supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportcited insimilar papers Open access

Acta Cryst. (2009). E65, o1519    [ doi:10.1107/S1600536809021011 ]

2,3-Diaminopyridinium benzoate

K. Balasubramani and H.-K. Fun

Abstract top

In the title compound, C5H8N3+·C7H5O2-, the pyridine N atom is protonated. The carboxylate group of the benzoate anion is twisted away from the attached ring by 10.91 (9)°. In the crystal structure, N-H...O hydrogen bonds between 2,3-diaminopyridinium cations and benzoate anions, and [pi]-[pi] interactions between the pyridinium rings [centroid-centroid distance = 3.6467 (9) Å] form a two-dimensional network parallel to (001). In the network, N-H...O hydrogen bonds form R22(8) and R21(7) ring motifs.

Comment top

Pyridine and its derivatives play an important role in heterocyclic chemistry (Pozharski et al., 1997; Katritzky et al., 1996). Pyridine and its substituted derivatives are often involved in hydrogen-bond interactions (Jeffrey & Saenger, 1991; Jeffrey, 1997; Scheiner, 1997). Since our aim is to study some interesting hydrogen-bonding interactions, the crystal structure of the title compound is presented here.

The asymmetric unit (Fig 1), contains a protonated 2,3-diaminopyridinium cation and a benzoate anion. The bond lengths (Allen et al.,1987) and angles are normal. In the 2,3-diaminopyridinium cation, the protonated N1 atom has lead to a slight increase in C8—N1—C12 angle to 123.30 (14)°. Moreover, the carboxylate group is twisted slightly out of the attached ring; the dihedral angle between C1—C6 and O1/O2/C7/C6 planes is 10.91 (9)°. The 2,3-diaminopyridinium cation is planar, with a maximum deviation of 0.0089 (17) Å for atom C9.

In the crystal packing, the protonated N1 atom and the 2-amino group (N2) is hydrogen-bonded to the carboxylate oxygen atoms (O1 and O2) via a pair of N—H···O hydrogen bonds forming an R22(8) ring motif (Bernstein et al., 1995). The two amino groups (N2 and N3) are involved in N—H···O hydrogen bonding interactions to form an R12(7) ring motif. The cationic and anionic units are linked through N—H···O hydrogen bonds (Table 1 and Fig 2) to form a two-dimensional network parallel to the (001) plane. The crystal structure is further stabilized by π-π stacking interactions between the pyridinium rings of the cations at (x, y, z) and (-x, 1-y, 1-z), with a centroid to centroid distance of 3.6467 (9) Å.

Related literature top

For general background to pyridine derivatives, see: Pozharski et al. (1997); Katritzky et al. (1996). For bond-length data, see: Allen et al. (1987). For details on hydrogen bonding, see: Jeffrey & Saenger (1991); Jeffrey (1997); Scheiner (1997). For hydrogen-bond motifs, see: Bernstein et al. (1995). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).

Experimental top

Hot methanol solutions (20 ml) of 2,3-diaminopyridine (27 mg, Aldrich) and benzoic acid (31 mg, Merck) were mixed and warmed over a heating magnetic stirrer for 5 minutes. The resulting solution was allowed to cool slowly at room temperature. Crystals of the title compound appeared from the mother liquor after a few days.

Refinement top

All H atoms were located in a difference Fourier map and allowed to refine freely [N-H = 0.89 (2)–0.95 (2) Å and C–H = 0.97 (18)–1.02 (2) Å].

