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Acta Crystallogr Sect E Struct Rep Online. 2010 August 1; 66(Pt 8): o1964.
Published online 2010 July 10. doi:  10.1107/S1600536810026280
PMCID: PMC3007480

2-Amino-5-bromo­pyridinium 4-carb­oxy­butano­ate

Abstract

In the title salt, C5H6BrN2 +·C5H7O4 , the 2-amino-5-bromo­pyridinium cation is essentially planar, with a maximum deviation of 0.005 (3) Å. In the crystal structure, the proton­ated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl­ate O atoms of the anion via a pair of N—H(...)O hydrogen bonds, forming an R 2 2(8) ring motif. The ion pairs are further connected via O—H(...)O, N—H(...)O and C—H(...)O hydrogen bonds, forming a two-dimensional network parallel to the bc plane. In the network, the hydrogen glutarate (4-carb­oxy­butano­ate) anions self-assemble through O—H(...)O hydrogen bonds, forming a supra­molecular chain along the c axis.

Related literature

For applications of weak intermolecular inter­actions, see: Moghimi et al. (2002 [triangle]); Aghabozorg et al. (2005 [triangle]); Lehn (1992 [triangle]). For the conformation of glutaric acid, see: Saraswathi et al. (2001 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]).

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Object name is e-66-o1964-scheme1.jpg

Experimental

Crystal data

  • C5H6BrN2 +·C5H7O4
  • M r = 305.13
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1964-efi1.jpg
  • a = 5.1499 (12) Å
  • b = 14.858 (4) Å
  • c = 16.022 (4) Å
  • V = 1226.0 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 3.36 mm−1
  • T = 296 K
  • 0.72 × 0.31 × 0.15 mm

Data collection

  • Bruker APEXII DUO CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.195, T max = 0.628
  • 8937 measured reflections
  • 4149 independent reflections
  • 2911 reflections with I > 2σ(I)
  • R int = 0.035

Refinement

  • R[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.116
  • S = 1.02
  • 4149 reflections
  • 170 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.59 e Å−3
  • Δρmin = −0.42 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1734 Friedel pairs
  • Flack parameter: 0.024 (9)

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810026280/is2573sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810026280/is2573Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

MH and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012. MH also thanks Universiti Sains Malaysia for a post-doctoral research fellowship.

supplementary crystallographic information

Comment

Weak interactions, such as hydrogen bonding and π–π stacking, have attracted much interest as a result of their significance in chemistry and biology, especially in the field of crystal engineering (Moghimi et al., 2002; Aghabozorg et al., 2005). The design of highly specific solid-state compounds is of considerable significance in organic chemistry due to the important applications of these compounds in the development of new optical, magnetic and electronic systems (Lehn, 1992). The present work is part of a structural study of complexes of 2-amino pyridinium systems with hydrogen-bond donors and we report here the structure of 2-amino-5-bromopyridinium hydrogen glutarate, (I).

The asymmetric unit (Fig. 1) contains a 2-amino-5-bromopyridinium cation and a hydrogen glutarate anion. The 2-amino-5-bromopyridinium cation is essentially planar, with a maximum deviation of 0.005 (3) Å for atom C5. In the 2-amino-5-bromopyridinium cation, a wider than normal angle [C6—N1—C2 = 123.8 (2)°] is subtented at the protonated N1 atom. The backbone conformation of the hydrogen glutarate anion can be described by the two torsion angles C8-C9-C10-C11 of -178.0 (2)° and C7-C8-C9-C10 of -71.7 (3)°. As evident from the torsion angles, the backbone 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 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 intermolecular N1—H1N1···O2 and N2–H1N2···O1 hydrogen bonds forming a ring motif R22(8) (Bernstein et al., 1995). The ion pairs are further connected via N2—H2N2···O1, O4—H1O4···O2 and C6—H6A···O3 (Table 1) hydrogen bonds, forming a two-dimensional network parallel to the bc-plane (Fig. 2). The hydrogen glutarate anions self-assemble through O4—H1O4···O2 hydrogen bonds, forming one-dimensional supramolecular chains along the c-axis (Fig. 3). Furthermore, the ion pairs are stacked down along the a-axis, forming a three-dimensional network as shown in Fig. 4.

