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ISSN: 2414-3146

2-Amino-5-bromo­pyridinium 2-phen­­oxy­acetate

CROSSMARK_Color_square_no_text.svg

aDepartment of Chemistry, Dhanalakshmi Srinivasan Institute of Technology, Samayapuram, Tiruchirappalli 621 112, Tamil Nadu, India, bDepartment of Chemistry, St. Joseph College (Autonomous), Tiruchirappalli 620 002, Tamil Nadu, India, cDepartment of Chemistry, Government Arts College, Tiruchirappalli 620 022, Tamil Nadu, India, and dSchool of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: chemdhanabalan@gmail.com

Edited by H. Ishida, Okayama University, Japan (Received 15 November 2016; accepted 3 December 2016; online 9 December 2016)

The phen­oxy­acetate anion of the title salt, C5H6BrN2+·C8H7O3, is essentially planar, with a dihedral angle of 7.6 (5)° between the carboxyl­ate group and the benzene ring. In the crystal, the cation and the anion are linked via N—H⋯O hydrogen bonds, forming a helical chain along a 21 screw axis. In the chain, a ππ stacking inter­action between the pyridinium and benzene rings, with a centroid–centroid distance of 3.854 (2) Å, and a C—H⋯O inter­action are observed. The chains are further linked through another C—H⋯O hydrogen bond, forming a three-dimensional network.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Supra­molecular architectures assembled via various delicate non-covalent inter­actions, such as hydrogen bonds, ππ stacking and electrostatic inter­actions, etc. have attracted intense inter­est in recent years because of their fascinating structural diversity and potential applications for functional materials (Desiraju, 2007[Desiraju, G. R. (2007). Angew. Chem. Int. Ed. 46, 8342-8356.]). In particular, the application of inter­molecular hydrogen bonds is a well known and efficient tool in the field of organic crystal design owing to its strength and directional properties (Aakeröy & Seddon, 1993[Aakeröy, C. B. & Seddon, K. R. (1993). Chem. Soc. Rev. 22, 397-407.]). Pyridine and its derivatives play an important role in heterocyclic chemistry (Pozharski et al., 1997[Pozharski, A. F., Soldatenkov, A. T. & Katritzky, A. R. (1997). In Heterocycles in Life and Society. New York: Wiley.]; Katritzky et al., 1996[Katritzky, A. R., Rees, C. W. & Scriven, E. F. V. (1996). In Comprehensive Heterocyclic Chemistry II. Oxford: Pergamon Press.]). They are often involved in hydrogen-bond inter­actions. Aryl­oxyacetic acid derivatives possess a wide array of diverse bioactivities including anti­mycobacterial (Ali & Shanharyar, 2007[Ali, M. A. & Shaharyar, M. (2007). Bioorg. Med. Chem. 15, 1896-1902.]; Shaharyar et al., 2006[Shaharyar, M., Siddiqui, A. A. & Asraf Ali, M. (2006). Bioorg. Med. Chem. Lett. 16, 4571-4574.]), anti-inflammatory and anti­oxidant (Kunsch et al., 2005[Kunsch, C., Luchoomun, J., Chen, X. L., Dodd, G. L., Karu, K. S., Meng, C. Q., Marino, E. M., Olliff, L. K., Piper, J. D., Qiu, F. H., Sikorski, J. A., Somers, P. K., Suen, K.-L., Thomas, S., Whalen, A. M., Wasserman, M. A. & Sundell, C. L. (2005). J. Pharmacol. Exp. Ther. 313, 492-501.]), anti­bacterial (Iqbal et al., 2007[Iqbal, A., Siddiqui, H. L., Ashraf, C. M., Ahmad, M. & Weaver, G. W. (2007). Molecules, 12, 245-254.]), anti­lipaemic and anti­platelet (Pérez-Pastén et al., 2006[Pérez-Pastén, R., García, R. V., Garduño, L., Reyes, E., Labarrios, F., Tamariz, J. & Chamorro, G. (2006). J. Pharm. Pharmacol. 58, 1343-1349.]) and inhibitory activity of cathepsin K and aldose reductase (Shinozuka et al., 2006[Shinozuka, T., Shimada, K., Matsui, S., Yamane, T., Ama, M., Fukuda, T., Taki, M. & Naito, S. (2006). Bioorg. Med. Chem. Lett. 16, 1502-1505.]). In order to study some hydrogen-bonding inter­actions, the structure of the title salt was determined.

The asymmetric unit (Fig. 1[link]) contains one 2-amino-5-bromo­pyridinium cation and one phen­oxy­acetate anion, in which the carboxyl group of the phen­oxy­acetate acid is ionized by proton transfer to the nitro­gen atom of bromo­pyridine. The carboxyl­ate anion is also confirmed by the bond distances O2—C6 = 1.242 (4) Å and O3—C6 = 1.270 (4) Å. In the 2-amino-5-bromo­pyridinium cation, a wider than normal angle [C1—N1—C5 = 122.1 (3)°] is subtended at the protonated N1 atom. This type of protonation is observed in various amino­pyridine acid complexes (Hemamalini & Fun 2010[Hemamalini, M. & Fun, H.-K. (2010). Acta Cryst. E66, o664.]; Khalib et al., 2013[Khalib, N. C., Thanigaimani, K., Arshad, S. & Razak, I. A. (2013). Acta Cryst. E69, o1120.]). The non-H atoms of the 2-amino-5-bromo­pyridinium cation are essentially co-planar, with a maximum deviation of 0.016 (3) Å for atom N2. The dihedral angle between the pyridine (N1/C1–C5) and benzene (C8–C13) rings is 10.22 (18)°. The anion is essentially planar, with a dihedral angle of 7.6 (5)° between the benzene (C8–C13) ring and the carboxyl­ate (O2/O3/C6) group and with a C8—O1—C7—C6 torsion angle of 172.7 (3)°. All the bond lengths and angles are normal.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the atom labels and 50% probability displacement ellipsoids. Hydrogen bonds are shown as dashed lines.

In the crystal, the cation and the anion are linked via N1—H1N1⋯O3 and N2—H1N2⋯O2 hydrogen bonds, forming an R22(8) ring motif. The cation further inter­acts with the anions through a bifurcated N2—H2N2⋯(O1i,O2i) hydrogen bond and a C2—H2A⋯O2i inter­action (symmetry code in Table 1[link]) with R12(5) and R21(6) ring motifs, forming a helical chain (Fig. 2[link]). A ππ stacking inter­action between the pyridinium (C1–C5/N1) and benzene (C8–C13; symmetry code: x, y − 1, z) rings with a centroid–centroid distance of 3.854 (2) Å is observed in the chain. Finally, a weak C5—H5A⋯O3ii hydrogen bond (symmetry code in Table 1[link]), leads to the formation of a three-dimensional network.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1N1⋯O3 0.88 (1) 1.70 (3) 2.579 (4) 176 (5)
N2—H1N2⋯O2 0.87 (1) 2.01 (3) 2.877 (4) 177 (4)
N2—H2N2⋯O1i 0.87 (1) 2.41 (3) 3.140 (4) 142 (5)
N2—H2N2⋯O2i 0.87 (1) 2.13 (3) 2.900 (4) 146 (5)
C2—H2A⋯O2i 0.95 2.55 3.193 (4) 125
C5—H5A⋯O3ii 0.95 2.42 3.047 (4) 123
Symmetry codes: (i) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{5\over 4}}]; (ii) y, x, -z+1.
[Figure 2]
Figure 2
A partial packing diagram of the title compound. The N—H⋯O and C—H⋯O hydrogen bonds are shown as dashed lines.

Synthesis and crystallization

A hot methanol solution (20 ml) of 2-amino-5-bromo­pyridine (43 mg, Aldrich) and phen­oxy­acetic acid (38 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

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C5H6BrN2+·C8H7O3
Mr 325.16
Crystal system, space group Tetragonal, P41212
Temperature (K) 100
a, c (Å) 8.6944 (1), 35.2843 (7)
V3) 2667.23 (7)
Z 8
Radiation type Mo Kα
μ (mm−1) 3.09
Crystal size (mm) 0.34 × 0.21 × 0.13
 
Data collection
Diffractometer Bruker SMART APEXII CCD area-detector
Absorption correction Multi-scan (SADABS; Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.419, 0.688
No. of measured, independent and observed [I > 2σ(I)] reflections 38666, 3407, 2790
Rint 0.076
(sin θ/λ)max−1) 0.673
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.078, 1.17
No. of reflections 3407
No. of parameters 184
No. of restraints 3
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.52, −0.52
Absolute structure Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1324 Fridel pairs
Absolute structure parameter 0.072 (13)
Computer programs: APEX2 and SAINT (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Structural data


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).

