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ISSN: 2056-9890
Volume 69| Part 1| January 2013| Pages o92-o93

2,3-Di­amino­pyridinium hydrogen malonate

aSchool of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: arazaki@usm.my

(Received 4 December 2012; accepted 11 December 2012; online 15 December 2012)

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[Amr, A. G., Mohamed, A. M., Mohamed, S. F., Abdel-Hafez, N. A. & Hammam, A. G. (2006). Bioorg. Med. Chem. 14, 5481-5488.]); Bart et al. (2001[Bart, A., Jansen, J., Zwan, J. V., Dulk, H., Brouwer, J. & Reedijk, J. (2001). J. Med. Chem. 44, 245-249.]); Shinkai et al. (2000[Shinkai, H., Ito, T., Iida, T., Kitao, Y., Yamada, H. & Uchida, I. (2000). J. Med. Chem. 43, 4667-4677.]). For related structures, see: Betz et al. (2011[Betz, R., Gerber, T., Hosten, E. & Schalekamp, H. (2011). Acta Cryst. E67, o2154.]); Hemamalini et al. (2011[Hemamalini, M., Goh, J. H. & Fun, H.-K. (2011). Acta Cryst. E67, o3121.]); Balasubramani & Fun (2009[Balasubramani, K. & Fun, H.-K. (2009). Acta Cryst. E65, o1519.]); Fun & Balasubramani (2009[Fun, H.-K. & Balasubramani, K. (2009). Acta Cryst. E65, o1496-o1497.]). For the conformation of the malonate ion, see: Djinović et al. (1990[Djinović, K., Golič, L. & Leban, I. (1990). Acta Cryst. C46, 281-286.]). For hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]). For bond-length data, see: Allen et al. (1987[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.]). For stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]).

[Scheme 1]

Experimental

Crystal data
  • C5H8N3+·C3H3O4

  • Mr = 213.20

  • Monoclinic, P 21

  • a = 5.0843 (1) Å

  • b = 8.0771 (1) Å

  • c = 11.1928 (2) Å

  • β = 91.214 (1)°

  • V = 459.55 (1) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.13 mm−1

  • T = 100 K

  • 0.28 × 0.25 × 0.14 mm

Data collection
  • Bruker SMART APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.966, Tmax = 0.983

  • 6631 measured reflections

  • 1778 independent reflections

  • 1695 reflections with I > 2σ(I)

  • Rint = 0.024

Refinement
  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 0.094

  • S = 1.07

  • 1778 reflections

  • 160 parameters

  • 1 restraint

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.35 e Å−3

  • Δρmin = −0.26 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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+{\script{1\over 2}}, -z+1]; (iii) x+1, y, z; (iv) [-x+1, y-{\script{1\over 2}}, -z+1].

Data collection: APEX2 (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

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.

Related literature top

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 top

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.

Refinement top

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 refinement, 1237 Friedel pairs were merged.

