organic compounds
2,3-Diaminopyridinium benzoate
aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my
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 N—H⋯O hydrogen bonds between 2,3-diaminopyridinium cations and benzoate anions, and π–π 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.
Related literature
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 of 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
Crystal data
|
Refinement
|
Data collection: APEX2 (Bruker, 2005); cell SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536809021011/ci2821sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809021011/ci2821Isup2.hkl
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.
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].
Data collection: APEX2 (Bruker, 2005); cell
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).Fig. 1. The asymmetric unit of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme. Dashed lines indicate hydrogen bonds. | |
Fig. 2. Part of the crystal packing of the title compound. Dashed lines indicate hydrogen bonds. |
C5H8N3+·C7H5O2− | F(000) = 976 |
Mr = 231.25 | Dx = 1.319 Mg m−3 |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 3782 reflections |
a = 10.1498 (3) Å | θ = 2.8–27.9° |
b = 11.0656 (3) Å | µ = 0.09 mm−1 |
c = 20.7368 (7) Å | T = 100 K |
V = 2329.03 (12) Å3 | Plate, brown |
Z = 8 | 0.43 × 0.40 × 0.03 mm |
Bruker SMART APEXII CCD area-detector diffractometer | 3443 independent reflections |
Radiation source: fine-focus sealed tube | 2559 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.070 |
ϕ and ω scans | θmax = 30.1°, θmin = 2.9° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −14→14 |
Tmin = 0.935, Tmax = 0.998 | k = −15→15 |
27109 measured reflections | l = −26→29 |
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)] = 0.065 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.124 | H 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 parameters | Δρmax = 0.26 e Å−3 |
0 restraints | Δρmin = −0.22 e Å−3 |
C5H8N3+·C7H5O2− | V = 2329.03 (12) Å3 |
Mr = 231.25 | Z = 8 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 10.1498 (3) Å | µ = 0.09 mm−1 |
b = 11.0656 (3) Å | T = 100 K |
c = 20.7368 (7) Å | 0.43 × 0.40 × 0.03 mm |
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 = 0.998 | Rint = 0.070 |
27109 measured reflections |
R[F2 > 2σ(F2)] = 0.065 | 0 restraints |
wR(F2) = 0.124 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.09 | Δρmax = 0.26 e Å−3 |
3443 reflections | Δρmin = −0.22 e Å−3 |
206 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.41320 (11) | 0.39789 (9) | 0.63510 (5) | 0.0253 (3) | |
O2 | 0.39681 (11) | 0.57595 (9) | 0.58541 (5) | 0.0257 (3) | |
C6 | 0.54129 (15) | 0.55976 (13) | 0.67572 (8) | 0.0217 (3) | |
C1 | 0.57778 (16) | 0.49395 (15) | 0.73019 (8) | 0.0271 (4) | |
C2 | 0.66687 (18) | 0.54115 (17) | 0.77390 (10) | 0.0347 (4) | |
C3 | 0.72160 (19) | 0.65474 (16) | 0.76378 (10) | 0.0365 (4) | |
C4 | 0.68658 (19) | 0.72004 (16) | 0.70966 (10) | 0.0375 (5) | |
C5 | 0.59687 (17) | 0.67368 (14) | 0.66578 (9) | 0.0296 (4) | |
C7 | 0.44423 (15) | 0.50698 (13) | 0.62917 (7) | 0.0211 (3) | |
C9 | 0.06661 (15) | 0.32936 (13) | 0.46855 (8) | 0.0220 (3) | |
C8 | 0.15562 (15) | 0.37759 (13) | 0.51515 (8) | 0.0211 (3) | |