Experimental

A hot methanol solution (20 ml) of 2-amino-5-bromopyridine (86 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 crystals of the title compound appeared after a few days.

Refinement

Atoms H1N1, H1N2, H2N2 and H1O4 were located from a difference Fourier map and were refined freely [N—H= 0.83 (4)–0.94 (3) Å and O—H = 0.69 (5) Å]. The remaining hydrogen atoms were positioned geometrically [C—H = 0.93 or 0.97 Å] and were refined using a riding model, with Uiso(H) = 1.2Ueq(C). 1734 Friedel pairs were used to determine the absolute configuration.

Figures

Fig. 1.
The asymmetric unit of the title compound. Displacement ellipsoids are drawn at the 30% probability level.
Fig. 2.
The crystal packing of (I), showing hydrogen-bonded (dashed lines) 2D networks parallel to to the bc-plane. H atoms not involved in the intermolecular interactions have been omitted for clarity.
Fig. 3.
Carboxyl-carboxylate interactions made up of hydrogen glutarate anion.
Fig. 4.
The crystal packing of the title compound (I), showing the stacking of the molecules down the a-axis. H atoms not involved in the intermolecular interactions have been omitted for clarity.

Crystal data

C5H6BrN2+·C5H7O4F(000) = 616
Mr = 305.13Dx = 1.653 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 2942 reflections
a = 5.1499 (12) Åθ = 2.7–26.8°
b = 14.858 (4) ŵ = 3.36 mm1
c = 16.022 (4) ÅT = 296 K
V = 1226.0 (5) Å3Block, colourless
Z = 40.72 × 0.31 × 0.15 mm

Data collection

Bruker APEXII DUO CCD area-detector diffractometer4149 independent reflections
Radiation source: fine-focus sealed tube2911 reflections with I > 2σ(I)
graphiteRint = 0.035
[var phi] and ω scansθmax = 31.8°, θmin = 2.7°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −7→7
Tmin = 0.195, Tmax = 0.628k = −22→21
8937 measured reflectionsl = −21→23

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.041H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.116w = 1/[σ2(Fo2) + (0.0414P)2] where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max = 0.001
4149 reflectionsΔρmax = 0.59 e Å3
170 parametersΔρmin = −0.42 e Å3
0 restraintsAbsolute structure: Flack (1983), 1734 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.024 (9)

Special details

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)