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The asymmetric unit of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme. Dashed lines indicate hydrogen bonds.
[Figure 2] Fig. 2. Part of the crystal packing of the title compound. Dashed lines indicate hydrogen bonds.
2,3-Diaminopyridinium benzoate top
Crystal data top
C5H8N3+·C7H5O2−F(000) = 976
Mr = 231.25Dx = 1.319 Mg m−3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 3782 reflections
a = 10.1498 (3) Åθ = 2.8–27.9°
b = 11.0656 (3) ŵ = 0.09 mm−1
c = 20.7368 (7) ÅT = 100 K
V = 2329.03 (12) Å3Plate, brown
Z = 80.43 × 0.40 × 0.03 mm
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer		3443 independent reflections
Radiation source: fine-focus sealed tube2559 reflections with I > 2σ(I)
graphiteRint = 0.070
φ and ω scansθmax = 30.1°, θmin = 2.9°
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		h = −14→14
Tmin = 0.935, Tmax = 0.998k = −15→15
27109 measured reflectionsl = −26→29
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.065Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.124H atoms treated by a mixture of independent and constrained refinement
S = 1.09 w = 1/[σ2(Fo2) + (0.0394P)2 + 1.0527P]
where P = (Fo2 + 2Fc2)/3
3443 reflections(Δ/σ)max = 0.001
206 parametersΔρmax = 0.26 e Å−3
0 restraintsΔρmin = −0.22 e Å−3
Crystal data top
C5H8N3+·C7H5O2−V = 2329.03 (12) Å3
Mr = 231.25Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 10.1498 (3) ŵ = 0.09 mm−1
b = 11.0656 (3) ÅT = 100 K
c = 20.7368 (7) Å0.43 × 0.40 × 0.03 mm
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer		3443 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		2559 reflections with I > 2σ(I)
Tmin = 0.935, Tmax = 0.998Rint = 0.070
27109 measured reflectionsθmax = 30.1°
Refinement top
R[F2 > 2σ(F2)] = 0.065H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.124Δρmax = 0.26 e Å−3
S = 1.09Δρmin = −0.22 e Å−3
3443 reflectionsAbsolute structure: ?
206 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

