	0.2403	0.044*
C2	1.0214 (3)	0.78119 (13)	0.10227 (11)	0.0293 (4)
C4	0.7351 (4)	0.84350 (14)	0.22213 (12)	0.0371 (4)
H4	0.6060	0.8304	0.2668	0.045*
C3	0.8357 (4)	0.76140 (14)	0.17102 (12)	0.0349 (4)
H3	0.7788	0.6924	0.1826	0.042*
Cl1	0.40819 (11)	0.14752 (3)	0.10233 (3)	0.04427 (15)
N2	1.0124 (3)	0.96146 (11)	0.14194 (10)	0.0367 (4)
H2	1.0724	1.0249	0.1336	0.044*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl2	0.0384 (2)	0.0291 (2)	0.0340 (2)	−0.00167 (16)	0.01032 (17)	−0.00133 (16)
N1	0.0389 (8)	0.0256 (7)	0.0362 (8)	0.0047 (6)	0.0099 (6)	−0.0021 (6)
C6	0.0310 (9)	0.0315 (9)	0.0479 (11)	0.0040 (7)	0.0086 (8)	−0.0028 (8)
C1	0.0347 (9)	0.0314 (9)	0.0352 (9)	0.0001 (7)	0.0041 (7)	0.0029 (7)
C5	0.0440 (10)	0.0354 (10)	0.0311 (9)	0.0044 (8)	−0.0011 (8)	−0.0071 (7)
C2	0.0260 (8)	0.0284 (8)	0.0331 (9)	0.0020 (6)	−0.0008 (7)	−0.0010 (7)
C4	0.0406 (10)	0.0407 (10)	0.0306 (9)	−0.0030 (8)	0.0064 (8)	−0.0032 (7)
C3	0.0390 (10)	0.0297 (9)	0.0363 (10)	−0.0038 (7)	0.0044 (8)	0.0005 (7)
Cl1	0.0486 (3)	0.0305 (2)	0.0547 (3)	0.00301 (18)	0.0108 (2)	0.00943 (19)
N2	0.0462 (9)	0.0237 (7)	0.0397 (9)	−0.0029 (6)	−0.0014 (7)	0.0013 (6)

Geometric parameters (Å, º) top

N1—C6	1.478 (2)	C1—H1	0.9300
N1—H1A	0.8900	C5—N2	1.334 (2)
N1—H1B	0.8900	C5—C4	1.369 (3)
N1—H1C	0.8900	C5—H5	0.9300
C6—C2	1.504 (2)	C2—C3	1.391 (2)
C6—H6A	0.9700	C4—C3	1.382 (2)
C6—H6B	0.9700	C4—H4	0.9300
C1—N2	1.338 (2)	C3—H3	0.9300
C1—C2	1.379 (2)	N2—H2	0.8600

C6—N1—H1A	109.5	N2—C5—C4	119.33 (16)
C6—N1—H1B	109.5	N2—C5—H5	120.3
H1A—N1—H1B	109.5	C4—C5—H5	120.3
C6—N1—H1C	109.5	C1—C2—C3	117.69 (16)
H1A—N1—H1C	109.5	C1—C2—C6	118.97 (16)
H1B—N1—H1C	109.5	C3—C2—C6	123.31 (15)
N1—C6—C2	112.88 (13)	C5—C4—C3	119.34 (17)
N1—C6—H6A	109.0	C5—C4—H4	120.3
C2—C6—H6A	109.0	C3—C4—H4	120.3
N1—C6—H6B	109.0	C4—C3—C2	120.47 (16)
C2—C6—H6B	109.0	C4—C3—H3	119.8
H6A—C6—H6B	107.8	C2—C3—H3	119.8
N2—C1—C2	120.23 (16)	C5—N2—C1	122.89 (15)
N2—C1—H1	119.9	C5—N2—H2	118.6
C2—C1—H1	119.9	C1—N2—H2	118.6

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···Cl2ⁱ	0.89	2.35	3.1914 (16)	157
N1—H1B···Cl2ⁱⁱ	0.89	2.27	3.1206 (16)	159
N1—H1C···Cl1ⁱⁱⁱ	0.89	2.28	3.1622 (16)	170
N2—H2···Cl1^iv	0.86	2.25	3.0520 (16)	154
C3—H3···Cl2ⁱ	0.93	2.77	3.606 (2)	150
C6—H6A···Cl1^v	0.97	2.74	3.676 (2)	163
C6—H6B···Cl2^vi	0.97	2.82	3.700 (2)	152

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

Experimental details

Crystal data
Chemical formula	C₆H₁₀N₂²⁺·2Cl⁻
M_r	181.06
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	4.5874 (9), 12.650 (3), 14.814 (3)
β (°)	93.61 (3)
V (Å³)	857.9 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.69
Crystal size (mm)	0.50 × 0.45 × 0.15

Data collection
Diffractometer	Rigaku SCXmini diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku, 2005)
T_min, T_max	0.720, 0.909
No. of measured, independent and observed [I > 2σ(I)] reflections	8831, 1961, 1684
R_int	0.035
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.033, 0.076, 1.08
No. of reflections	1961
No. of parameters	92
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.19

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PRPKAPPA (Ferguson, 1999).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···Cl2ⁱ	0.89	2.35	3.1914 (16)	157
N1—H1B···Cl2ⁱⁱ	0.89	2.27	3.1206 (16)	159
N1—H1C···Cl1ⁱⁱⁱ	0.89	2.28	3.1622 (16)	170
N2—H2···Cl1^iv	0.86	2.25	3.0520 (16)	154
C3—H3···Cl2ⁱ	0.93	2.77	3.606 (2)	150
C6—H6A···Cl1^v	0.97	2.74	3.676 (2)	163
C6—H6B···Cl2^vi	0.97	2.82	3.700 (2)	152

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

Acknowledgements

This work was supported by the Technical Fund Financing Projects (No. 9207042464 and 9207041482) from Southeast University to ZRQ.

References

Chtioui, A. & Jouini, A. (2004). J. Chem. Crystallogr. A34, 43–49. Web of Science CSD CrossRef Google Scholar
Ferguson, G. (1999). PRPKAPPA. University of Guelph, Canada. Google Scholar
Genet, F. (1965). Bull. Soc. Fr. Mineral. Cristallogr. 88, 463–470. CAS Google Scholar
Long, G. S., Wei, M. & Willett, R. D. (1997). Inorg. Chem. 36, 3102–3107. CSD CrossRef PubMed CAS Web of Science Google Scholar
Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar