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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 11| November 2011| Page o3123
doi:10.1107/S1600536811044473

2,3-Di­amino­pyridinium 4-carb­­oxy­butano­ate

Madhukar Hemamalini,a Jia Hao Goha‡ and Hoong-Kun Funa*§

aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my

(Received 19 October 2011; accepted 25 October 2011; online 29 October 2011)

In the title mol­ecular salt, C5H8N3+·C5H7O4−, the 2,3-diamino­pyridine mol­ecule is protonated at the pyridine N atom. The cation is essentially planar, with a maximum deviation of 0.015 (2) Å, and the anion adopts an extended conformation. In the crystal, the hydrogen glutarate (4-carb­oxy­butano­ate) anions are self-assembled through O—H⋯O hydrogen bonds, forming chains. The cations are connected to the anion chains via N—H⋯O hydrogen bonds, forming a three-dimensional network. The crystal structure also features aromatic π–π inter­actions between the pyridinium cations, with a centroid–centroid distance of 3.4464 (10) Å.

Related literature

For applications of 2-amino­pyridine derivatives, see: Bis et al. (2006[Bis, J. A., McLaughlin, O. L., Vishweshwar, P. & Zaworotko, M. J. (2006). Cryst. Growth Des. 6, 2648-2650.]); Gellert & Hsu (1988[Gellert, R. W. & Hsu, I.-N. (1988). Acta Cryst. C44, 311-313.]). For glutaric acid conformations, see: Saraswathi et al. (2001[Saraswathi, N. T., Manoj, N. & Vijayan, M. (2001). Acta Cryst. B57, 366-371.]). 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 the stability of the temperature controller used in 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+·C5H7O4−

  • Mr = 241.25

  • Monoclinic, P 21 /c

  • a = 7.7052 (1) Å

  • b = 21.4626 (4) Å

  • c = 7.8450 (1) Å

  • β = 119.473 (1)°

  • V = 1129.46 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 100 K

  • 0.35 × 0.18 × 0.05 mm
Data collection

  • Bruker APEXII DUO CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.962, Tmax = 0.994

  • 9826 measured reflections

  • 3281 independent reflections

  • 2475 reflections with I > 2σ(I)

  • Rint = 0.030
Refinement

  • R[F2 > 2σ(F2)] = 0.050

  • wR(F2) = 0.123

  • S = 1.04

  • 3281 reflections

  • 191 parameters

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

  • Δρmax = 0.43 e Å−3

  • Δρmin = −0.35 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1N1⋯O2i 0.86 1.94 2.7571 (18) 159
N2—H2N1⋯O1i 0.86 2.13 2.9077 (19) 151
N2—H2N2⋯O1ii 0.86 2.04 2.8766 (18) 164
N3—H3N1⋯O4iii 0.86 2.16 3.0054 (18) 168
N3—H3N2⋯O1ii 0.86 2.17 3.0194 (18) 167
O3—H1O1⋯O2iv 0.82 1.74 2.5546 (18) 171
Symmetry codes: (i) x, y, z+1; (ii) -x+1, -y+2, -z+2; (iii) [-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iv) [x+1, -y+{\script{3\over 2}}, z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. 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

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811044473/hb6458sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811044473/hb6458Isup2.hkl

checkCIF report


Comment top

2-Aminopyridine and its derivatives are some of the most frequently-used synthons in supramolecular chemistry based on hydrogen bonds (Bis et al., 2006; Gellert & Hsu, 1988). Glutaric acid is found in the blood and urine. It is used in the synthesis of pharmaceuticals, surfactants and metal finishing compounds. Herein, we report the crystal structure determination of the title compound, (I).

The asymmetric unit (Fig. 1) contains a 2,3-diaminopyridinium cation and hydrogenglutarate anion. The cation is essentially planar, with a maximum deviation of 0.015 (2) Å for atom C1. In the 2,3-diaminopyridinium cation, a wide angle [123.94 (14)°] is subtended at the protonated N1 atom. The conformation of the hydrogenglutarate anion can be described by the two torsion angles C6-C7-C8-C9 of 58.61 (16)° and C7-C8-C9-C10 of 175.91 (13)°. As evident from the torsion angles, the hydrogenglutarate anion is in a fully extended conformation (Saraswathi et al., 2001). Of the two carboxyl groups, one is deprotonated while the other is not. The bond lengths (Allen et al., 1987) and angles are within normal ranges.