xyzUiso*/Ueq
Br10.34848 (8)0.78522 (2)0.59104 (2)0.06364 (14)
N1−0.1456 (5)0.72632 (14)0.78238 (14)0.0388 (5)
N2−0.2377 (6)0.7831 (2)0.91338 (17)0.0548 (6)
C6−0.0182 (6)0.72501 (17)0.70949 (16)0.0400 (6)
H6A−0.05630.68120.66990.048*
C50.1666 (6)0.78770 (17)0.69349 (17)0.0424 (5)
C40.2211 (6)0.8540 (2)0.7532 (2)0.0508 (7)
H4A0.34580.89770.74250.061*
C30.0906 (6)0.8540 (2)0.8269 (2)0.0506 (7)
H3A0.12710.89770.86680.061*
C2−0.1011 (6)0.78778 (19)0.84360 (16)0.0412 (6)
O10.3976 (5)0.64368 (15)0.92821 (11)0.0543 (6)
O20.5093 (4)0.59455 (14)0.80384 (11)0.0464 (5)
O3−0.1981 (4)0.44309 (18)1.10571 (14)0.0577 (6)
O40.1873 (5)0.46064 (19)1.16336 (14)0.0582 (6)
C70.3666 (5)0.59209 (17)0.86815 (13)0.0345 (5)
C80.1501 (6)0.52312 (18)0.86922 (15)0.0402 (5)
H8A0.22320.46480.85540.048*
H8B0.02670.53840.82570.048*
C90.0036 (6)0.5146 (2)0.95136 (17)0.0405 (6)
H9A−0.04720.57400.97060.049*
H9B−0.15290.47950.94270.049*
C100.1701 (6)0.46966 (19)1.01720 (16)0.0426 (6)
H10A0.22640.41150.99650.051*
H10B0.32390.50601.02660.051*
C110.0308 (5)0.45656 (16)1.09925 (16)0.0369 (5)
H1N1−0.270 (6)0.681 (2)0.7886 (19)0.037 (7)*
H1N2−0.335 (8)0.740 (3)0.923 (2)0.045 (9)*
H2N2−0.188 (8)0.813 (2)0.954 (2)0.054 (10)*
H1O40.132 (11)0.454 (3)1.202 (3)0.077 (15)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Br10.0722 (2)0.05631 (18)0.0624 (2)−0.00719 (18)0.02248 (18)0.00228 (16)
N10.0394 (12)0.0371 (10)0.0400 (11)−0.0100 (11)−0.0015 (9)−0.0063 (8)
N20.0634 (16)0.0631 (15)0.0380 (12)−0.0189 (14)−0.0009 (11)−0.0141 (14)
C60.0444 (15)0.0366 (12)0.0390 (12)−0.0025 (12)−0.0050 (11)−0.0050 (10)
C50.0438 (14)0.0356 (11)0.0479 (13)−0.0004 (14)0.0004 (12)0.0015 (11)
C40.0439 (16)0.0413 (14)0.067 (2)−0.0096 (13)0.0036 (14)−0.0033 (13)
C30.0520 (18)0.0437 (13)0.0562 (17)−0.0128 (14)−0.0056 (14)−0.0111 (13)
C20.0463 (15)0.0392 (12)0.0380 (12)−0.0033 (12)−0.0070 (11)−0.0055 (11)
O10.0721 (16)0.0581 (11)0.0327 (9)−0.0205 (12)0.0154 (9)−0.0153 (8)
O20.0526 (12)0.0619 (11)0.0247 (8)−0.0177 (11)0.0048 (8)−0.0074 (8)
O30.0367 (11)0.0894 (16)0.0470 (12)−0.0027 (11)0.0051 (9)0.0139 (11)
O40.0492 (13)0.0935 (18)0.0320 (10)−0.0119 (13)0.0026 (10)0.0173 (11)
C70.0397 (13)0.0409 (12)0.0229 (10)−0.0022 (12)−0.0023 (10)0.0006 (8)
C80.0458 (14)0.0450 (13)0.0299 (11)−0.0065 (13)−0.0016 (11)0.0015 (10)
C90.0369 (14)0.0496 (13)0.0349 (12)−0.0016 (12)0.0020 (11)0.0095 (11)
C100.0399 (14)0.0534 (14)0.0344 (12)0.0064 (14)0.0079 (11)0.0096 (10)
C110.0432 (14)0.0351 (11)0.0324 (12)0.0038 (10)0.0077 (11)0.0064 (10)

Geometric parameters (Å, °)

