organic compounds
2,3-Diaminopyridinium hydrogen malonate
aSchool of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: arazaki@usm.my
In the title molecular salt, C5H8N3+·C3H3O4−, the cation is essentially planar, with a maximum deviation of 0.005 (1) Å for all non-H atoms. In the anion, an intramolecular O—H⋯O hydrogen bond generates an S(6) ring. In the crystal, the cations and anions are connected via N—H⋯O hydrogen bonds and a weak C—H⋯O interaction, forming layers parallel to the ab plane.
Related literature
For backgroup to the chemistry of substituted pyridines, see: Amr et al. (2006); Bart et al. (2001); Shinkai et al. (2000). For related structures, see: Betz et al. (2011); Hemamalini et al. (2011); Balasubramani & Fun (2009); Fun & Balasubramani (2009). For the conformation of the malonate ion, see: Djinović et al. (1990). For hydrogen-bond motifs, see: Bernstein et al. (1995). For bond-length data, see: Allen et al. (1987). For stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
|
Refinement
|
Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); 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
https://doi.org/10.1107/S1600536812050386/is5228sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812050386/is5228Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S1600536812050386/is5228Isup3.cml
Hot methanol solutions (20 ml) of 2,3-diaminopyrimidine (27 mg, Aldrich) and malonic acid (26 mg, Merck) were mixed and warmed over a heating magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature and crystals of the title compound (I) appeared after a few days.
O- and N-bound H atoms were located in a difference Fourier map and allowed to be refined freely [O—H = 0.93 (4) Å and N—H = 0.87 (3)–0.92 (3) Å]. The remaining hydrogen atoms were positioned geometrically (C—H = 0.95 or 0.99 Å) and refined using a riding model, with Uiso(H) = 1.2Ueq(C). In the final
1237 Friedel pairs were merged.Pyridine and its derivatives continue to attract great interest due to the wide variety of interesting biological activities observed for these compounds, such as anticancer, analgesic, antimicrobial and antidepressant activities (Amr et al., 2006; Bart et al., 2001; Shinkai et al., 2000). They are also often involved in hydrogen-bond interactions. The related crystal structures of 2,3-diaminopyridinium 2-hydroxybenzoate (Hemamalini et al., 2011), 2,3-diaminopyrimidinium benzoate (Balasubramani & Fun, 2009) and 2,3-diaminopyridinium 4-hydroxybenzoate (Fun & Balasubramani, 2009) have been recently reported. In order to study potential hydrogen bonding interactions, the
determination of the title compound (I) was carried out.The
(Fig. 1) contains one 2,3-Diaminopyridinium cation and one hydrogen malonate anion. The proton transfers from one of the carboxyl group oxygen atom (O1) to atom N1 of 2,3-diaminopyridine resulted in widening of C1—N1—C5 angle of the pyridinium ring to 123.69 (13)°, compared to the corresponding angle of 118.97 (15)° in neutral 2,3-diaminopyridine (Betz et al., 2011). The 2,4-diaminopyrinium cation is planar, with a maximum deviation of 0.005 (1) Å for atom N1. The bond lengths (Allen et al., 1987) and angles are normal.In the crystal packing (Fig. 2), 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 intermolecular N1—H1N1···O1iii and N2—H1N2···O2iii hydrogen bonds (symmetry code in Table 1), forming a ring motif R22(8) (Bernstein et al., 1995). Atom O3 of the carboxyl group of the hydrogen malonate anion forms an intramolecular O3—H1O3···O1 hydrogen bond with the O atom of the carboxylate group (O1) [with graph-set notation S(6)], leading to a folded conformation. A similar intramolecular hydrogen bond has been observed in the crystal structures of benzylammonium hydrogen malonate and 4-picolinium hydrogen malonate (Djinović et al., 1990). The 2-amino groups (N2 and N3) are involved in the intermolecular N—H···O hydrogen bonds with hydrogen malonate oxygen atom (O2), forming an R21(7) ring motif. The
is further stabilized by a weak C7—H7B···O2iv interaction (symmetry code in Table 1), forming a layer lying parallel to the ab plane.For backgroup to the chemistry of substituted pyridines, see: Amr et al. (2006); Bart et al. (2001); Shinkai et al. (2000). For related structures, see: Betz et al. (2011); Hemamalini et al. (2011); Balasubramani & Fun (2009); Fun & Balasubramani (2009). For the conformation of the malonate ion, see: Djinović et al. (1990). For hydrogen-bond motifs, see: Bernstein et al. (1995). For bond-length data, see: Allen et al. (1987). For stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).