In the crystal (Fig. 2), the protonated N1 atom and the 2-amino group (N2) are hydrogen-bonded to the carboxylate oxygen atoms (O1 and O2) via a pair of intermolecular N—H···O hydrogen bonds, forming a ring motif R22(8) (Bernstein et al., 1995). The hydrogen glutarate anions self-assemble through O—H···O hydrogen bonds, forming chains. Furthermore, the cations are connected via N—H···O hydrogen bonds (Table 1) to these anoinic chains to form a three-dimensional network. The crystal structure is further stabilized by weak π–π interactions between the pyridinium (Cg1 = N1/C1–C5) cations [Cg1···Cg1 = 3.4464 (10) Å; -x, 2-y, 2-z].

Related literature top

For applications of 2-aminopyridine derivatives, see: Bis et al. (2006); Gellert & Hsu (1988). For glutaric acid conformations, see: Saraswathi et al. (2001). For hydrogen-bond motifs, see: Bernstein et al. (1995). For bond-length data, see: Allen et al. (1987). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).

Experimental top

Hot methanol solution (20 ml) of 2,3-diaminopyridine (52 mg, Aldrich) and glutaric acid (66 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 brown plates of the title compound appeared after a few days.

Refinement top

The C-bonded hydrogen atoms were located from a difference Fourier maps and refined freely [C–H = 0.96 (2)–1.00 (2) Å] and C–H = 0.93 (2)–1.01 (2) Å]. The O- and N- bonded hydrogen atoms can also be located but in the final refinement, these hydrogen were positioned geometrically [N–H = 0.86 Å and O–H = 0.82°] and were refined using a riding model, with Uiso(H) = 1.2 or 1.5 Ueq(C).

