Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807031042/kp2115sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807031042/kp2115Isup2.hkl |
CCDC reference: 655056
Key indicators
- Single-crystal X-ray study
- T = 294 K
- Mean (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
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).
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.
Hydrogen atoms were put in idealized positions and refined as 'riding model' with Uiso set at 1.2 times Ueq of appropriate carrier atoms. The disordered atoms of the anion were found in difference Fourier map and anisotropically refined without restraints.
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).
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).
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.
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) Å3 | 0.25 × 0.15 × 0.1 mm |
Z = 2 |
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 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)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.097 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0437P)2 + 0.0483P] where P = (Fo2 + 2Fc2)/3 |
868 reflections | (Δ/σ)max < 0.001 |
79 parameters | Δρmax = 0.22 e Å−3 |
0 restraints | Δρmin = −0.22 e Å−3 |
C5H8N3+·ClO4− | V = 420.13 (12) Å3 |
Mr = 209.59 | Z = 2 |
Monoclinic, P21/m | Mo Kα radiation |
a = 5.0007 (8) Å | µ = 0.44 mm−1 |
b = 10.3776 (17) Å | T = 294 K |
c = 8.2345 (14) Å | 0.25 × 0.15 × 0.1 mm |
β = 100.535 (17)° |
Kuma KM-4-CCD four-circle diffractometer | 638 reflections with I > 2σ(I) |
2095 measured reflections | Rint = 0.028 |
868 independent reflections |
R[F2 > 2σ(F2)] = 0.044 | 0 restraints |
wR(F2) = 0.097 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.22 e Å−3 |
868 reflections | Δρmin = −0.22 e Å−3 |
79 parameters |
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. |
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 |
U11 | U22 | U33 | U12 | U13 | U23 | |
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) |
N1—C2i | 1.356 (3) | C4—C3i | 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—O2i | 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—O2Ai | 1.424 (9) |
C3—C4 | 1.371 (3) | Cl1—O3i | 1.426 (4) |
C3—H3 | 0.9300 | Cl1—O3 | 1.426 (4) |
C2i—N1—C2 | 124.7 (3) | C3—C4—H4 | 118.6 |
C2i—N1—H1 | 117.6 | O2—Cl1—O1 | 110.9 (4) |
C2—N1—H1 | 117.6 | O2i—Cl1—O1 | 110.9 (4) |
N2—C2—N1 | 117.3 (2) | O2i—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—O2Ai | 107.8 (4) |
C2—N2—H2A | 120.0 | O1—Cl1—O2Ai | 108.6 (4) |
C2—N2—H2B | 120.0 | O2—Cl1—O3i | 107.2 (4) |
H2A—N2—H2B | 120.0 | O1—Cl1—O3i | 110.04 (19) |
C4—C3—C2 | 118.5 (3) | O2Ai—Cl1—O3i | 112.2 (5) |
C4—C3—H3 | 120.8 | O2i—Cl1—O3 | 107.2 (4) |
C2—C3—H3 | 120.8 | O1—Cl1—O3 | 110.04 (18) |
C3i—C4—C3 | 122.8 (4) | O2A—Cl1—O3 | 112.2 (5) |
C3i—C4—H4 | 118.6 | ||
C2i—N1—C2—N2 | −179.11 (18) | N1—C2—C3—C4 | −0.3 (4) |
C2i—N1—C2—C3 | 0.1 (4) | C2—C3—C4—C3i | 0.6 (5) |
N2—C2—C3—C4 | 178.8 (3) |
Symmetry code: (i) x, −y+1/2, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2ii | 0.86 | 2.19 | 2.988 (9) | 154 |
N2—H2A···O2ii | 0.86 | 2.26 | 3.034 (10) | 149 |
N2—H2B···O1iii | 0.86 | 2.45 | 3.025 (2) | 124 |
C4—H4···O3iv | 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. |
Experimental details
Crystal data | |
Chemical formula | C5H8N3+·ClO4− |
Mr | 209.59 |
Crystal system, space group | Monoclinic, P21/m |
Temperature (K) | 294 |
a, b, c (Å) | 5.0007 (8), 10.3776 (17), 8.2345 (14) |
β (°) | 100.535 (17) |
V (Å3) | 420.13 (12) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.44 |
Crystal size (mm) | 0.25 × 0.15 × 0.1 |
Data collection | |
Diffractometer | Kuma KM-4-CCD four-circle |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2095, 868, 638 |
Rint | 0.028 |
(sin θ/λ)max (Å−1) | 0.617 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.097, 1.06 |
No. of reflections | 868 |
No. of parameters | 79 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.22, −0.22 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2002), CrysAlis CCD, CrysAlis RED (Oxford Diffraction, 2002), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), Stereochemical Workstation (Siemens, 1989), SHELXL97.
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 0.86 | 2.19 | 2.988 (9) | 154.3 |
N2—H2A···O2i | 0.86 | 2.26 | 3.034 (10) | 148.9 |
N2—H2B···O1ii | 0.86 | 2.45 | 3.025 (2) | 124.4 |
C4—H4···O3iii | 0.93 | 2.56 | 3.474 (5) | 168.5 |
Symmetry codes: (i) x, −y+1/2, z−1; (ii) −x+2, −y, −z+1; (iii) x−1, −y+1/2, z. |
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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).