Data collection: APEX2 (Bruker, 2009); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); 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 the title compound with atom labels with 50% probability displacement ellipsoids. | |
Fig. 2. The crystal packing of the title compound. The H atoms not involved in the intermolecular interactions (dashed lines) have been omitted for clarity. |
C5H8N3+·C3H3O4− | F(000) = 224 |
Mr = 213.20 | Dx = 1.541 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 3153 reflections |
a = 5.0843 (1) Å | θ = 3.1–32.6° |
b = 8.0771 (1) Å | µ = 0.13 mm−1 |
c = 11.1928 (2) Å | T = 100 K |
β = 91.214 (1)° | Block, brown |
V = 459.55 (1) Å3 | 0.28 × 0.25 × 0.14 mm |
Z = 2 |
Bruker SMART APEXII CCD area-detector diffractometer | 1778 independent reflections |
Radiation source: fine-focus sealed tube | 1695 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.024 |
φ and ω scans | θmax = 32.7°, θmin = 1.8° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −7→7 |
Tmin = 0.966, Tmax = 0.983 | k = −10→12 |
6631 measured reflections | l = −17→16 |
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)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.094 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0564P)2 + 0.057P] where P = (Fo2 + 2Fc2)/3 |
1778 reflections | (Δ/σ)max < 0.001 |
160 parameters | Δρmax = 0.35 e Å−3 |
1 restraint | Δρmin = −0.26 e Å−3 |
C5H8N3+·C3H3O4− | V = 459.55 (1) Å3 |
Mr = 213.20 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 5.0843 (1) Å | µ = 0.13 mm−1 |
b = 8.0771 (1) Å | T = 100 K |
c = 11.1928 (2) Å | 0.28 × 0.25 × 0.14 mm |
β = 91.214 (1)° |
Bruker SMART APEXII CCD area-detector diffractometer | 1778 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 1695 reflections with I > 2σ(I) |
Tmin = 0.966, Tmax = 0.983 | Rint = 0.024 |
6631 measured reflections |
R[F2 > 2σ(F2)] = 0.037 | 1 restraint |
wR(F2) = 0.094 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | Δρmax = 0.35 e Å−3 |
1778 reflections | Δρmin = −0.26 e Å−3 |
160 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 | ||
O1 | 0.4162 (2) | 0.50089 (15) | 0.24888 (10) | 0.0139 (2) | |
O2 | 0.3017 (2) | 0.50412 (15) | 0.44060 (10) | 0.0139 (2) | |
O3 | 0.7878 (2) | 0.31758 (17) | 0.18357 (11) | 0.0209 (3) | |
O4 | 1.0228 (2) | 0.17757 (17) | 0.31863 (13) | 0.0222 (3) | |
N1 | 0.9986 (2) | 0.70786 (17) | 0.18711 (12) | 0.0123 (2) | |
N2 | 0.8913 (3) | 0.75149 (17) | 0.38452 (12) | 0.0136 (3) | |
N3 | 0.4668 (3) | 0.95043 (19) | 0.30805 (14) | 0.0163 (3) | |
C1 | 0.8441 (3) | 0.78141 (18) | 0.26789 (13) | 0.0107 (3) | |
C2 | 0.6311 (3) | 0.88272 (18) | 0.22541 (14) | 0.0119 (3) | |
C3 | 0.5946 (3) | 0.8991 (2) | 0.10331 (14) | 0.0142 (3) | |
H3A | 0.4551 | 0.9663 | 0.0730 | 0.017* | |
C4 | 0.7607 (3) | 0.8179 (2) | 0.02293 (14) | 0.0161 (3) | |
H4A | 0.7326 | 0.8294 | −0.0608 | 0.019* | |