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with atom labels with 50% probability displacement ellipsoids.
[Figure 2] 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.
2,3-Diaminopyridinium hydrogen malonate top
Crystal data top
C5H8N3+·C3H3O4F(000) = 224
Mr = 213.20Dx = 1.541 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 3153 reflections
a = 5.0843 (1) Åθ = 3.1–32.6°
b = 8.0771 (1) ŵ = 0.13 mm1
c = 11.1928 (2) ÅT = 100 K
β = 91.214 (1)°Block, brown
V = 459.55 (1) Å30.28 × 0.25 × 0.14 mm
Z = 2
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
1778 independent reflections
Radiation source: fine-focus sealed tube1695 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
ϕ and ω scansθmax = 32.7°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 77
Tmin = 0.966, Tmax = 0.983k = 1012
6631 measured reflectionsl = 1716
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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.094H 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 parametersΔρmax = 0.35 e Å3
1 restraintΔρmin = 0.26 e Å3
Crystal data top
C5H8N3+·C3H3O4V = 459.55 (1) Å3
Mr = 213.20Z = 2
Monoclinic, P21Mo Kα radiation
a = 5.0843 (1) ŵ = 0.13 mm1
b = 8.0771 (1) ÅT = 100 K
c = 11.1928 (2) Å0.28 × 0.25 × 0.14 mm
β = 91.214 (1)°
Data collection top
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 = 0.983Rint = 0.024
6631 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0371 restraint
wR(F2) = 0.094H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.35 e Å3
1778 reflectionsΔρmin = 0.26 e Å3
160 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.4162 (2)0.50089 (15)0.24888 (10)0.0139 (2)
O20.3017 (2)0.50412 (15)0.44060 (10)0.0139 (2)
O30.7878 (2)0.31758 (17)0.18357 (11)0.0209 (3)
O41.0228 (2)0.17757 (17)0.31863 (13)0.0222 (3)
N10.9986 (2)0.70786 (17)0.18711 (12)0.0123 (2)
N20.8913 (3)0.75149 (17)0.38452 (12)0.0136 (3)
N30.4668 (3)0.95043 (19)0.30805 (14)0.0163 (3)
C10.8441 (3)0.78141 (18)0.26789 (13)0.0107 (3)
C20.6311 (3)0.88272 (18)0.22541 (14)0.0119 (3)
C30.5946 (3)0.8991 (2)0.10331 (14)0.0142 (3)
H3A0.45510.96630.07300.017*
C40.7607 (3)0.8179 (2)0.02293 (14)0.0161 (3)
H4A0.73260.82940.06080.019*
C50.9617 (3)0.7228 (2)0.06655 (14)0.0153 (3)
H5A1.07540.66730.01350.018*
C60.4477 (3)0.45888 (19)0.35774 (14)0.0112 (3)
C70.6803 (3)0.34858 (19)0.39221 (14)0.0129 (3)
H7A0.79970.41420.44480.016*
H7B0.61220.25640.44100.016*
C80.8449 (3)0.27351 (19)0.29470 (15)0.0148 (3)
H2N30.343 (5)1.013 (4)0.276 (2)0.023 (6)*
H2N20.814 (5)0.817 (4)0.434 (2)0.026 (6)*
H1N11.136 (6)0.645 (4)0.218 (3)0.044 (8)*
H1N21.043 (5)0.703 (4)0.401 (2)0.029 (6)*
H1N30.534 (5)0.963 (3)0.380 (2)0.018 (5)*
H1O30.654 (6)0.395 (5)0.190 (3)0.048 (9)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0137 (4)0.0153 (5)0.0126 (5)0.0024 (4)0.0005 (4)0.0011 (4)
O20.0129 (4)0.0152 (5)0.0136 (5)0.0025 (4)0.0018 (3)0.0004 (4)
O30.0217 (5)0.0231 (6)0.0183 (6)0.0068 (5)0.0060 (4)0.0012 (5)
O40.0143 (5)0.0164 (6)0.0360 (8)0.0056 (4)0.0016 (4)0.0008 (5)
N10.0115 (5)0.0135 (6)0.0119 (6)0.0010 (4)0.0004 (4)0.0006 (5)
N20.0134 (5)0.0160 (6)0.0114 (6)0.0024 (4)0.0001 (4)0.0004 (5)
N30.0115 (5)0.0211 (6)0.0162 (6)0.0053 (5)0.0001 (4)0.0023 (5)
C10.0096 (5)0.0114 (6)0.0112 (6)0.0005 (4)0.0006 (4)0.0001 (5)
C20.0099 (5)0.0112 (6)0.0147 (7)0.0001 (5)0.0005 (4)0.0005 (5)
C30.0124 (5)0.0154 (6)0.0148 (7)0.0012 (5)0.0022 (5)0.0026 (6)
C40.0168 (6)0.0201 (7)0.0114 (7)0.0012 (5)0.0011 (5)0.0021 (6)
C50.0165 (6)0.0184 (7)0.0111 (6)0.0015 (6)0.0022 (5)0.0002 (6)
C60.0089 (5)0.0101 (6)0.0145 (6)0.0006 (5)0.0007 (4)0.0002 (5)
C70.0118 (5)0.0130 (6)0.0140 (6)0.0028 (5)0.0007 (4)0.0012 (5)
C80.0113 (6)0.0114 (6)0.0219 (8)0.0008 (5)0.0032 (5)0.0019 (6)
Geometric parameters (Å, º) top
O1—C61.2716 (19)N3—H1N30.87 (2)
O2—C61.2542 (17)C1—C21.4305 (19)
O3—C81.320 (2)C2—C31.382 (2)
O3—H1O30.93 (4)C3—C41.409 (2)
O4—C81.2168 (19)C3—H3A0.9500
N1—C11.3482 (18)C4—C51.361 (2)
N1—C51.3638 (19)C4—H4A0.9500
N1—H1N10.92 (3)C5—H5A0.9500
N2—C11.344 (2)C6—C71.524 (2)
N2—H2N20.87 (3)C7—C81.516 (2)
N2—H1N20.88 (3)C7—H7A0.9900
N3—C21.3731 (19)C7—H7B0.9900
N3—H2N30.88 (3)
C8—O3—H1O3104.9 (19)C5—C4—C3119.31 (14)
C1—N1—C5123.70 (13)C5—C4—H4A120.3
C1—N1—H1N1116.0 (18)C3—C4—H4A120.3
C5—N1—H1N1120.3 (18)C4—C5—N1119.42 (14)
C1—N2—H2N2115.8 (16)C4—C5—H5A120.3
C1—N2—H1N2114.6 (16)N1—C5—H5A120.3
H2N2—N2—H1N2123 (2)O2—C6—O1124.51 (13)
C2—N3—H2N3113.0 (16)O2—C6—C7116.82 (13)
C2—N3—H1N3115.7 (15)O1—C6—C7118.66 (12)
H2N3—N3—H1N3125 (2)C8—C7—C6119.27 (13)
N2—C1—N1118.52 (13)C8—C7—H7A107.5
N2—C1—C2122.95 (13)C6—C7—H7A107.5
N1—C1—C2118.48 (13)C8—C7—H7B107.5
N3—C2—C3123.85 (13)C6—C7—H7B107.5
N3—C2—C1118.10 (13)H7A—C7—H7B107.0
C3—C2—C1117.95 (12)O4—C8—O3121.78 (15)
C2—C3—C4121.14 (13)O4—C8—C7121.03 (16)
C2—C3—H3A119.4O3—C8—C7117.19 (13)
C4—C3—H3A119.4
C5—N1—C1—N2176.82 (14)C2—C3—C4—C50.5 (2)
C5—N1—C1—C20.8 (2)C3—C4—C5—N10.0 (2)
N2—C1—C2—N30.7 (2)C1—N1—C5—C40.7 (2)
N1—C1—C2—N3176.80 (14)O2—C6—C7—C8172.90 (13)
N2—C1—C2—C3177.26 (15)O1—C6—C7—C88.2 (2)
N1—C1—C2—C30.3 (2)C6—C7—C8—O4175.86 (14)
N3—C2—C3—C4175.92 (16)C6—C7—C8—O34.6 (2)
C1—C2—C3—C40.4 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H1O3···O10.93 (4)1.63 (3)2.5208 (16)159 (3)
N3—H2N3···O4i0.88 (3)2.16 (3)2.9133 (19)143 (2)
N2—H2N2···O2ii0.87 (3)2.15 (3)3.0066 (18)168 (2)
N1—H1N1···O1iii0.92 (3)1.87 (3)2.7782 (16)168 (3)
N2—H1N2···O2iii0.88 (3)2.12 (3)2.9470 (18)157 (3)
N3—H1N3···O2ii0.87 (2)2.18 (2)3.0574 (19)178 (3)
C7—H7B···O2iv0.992.463.3532 (19)149
Symmetry codes: (i) x1, y+1, z; (ii) x+1, y+1/2, z+1; (iii) x+1, y, z; (iv) x+1, y1/2, z+1.

