2,6-Diamino­pyridinium perchlorate

In the title salt, C₅H₈N₃⁺·ClO₄⁻, a mirror plane runs through the ring N atom and the para-C atom of the cation, and also through Cl and one O atom of the anion. The anion is disordered equally over two positions. A network of N—H...O hydrogen bonds connects the cations and anions into layers, forming a stair-like structure.

Key indicators

• Single-crystal X-ray study
• T = 294 K
• Mean [sigma](C-C) = 0.004 Å
• Disorder in main residue
• R factor = 0.044
• wR factor = 0.097
• Data-to-parameter ratio = 11.0

checkCIF/PLATON results

No syntax errors found





Alert level B
PLAT241_ALERT_2_B Check High      Ueq as Compared to Neighbors for        O2A
PLAT242_ALERT_2_B Check Low       Ueq as Compared to Neighbors for        Cl1

Alert level C
PLAT301_ALERT_3_C Main Residue  Disorder .........................      19.00 Perc.

   0 ALERT level A = In general: serious problem
   2 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

The 2,6-diaminopyridine is used as component for the self-assembled supramolecular architectures displaying interesting structures (Liu et al., 2001) useful as a pharmaceutical intermediate for the synthesis of analgesic drugs (Scriven et al., 1996) and in the construction of electrochemical sensor for detection of ascorbic acid (Cao et al., 2006). The title compound was isolated in the course of our studies of Schiff base metal complexes with novel physico-chemical properties and potential applications.

The compound I (Fig. 1) crystallizes in the monoclinic space group P2₁/m with two molecules in the unit cell with asymmetric unit comprising half of a molecule. The crystallographic mirror plane passes the pyridinium ring along N1···C4 line (H1, N1 and C4 all lie in the plane) while in the anion Cl and one of oxygen atoms are in this plane. The anion is moreover disordered over two positions with occupancy factors 0.5 for involving atoms. The attempts to refine the structure in non-centrosymmetric P2₁ space group gave results inferior to the centrosymmetric model. The cations and anions are connected by means of N—H···O hydrogen bonds into layers (Tale 1, Fig. 2). These layers are also connected by N—H···O hydrogen bonds into the stair-like structure (Fig. 3).

Related literature

There are a number of structures of 2,6-diaminopyridinium salts with different anions. For example, see Bertolasi et al. (2001). For related literature, see Cao et al. (2006), Liu et al. (2001), Scriven et al. (1996).

S2. Experimental

To a solution of lanthanum(III) perchlorate (0.1 mmol) in acetonitrile (10 ml), 2,6-diaminopyridine (0.2 mmol) in acetonitrile (10 ml) was added with stirring. The reaction was carried out for 24 h at room temperature. The solution volume was then reduced to 10 ml by roto-evaporation and very small amount of precipitate was formed on addition of diethyl ether. The solution over the precipitate was separated and left to evaporate at room temperature affording transparent long needles of I after three days.

S3. Refinement

Hydrogen atoms were put in idealized positions and refined as 'riding model' with U_iso set at 1.2 times U_eq of appropriate carrier atoms. The disordered atoms of the anion were found in difference Fourier map and anisotropically refined without restraints.

Computing details

Data collection: CrysAlis CCD (Oxford Diffraction, 2002); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Stereochemical Workstation (Siemens, 1989); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. Molecular structure of I with displacement parameters scalled at the 50% probability level (Siemens, 1989) and numbering scheme. The hydrogen atoms are drawn as spheres with arbitrary radii. Only one orientation of disordered perchlorate anion is shown.
	Fig. 2. The layer of the cations and anions connected by hydrogen bonds (Siemens, 1989). Hydrogen bonds are drawn as dashed lines. The symmetry codes used: (i) x, y, z; (ii) x, y, -1 + z; (ii) 2 - x, -y, -z; (iv) 2 - x, -y, 1 - z; (v) 2 - x, 1/2 + y, -z; (vi) 2 - x, 1/2 + y, 1 - z; (vii) x, 1 + y, z; (viii) x, 1 + y, -1 + z.
	Fig. 3. The crystal packing along a direction (Siemens, 1989). Hydrogen bonds are shown as dashed lines.

2,6-Diaminopyridinium perchlorate

Crystal data

C5H8N3^+·ClO4^−	F(000) = 216
Mr = 209.59	Dx = 1.657 Mg m^−3
Monoclinic, P21/m	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yb	Cell parameters from 2311 reflections
a = 5.0007 (8) Å	θ = 4–24°
b = 10.3776 (17) Å	µ = 0.44 mm^−1
c = 8.2345 (14) Å	T = 294 K
β = 100.535 (17)°	Block, colourless
V = 420.13 (12) Å^3	0.25 × 0.15 × 0.1 mm
Z = 2

Data collection

Kuma KM-4-CCD four-circle diffractometer	638 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.028
Graphite monochromator	θmax = 26.0°, θmin = 3.2°
ω scan	h = −6→5
2095 measured reflections	k = −12→12
868 independent reflections	l = −8→10