C5 | 0.9617 (3) | 0.7228 (2) | 0.06655 (14) | 0.0153 (3) | |
H5A | 1.0754 | 0.6673 | 0.0135 | 0.018* | |
C6 | 0.4477 (3) | 0.45888 (19) | 0.35774 (14) | 0.0112 (3) | |
C7 | 0.6803 (3) | 0.34858 (19) | 0.39221 (14) | 0.0129 (3) | |
H7A | 0.7997 | 0.4142 | 0.4448 | 0.016* | |
H7B | 0.6122 | 0.2564 | 0.4410 | 0.016* | |
C8 | 0.8449 (3) | 0.27351 (19) | 0.29470 (15) | 0.0148 (3) | |
H2N3 | 0.343 (5) | 1.013 (4) | 0.276 (2) | 0.023 (6)* | |
H2N2 | 0.814 (5) | 0.817 (4) | 0.434 (2) | 0.026 (6)* | |
H1N1 | 1.136 (6) | 0.645 (4) | 0.218 (3) | 0.044 (8)* | |
H1N2 | 1.043 (5) | 0.703 (4) | 0.401 (2) | 0.029 (6)* | |
H1N3 | 0.534 (5) | 0.963 (3) | 0.380 (2) | 0.018 (5)* | |
H1O3 | 0.654 (6) | 0.395 (5) | 0.190 (3) | 0.048 (9)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0137 (4) | 0.0153 (5) | 0.0126 (5) | 0.0024 (4) | −0.0005 (4) | 0.0011 (4) |
O2 | 0.0129 (4) | 0.0152 (5) | 0.0136 (5) | 0.0025 (4) | 0.0018 (3) | 0.0004 (4) |
O3 | 0.0217 (5) | 0.0231 (6) | 0.0183 (6) | 0.0068 (5) | 0.0060 (4) | −0.0012 (5) |
O4 | 0.0143 (5) | 0.0164 (6) | 0.0360 (8) | 0.0056 (4) | 0.0016 (4) | −0.0008 (5) |
N1 | 0.0115 (5) | 0.0135 (6) | 0.0119 (6) | 0.0010 (4) | 0.0004 (4) | 0.0006 (5) |
N2 | 0.0134 (5) | 0.0160 (6) | 0.0114 (6) | 0.0024 (4) | −0.0001 (4) | 0.0004 (5) |
N3 | 0.0115 (5) | 0.0211 (6) | 0.0162 (6) | 0.0053 (5) | 0.0001 (4) | −0.0023 (5) |
C1 | 0.0096 (5) | 0.0114 (6) | 0.0112 (6) | −0.0005 (4) | 0.0006 (4) | 0.0001 (5) |
C2 | 0.0099 (5) | 0.0112 (6) | 0.0147 (7) | −0.0001 (5) | −0.0005 (4) | 0.0005 (5) |
C3 | 0.0124 (5) | 0.0154 (6) | 0.0148 (7) | 0.0012 (5) | −0.0022 (5) | 0.0026 (6) |
C4 | 0.0168 (6) | 0.0201 (7) | 0.0114 (7) | 0.0012 (5) | −0.0011 (5) | 0.0021 (6) |
C5 | 0.0165 (6) | 0.0184 (7) | 0.0111 (6) | 0.0015 (6) | 0.0022 (5) | 0.0002 (6) |
C6 | 0.0089 (5) | 0.0101 (6) | 0.0145 (6) | −0.0006 (5) | −0.0007 (4) | 0.0002 (5) |
C7 | 0.0118 (5) | 0.0130 (6) | 0.0140 (6) | 0.0028 (5) | −0.0007 (4) | 0.0012 (5) |
C8 | 0.0113 (6) | 0.0114 (6) | 0.0219 (8) | −0.0008 (5) | 0.0032 (5) | −0.0019 (6) |
O1—C6 | 1.2716 (19) | N3—H1N3 | 0.87 (2) |
O2—C6 | 1.2542 (17) | C1—C2 | 1.4305 (19) |
O3—C8 | 1.320 (2) | C2—C3 | 1.382 (2) |
O3—H1O3 | 0.93 (4) | C3—C4 | 1.409 (2) |
O4—C8 | 1.2168 (19) | C3—H3A | 0.9500 |
N1—C1 | 1.3482 (18) | C4—C5 | 1.361 (2) |
N1—C5 | 1.3638 (19) | C4—H4A | 0.9500 |
N1—H1N1 | 0.92 (3) | C5—H5A | 0.9500 |
N2—C1 | 1.344 (2) | C6—C7 | 1.524 (2) |
N2—H2N2 | 0.87 (3) | C7—C8 | 1.516 (2) |
N2—H1N2 | 0.88 (3) | C7—H7A | 0.9900 |
N3—C2 | 1.3731 (19) | C7—H7B | 0.9900 |
N3—H2N3 | 0.88 (3) | ||
C8—O3—H1O3 | 104.9 (19) | C5—C4—C3 | 119.31 (14) |
C1—N1—C5 | 123.70 (13) | C5—C4—H4A | 120.3 |
C1—N1—H1N1 | 116.0 (18) | C3—C4—H4A | 120.3 |
C5—N1—H1N1 | 120.3 (18) | C4—C5—N1 | 119.42 (14) |
C1—N2—H2N2 | 115.8 (16) | C4—C5—H5A | 120.3 |
C1—N2—H1N2 | 114.6 (16) | N1—C5—H5A | 120.3 |
