organic compounds
2,3-Diaminopyridinium 3-aminobenzoate
aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my
In the title salt, C5H8N3+·C7H6NO2−, the pyridine N atom of the 2,3-diaminopyridine molecule is protonated. The protonated N atom and one of the two N atoms of the 2-amino groups are hydrogen bonded to the 3-aminobenzoate anion through a pair of N—H⋯O hydrogen bonds, forming an R22(8) ring motif. The carboxylate mean plane of the 3-aminobenzoate anion is twisted by 8.81 (7)° from the attached ring. The is further stabilized by π–π interactions [centroid–centroid distance 3.6827 (7) Å].
Related literature
For substituted pyridines, see: Pozharski et al. (1997); Katritzky et al. (1996). For hydrogen bonding in pyridine and its substituted derivatives, see: Jeffrey & Saenger (1991); Jeffrey (1997); Scheiner (1997). For related structures, see: Fun & Balasubramani (2009); Balasubramani & Fun (2009a,b). For bond-length data, see: Allen et al. (1987). 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
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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/S1600536809024362/bt2977sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809024362/bt2977Isup2.hkl
Hot methanol solutions (20 ml) of 2,3-diaminopyridine (27 mg, Aldrich) and 3-aminobenzoic acid (35 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 (I) appeared from the mother liquor after a few days.
All the H atoms were located from the difference Fourier map and allowed to refine freely.
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 molecular structure of (I), showing 50% probability displacement ellipsoids and the atom numbering scheme. Dashed lines indicate the hydrogen bonding. | |
Fig. 2. Part of the crystal packing of (I). Dashed lines indicate the hydrogen bonding. |
C5H8N3+·C7H6NO2− | F(000) = 520 |
Mr = 246.27 | Dx = 1.366 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 3436 reflections |
a = 9.9119 (2) Å | θ = 2.9–32.6° |
b = 10.1751 (2) Å | µ = 0.10 mm−1 |
c = 12.4060 (2) Å | T = 100 K |
β = 106.811 (1)° | Plate, brown |
V = 1197.73 (4) Å3 | 0.46 × 0.14 × 0.06 mm |
Z = 4 |
Bruker SMART APEXII CCD area-detector diffractometer | 4434 independent reflections |
Radiation source: fine-focus sealed tube | 2965 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.046 |
ϕ and ω scans | θmax = 32.8°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −14→15 |
Tmin = 0.957, Tmax = 0.994 | k = −12→15 |
19514 measured reflections | l = −18→18 |
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)] = 0.050 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.142 | All H-atom parameters refined |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0681P)2 + 0.0752P] where P = (Fo2 + 2Fc2)/3 |