2-Amino-5-bromopyridinium 2-phenoxyacetate top
Crystal data top
C5H6BrN2+·C8H7O3Dx = 1.620 Mg m3
Mr = 325.16Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P41212Cell parameters from 9890 reflections
Hall symbol: P 4abw 2nwθ = 2.3–26.4°
a = 8.6944 (1) ŵ = 3.09 mm1
c = 35.2843 (7) ÅT = 100 K
V = 2667.23 (7) Å3Block, colourless
Z = 80.34 × 0.21 × 0.13 mm
F(000) = 1312
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
3407 independent reflections
Radiation source: fine-focus sealed tube2790 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.076
φ and ω scansθmax = 28.6°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 1111
Tmin = 0.419, Tmax = 0.688k = 1111
38666 measured reflectionsl = 4747
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.042H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.078 w = 1/[σ2(Fo2) + (0.P)2 + 4.511P]
where P = (Fo2 + 2Fc2)/3
S = 1.17(Δ/σ)max = 0.001
3407 reflectionsΔρmax = 0.52 e Å3
184 parametersΔρmin = 0.52 e Å3
3 restraintsAbsolute structure: Flack (1983), 1324 Fridel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.072 (13)
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 esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
Br10.85535 (5)1.53676 (5)0.471862 (11)0.02404 (10)
O11.0287 (3)0.5443 (3)0.58802 (7)0.0207 (6)
O20.8557 (3)0.7960 (3)0.58999 (7)0.0251 (6)
O30.9831 (3)0.9012 (3)0.54112 (7)0.0228 (6)
N10.8335 (3)1.1573 (4)0.54085 (8)0.0168 (6)
N20.7130 (4)1.0932 (4)0.59699 (10)0.0218 (7)
C10.7426 (4)1.1976 (4)0.57033 (10)0.0171 (8)
C20.6803 (4)1.3478 (5)0.57085 (10)0.0204 (8)
H2A0.61541.37900.59110.024*
C30.7137 (4)1.4481 (5)0.54222 (11)0.0220 (8)
H3A0.67271.54940.54260.026*
C40.8083 (4)1.4014 (4)0.51234 (10)0.0193 (8)
C50.8671 (4)1.2562 (4)0.51232 (10)0.0177 (7)
H5A0.93221.22410.49220.021*
C60.9580 (5)0.7964 (4)0.56542 (10)0.0177 (8)
C71.0704 (4)0.6625 (4)0.56195 (10)0.0196 (8)
H7A1.06830.62160.53580.024*
H7B1.17610.69860.56740.024*
C81.1075 (4)0.4079 (4)0.58550 (10)0.0178 (8)
C91.0630 (5)0.2962 (4)0.61188 (10)0.0211 (9)
H9A0.98480.31750.62990.025*
C101.1351 (5)0.1534 (5)0.61129 (11)0.0254 (9)
H10A1.10490.07690.62900.030*
C111.2500 (5)0.1206 (5)0.58536 (11)0.0277 (10)
H11A1.29910.02300.58540.033*
C121.2921 (5)0.2316 (5)0.55947 (12)0.0283 (10)
H12A1.36990.20920.54140.034*
C131.2226 (5)0.3765 (5)0.55927 (11)0.0235 (9)
H13A1.25350.45240.54150.028*
H1N10.881 (5)1.068 (3)0.5407 (12)0.044 (14)*
H1N20.754 (5)1.002 (3)0.5955 (13)0.048 (16)*
H2N20.665 (5)1.123 (6)0.6174 (9)0.066 (18)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0268 (2)0.0230 (2)0.02226 (17)0.00121 (18)0.00088 (18)0.00592 (17)
O10.0260 (14)0.0159 (13)0.0203 (13)0.0051 (13)0.0058 (12)0.0047 (11)
O20.0299 (16)0.0215 (14)0.0241 (13)0.0079 (13)0.0103 (13)0.0050 (11)
O30.0276 (16)0.0194 (14)0.0215 (13)0.0050 (12)0.0059 (12)0.0068 (11)
N10.0152 (16)0.0165 (16)0.0185 (14)0.0039 (13)0.0002 (12)0.0002 (13)
N20.0267 (19)0.0196 (18)0.0191 (17)0.0015 (14)0.0049 (15)0.0023 (14)
C10.0165 (19)0.0163 (19)0.0184 (19)0.0002 (15)0.0003 (15)0.0009 (15)