H2N2—N2—H1N2 | 123 (2) | O2—C6—O1 | 124.51 (13) |
C2—N3—H2N3 | 113.0 (16) | O2—C6—C7 | 116.82 (13) |
C2—N3—H1N3 | 115.7 (15) | O1—C6—C7 | 118.66 (12) |
H2N3—N3—H1N3 | 125 (2) | C8—C7—C6 | 119.27 (13) |
N2—C1—N1 | 118.52 (13) | C8—C7—H7A | 107.5 |
N2—C1—C2 | 122.95 (13) | C6—C7—H7A | 107.5 |
N1—C1—C2 | 118.48 (13) | C8—C7—H7B | 107.5 |
N3—C2—C3 | 123.85 (13) | C6—C7—H7B | 107.5 |
N3—C2—C1 | 118.10 (13) | H7A—C7—H7B | 107.0 |
C3—C2—C1 | 117.95 (12) | O4—C8—O3 | 121.78 (15) |
C2—C3—C4 | 121.14 (13) | O4—C8—C7 | 121.03 (16) |
C2—C3—H3A | 119.4 | O3—C8—C7 | 117.19 (13) |
C4—C3—H3A | 119.4 | ||
C5—N1—C1—N2 | 176.82 (14) | C2—C3—C4—C5 | −0.5 (2) |
C5—N1—C1—C2 | −0.8 (2) | C3—C4—C5—N1 | 0.0 (2) |
N2—C1—C2—N3 | −0.7 (2) | C1—N1—C5—C4 | 0.7 (2) |
N1—C1—C2—N3 | 176.80 (14) | O2—C6—C7—C8 | 172.90 (13) |
N2—C1—C2—C3 | −177.26 (15) | O1—C6—C7—C8 | −8.2 (2) |
N1—C1—C2—C3 | 0.3 (2) | C6—C7—C8—O4 | −175.86 (14) |
N3—C2—C3—C4 | −175.92 (16) | C6—C7—C8—O3 | 4.6 (2) |
C1—C2—C3—C4 | 0.4 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H1O3···O1 | 0.93 (4) | 1.63 (3) | 2.5208 (16) | 159 (3) |
N3—H2N3···O4i | 0.88 (3) | 2.16 (3) | 2.9133 (19) | 143 (2) |
N2—H2N2···O2ii | 0.87 (3) | 2.15 (3) | 3.0066 (18) | 168 (2) |
N1—H1N1···O1iii | 0.92 (3) | 1.87 (3) | 2.7782 (16) | 168 (3) |
N2—H1N2···O2iii | 0.88 (3) | 2.12 (3) | 2.9470 (18) | 157 (3) |
N3—H1N3···O2ii | 0.87 (2) | 2.18 (2) | 3.0574 (19) | 178 (3) |
C7—H7B···O2iv | 0.99 | 2.46 | 3.3532 (19) | 149 |
Symmetry codes: (i) x−1, y+1, z; (ii) −x+1, y+1/2, −z+1; (iii) x+1, y, z; (iv) −x+1, y−1/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C5H8N3+·C3H3O4− |
Mr | 213.20 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 100 |
a, b, c (Å) | 5.0843 (1), 8.0771 (1), 11.1928 (2) |
β (°) | 91.214 (1) |
V (Å3) | 459.55 (1) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.13 |
Crystal size (mm) | 0.28 × 0.25 × 0.14 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.966, 0.983 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6631, 1778, 1695 |
Rint | 0.024 |
(sin θ/λ)max (Å−1) | 0.761 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.094, 1.07 |
No. of reflections | 1778 |
No. of parameters | 160 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.35, −0.26 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H1O3···O1 | 0.93 (4) | 1.63 (3) | 2.5208 (16) | 159 (3) |
N3—H2N3···O4i | 0.88 (3) | 2.16 (3) | 2.9133 (19) | 143 (2) |
N2—H2N2···O2ii | 0.87 (3) | 2.15 (3) | 3.0066 (18) | 168 (2) |
N1—H1N1···O1iii | 0.92 (3) | 1.87 (3) | 2.7782 (16) | 168 (3) |
N2—H1N2···O2iii | 0.88 (3) | 2.12 (3) | 2.9470 (18) | 157 (3) |
N3—H1N3···O2ii | 0.87 (2) | 2.18 (2) | 3.0574 (19) | 178 (3) |
C7—H7B···O2iv | 0.99 | 2.46 | 3.3532 (19) | 149 |
Symmetry codes: (i) x−1, y+1, z; (ii) −x+1, y+1/2, −z+1; (iii) x+1, y, z; (iv) −x+1, y−1/2, −z+1. |
Footnotes
‡Thomson Reuters ResearcherID: A-5599-2009.
