2-Amino-5-bromo­pyridinium 2-phen­oxy­acetate

Dhanabalan, N.; Thanigaimani, K.; Khalib, N.C.; Santhanaraj, K.J.; Razak, I.A.

doi:10.1107/S2414314616019398

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 12| December 2016| x161939

https://doi.org/10.1107/S2414314616019398

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2-Amino-5-bromopyridinium 2-phenoxyacetate

Nallathambi Dhanabalan,^a,^b ^* Kaliyaperumal Thanigaimani,^c Nuridayanti Che Khalib,^d K. Joseph Santhanaraj ^b and Ibrahim Abdul Razak ^d ‡

^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 π–π 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.

Keywords: crystal structure; phenoxyacetic acid; 2-amino-5-bromopyridine; hydrogen bond.

CCDC reference: 1520598

Structure description

Supramolecular architectures assembled via various delicate non-covalent interactions, such as hydrogen bonds, π–π 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 ). 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 ). Pyridine and its derivatives play an important role in heterocyclic chemistry (Pozharski et al., 1997 ; Katritzky et al., 1996 ). They are often involved in hydrogen-bond interactions. Aryloxyacetic acid derivatives possess a wide array of diverse bioactivities including antimycobacterial (Ali & Shanharyar, 2007 ; Shaharyar et al., 2006 ), anti-inflammatory and antioxidant (Kunsch et al., 2005 ), antibacterial (Iqbal et al., 2007 ), antilipaemic and antiplatelet (Pérez-Pastén et al., 2006 ) and inhibitory activity of cathepsin K and aldose reductase (Shinozuka et al., 2006 ). In order to study some hydrogen-bonding interactions, the structure of the title salt was determined.

The asymmetric unit (Fig. 1) 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 ; Khalib et al., 2013 ). 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
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) with R₁²(5) and R₂¹(6) ring motifs, forming a helical chain (Fig. 2). A π–π 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), leads to the formation of a three-dimensional network.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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
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.

Table 2
Experimental details

Crystal data
Chemical formula	C₅H₆BrN₂⁺·C₈H₇O₃⁻
M_r	325.16
Crystal system, space group	Tetragonal, P4₁2₁2
Temperature (K)	100
a, c (Å)	8.6944 (1), 35.2843 (7)
V (Å³)	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 )
T_min, T_max	0.419, 0.688
No. of measured, independent and observed [I > 2σ(I)] reflections	38666, 3407, 2790
R_int	0.076
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.52, −0.52
Absolute structure	Flack (1983 ), 1324 Fridel pairs
Absolute structure parameter	0.072 (13)
Computer programs: APEX2 and SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008 ) and PLATON (Spek, 2009 ).

Structural data

CCDC reference: 1520598

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314616019398/is5465sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616019398/is5465Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314616019398/is5465Isup3.cml

checkCIF report

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⁺·C₈H₇O₃⁻	D_x = 1.620 Mg m⁻³
M_r = 325.16	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P4₁2₁2	Cell parameters from 9890 reflections
Hall symbol: P 4abw 2nw	θ = 2.3–26.4°
a = 8.6944 (1) Å	µ = 3.09 mm⁻¹
c = 35.2843 (7) Å	T = 100 K
V = 2667.23 (7) Å³	Block, colourless
Z = 8	0.34 × 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 tube	2790 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.076
φ and ω scans	θ_max = 28.6°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −11→11
T_min = 0.419, T_max = 0.688	k = −11→11
38666 measured reflections	l = −47→47

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.042	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.078	w = 1/[σ²(F_o²) + (0.P)² + 4.511P] where P = (F_o² + 2F_c²)/3
S = 1.17	(Δ/σ)_max = 0.001
3407 reflections	Δρ_max = 0.52 e Å⁻³
184 parameters	Δρ_min = −0.52 e Å⁻³
3 restraints	Absolute structure: Flack (1983), 1324 Fridel pairs
Primary atom site location: structure-invariant direct methods	Absolute 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