4434 reflections | (Δ/σ)max < 0.001 |
219 parameters | Δρmax = 0.33 e Å−3 |
0 restraints | Δρmin = −0.23 e Å−3 |
C5H8N3+·C7H6NO2− | V = 1197.73 (4) Å3 |
Mr = 246.27 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.9119 (2) Å | µ = 0.10 mm−1 |
b = 10.1751 (2) Å | T = 100 K |
c = 12.4060 (2) Å | 0.46 × 0.14 × 0.06 mm |
β = 106.811 (1)° |
Bruker SMART APEXII CCD area-detector diffractometer | 4434 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 2965 reflections with I > 2σ(I) |
Tmin = 0.957, Tmax = 0.994 | Rint = 0.046 |
19514 measured reflections |
R[F2 > 2σ(F2)] = 0.050 | 0 restraints |
wR(F2) = 0.142 | All H-atom parameters refined |
S = 1.06 | Δρmax = 0.33 e Å−3 |
4434 reflections | Δρmin = −0.23 e Å−3 |
219 parameters |
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems 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 | ||
N1 | 0.45804 (11) | 0.32315 (11) | 0.46427 (8) | 0.0219 (2) | |
N2 | 0.56864 (12) | 0.28026 (12) | 0.32806 (9) | 0.0252 (2) | |
N3 | 0.36894 (13) | 0.43692 (12) | 0.17546 (9) | 0.0275 (2) | |
C8 | 0.46690 (12) | 0.34222 (12) | 0.35929 (10) | 0.0199 (2) | |
C9 | 0.36669 (13) | 0.42721 (12) | 0.28567 (10) | 0.0223 (2) | |
C10 | 0.26897 (14) | 0.48893 (14) | 0.32782 (11) | 0.0276 (3) | |
C11 | 0.26420 (14) | 0.46612 (14) | 0.43889 (12) | 0.0286 (3) | |
C12 | 0.35938 (13) | 0.38245 (13) | 0.50509 (11) | 0.0252 (3) | |
H10 | 0.1974 (16) | 0.5508 (16) | 0.2749 (13) | 0.032 (4)* | |
H11 | 0.1881 (16) | 0.5151 (16) | 0.4685 (13) | 0.033 (4)* | |
H12 | 0.3671 (16) | 0.3657 (15) | 0.5851 (13) | 0.028 (4)* | |
H1N1 | 0.5279 (18) | 0.2611 (17) | 0.5122 (14) | 0.040 (5)* | |
H1N2 | 0.6338 (18) | 0.2303 (17) | 0.3822 (15) | 0.040 (5)* | |
H2N2 | 0.5864 (19) | 0.2985 (18) | 0.2620 (16) | 0.045 (5)* | |
H1N3 | 0.453 (2) | 0.4228 (19) | 0.1593 (16) | 0.056 (6)* | |
H2N3 | 0.311 (2) | 0.504 (2) | 0.1305 (16) | 0.053 (5)* | |
C4 | 0.96875 (12) | −0.19646 (13) | 0.66376 (10) | 0.0226 (2) | |
C5 | 0.89408 (12) | −0.08847 (12) | 0.60585 (10) | 0.0206 (2) | |
H1 | 0.7131 (18) | −0.0025 (17) | 0.7829 (14) | 0.042 (5)* | |
H2 | 0.8458 (18) | −0.1824 (17) | 0.8828 (15) | 0.039 (4)* | |
H3 | 1.0060 (16) | −0.3052 (16) | 0.8108 (13) | 0.032 (4)* | |
H5 | 0.9082 (15) | −0.0651 (14) | 0.5321 (12) | 0.023 (4)* | |
C6 | 0.80059 (12) | −0.01887 (12) | 0.64902 (9) | 0.0191 (2) | |
C7 | 0.72259 (12) | 0.09741 (12) | 0.58352 (9) | 0.0198 (2) | |
O1 | 0.75796 (9) | 0.13487 (9) | 0.49856 (7) | 0.0232 (2) | |
O2 | 0.62586 (10) | 0.15115 (9) | 0.61617 (7) | 0.0259 (2) | |
N4 | 1.05563 (14) | −0.26916 (14) | 0.61717 (11) | 0.0347 (3) | |
C1 | 0.78080 (13) | −0.05510 (13) | 0.75193 (10) | 0.0231 (2) | |