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 asymmetric unit of the title compound, showing 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. The crystal packing of title compound (I).
2,3-Diaminopyridinium 4-carboxybutanoate top
Crystal data top
C5H8N3+·C5H7O4−F(000) = 512
Mr = 241.25Dx = 1.419 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3028 reflections
a = 7.7052 (1) Åθ = 3.1–30.0°
b = 21.4626 (4) ŵ = 0.11 mm−1
c = 7.8450 (1) ÅT = 100 K
β = 119.473 (1)°Plate, brown
V = 1129.46 (3) Å30.35 × 0.18 × 0.05 mm
Z = 4
Data collection top
Bruker APEXII DUO CCD
diffractometer		3281 independent reflections
Radiation source: fine-focus sealed tube2475 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
ϕ and ω scansθmax = 30.1°, θmin = 3.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		h = −10→9
Tmin = 0.962, Tmax = 0.994k = −30→16
9826 measured reflectionsl = −11→10
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)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.123H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0439P)2 + 0.6889P]
where P = (Fo2 + 2Fc2)/3
3281 reflections(Δ/σ)max = 0.001
191 parametersΔρmax = 0.43 e Å−3
0 restraintsΔρmin = −0.35 e Å−3
Crystal data top
C5H8N3+·C5H7O4−V = 1129.46 (3) Å3
Mr = 241.25Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.7052 (1) ŵ = 0.11 mm−1
b = 21.4626 (4) ÅT = 100 K
c = 7.8450 (1) Å0.35 × 0.18 × 0.05 mm
β = 119.473 (1)°
Data collection top
Bruker APEXII DUO CCD
diffractometer		3281 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		2475 reflections with I > 2σ(I)
Tmin = 0.962, Tmax = 0.994Rint = 0.030
9826 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0500 restraints
wR(F2) = 0.123H atoms treated by a mixture of independent and constrained refinement
S = 1.04Δρmax = 0.43 e Å−3
3281 reflectionsΔρmin = −0.35 e Å−3
191 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 s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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
N10.1547 (2)0.91493 (6)1.0497 (2)0.0199 (3)
H1N10.17630.88951.14280.024*
N20.4178 (2)0.97294 (6)1.27871 (19)0.0227 (3)
H2N10.43580.94541.36570.027*
H2N20.49411.00511.31050.027*
N30.3437 (2)1.06274 (6)0.9866 (2)0.0236 (3)
H3N10.32061.08970.89670.028*
H3N20.43821.06901.10440.028*
C10.2710 (2)0.96571 (7)1.0940 (2)0.0174 (3)
C20.2301 (2)1.00984 (7)0.9422 (2)0.0179 (3)
C30.0765 (3)0.99662 (8)0.7572 (2)0.0218 (3)
C4−0.0356 (3)0.94140 (8)0.7180 (2)0.0243 (3)
C50.0045 (2)0.90133 (8)0.8661 (2)0.0230 (3)
O10.37775 (18)0.91001 (5)0.58579 (17)0.0259 (3)
O20.14921 (17)0.85057 (5)0.35117 (16)0.0231 (3)
O30.89545 (17)0.73680 (5)0.77123 (18)0.0250 (3)
H1O10.96960.70650.80030.037*
O40.68383 (19)0.66708 (5)0.78111 (19)0.0286 (3)
C60.2633 (2)0.86410 (7)0.5313 (2)0.0184 (3)
C70.2679 (2)0.81908 (7)0.6837 (2)0.0180 (3)
C80.3856 (2)0.76040 (7)0.6920 (2)0.0177 (3)
C90.5983 (2)0.77618 (7)0.7421 (2)0.0181 (3)
C100.7278 (2)0.72033 (7)0.7669 (2)0.0190 (3)
H3A0.044 (3)1.0263 (9)0.654 (3)0.031 (5)*
H4A−0.143 (3)0.9321 (9)0.589 (3)0.031 (5)*
H5A−0.066 (3)0.8624 (9)0.854 (3)0.026 (5)*
H7A0.331 (3)0.8398 (8)0.812 (3)0.019 (4)*
H7B0.131 (3)0.8081 (9)0.649 (3)0.025 (5)*
H8A0.317 (3)0.7388 (8)0.562 (3)0.019 (4)*
H8B0.389 (3)0.7319 (8)0.792 (3)0.018 (4)*
H9A0.601 (3)0.8033 (9)0.642 (3)0.025 (5)*
H9B0.664 (3)0.8000 (9)0.867 (3)0.028 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0211 (6)0.0171 (6)0.0228 (7)−0.0007 (5)0.0118 (5)0.0011 (5)
N20.0241 (7)0.0215 (6)0.0182 (7)−0.0050 (5)0.0071 (6)0.0039 (5)
N30.0300 (7)0.0199 (6)0.0181 (6)−0.0049 (5)0.0097 (6)0.0028 (5)
C10.0182 (7)0.0157 (7)0.0196 (7)0.0011 (5)0.0102 (6)0.0001 (5)
C20.0208 (7)0.0160 (6)0.0192 (7)0.0014 (5)0.0117 (6)0.0006 (5)
C30.0251 (8)0.0238 (8)0.0168 (7)0.0010 (6)0.0105 (6)0.0009 (6)
C40.0223 (8)0.0294 (8)0.0189 (8)−0.0003 (6)0.0085 (7)−0.0058 (6)
C50.0218 (8)0.0218 (8)0.0272 (8)−0.0022 (6)0.0134 (7)−0.0072 (6)
O10.0285 (6)0.0209 (6)0.0233 (6)−0.0069 (5)0.0091 (5)0.0011 (4)
O20.0226 (6)0.0232 (6)0.0196 (6)−0.0046 (4)0.0073 (5)0.0025 (4)
O30.0194 (6)0.0228 (6)0.0316 (7)0.0047 (4)0.0117 (5)0.0022 (5)
O40.0326 (7)0.0179 (6)0.0386 (7)0.0018 (5)0.0200 (6)−0.0013 (5)