	x	y	z	U_iso*/U_eq
Br1	0.85535 (5)	1.53676 (5)	0.471862 (11)	0.02404 (10)
O1	1.0287 (3)	0.5443 (3)	0.58802 (7)	0.0207 (6)
O2	0.8557 (3)	0.7960 (3)	0.58999 (7)	0.0251 (6)
O3	0.9831 (3)	0.9012 (3)	0.54112 (7)	0.0228 (6)
N1	0.8335 (3)	1.1573 (4)	0.54085 (8)	0.0168 (6)
N2	0.7130 (4)	1.0932 (4)	0.59699 (10)	0.0218 (7)
C1	0.7426 (4)	1.1976 (4)	0.57033 (10)	0.0171 (8)
C2	0.6803 (4)	1.3478 (5)	0.57085 (10)	0.0204 (8)
H2A	0.6154	1.3790	0.5911	0.024*
C3	0.7137 (4)	1.4481 (5)	0.54222 (11)	0.0220 (8)
H3A	0.6727	1.5494	0.5426	0.026*
C4	0.8083 (4)	1.4014 (4)	0.51234 (10)	0.0193 (8)
C5	0.8671 (4)	1.2562 (4)	0.51232 (10)	0.0177 (7)
H5A	0.9322	1.2241	0.4922	0.021*
C6	0.9580 (5)	0.7964 (4)	0.56542 (10)	0.0177 (8)
C7	1.0704 (4)	0.6625 (4)	0.56195 (10)	0.0196 (8)
H7A	1.0683	0.6216	0.5358	0.024*
H7B	1.1761	0.6986	0.5674	0.024*
C8	1.1075 (4)	0.4079 (4)	0.58550 (10)	0.0178 (8)
C9	1.0630 (5)	0.2962 (4)	0.61188 (10)	0.0211 (9)
H9A	0.9848	0.3175	0.6299	0.025*
C10	1.1351 (5)	0.1534 (5)	0.61129 (11)	0.0254 (9)
H10A	1.1049	0.0769	0.6290	0.030*
C11	1.2500 (5)	0.1206 (5)	0.58536 (11)	0.0277 (10)
H11A	1.2991	0.0230	0.5854	0.033*
C12	1.2921 (5)	0.2316 (5)	0.55947 (12)	0.0283 (10)
H12A	1.3699	0.2092	0.5414	0.034*
C13	1.2226 (5)	0.3765 (5)	0.55927 (11)	0.0235 (9)
H13A	1.2535	0.4524	0.5415	0.028*
H1N1	0.881 (5)	1.068 (3)	0.5407 (12)	0.044 (14)*
H1N2	0.754 (5)	1.002 (3)	0.5955 (13)	0.048 (16)*
H2N2	0.665 (5)	1.123 (6)	0.6174 (9)	0.066 (18)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br1	0.0268 (2)	0.0230 (2)	0.02226 (17)	0.00121 (18)	0.00088 (18)	0.00592 (17)
O1	0.0260 (14)	0.0159 (13)	0.0203 (13)	0.0051 (13)	0.0058 (12)	0.0047 (11)
O2	0.0299 (16)	0.0215 (14)	0.0241 (13)	0.0079 (13)	0.0103 (13)	0.0050 (11)
O3	0.0276 (16)	0.0194 (14)	0.0215 (13)	0.0050 (12)	0.0059 (12)	0.0068 (11)
N1	0.0152 (16)	0.0165 (16)	0.0185 (14)	0.0039 (13)	−0.0002 (12)	0.0002 (13)
N2	0.0267 (19)	0.0196 (18)	0.0191 (17)	0.0015 (14)	0.0049 (15)	−0.0023 (14)
C1	0.0165 (19)	0.0163 (19)	0.0184 (19)	−0.0002 (15)	−0.0003 (15)	−0.0009 (15)
C2	0.021 (2)	0.022 (2)	0.0188 (17)	0.0049 (16)	0.0010 (15)	−0.0012 (16)
C3	0.024 (2)	0.017 (2)	0.0245 (19)	0.0036 (17)	−0.0018 (16)	0.0000 (16)
C4	0.020 (2)	0.020 (2)	0.0173 (17)	−0.0003 (15)	0.0007 (15)	−0.0013 (15)
C5	0.0171 (19)	0.0211 (19)	0.0149 (16)	−0.0009 (15)	0.0034 (15)	−0.0011 (15)
C6	0.0188 (19)	0.0177 (18)	0.0167 (18)	0.0003 (16)	−0.0011 (16)	−0.0006 (14)
C7	0.023 (2)	0.018 (2)	0.0177 (17)	0.0005 (16)	0.0042 (15)	−0.0003 (15)
C8	0.021 (2)	0.0114 (17)	0.0208 (18)	0.0018 (14)	−0.0052 (16)	−0.0048 (15)
C9	0.028 (2)	0.0173 (19)	0.0186 (18)	−0.0009 (16)	−0.0017 (16)	0.0010 (15)
C10	0.031 (2)	0.0176 (19)	0.028 (2)	−0.001 (2)	−0.0101 (18)	0.0037 (17)
C11	0.029 (2)	0.018 (2)	0.036 (2)	0.0082 (18)	−0.0110 (19)	−0.0085 (18)
C12	0.028 (2)	0.026 (2)	0.032 (2)	0.0052 (19)	0.0004 (19)	−0.0031 (19)
C13	0.026 (2)	0.022 (2)	0.023 (2)	0.0039 (17)	−0.0006 (17)	0.0008 (17)