C2 | 0.85824 (14) | −0.16013 (13) | 0.81132 (11) | 0.0261 (3) | |
C3 | 0.94998 (13) | −0.23049 (13) | 0.76778 (11) | 0.0249 (3) | |
H1N4 | 1.097 (2) | −0.224 (2) | 0.5680 (17) | 0.057 (6)* | |
H2N4 | 1.109 (2) | −0.329 (2) | 0.6604 (17) | 0.053 (5)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0232 (5) | 0.0234 (5) | 0.0198 (5) | 0.0005 (4) | 0.0075 (4) | 0.0013 (4) |
N2 | 0.0283 (5) | 0.0289 (6) | 0.0206 (5) | 0.0065 (4) | 0.0105 (4) | 0.0062 (4) |
N3 | 0.0298 (6) | 0.0314 (6) | 0.0196 (5) | 0.0039 (5) | 0.0045 (4) | 0.0048 (4) |
C8 | 0.0208 (5) | 0.0193 (5) | 0.0196 (5) | −0.0018 (4) | 0.0059 (4) | 0.0005 (4) |
C9 | 0.0225 (5) | 0.0220 (6) | 0.0204 (5) | −0.0007 (5) | 0.0031 (4) | 0.0010 (4) |
C10 | 0.0238 (6) | 0.0285 (7) | 0.0283 (6) | 0.0038 (5) | 0.0041 (5) | 0.0003 (5) |
C11 | 0.0252 (6) | 0.0307 (7) | 0.0310 (7) | 0.0016 (5) | 0.0097 (5) | −0.0041 (5) |
C12 | 0.0262 (6) | 0.0280 (7) | 0.0234 (6) | −0.0009 (5) | 0.0104 (5) | −0.0029 (5) |
C4 | 0.0201 (5) | 0.0230 (6) | 0.0257 (6) | −0.0015 (5) | 0.0083 (4) | 0.0014 (5) |
C5 | 0.0209 (5) | 0.0223 (6) | 0.0187 (5) | −0.0014 (4) | 0.0057 (4) | 0.0012 (4) |
C6 | 0.0200 (5) | 0.0196 (5) | 0.0171 (5) | −0.0019 (4) | 0.0043 (4) | −0.0002 (4) |
C7 | 0.0231 (5) | 0.0207 (6) | 0.0151 (5) | −0.0020 (4) | 0.0046 (4) | −0.0015 (4) |
O1 | 0.0251 (4) | 0.0266 (5) | 0.0183 (4) | 0.0010 (4) | 0.0072 (3) | 0.0034 (3) |
O2 | 0.0318 (5) | 0.0272 (5) | 0.0213 (4) | 0.0078 (4) | 0.0116 (4) | 0.0033 (3) |
N4 | 0.0351 (6) | 0.0352 (7) | 0.0405 (7) | 0.0139 (5) | 0.0216 (5) | 0.0126 (6) |
C1 | 0.0257 (6) | 0.0234 (6) | 0.0217 (6) | 0.0010 (5) | 0.0096 (5) | 0.0016 (5) |
C2 | 0.0302 (6) | 0.0279 (7) | 0.0223 (6) | 0.0012 (5) | 0.0107 (5) | 0.0061 (5) |
C3 | 0.0235 (6) | 0.0243 (6) | 0.0273 (6) | 0.0016 (5) | 0.0078 (5) | 0.0067 (5) |
N1—C8 | 1.3445 (15) | C4—N4 | 1.3822 (17) |
N1—C12 | 1.3650 (16) | C4—C3 | 1.3995 (17) |
N1—H1N1 | 0.997 (18) | C4—C5 | 1.4013 (17) |
N2—C8 | 1.3382 (16) | C5—C6 | 1.3907 (16) |
N2—H1N2 | 0.936 (18) | C5—H5 | 0.994 (14) |
N2—H2N2 | 0.906 (19) | C6—C1 | 1.3961 (16) |
N3—C9 | 1.3775 (16) | C6—C7 | 1.5147 (17) |
N3—H1N3 | 0.92 (2) | C7—O1 | 1.2621 (14) |
N3—H2N3 | 0.96 (2) | C7—O2 | 1.2677 (14) |
C8—C9 | 1.4296 (16) | N4—H1N4 | 0.95 (2) |
C9—C10 | 1.3781 (18) | N4—H2N4 | 0.88 (2) |
C10—C11 | 1.4115 (19) | C1—C2 | 1.3954 (18) |
C10—H10 | 1.030 (16) | C1—H1 | 1.017 (17) |
C11—C12 | 1.3569 (19) | C2—C3 | 1.3839 (18) |
C11—H11 | 1.054 (16) | C2—H2 | 0.957 (17) |
C12—H12 | 0.988 (15) | C3—H3 | 1.000 (16) |
C8—N1—C12 | 123.37 (11) | N4—C4—C3 | 121.21 (12) |
C8—N1—H1N1 | 116.1 (10) | N4—C4—C5 | 120.39 (11) |
C12—N1—H1N1 | 120.5 (10) | C3—C4—C5 | 118.38 (11) |