Br1—C51.890 (3)O2—C71.266 (3)
N1—C61.340 (4)O3—C111.201 (4)
N1—C21.360 (3)O4—C111.307 (4)
N1—H1N10.94 (3)O4—H1O40.69 (5)
N2—C21.323 (4)C7—C81.514 (4)
N2—H1N20.83 (4)C8—C91.522 (4)
N2—H2N20.83 (4)C8—H8A0.9700
C6—C51.356 (4)C8—H8B0.9700
C6—H6A0.9300C9—C101.515 (4)
C5—C41.402 (4)C9—H9A0.9700
C4—C31.359 (5)C9—H9B0.9700
C4—H4A0.9300C10—C111.510 (4)
C3—C21.419 (4)C10—H10A0.9700
C3—H3A0.9300C10—H10B0.9700
O1—C71.241 (3)
C6—N1—C2123.8 (2)O1—C7—C8120.3 (2)
C6—N1—H1N1114.6 (19)O2—C7—C8117.1 (2)
C2—N1—H1N1121.7 (19)C7—C8—C9115.5 (2)
C2—N2—H1N2122 (2)C7—C8—H8A108.4
C2—N2—H2N2119 (3)C9—C8—H8A108.4
H1N2—N2—H2N2116 (4)C7—C8—H8B108.4
N1—C6—C5119.9 (2)C9—C8—H8B108.4
N1—C6—H6A120.0H8A—C8—H8B107.5
C5—C6—H6A120.0C10—C9—C8111.0 (2)
C6—C5—C4119.6 (3)C10—C9—H9A109.4
C6—C5—Br1119.9 (2)C8—C9—H9A109.4
C4—C5—Br1120.5 (2)C10—C9—H9B109.4
C3—C4—C5119.6 (3)C8—C9—H9B109.4
C3—C4—H4A120.2H9A—C9—H9B108.0
C5—C4—H4A120.2C11—C10—C9113.2 (2)
C4—C3—C2120.5 (3)C11—C10—H10A108.9
C4—C3—H3A119.7C9—C10—H10A108.9
C2—C3—H3A119.7C11—C10—H10B108.9
N2—C2—N1119.0 (3)C9—C10—H10B108.9
N2—C2—C3124.4 (3)H10A—C10—H10B107.7
N1—C2—C3116.6 (3)O3—C11—O4123.1 (3)
C11—O4—H1O4117 (5)O3—C11—C10124.3 (3)
O1—C7—O2122.6 (3)O4—C11—C10112.7 (2)
C2—N1—C6—C5−0.2 (4)C4—C3—C2—N2−179.7 (3)
N1—C6—C5—C4−0.6 (4)C4—C3—C2—N1−0.4 (4)
N1—C6—C5—Br1179.5 (2)O1—C7—C8—C9−7.5 (4)
C6—C5—C4—C30.8 (5)O2—C7—C8—C9173.0 (2)
Br1—C5—C4—C3−179.2 (3)C7—C8—C9—C10−71.7 (3)
C5—C4—C3—C2−0.3 (5)C8—C9—C10—C11−178.0 (2)
C6—N1—C2—N2−179.9 (3)C9—C10—C11—O332.0 (4)
C6—N1—C2—C30.7 (4)C9—C10—C11—O4−148.6 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N1···O2i0.94 (3)1.73 (3)2.666 (3)177 (2)
N2—H1N2···O1i0.83 (4)1.99 (4)2.806 (4)170 (4)
N2—H2N2···O1ii0.83 (3)2.04 (3)2.848 (3)164 (3)
O4—H1O4···O2iii0.69 (5)1.93 (5)2.601 (3)166 (5)
C3—H3A···O3iv0.932.573.382 (4)146
C6—H6A···O3v0.932.463.337 (4)157

Symmetry codes: (i) x−1, y, z; (ii) x−1/2, −y+3/2, −z+2; (iii) −x+1/2, −y+1, z+1/2; (iv) x+1/2, −y+3/2, −z+2; (v) −x−1/2, −y+1, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS2573).

References

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  • Bruker (2009). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
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  • Moghimi, A., Ranibar, M., Aghabozorg, H., Jalali, F., Shamsipur, M., Yap, G. P. A. & Rahbarnoohi, H. (2002). J. Mol. Struct.605, 133–149.
  • Saraswathi, N. T., Manoj, N. & Vijayan, M. (2001). Acta Cryst. B57, 366–371. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

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