Geometric parameters (Å, º) top

Br1—C4	1.895 (4)	C4—C5	1.362 (5)
O1—C8	1.372 (4)	C5—H5A	0.9500
O1—C7	1.427 (4)	C6—C7	1.524 (5)
O2—C6	1.242 (4)	C7—H7A	0.9900
O3—C6	1.270 (4)	C7—H7B	0.9900
N1—C1	1.353 (5)	C8—C13	1.390 (5)
N1—C5	1.356 (4)	C8—C9	1.400 (5)
N1—H1N1	0.876 (10)	C9—C10	1.390 (5)
N2—C1	1.332 (5)	C9—H9A	0.9500
N2—H1N2	0.872 (10)	C10—C11	1.384 (6)
N2—H2N2	0.870 (10)	C10—H10A	0.9500
C1—C2	1.414 (5)	C11—C12	1.379 (6)
C2—C3	1.366 (5)	C11—H11A	0.9500
C2—H2A	0.9500	C12—C13	1.398 (6)
C3—C4	1.398 (5)	C12—H12A	0.9500
C3—H3A	0.9500	C13—H13A	0.9500

C8—O1—C7	117.0 (3)	O1—C7—C6	109.6 (3)
C1—N1—C5	122.1 (3)	O1—C7—H7A	109.7
C1—N1—H1N1	121 (3)	C6—C7—H7A	109.7
C5—N1—H1N1	117 (3)	O1—C7—H7B	109.7
C1—N2—H1N2	120 (3)	C6—C7—H7B	109.7
C1—N2—H2N2	118 (4)	H7A—C7—H7B	108.2
H1N2—N2—H2N2	121 (5)	O1—C8—C13	124.9 (3)
N2—C1—N1	118.6 (3)	O1—C8—C9	114.8 (3)
N2—C1—C2	123.1 (3)	C13—C8—C9	120.3 (3)
N1—C1—C2	118.2 (3)	C10—C9—C8	119.0 (4)
C3—C2—C1	119.9 (3)	C10—C9—H9A	120.5
C3—C2—H2A	120.0	C8—C9—H9A	120.5
C1—C2—H2A	120.0	C11—C10—C9	121.3 (4)
C2—C3—C4	119.8 (4)	C11—C10—H10A	119.4
C2—C3—H3A	120.1	C9—C10—H10A	119.4
C4—C3—H3A	120.1	C12—C11—C10	119.0 (4)
C5—C4—C3	119.4 (3)	C12—C11—H11A	120.5
C5—C4—Br1	119.6 (3)	C10—C11—H11A	120.5
C3—C4—Br1	121.0 (3)	C11—C12—C13	121.3 (4)
N1—C5—C4	120.5 (3)	C11—C12—H12A	119.3
N1—C5—H5A	119.8	C13—C12—H12A	119.3
C4—C5—H5A	119.8	C8—C13—C12	119.0 (4)
O2—C6—O3	126.6 (4)	C8—C13—H13A	120.5
O2—C6—C7	120.9 (3)	C12—C13—H13A	120.5
O3—C6—C7	112.6 (3)

C5—N1—C1—N2	179.0 (3)	O3—C6—C7—O1	−175.6 (3)
C5—N1—C1—C2	0.6 (5)	C7—O1—C8—C13	−0.9 (5)
N2—C1—C2—C3	−179.0 (4)	C7—O1—C8—C9	179.6 (3)
N1—C1—C2—C3	−0.5 (5)	O1—C8—C9—C10	179.3 (3)
C1—C2—C3—C4	0.5 (6)	C13—C8—C9—C10	−0.3 (6)
C2—C3—C4—C5	−0.5 (6)	C8—C9—C10—C11	0.4 (6)
C2—C3—C4—Br1	179.3 (3)	C9—C10—C11—C12	−0.7 (6)
C1—N1—C5—C4	−0.5 (5)	C10—C11—C12—C13	0.8 (6)
C3—C4—C5—N1	0.5 (5)	O1—C8—C13—C12	−179.1 (4)
Br1—C4—C5—N1	−179.3 (3)	C9—C8—C13—C12	0.5 (6)
C8—O1—C7—C6	172.7 (3)	C11—C12—C13—C8	−0.7 (6)
O2—C6—C7—O1	4.5 (5)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+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.

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