C8—N2—H1N2 | 118.0 (10) | C6—C5—C4 | 120.92 (11) |
C8—N2—H2N2 | 121.7 (12) | C6—C5—H5 | 121.3 (8) |
H1N2—N2—H2N2 | 119.1 (15) | C4—C5—H5 | 117.7 (8) |
C9—N3—H1N3 | 118.6 (12) | C5—C6—C1 | 120.21 (11) |
C9—N3—H2N3 | 116.7 (11) | C5—C6—C7 | 118.99 (10) |
H1N3—N3—H2N3 | 114.2 (16) | C1—C6—C7 | 120.79 (11) |
N2—C8—N1 | 118.57 (11) | O1—C7—O2 | 123.71 (11) |
N2—C8—C9 | 122.86 (11) | O1—C7—C6 | 117.51 (10) |
N1—C8—C9 | 118.57 (11) | O2—C7—C6 | 118.77 (10) |
N3—C9—C10 | 123.98 (12) | C4—N4—H1N4 | 116.5 (12) |
N3—C9—C8 | 118.02 (11) | C4—N4—H2N4 | 117.0 (12) |
C10—C9—C8 | 117.90 (11) | H1N4—N4—H2N4 | 115.6 (17) |
C9—C10—C11 | 121.41 (12) | C2—C1—C6 | 118.93 (12) |
C9—C10—H10 | 117.8 (8) | C2—C1—H1 | 121.7 (10) |
C11—C10—H10 | 120.8 (8) | C6—C1—H1 | 119.3 (10) |
C12—C11—C10 | 118.71 (12) | C3—C2—C1 | 120.88 (12) |
C12—C11—H11 | 121.8 (9) | C3—C2—H2 | 121.0 (10) |
C10—C11—H11 | 119.4 (9) | C1—C2—H2 | 118.1 (10) |
C11—C12—N1 | 120.00 (12) | C2—C3—C4 | 120.64 (12) |
C11—C12—H12 | 123.7 (9) | C2—C3—H3 | 120.7 (9) |
N1—C12—H12 | 116.1 (9) | C4—C3—H3 | 118.6 (9) |
C12—N1—C8—N2 | 179.31 (11) | C4—C5—C6—C1 | 0.65 (18) |
C12—N1—C8—C9 | −1.04 (17) | C4—C5—C6—C7 | 179.83 (11) |
N2—C8—C9—N3 | 5.26 (18) | C5—C6—C7—O1 | −7.75 (16) |
N1—C8—C9—N3 | −174.37 (11) | C1—C6—C7—O1 | 171.43 (11) |
N2—C8—C9—C10 | −178.13 (12) | C5—C6—C7—O2 | 171.97 (11) |
N1—C8—C9—C10 | 2.23 (17) | C1—C6—C7—O2 | −8.85 (17) |
N3—C9—C10—C11 | 174.31 (12) | C5—C6—C1—C2 | 1.28 (18) |
C8—C9—C10—C11 | −2.08 (19) | C7—C6—C1—C2 | −177.89 (11) |
C9—C10—C11—C12 | 0.7 (2) | C6—C1—C2—C3 | −2.1 (2) |
C10—C11—C12—N1 | 0.6 (2) | C1—C2—C3—C4 | 1.0 (2) |
C8—N1—C12—C11 | −0.41 (19) | N4—C4—C3—C2 | −177.33 (13) |
N4—C4—C5—C6 | 176.53 (12) | C5—C4—C3—C2 | 0.93 (19) |
C3—C4—C5—C6 | −1.75 (18) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N2···O2i | 0.91 (2) | 2.02 (2) | 2.9293 (14) | 177.1 (17) |
N3—H1N3···O2i | 0.92 (2) | 2.08 (2) | 2.9854 (16) | 167.3 (18) |
N3—H2N3···O1ii | 0.96 (2) | 2.04 (2) | 2.9544 (14) | 158.1 (16) |
N4—H1N4···O1iii | 0.95 (2) | 2.06 (2) | 2.9794 (15) | 162.3 (18) |
N1—H1N1···O2 | 0.99 (2) | 1.77 (2) | 2.7510 (13) | 167.1 (15) |
N2—H1N2···O1 | 0.94 (2) | 1.87 (2) | 2.8086 (14) | 175.7 (16) |
Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) −x+1, y+1/2, −z+1/2; (iii) −x+2, −y, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C5H8N3+·C7H6NO2− |
Mr | 246.27 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 9.9119 (2), 10.1751 (2), 12.4060 (2) |
β (°) | 106.811 (1) |
V (Å3) | 1197.73 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.46 × 0.14 × 0.06 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.957, 0.994 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 19514, 4434, 2965 |
Rint | 0.046 |
