organic compounds
2-Amino-5-bromopyridinium 5-chloro-2-hydroxybenzoate
aSchool of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: arazaki@usm.my
In the 5-chlorosalicylate anion of the title salt, C5H6BrN2+·C7H4ClO3−, an intramolecular O—H⋯O hydrogen bond with an S(6) graph-set motif is formed, so that the anion is essentially planar with a dihedral angle of 1.3 (5)° between the benzene ring and the carboxylate group. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxylate O atoms via a pair of N—H⋯O hydrogen bonds, forming an R22(8) ring motif. The also features N—H⋯O and weak C—H⋯O interactions, resulting in a layer parallel to the (10-1) plane.
Related literature
For background to the chemistry of substituted pyridines, see: Pozharski et al. (1997); Katritzky et al. (1996). For related structures, see: Goubitz et al. (2001); Quah et al. (2010); Thanigaimani et al. (2013); Raza et al. (2010). 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 data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
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Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); data reduction: SAINT ; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
10.1107/S160053681300665X/is5251sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S160053681300665X/is5251Isup2.hkl
Supporting information file. DOI: 10.1107/S160053681300665X/is5251Isup3.cml
Hot methanol solutions (20 ml) of 2-amino-5-bromopyridine (43 mg, Aldrich) and 5-chlorosalicylic acid (43 mg, Aldrich) 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.
O- and N-bound H atoms were located in a difference Fourier map and allowed to be refined freely [O—H = 0.77 (8) Å and N—H = 0.86 (5)–0.96 (6) Å]. The remaining H atoms were positioned geometrically (C—H = 0.95 Å) and refined using a riding model, with Uiso(H) = 1.2Ueq(C). Eight outliers were omitted (-4 -3 1, -1 -2 2, 1 0 5, 3 2 7, -1 -2 3, -1 0 5, 2 4 0, 2 -4 0) in the final refinement.
Data collection: APEX2 (Bruker, 2009); cell
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).Fig. 1. The molecular structure of the title compound with atom labels with 50% probability displacement ellipsoids. | |
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. |
C5H6BrN2+·C7H4ClO3− | F(000) = 344 |
Mr = 345.58 | Dx = 1.771 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 1541 reflections |
a = 8.9769 (17) Å | θ = 3.9–25.8° |
b = 5.6601 (12) Å | µ = 3.38 mm−1 |
c = 12.753 (2) Å | T = 100 K |
β = 90.662 (5)° | Needle, colourless |
V = 647.9 (2) Å3 | 0.31 × 0.04 × 0.03 mm |
Z = 2 |
Bruker SMART APEXII DUO CCD area-detector diffractometer | 4233 independent reflections |
Radiation source: fine-focus sealed tube | 3014 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.087 |
ϕ and ω scans | θmax = 32.7°, θmin = 2.3° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −13→13 |
Tmin = 0.417, Tmax = 0.894 | k = −7→8 |
8030 measured reflections | l = −19→19 |
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)] = 0.046 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.091 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.91 | (Δ/σ)max < 0.001 |
4233 reflections | Δρmax = 0.84 e Å−3 |
188 parameters | Δρmin = −0.98 e Å−3 |
1 restraint | Absolute structure: Flack (1983), 1558 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.037 (11) |
C5H6BrN2+·C7H4ClO3− | V = 647.9 (2) Å3 |
Mr = 345.58 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 8.9769 (17) Å | µ = 3.38 mm−1 |
b = 5.6601 (12) Å | T = 100 K |
c = 12.753 (2) Å | 0.31 × 0.04 × 0.03 mm |
β = 90.662 (5)° |