N1 | 0.22115 (13) | 0.47997 (11) | 0.50049 (7) | 0.0230 (3) | |
N2 | 0.17608 (14) | 0.32713 (12) | 0.57320 (7) | 0.0239 (3) | |
N3 | −0.00614 (14) | 0.22766 (12) | 0.48334 (8) | 0.0273 (3) | |
C12 | 0.20715 (17) | 0.53936 (14) | 0.44310 (9) | 0.0270 (4) | |
C11 | 0.12491 (17) | 0.49519 (15) | 0.39762 (9) | 0.0288 (4) | |
C10 | 0.05443 (17) | 0.38821 (14) | 0.41056 (9) | 0.0268 (4) | |
H12A | 0.262 (2) | 0.6122 (17) | 0.4384 (9) | 0.039 (5)* | |
H11A | 0.1152 (17) | 0.5333 (16) | 0.3555 (9) | 0.028 (5)* | |
H10A | −0.0033 (18) | 0.3556 (15) | 0.3778 (9) | 0.027 (5)* | |
H1A | 0.5401 (19) | 0.4138 (17) | 0.7363 (9) | 0.037 (5)* | |
H2A | 0.690 (2) | 0.4955 (18) | 0.8134 (10) | 0.045 (6)* | |
H3A | 0.785 (2) | 0.6890 (17) | 0.7969 (10) | 0.043 (6)* | |
H4A | 0.726 (2) | 0.7970 (19) | 0.7013 (10) | 0.051 (6)* | |
H5A | 0.5737 (18) | 0.7200 (17) | 0.6276 (9) | 0.032 (5)* | |
H1N1 | 0.283 (2) | 0.5096 (18) | 0.5312 (9) | 0.039 (5)* | |
H1N2 | 0.248 (2) | 0.3487 (16) | 0.5959 (9) | 0.033 (5)* | |
H2N2 | 0.146 (2) | 0.253 (2) | 0.5800 (10) | 0.047 (6)* | |
H1N3 | 0.021 (2) | 0.1812 (18) | 0.5170 (10) | 0.042 (6)* | |
H2N3 | −0.043 (2) | 0.1882 (17) | 0.4469 (10) | 0.041 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0278 (6) | 0.0181 (5) | 0.0298 (6) | −0.0009 (4) | −0.0021 (5) | 0.0002 (4) |
O2 | 0.0280 (6) | 0.0205 (5) | 0.0285 (6) | −0.0020 (4) | −0.0058 (5) | 0.0020 (4) |
C6 | 0.0181 (7) | 0.0209 (7) | 0.0261 (8) | 0.0037 (5) | 0.0001 (6) | −0.0025 (6) |
C1 | 0.0252 (8) | 0.0271 (8) | 0.0291 (9) | 0.0039 (6) | −0.0009 (7) | 0.0015 (7) |
C2 | 0.0335 (10) | 0.0398 (10) | 0.0308 (10) | 0.0067 (8) | −0.0089 (8) | 0.0007 (8) |
C3 | 0.0339 (10) | 0.0346 (9) | 0.0410 (11) | 0.0058 (7) | −0.0150 (8) | −0.0104 (8) |
C4 | 0.0361 (10) | 0.0245 (8) | 0.0520 (12) | −0.0009 (7) | −0.0165 (9) | −0.0026 (8) |
C5 | 0.0298 (9) | 0.0227 (7) | 0.0364 (10) | 0.0003 (6) | −0.0111 (8) | 0.0019 (7) |
C7 | 0.0197 (7) | 0.0210 (7) | 0.0226 (8) | 0.0019 (5) | 0.0027 (6) | −0.0013 (6) |
C9 | 0.0194 (7) | 0.0182 (7) | 0.0285 (9) | 0.0017 (5) | −0.0004 (6) | −0.0027 (6) |
C8 | 0.0192 (7) | 0.0175 (6) | 0.0265 (8) | 0.0028 (5) | 0.0011 (6) | −0.0016 (6) |
N1 | 0.0223 (7) | 0.0186 (6) | 0.0281 (7) | −0.0011 (5) | −0.0013 (6) | −0.0012 (5) |
N2 | 0.0237 (7) | 0.0213 (6) | 0.0269 (8) | −0.0029 (5) | −0.0020 (6) | 0.0014 (5) |
N3 | 0.0288 (7) | 0.0217 (6) | 0.0314 (8) | −0.0048 (5) | −0.0055 (7) | 0.0010 (6) |
C12 | 0.0286 (9) | 0.0204 (7) | 0.0320 (9) | −0.0014 (6) | 0.0008 (7) | 0.0038 (6) |
C11 | 0.0319 (9) | 0.0260 (8) | 0.0285 (9) | 0.0006 (7) | −0.0019 (7) | 0.0054 (7) |
C10 | 0.0252 (8) | 0.0269 (8) | 0.0283 (9) | 0.0000 (6) | −0.0043 (7) | −0.0014 (7) |
O1—C7 | 1.2537 (17) | C9—N3 | 1.3805 (19) |
O2—C7 | 1.2796 (18) | C9—C8 | 1.427 (2) |
C6—C1 | 1.394 (2) | C8—N2 | 1.343 (2) |
C6—C5 | 1.396 (2) | C8—N1 | 1.3484 (19) |
C6—C7 | 1.498 (2) | N1—C12 | 1.367 (2) |
C1—C2 | 1.383 (2) | N1—H1N1 | 0.96 (2) |
C1—H1A | 0.974 (19) | N2—H1N2 | 0.90 (2) |
C2—C3 | 1.390 (3) | N2—H2N2 | 0.88 (2) |
C2—H2A | 0.99 (2) | N3—H1N3 | 0.91 (2) |
C3—C4 | 1.381 (3) | N3—H2N3 | 0.95 (2) |
C3—H3A | 1.02 (2) | C12—C11 | 1.351 (2) |
C4—C5 | 1.386 (2) | C12—H12A | 0.99 (2) |
C4—H4A | 0.96 (2) | C11—C10 | 1.409 (2) |
C5—H5A | 0.972 (19) | C11—H11A | 0.975 (18) |
C9—C10 | 1.373 (2) | C10—H10A | 0.966 (18) |