Experimental details

Crystal data
Chemical formulaC5H8N3+·C3H3O4
Mr213.20
Crystal system, space groupMonoclinic, P21
Temperature (K)100
a, b, c (Å)5.0843 (1), 8.0771 (1), 11.1928 (2)
β (°) 91.214 (1)
V3)459.55 (1)
Z2
Radiation typeMo Kα
µ (mm1)0.13
Crystal size (mm)0.28 × 0.25 × 0.14
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.966, 0.983
No. of measured, independent and
observed [I > 2σ(I)] reflections
6631, 1778, 1695
Rint0.024
(sin θ/λ)max1)0.761
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.094, 1.07
No. of reflections1778
No. of parameters160
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.35, 0.26

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H1O3···O10.93 (4)1.63 (3)2.5208 (16)159 (3)
N3—H2N3···O4i0.88 (3)2.16 (3)2.9133 (19)143 (2)
N2—H2N2···O2ii0.87 (3)2.15 (3)3.0066 (18)168 (2)
N1—H1N1···O1iii0.92 (3)1.87 (3)2.7782 (16)168 (3)
N2—H1N2···O2iii0.88 (3)2.12 (3)2.9470 (18)157 (3)
N3—H1N3···O2ii0.87 (2)2.18 (2)3.0574 (19)178 (3)
C7—H7B···O2iv0.992.463.3532 (19)149
Symmetry codes: (i) x1, y+1, z; (ii) x+1, y+1/2, z+1; (iii) x+1, y, z; (iv) x+1, y1/2, 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

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Volume 69| Part 1| January 2013| Pages o92-o93
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