C60.0172 (7)0.0160 (7)0.0214 (8)0.0018 (5)0.0090 (6)0.0020 (5)
C70.0191 (7)0.0174 (7)0.0190 (7)−0.0002 (6)0.0105 (6)0.0006 (5)
C80.0208 (7)0.0154 (6)0.0180 (7)0.0004 (5)0.0104 (6)0.0016 (5)
C90.0192 (7)0.0155 (7)0.0189 (7)0.0015 (5)0.0088 (6)0.0005 (5)
C100.0219 (7)0.0187 (7)0.0147 (7)0.0020 (6)0.0076 (6)−0.0013 (5)
Geometric parameters (Å, º) top
N1—C11.3435 (19)O1—C61.2491 (18)
N1—C51.364 (2)O2—C61.2774 (19)
N1—H1N10.8600O3—C101.3235 (19)
N2—C11.338 (2)O3—H1O10.8200
N2—H2N10.8600O4—C101.2125 (19)
N2—H2N20.8600C6—C71.524 (2)
N3—C21.3698 (19)C7—C81.535 (2)
N3—H3N10.8600C7—H7A0.981 (18)
N3—H3N20.8600C7—H7B0.98 (2)
C1—C21.430 (2)C8—C91.523 (2)
C2—C31.378 (2)C8—H8A0.999 (18)
C3—C41.408 (2)C8—H8B0.987 (18)
C3—H3A0.96 (2)C9—C101.510 (2)
C4—C51.353 (2)C9—H9A0.98 (2)
C4—H4A0.96 (2)C9—H9B1.00 (2)
C5—H5A0.97 (2)
C1—N1—C5123.94 (14)O1—C6—O2122.93 (14)
C1—N1—H1N1118.0O1—C6—C7119.46 (14)
C5—N1—H1N1118.0O2—C6—C7117.48 (13)
C1—N2—H2N1120.0C6—C7—C8109.78 (12)
C1—N2—H2N2120.0C6—C7—H7A108.9 (11)
H2N1—N2—H2N2120.0C8—C7—H7A110.1 (11)
C2—N3—H3N1120.0C6—C7—H7B109.2 (11)
C2—N3—H3N2120.0C8—C7—H7B110.4 (11)
H3N1—N3—H3N2120.0H7A—C7—H7B108.4 (16)
N2—C1—N1118.36 (13)C9—C8—C7111.52 (12)
N2—C1—C2123.19 (14)C9—C8—H8A109.1 (10)
N1—C1—C2118.44 (14)C7—C8—H8A109.5 (10)
N3—C2—C3123.32 (14)C9—C8—H8B109.2 (10)
N3—C2—C1119.05 (14)C7—C8—H8B109.0 (10)
C3—C2—C1117.63 (14)H8A—C8—H8B108.5 (14)
C2—C3—C4121.33 (15)C10—C9—C8114.57 (13)
C2—C3—H3A118.8 (13)C10—C9—H9A107.5 (12)
C4—C3—H3A119.9 (12)C8—C9—H9A111.5 (12)
C5—C4—C3119.41 (15)C10—C9—H9B107.4 (11)
C5—C4—H4A119.1 (12)C8—C9—H9B109.1 (12)
C3—C4—H4A121.5 (12)H9A—C9—H9B106.4 (16)
C4—C5—N1119.17 (15)O4—C10—O3124.24 (14)
C4—C5—H5A125.4 (12)O4—C10—C9124.27 (15)
N1—C5—H5A115.4 (11)O3—C10—C9111.48 (13)
C10—O3—H1O1109.5
C5—N1—C1—N2−177.92 (14)C3—C4—C5—N1−0.9 (2)
C5—N1—C1—C23.0 (2)C1—N1—C5—C4−1.6 (2)
N2—C1—C2—N3−1.0 (2)O1—C6—C7—C8−101.51 (16)
N1—C1—C2—N3178.07 (14)O2—C6—C7—C874.36 (17)
N2—C1—C2—C3179.09 (15)C6—C7—C8—C958.61 (16)
N1—C1—C2—C3−1.8 (2)C7—C8—C9—C10175.91 (13)
N3—C2—C3—C4179.59 (15)C8—C9—C10—O4−12.6 (2)
C1—C2—C3—C4−0.5 (2)C8—C9—C10—O3167.48 (13)
C2—C3—C4—C51.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O2i0.861.942.7571 (18)159
N2—H2N1···O1i0.862.132.9077 (19)151
N2—H2N2···O1ii0.862.042.8766 (18)164
N3—H3N1···O4iii0.862.163.0054 (18)168
N3—H3N2···O1ii0.862.173.0194 (18)167
O3—H1O1···O2iv0.821.742.5546 (18)171
Symmetry codes: (i) x, y, z+1; (ii) −x+1, −y+2, −z+2; (iii) −x+1, y+1/2, −z+3/2; (iv) x+1, −y+3/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC5H8N3+·C5H7O4−
Mr241.25
Crystal system, space groupMonoclinic, P21/c
Temperature (K)100
a, b, c (Å)7.7052 (1), 21.4626 (4), 7.8450 (1)
β (°) 119.473 (1)
V (Å3)1129.46 (3)
Z4
Radiation typeMo Kα
µ (mm−1)0.11
Crystal size (mm)0.35 × 0.18 × 0.05
Data collection
DiffractometerBruker APEXII DUO CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.962, 0.994
No. of measured, independent and
observed [I > 2σ(I)] reflections		9826, 3281, 2475
Rint0.030
(sin θ/λ)max (Å−1)0.706
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.050, 0.123, 1.04
No. of reflections3281
No. of parameters191
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.43, −0.35

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
N1—H1N1···O2i0.861.942.7571 (18)159
N2—H2N1···O1i0.862.132.9077 (19)151
N2—H2N2···O1ii0.862.042.8766 (18)164
N3—H3N1···O4iii0.862.163.0054 (18)168
N3—H3N2···O1ii0.862.173.0194 (18)167
O3—H1O1···O2iv0.821.742.5546 (18)171
Symmetry codes: (i) x, y, z+1; (ii) −x+1, −y+2, −z+2; (iii) −x+1, y+1/2, −z+3/2; (iv) x+1, −y+3/2, z+1/2.
 

Footnotes

‡Thomson Reuters ResearcherID: C-7576-2009.

§Thomson Reuters ResearcherID: A-3561-2009.

Acknowledgements

MH, JHG and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Research University Grant No. 1001/PFIZIK/811160. MH also thanks Universiti Sains Malaysia for a post-doctoral research fellowship.

References

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ISSN: 2056-9890
Volume 67| Part 11| November 2011| Page o3123
doi:10.1107/S1600536811044473
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