C20.021 (2)0.022 (2)0.0188 (17)0.0049 (16)0.0010 (15)0.0012 (16)
C30.024 (2)0.017 (2)0.0245 (19)0.0036 (17)0.0018 (16)0.0000 (16)
C40.020 (2)0.020 (2)0.0173 (17)0.0003 (15)0.0007 (15)0.0013 (15)
C50.0171 (19)0.0211 (19)0.0149 (16)0.0009 (15)0.0034 (15)0.0011 (15)
C60.0188 (19)0.0177 (18)0.0167 (18)0.0003 (16)0.0011 (16)0.0006 (14)
C70.023 (2)0.018 (2)0.0177 (17)0.0005 (16)0.0042 (15)0.0003 (15)
C80.021 (2)0.0114 (17)0.0208 (18)0.0018 (14)0.0052 (16)0.0048 (15)
C90.028 (2)0.0173 (19)0.0186 (18)0.0009 (16)0.0017 (16)0.0010 (15)
C100.031 (2)0.0176 (19)0.028 (2)0.001 (2)0.0101 (18)0.0037 (17)
C110.029 (2)0.018 (2)0.036 (2)0.0082 (18)0.0110 (19)0.0085 (18)
C120.028 (2)0.026 (2)0.032 (2)0.0052 (19)0.0004 (19)0.0031 (19)
C130.026 (2)0.022 (2)0.023 (2)0.0039 (17)0.0006 (17)0.0008 (17)
Geometric parameters (Å, º) top
Br1—C41.895 (4)C4—C51.362 (5)
O1—C81.372 (4)C5—H5A0.9500
O1—C71.427 (4)C6—C71.524 (5)
O2—C61.242 (4)C7—H7A0.9900
O3—C61.270 (4)C7—H7B0.9900
N1—C11.353 (5)C8—C131.390 (5)
N1—C51.356 (4)C8—C91.400 (5)
N1—H1N10.876 (10)C9—C101.390 (5)
N2—C11.332 (5)C9—H9A0.9500
N2—H1N20.872 (10)C10—C111.384 (6)
N2—H2N20.870 (10)C10—H10A0.9500
C1—C21.414 (5)C11—C121.379 (6)
C2—C31.366 (5)C11—H11A0.9500
C2—H2A0.9500C12—C131.398 (6)
C3—C41.398 (5)C12—H12A0.9500
C3—H3A0.9500C13—H13A0.9500
C8—O1—C7117.0 (3)O1—C7—C6109.6 (3)
C1—N1—C5122.1 (3)O1—C7—H7A109.7
C1—N1—H1N1121 (3)C6—C7—H7A109.7
C5—N1—H1N1117 (3)O1—C7—H7B109.7
C1—N2—H1N2120 (3)C6—C7—H7B109.7
C1—N2—H2N2118 (4)H7A—C7—H7B108.2
H1N2—N2—H2N2121 (5)O1—C8—C13124.9 (3)
N2—C1—N1118.6 (3)O1—C8—C9114.8 (3)
N2—C1—C2123.1 (3)C13—C8—C9120.3 (3)
N1—C1—C2118.2 (3)C10—C9—C8119.0 (4)
C3—C2—C1119.9 (3)C10—C9—H9A120.5
C3—C2—H2A120.0C8—C9—H9A120.5
C1—C2—H2A120.0C11—C10—C9121.3 (4)
C2—C3—C4119.8 (4)C11—C10—H10A119.4
C2—C3—H3A120.1C9—C10—H10A119.4
C4—C3—H3A120.1C12—C11—C10119.0 (4)
C5—C4—C3119.4 (3)C12—C11—H11A120.5
C5—C4—Br1119.6 (3)C10—C11—H11A120.5
C3—C4—Br1121.0 (3)C11—C12—C13121.3 (4)
N1—C5—C4120.5 (3)C11—C12—H12A119.3
N1—C5—H5A119.8C13—C12—H12A119.3
C4—C5—H5A119.8C8—C13—C12119.0 (4)
O2—C6—O3126.6 (4)C8—C13—H13A120.5
O2—C6—C7120.9 (3)C12—C13—H13A120.5
O3—C6—C7112.6 (3)
C5—N1—C1—N2179.0 (3)O3—C6—C7—O1175.6 (3)
C5—N1—C1—C20.6 (5)C7—O1—C8—C130.9 (5)
N2—C1—C2—C3179.0 (4)C7—O1—C8—C9179.6 (3)
N1—C1—C2—C30.5 (5)O1—C8—C9—C10179.3 (3)
C1—C2—C3—C40.5 (6)C13—C8—C9—C100.3 (6)
C2—C3—C4—C50.5 (6)C8—C9—C10—C110.4 (6)
C2—C3—C4—Br1179.3 (3)C9—C10—C11—C120.7 (6)
C1—N1—C5—C40.5 (5)C10—C11—C12—C130.8 (6)
C3—C4—C5—N10.5 (5)O1—C8—C13—C12179.1 (4)
Br1—C4—C5—N1179.3 (3)C9—C8—C13—C120.5 (6)
C8—O1—C7—C6172.7 (3)C11—C12—C13—C80.7 (6)
O2—C6—C7—O14.5 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O30.88 (1)1.70 (3)2.579 (4)176 (5)
N2—H1N2···O20.87 (1)2.01 (3)2.877 (4)177 (4)
N2—H2N2···O1i0.87 (1)2.41 (3)3.140 (4)142 (5)
N2—H2N2···O2i0.87 (1)2.13 (3)2.900 (4)146 (5)
C2—H2A···O2i0.952.553.193 (4)125
C5—H5A···O3ii0.952.423.047 (4)123
Symmetry codes: (i) x+3/2, y+1/2, z+5/4; (ii) y, x, 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 the TWAS–USM fellowship.

References

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