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
xyzUiso*/Ueq
O10.41320 (11)0.39789 (9)0.63510 (5)0.0253 (3)
O20.39681 (11)0.57595 (9)0.58541 (5)0.0257 (3)
C60.54129 (15)0.55976 (13)0.67572 (8)0.0217 (3)
C10.57778 (16)0.49395 (15)0.73019 (8)0.0271 (4)
C20.66687 (18)0.54115 (17)0.77390 (10)0.0347 (4)
C30.72160 (19)0.65474 (16)0.76378 (10)0.0365 (4)
C40.68658 (19)0.72004 (16)0.70966 (10)0.0375 (5)
C50.59687 (17)0.67368 (14)0.66578 (9)0.0296 (4)
C70.44423 (15)0.50698 (13)0.62917 (7)0.0211 (3)
C90.06661 (15)0.32936 (13)0.46855 (8)0.0220 (3)
C80.15562 (15)0.37759 (13)0.51515 (8)0.0211 (3)
N10.22115 (13)0.47997 (11)0.50049 (7)0.0230 (3)
N20.17608 (14)0.32713 (12)0.57320 (7)0.0239 (3)
N3−0.00614 (14)0.22766 (12)0.48334 (8)0.0273 (3)
C120.20715 (17)0.53936 (14)0.44310 (9)0.0270 (4)
C110.12491 (17)0.49519 (15)0.39762 (9)0.0288 (4)
C100.05443 (17)0.38821 (14)0.41056 (9)0.0268 (4)
H12A0.262 (2)0.6122 (17)0.4384 (9)0.039 (5)*
H11A0.1152 (17)0.5333 (16)0.3555 (9)0.028 (5)*
H10A−0.0033 (18)0.3556 (15)0.3778 (9)0.027 (5)*
H1A0.5401 (19)0.4138 (17)0.7363 (9)0.037 (5)*
H2A0.690 (2)0.4955 (18)0.8134 (10)0.045 (6)*
H3A0.785 (2)0.6890 (17)0.7969 (10)0.043 (6)*
H4A0.726 (2)0.7970 (19)0.7013 (10)0.051 (6)*
H5A0.5737 (18)0.7200 (17)0.6276 (9)0.032 (5)*
H1N10.283 (2)0.5096 (18)0.5312 (9)0.039 (5)*
H1N20.248 (2)0.3487 (16)0.5959 (9)0.033 (5)*
H2N20.146 (2)0.253 (2)0.5800 (10)0.047 (6)*
H1N30.021 (2)0.1812 (18)0.5170 (10)0.042 (6)*
H2N3−0.043 (2)0.1882 (17)0.4469 (10)0.041 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0278 (6)0.0181 (5)0.0298 (6)−0.0009 (4)−0.0021 (5)0.0002 (4)
O20.0280 (6)0.0205 (5)0.0285 (6)−0.0020 (4)−0.0058 (5)0.0020 (4)
C60.0181 (7)0.0209 (7)0.0261 (8)0.0037 (5)0.0001 (6)−0.0025 (6)
C10.0252 (8)0.0271 (8)0.0291 (9)0.0039 (6)−0.0009 (7)0.0015 (7)
C20.0335 (10)0.0398 (10)0.0308 (10)0.0067 (8)−0.0089 (8)0.0007 (8)
C30.0339 (10)0.0346 (9)0.0410 (11)0.0058 (7)−0.0150 (8)−0.0104 (8)
C40.0361 (10)0.0245 (8)0.0520 (12)−0.0009 (7)−0.0165 (9)−0.0026 (8)
C50.0298 (9)0.0227 (7)0.0364 (10)0.0003 (6)−0.0111 (8)0.0019 (7)
C70.0197 (7)0.0210 (7)0.0226 (8)0.0019 (5)0.0027 (6)−0.0013 (6)
C90.0194 (7)0.0182 (7)0.0285 (9)0.0017 (5)−0.0004 (6)−0.0027 (6)
C80.0192 (7)0.0175 (6)0.0265 (8)0.0028 (5)0.0011 (6)−0.0016 (6)
N10.0223 (7)0.0186 (6)0.0281 (7)−0.0011 (5)−0.0013 (6)−0.0012 (5)
N20.0237 (7)0.0213 (6)0.0269 (8)−0.0029 (5)−0.0020 (6)0.0014 (5)
N30.0288 (7)0.0217 (6)0.0314 (8)−0.0048 (5)−0.0055 (7)0.0010 (6)
C120.0286 (9)0.0204 (7)0.0320 (9)−0.0014 (6)0.0008 (7)0.0038 (6)
C110.0319 (9)0.0260 (8)0.0285 (9)0.0006 (7)−0.0019 (7)0.0054 (7)
C100.0252 (8)0.0269 (8)0.0283 (9)0.0000 (6)−0.0043 (7)−0.0014 (7)
Geometric parameters (Å, °) top
O1—C71.2537 (17)C9—N31.3805 (19)
O2—C71.2796 (18)C9—C81.427 (2)
C6—C11.394 (2)C8—N21.343 (2)
C6—C51.396 (2)C8—N11.3484 (19)
C6—C71.498 (2)N1—C121.367 (2)
C1—C21.383 (2)N1—H1N10.96 (2)
C1—H1A0.974 (19)N2—H1N20.90 (2)
C2—C31.390 (3)N2—H2N20.88 (2)
C2—H2A0.99 (2)N3—H1N30.91 (2)
C3—C41.381 (3)N3—H2N30.95 (2)
C3—H3A1.02 (2)C12—C111.351 (2)
C4—C51.386 (2)C12—H12A0.99 (2)
C4—H4A0.96 (2)C11—C101.409 (2)
C5—H5A0.972 (19)C11—H11A0.975 (18)
C9—C101.373 (2)C10—H10A0.966 (18)
C1—C6—C5118.94 (15)N3—C9—C8119.55 (15)
C1—C6—C7119.56 (14)N2—C8—N1118.36 (14)