C1—C6—C5 | 118.94 (15) | N3—C9—C8 | 119.55 (15) |
C1—C6—C7 | 119.56 (14) | N2—C8—N1 | 118.36 (14) |
C5—C6—C7 | 121.50 (14) | N2—C8—C9 | 123.34 (14) |
C2—C1—C6 | 120.50 (16) | N1—C8—C9 | 118.29 (14) |
C2—C1—H1A | 121.0 (12) | C8—N1—C12 | 123.30 (14) |
C6—C1—H1A | 118.5 (12) | C8—N1—H1N1 | 117.7 (12) |
C1—C2—C3 | 120.25 (17) | C12—N1—H1N1 | 119.0 (12) |
C1—C2—H2A | 120.4 (12) | C8—N2—H1N2 | 118.9 (12) |
C3—C2—H2A | 119.3 (12) | C8—N2—H2N2 | 118.3 (14) |
C4—C3—C2 | 119.53 (17) | H1N2—N2—H2N2 | 116.3 (18) |
C4—C3—H3A | 121.2 (11) | C9—N3—H1N3 | 117.9 (13) |
C2—C3—H3A | 119.3 (11) | C9—N3—H2N3 | 114.0 (12) |
C3—C4—C5 | 120.59 (17) | H1N3—N3—H2N3 | 118.1 (17) |
C3—C4—H4A | 120.4 (13) | C11—C12—N1 | 119.87 (15) |
C5—C4—H4A | 119.0 (13) | C11—C12—H12A | 125.2 (11) |
C4—C5—C6 | 120.18 (17) | N1—C12—H12A | 114.9 (11) |
C4—C5—H5A | 119.9 (11) | C12—C11—C10 | 118.99 (16) |
C6—C5—H5A | 119.9 (11) | C12—C11—H11A | 122.1 (11) |
O1—C7—O2 | 123.33 (14) | C10—C11—H11A | 118.9 (11) |
O1—C7—C6 | 118.52 (14) | C9—C10—C11 | 121.30 (16) |
O2—C7—C6 | 118.15 (13) | C9—C10—H10A | 119.5 (10) |
C10—C9—N3 | 122.21 (15) | C11—C10—H10A | 119.2 (10) |
C10—C9—C8 | 118.22 (14) | ||
C5—C6—C1—C2 | 0.5 (2) | C10—C9—C8—N2 | −179.52 (15) |
C7—C6—C1—C2 | −179.77 (15) | N3—C9—C8—N2 | 1.9 (2) |
C6—C1—C2—C3 | −0.3 (3) | C10—C9—C8—N1 | 1.4 (2) |
C1—C2—C3—C4 | −0.1 (3) | N3—C9—C8—N1 | −177.16 (13) |
C2—C3—C4—C5 | 0.5 (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—C10 | 0.2 (2) |
C1—C6—C7—O1 | −10.6 (2) | N3—C9—C10—C11 | 176.89 (15) |
C5—C6—C7—O1 | 169.17 (15) | C8—C9—C10—C11 | −1.7 (2) |
C1—C6—C7—O2 | 169.17 (14) | C12—C11—C10—C9 | 0.8 (3) |
C5—C6—C7—O2 | −11.1 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O2 | 0.96 (2) | 1.77 (2) | 2.7218 (18) | 176 (2) |
N2—H1N2···O1 | 0.90 (2) | 1.94 (2) | 2.8377 (18) | 173 (2) |
N2—H2N2···O2i | 0.88 (2) | 2.01 (2) | 2.8873 (17) | 170 (2) |
N3—H1N3···O2i | 0.91 (2) | 2.02 (2) | 2.9206 (19) | 173 (2) |
N3—H2N3···O1ii | 0.95 (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. |
Experimental details
Crystal data | |
Chemical formula | C5H8N3+·C7H5O2− |
Mr | 231.25 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 100 |
a, b, c (Å) | 10.1498 (3), 11.0656 (3), 20.7368 (7) |
V (Å3) | 2329.03 (12) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.43 × 0.40 × 0.03 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.935, 0.998 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 27109, 3443, 2559 |
Rint | 0.070 |
(sin θ/λ)max (Å−1) | 0.706 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.065, 0.124, 1.09 |
No. of reflections | 3443 |
No. of parameters | 206 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.26, −0.22 |
Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O2 | 0.96 (2) | 1.77 (2) | 2.7218 (18) | 176 (2) |
N2—H1N2···O1 | 0.90 (2) | 1.94 (2) | 2.8377 (18) | 173 (2) |
N2—H2N2···O2i | 0.88 (2) | 2.01 (2) | 2.8873 (17) | 170 (2) |
N3—H1N3···O2i | 0.91 (2) | 2.02 (2) | 2.9206 (19) | 173 (2) |
N3—H2N3···O1ii | 0.95 (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. |
Footnotes
‡Thomson Reuters ResearcherID: A-3561-2009.
Acknowledgements
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
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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.