Acknowledgements
The authors thank the Malaysian Government and Universiti Sains Malaysia (USM) for the research facilities and USM Short Term Grant No. 304/PFIZIK/6312078 to conduct this work. KT thanks The Academy of Sciences for the Developing World and USM for a TWAS–USM fellowship.
References
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. CSD CrossRef Web of Science Google Scholar
Amr, A. G., Mohamed, A. M., Mohamed, S. F., Abdel-Hafez, N. A. & Hammam, A. G. (2006). Bioorg. Med. Chem. 14, 5481–5488. Web of Science CrossRef PubMed CAS Google Scholar
Balasubramani, K. & Fun, H.-K. (2009). Acta Cryst. E65, o1519. Web of Science CSD CrossRef IUCr Journals Google Scholar
Bart, A., Jansen, J., Zwan, J. V., Dulk, H., Brouwer, J. & Reedijk, J. (2001). J. Med. Chem. 44, 245–249. Web of Science PubMed Google Scholar
Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. CrossRef CAS Web of Science Google Scholar
Betz, R., Gerber, T., Hosten, E. & Schalekamp, H. (2011). Acta Cryst. E67, o2154. Web of Science CSD CrossRef IUCr Journals Google Scholar
Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107. CrossRef CAS Web of Science IUCr Journals Google Scholar
Djinović, K., Golič, L. & Leban, I. (1990). Acta Cryst. C46, 281–286. CSD CrossRef Web of Science IUCr Journals Google Scholar
Fun, H.-K. & Balasubramani, K. (2009). Acta Cryst. E65, o1496–o1497. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Hemamalini, M., Goh, J. H. & Fun, H.-K. (2011). Acta Cryst. E67, o3121. Web of Science CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Shinkai, H., Ito, T., Iida, T., Kitao, Y., Yamada, H. & Uchida, I. (2000). J. Med. Chem. 43, 4667–4677. Web of Science CrossRef PubMed CAS Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
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 continue to attract great interest due to the wide variety of interesting biological activities observed for these compounds, such as anticancer, analgesic, antimicrobial and antidepressant activities (Amr et al., 2006; Bart et al., 2001; Shinkai et al., 2000). They are also often involved in hydrogen-bond interactions. The related crystal structures of 2,3-diaminopyridinium 2-hydroxybenzoate (Hemamalini et al., 2011), 2,3-diaminopyrimidinium benzoate (Balasubramani & Fun, 2009) and 2,3-diaminopyridinium 4-hydroxybenzoate (Fun & Balasubramani, 2009) have been recently reported. In order to study potential hydrogen bonding interactions, the crystal structure determination of the title compound (I) was carried out.
The asymmetric unit (Fig. 1) contains one 2,3-Diaminopyridinium cation and one hydrogen malonate anion. The proton transfers from one of the carboxyl group oxygen atom (O1) to atom N1 of 2,3-diaminopyridine resulted in widening of C1—N1—C5 angle of the pyridinium ring to 123.69 (13)°, compared to the corresponding angle of 118.97 (15)° in neutral 2,3-diaminopyridine (Betz et al., 2011). The 2,4-diaminopyrinium cation is planar, with a maximum deviation of 0.005 (1) Å for atom N1. The bond lengths (Allen et al., 1987) and angles are normal.
In the crystal packing (Fig. 2), 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 intermolecular N1—H1N1···O1iii and N2—H1N2···O2iii hydrogen bonds (symmetry code in Table 1), forming a ring motif R22(8) (Bernstein et al., 1995). Atom O3 of the carboxyl group of the hydrogen malonate anion forms an intramolecular O3—H1O3···O1 hydrogen bond with the O atom of the carboxylate group (O1) [with graph-set notation S(6)], leading to a folded conformation. A similar intramolecular hydrogen bond has been observed in the crystal structures of benzylammonium hydrogen malonate and 4-picolinium hydrogen malonate (Djinović et al., 1990). The 2-amino groups (N2 and N3) are involved in the intermolecular N—H···O hydrogen bonds with hydrogen malonate oxygen atom (O2), forming an R21(7) ring motif. The crystal structure is further stabilized by a weak C7—H7B···O2iv interaction (symmetry code in Table 1), forming a layer lying parallel to the ab plane.