C5—C6—C7121.50 (14)N2—C8—C9123.34 (14)
C2—C1—C6120.50 (16)N1—C8—C9118.29 (14)
C2—C1—H1A121.0 (12)C8—N1—C12123.30 (14)
C6—C1—H1A118.5 (12)C8—N1—H1N1117.7 (12)
C1—C2—C3120.25 (17)C12—N1—H1N1119.0 (12)
C1—C2—H2A120.4 (12)C8—N2—H1N2118.9 (12)
C3—C2—H2A119.3 (12)C8—N2—H2N2118.3 (14)
C4—C3—C2119.53 (17)H1N2—N2—H2N2116.3 (18)
C4—C3—H3A121.2 (11)C9—N3—H1N3117.9 (13)
C2—C3—H3A119.3 (11)C9—N3—H2N3114.0 (12)
C3—C4—C5120.59 (17)H1N3—N3—H2N3118.1 (17)
C3—C4—H4A120.4 (13)C11—C12—N1119.87 (15)
C5—C4—H4A119.0 (13)C11—C12—H12A125.2 (11)
C4—C5—C6120.18 (17)N1—C12—H12A114.9 (11)
C4—C5—H5A119.9 (11)C12—C11—C10118.99 (16)
C6—C5—H5A119.9 (11)C12—C11—H11A122.1 (11)
O1—C7—O2123.33 (14)C10—C11—H11A118.9 (11)
O1—C7—C6118.52 (14)C9—C10—C11121.30 (16)
O2—C7—C6118.15 (13)C9—C10—H10A119.5 (10)
C10—C9—N3122.21 (15)C11—C10—H10A119.2 (10)
C10—C9—C8118.22 (14)
C5—C6—C1—C20.5 (2)C10—C9—C8—N2−179.52 (15)
C7—C6—C1—C2−179.77 (15)N3—C9—C8—N21.9 (2)
C6—C1—C2—C3−0.3 (3)C10—C9—C8—N11.4 (2)
C1—C2—C3—C4−0.1 (3)N3—C9—C8—N1−177.16 (13)
C2—C3—C4—C50.5 (3)N2—C8—N1—C12−179.52 (14)
C3—C4—C5—C6−0.3 (3)C9—C8—N1—C12−0.4 (2)
C1—C6—C5—C4−0.1 (3)C8—N1—C12—C11−0.4 (2)
C7—C6—C5—C4−179.90 (16)N1—C12—C11—C100.2 (2)
C1—C6—C7—O1−10.6 (2)N3—C9—C10—C11176.89 (15)
C5—C6—C7—O1169.17 (15)C8—C9—C10—C11−1.7 (2)
C1—C6—C7—O2169.17 (14)C12—C11—C10—C90.8 (3)
C5—C6—C7—O2−11.1 (2)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O20.96 (2)1.77 (2)2.7218 (18)176 (2)
N2—H1N2···O10.90 (2)1.94 (2)2.8377 (18)173 (2)
N2—H2N2···O2i0.88 (2)2.01 (2)2.8873 (17)170 (2)
N3—H1N3···O2i0.91 (2)2.02 (2)2.9206 (19)173 (2)
N3—H2N3···O1ii0.95 (2)2.00 (2)2.9382 (19)170 (2)
Symmetry codes: (i) −x+1/2, y−1/2, z; (ii) x−1/2, −y+1/2, −z+1.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O20.96 (2)1.77 (2)2.7218 (18)176 (2)
N2—H1N2···O10.90 (2)1.94 (2)2.8377 (18)173 (2)
N2—H2N2···O2i0.88 (2)2.01 (2)2.8873 (17)170 (2)
N3—H1N3···O2i0.91 (2)2.02 (2)2.9206 (19)173 (2)
N3—H2N3···O1ii0.95 (2)2.00 (2)2.9382 (19)170 (2)
Symmetry codes: (i) −x+1/2, y−1/2, z; (ii) x−1/2, −y+1/2, −z+1.
Acknowledgements top

HKF and KB thank the Malaysian Government and Universiti Sains Malaysia for the Science Fund grant No. 305/PFIZIK/613312. KB thanks Universiti Sains Malaysia for a post–doctoral research fellowship. HKF also thanks Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012.

references
References top

Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.

Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.

Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.

Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107.

Jeffrey, G. A. (1997). In An Introduction to Hydrogen Bonding. Oxford University Press.

Jeffrey, G. A. & Saenger, W. (1991). In Hydrogen Bonding in Biological Structures. Berlin: Springer.

Katritzky, A. R., Rees, C. W. & Scriven, E. F. V. (1996). In Comprehensive Heterocyclic Chemistry II. Oxford: Pergamon Press.

Pozharski, A. F., Soldatenkov, A. T. & Katritzky, A. R. (1997). In Heterocycles in Life and Society. New York: Wiley.

Scheiner, S. (1997). In Hydrogen Bonding, A Theoretical Perspective. Oxford University Press.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Spek, A. L. (2009). Acta Cryst. D65, 148–155.