(sin θ/λ)max (Å−1) | 0.763 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.050, 0.142, 1.06 |
No. of reflections | 4434 |
No. of parameters | 219 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.33, −0.23 |
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 |
N2—H2N2···O2i | 0.91 (2) | 2.02 (2) | 2.9293 (14) | 177.1 (17) |
N3—H1N3···O2i | 0.92 (2) | 2.08 (2) | 2.9854 (16) | 167.3 (18) |
N3—H2N3···O1ii | 0.96 (2) | 2.04 (2) | 2.9544 (14) | 158.1 (16) |
N4—H1N4···O1iii | 0.95 (2) | 2.06 (2) | 2.9794 (15) | 162.3 (18) |
N1—H1N1···O2 | 0.99 (2) | 1.77 (2) | 2.7510 (13) | 167.1 (15) |
N2—H1N2···O1 | 0.94 (2) | 1.87 (2) | 2.8086 (14) | 175.7 (16) |
Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) −x+1, y+1/2, −z+1/2; (iii) −x+2, −y, −z+1. |
Footnotes
‡Thomson Reuters ResearcherID: A-3561-2009.
Acknowledgements
KBS and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Science Fund grant No. 305/PFIZIK/613312. KBS 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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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). The crystal structures of 2,3-diaminopyridinium 4-hydroxybenzoate (Fun & Balasubramani, 2009), 2,3-diaminopyridinium 4-nitrobenzoate (Balasubramani & Fun, 2009a) and 2,3-diaminopyridinium benzoate (Balasubramani & Fun, 2009b) have been reported by us recently. In the hope to study some interesting hydrogen-bonding interactions, the title compound (I) was synthesized. Its molecular and crystal structure is presented here.
The asymmetric unit of (I) (Fig 1), contains a protonated 2,3-diaminopyridinium cation and an 3-aminobenzoate 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 the C8—N1—C12 angle to 123.37 (11)°. The carboxylate group is twisted slightly from the ring with the dihedral angle between C1—C6 and O1/O2/C7/C6 planes being 8.81 (7)°. The 2,3-diaminopyridinium cation is planar, with a maximum deviation of 0.0126 (14) Å for atom C9.
In the crystal packing (Fig. 2), the protonated N1 atom and a nitrogen atom of the 2-amino group (N2) are hydrogen-bonded to the carboxylate oxygen atoms (O2 and O1) via a pair of N—H···O hydrogen bonds forming a ring motif R22(8) (Bernstein et al., 1995). The 2-amino groups (N2 and N3) are involved in N—H···O hydrogen bonding interactions to form a R12(7) ring motif. The symmetry-related 3-aminobenzoate molecules are linked through N—H···O hydrogen-bonding to form a R22(14) ring motif (Table 1 and Fig. 2). The cystal structure is further stabilized by a π-π stacking interaction between the aminopyridine rings (C8—C12/N1) with centroid-to-centroid distance of 3.6827 (7) Å, perpendicular interplanar distance of 3.3536 (5) Å.