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.044	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.097	H-atom parameters constrained
S = 1.06	w = 1/[σ^2(Fo^2) + (0.0437P)^2 + 0.0483P] where P = (Fo^2 + 2Fc^2)/3
868 reflections	(Δ/σ)max < 0.001
79 parameters	Δρmax = 0.22 e Å^−3
0 restraints	Δρmin = −0.22 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	Occ. (<1)
N1	0.5846 (5)	0.2500	0.2196 (3)	0.0384 (7)
H1	0.7017	0.2500	0.1550	0.046*
C2	0.4989 (5)	0.1342 (2)	0.2668 (3)	0.0410 (6)
N2	0.6064 (4)	0.0285 (2)	0.2109 (3)	0.0649 (7)
H2A	0.7248	0.0358	0.1477	0.078*
H2B	0.5571	−0.0466	0.2382	0.078*
C3	0.3110 (5)	0.1340 (3)	0.3701 (3)	0.0518 (7)
H3	0.2458	0.0569	0.4052	0.062*
C4	0.2224 (7)	0.2500	0.4198 (4)	0.0546 (11)
H4	0.0969	0.2500	0.4903	0.066*
Cl1	0.97841 (16)	0.2500	0.86291 (10)	0.0388 (3)
O1	1.2550 (4)	0.2500	0.8438 (3)	0.0529 (7)
O2	0.936 (2)	0.3390 (8)	0.9844 (9)	0.070 (2)	0.50
O3	0.8079 (6)	0.2124 (6)	0.7121 (4)	0.073 (3)	0.50
O2A	0.912 (2)	0.3748 (8)	0.9156 (12)	0.092 (3)	0.50

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0342 (15)	0.0461 (19)	0.0374 (16)	0.000	0.0135 (12)	0.000
C2	0.0370 (13)	0.0428 (16)	0.0416 (15)	−0.0033 (11)	0.0027 (11)	0.0009 (12)
N2	0.0677 (16)	0.0434 (15)	0.0858 (18)	0.0017 (12)	0.0201 (13)	−0.0080 (13)
C3	0.0452 (15)	0.064 (2)	0.0456 (16)	−0.0120 (13)	0.0057 (12)	0.0111 (13)
C4	0.040 (2)	0.089 (3)	0.037 (2)	0.000	0.0139 (16)	0.000
Cl1	0.0344 (5)	0.0420 (6)	0.0421 (5)	0.000	0.0128 (3)	0.000
O1	0.0330 (13)	0.0560 (17)	0.0736 (18)	0.000	0.0205 (11)	0.000
O2	0.087 (4)	0.065 (5)	0.066 (4)	−0.001 (4)	0.031 (3)	−0.026 (3)
O3	0.0501 (18)	0.124 (8)	0.0438 (19)	−0.023 (3)	0.0027 (14)	−0.003 (2)
O2A	0.095 (5)	0.038 (4)	0.161 (10)	0.026 (3)	0.071 (6)	0.002 (4)

Geometric parameters (Å, º)

N1—C2^i	1.356 (3)	C4—C3^i	1.371 (3)
N1—C2	1.356 (3)	C4—H4	0.9300
N1—H1	0.8600	Cl1—O2	1.406 (9)
C2—N2	1.339 (3)	Cl1—O2^i	1.406 (9)
C2—C3	1.378 (4)	Cl1—O1	1.421 (2)
N2—H2A	0.8600	Cl1—O2A	1.424 (9)
N2—H2B	0.8600	Cl1—O2A^i	1.424 (9)
C3—C4	1.371 (3)	Cl1—O3^i	1.426 (4)
C3—H3	0.9300	Cl1—O3	1.426 (4)
C2^i—N1—C2	124.7 (3)	C3—C4—H4	118.6
C2^i—N1—H1	117.6	O2—Cl1—O1	110.9 (4)
C2—N1—H1	117.6	O2^i—Cl1—O1	110.9 (4)
N2—C2—N1	117.3 (2)	O2^i—Cl1—O2A	107.8 (4)
N2—C2—C3	124.9 (3)	O1—Cl1—O2A	108.6 (4)
N1—C2—C3	117.7 (2)	O2—Cl1—O2A^i	107.8 (4)
C2—N2—H2A	120.0	O1—Cl1—O2A^i	108.6 (4)
C2—N2—H2B	120.0	O2—Cl1—O3^i	107.2 (4)
H2A—N2—H2B	120.0	O1—Cl1—O3^i	110.04 (19)
C4—C3—C2	118.5 (3)	O2A^i—Cl1—O3^i	112.2 (5)
C4—C3—H3	120.8	O2^i—Cl1—O3	107.2 (4)
C2—C3—H3	120.8	O1—Cl1—O3	110.04 (18)
C3^i—C4—C3	122.8 (4)	O2A—Cl1—O3	112.2 (5)
C3^i—C4—H4	118.6
C2^i—N1—C2—N2	−179.11 (18)	N1—C2—C3—C4	−0.3 (4)
C2^i—N1—C2—C3	0.1 (4)	C2—C3—C4—C3^i	0.6 (5)
N2—C2—C3—C4	178.8 (3)

Symmetry code: (i) x, −y+1/2, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2^ii	0.86	2.19	2.988 (9)	154
N2—H2A···O2^ii	0.86	2.26	3.034 (10)	149
N2—H2B···O1^iii	0.86	2.45	3.025 (2)	124
C4—H4···O3^iv	0.93	2.56	3.474 (5)	169

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