Redetermination of 3-(ammonio­meth­yl)pyridinium dichloride

Abstract

The crystal structure of the title compound, C₆H₁₀N₂ ²⁺·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

• C₆H₁₀N₂ ²⁺·2Cl⁻

• M _r = 181.06

• Monoclinic,

• a = 4.5874 (9) Å

• b = 12.650 (3) Å

• c = 14.814 (3) Å

• β = 93.61 (3)°

• V = 857.9 (3) ų

• 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[F ² > 2σ(F ²)] = 0.033

• wR(F ²) = 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

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 ▶).

Supplementary Material

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

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⋯Cl1iv	0.86	2.25	3.0520 (16)	154
C3—H3⋯Cl2i	0.93	2.77	3.606 (2)	150
C6—H6A⋯Cl1v	0.97	2.74	3.676 (2)	163
C6—H6B⋯Cl2vi	0.97	2.82	3.700 (2)	152

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) ; (vi) .

supplementary crystallographic information

Comment

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.

Experimental

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.

Refinement

Positional parameters of all the H atoms were calculated geometrically and were allowed to ride on their parent atoms, with C—H = 0.93-0.97 Å, N—H = 0.86-0.89 Å, and with U_iso(H) = 1.2 U_eq(C, N).

Figures

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.

Crystal data

C6H10N22+·2Cl−	F(000) = 376
Mr = 181.06	Dx = 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

Rigaku SCXmini diffractometer	1961 independent reflections
Radiation source: fine-focus sealed tube	1684 reflections with I > 2σ(I)
graphite	Rint = 0.035
Detector resolution: 13.662 pixels mm-1	θmax = 27.5°, θmin = 3.2°
CCD_Profile_fitting scans	h = −5→5
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −16→16
Tmin = 0.720, Tmax = 0.909	l = −19→19
8831 measured reflections

Refinement

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(Fo2) + (0.0293P)2 + 0.274P] where P = (Fo2 + 2Fc2)/3
1961 reflections	(Δ/σ)max = 0.001
92 parameters	Δρmax = 0.21 e Å−3
0 restraints	Δρmin = −0.19 e Å−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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, °)

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, °)

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···Cl1iv	0.86	2.25	3.0520 (16)	154
C3—H3···Cl2i	0.93	2.77	3.606 (2)	150
C6—H6A···Cl1v	0.97	2.74	3.676 (2)	163
C6—H6B···Cl2vi	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.