Bruker SMART APEXII DUO CCD area-detector diffractometer | 4233 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 3014 reflections with I > 2σ(I) |
Tmin = 0.417, Tmax = 0.894 | Rint = 0.087 |
8030 measured reflections |
R[F2 > 2σ(F2)] = 0.046 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.091 | Δρmax = 0.84 e Å−3 |
S = 0.91 | Δρmin = −0.98 e Å−3 |
4233 reflections | Absolute structure: Flack (1983), 1558 Friedel pairs |
188 parameters | Absolute structure parameter: 0.037 (11) |
1 restraint |
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. |
x | y | z | Uiso*/Ueq | ||
Br1 | 0.79689 (4) | 0.54521 (9) | 0.42592 (3) | 0.02463 (10) | |
Cl1 | 0.50091 (11) | 0.29983 (19) | 0.90762 (8) | 0.0253 (2) | |
O1 | 0.8634 (3) | 1.0293 (8) | 0.87224 (17) | 0.0248 (6) | |
O2 | 0.8465 (3) | 1.1615 (5) | 0.7080 (2) | 0.0205 (6) | |
O3 | 0.6812 (3) | 0.9496 (7) | 0.5736 (2) | 0.0239 (7) | |
N1 | 0.9596 (4) | 0.0044 (6) | 0.2466 (2) | 0.0190 (8) | |
N2 | 0.9338 (4) | −0.1193 (7) | 0.0762 (3) | 0.0209 (8) | |
C1 | 0.8982 (4) | 0.0324 (11) | 0.1506 (2) | 0.0177 (7) | |
C2 | 0.8005 (4) | 0.2245 (7) | 0.1337 (3) | 0.0196 (8) | |
H2A | 0.7561 | 0.2495 | 0.0666 | 0.024* | |
C3 | 0.7703 (4) | 0.3746 (7) | 0.2152 (3) | 0.0196 (8) | |
H3A | 0.7039 | 0.5034 | 0.2050 | 0.024* | |
C4 | 0.8375 (4) | 0.3379 (7) | 0.3134 (3) | 0.0188 (8) | |
C5 | 0.9301 (4) | 0.1523 (7) | 0.3275 (3) | 0.0207 (8) | |
H5A | 0.9748 | 0.1252 | 0.3943 | 0.025* | |
C6 | 0.7012 (4) | 0.8297 (7) | 0.7544 (3) | 0.0162 (7) | |
C7 | 0.6406 (4) | 0.8057 (8) | 0.6536 (3) | 0.0177 (7) | |
C8 | 0.5392 (4) | 0.6258 (7) | 0.6314 (3) | 0.0223 (9) | |
H8A | 0.4986 | 0.6110 | 0.5626 | 0.027* | |
C9 | 0.4971 (4) | 0.4687 (7) | 0.7085 (3) | 0.0210 (8) | |
H9A | 0.4290 | 0.3447 | 0.6932 | 0.025* | |
C10 | 0.5563 (4) | 0.4956 (7) | 0.8089 (3) | 0.0187 (9) | |
C11 | 0.6566 (4) | 0.6721 (7) | 0.8323 (3) | 0.0169 (8) | |
H11A | 0.6957 | 0.6868 | 0.9016 | 0.020* | |
C12 | 0.8105 (4) | 1.0173 (9) | 0.7811 (3) | 0.0188 (8) | |
H1O3 | 0.721 (5) | 1.068 (16) | 0.582 (4) | 0.025 (16)* | |
H1N1 | 1.027 (5) | −0.101 (9) | 0.256 (4) | 0.023 (12)* | |
H1N2 | 1.000 (6) | −0.248 (12) | 0.092 (4) | 0.039 (15)* | |
H2N2 | 0.898 (4) | −0.093 (8) | 0.013 (4) | 0.021 (11)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br1 | 0.02863 (18) | 0.02674 (19) | 0.01847 (16) | 0.0061 (3) | −0.00223 (12) | −0.0056 (2) |
Cl1 | 0.0287 (5) | 0.0241 (5) | 0.0232 (5) | −0.0076 (4) | −0.0007 (4) | 0.0025 (4) |
O1 | 0.0301 (12) | 0.0291 (17) | 0.0151 (11) | −0.0079 (18) | −0.0073 (9) | 0.0053 (16) |
O2 | 0.0256 (14) | 0.0202 (14) | 0.0158 (13) | −0.0045 (12) | −0.0028 (11) | 0.0015 (11) |
O3 | 0.0306 (18) | 0.0268 (18) | 0.0141 (14) | −0.0079 (15) | −0.0061 (12) | 0.0035 (12) |
N1 | 0.0225 (15) | 0.020 (2) | 0.0148 (13) | 0.0051 (15) | −0.0014 (11) | −0.0013 (13) |
N2 | 0.0232 (18) | 0.027 (2) | 0.0128 (16) | 0.0059 (15) | −0.0048 (13) | −0.0038 (14) |
C1 | 0.0196 (15) | 0.0188 (19) | 0.0147 (14) | 0.001 (2) | 0.0000 (11) | 0.005 (2) |
C2 | 0.023 (2) | 0.021 (2) | 0.0151 (17) | 0.0002 (16) | −0.0060 (15) | 0.0048 (15) |
C3 | 0.0193 (19) | 0.019 (2) | 0.0204 (19) | 0.0038 (16) | −0.0021 (15) | 0.0031 (15) |
C4 | 0.0206 (19) | 0.022 (2) | 0.0136 (17) | 0.0026 (16) | 0.0004 (14) | −0.0021 (15) |
C5 | 0.027 (2) | 0.022 (2) | 0.0129 (17) | −0.0013 (17) | −0.0025 (15) | 0.0010 (15) |
C6 | 0.0192 (18) | 0.0173 (19) | 0.0119 (16) | 0.0013 (15) | −0.0006 (13) | −0.0022 (14) |
C7 | 0.0157 (17) | 0.021 (2) | 0.0158 (17) | −0.0011 (16) | −0.0032 (13) | −0.0027 (16) |
C8 | 0.0209 (18) | 0.027 (2) | 0.0188 (18) | −0.0023 (16) | −0.0037 (15) | −0.0038 (15) |
C9 | 0.0183 (18) | 0.023 (2) | 0.0218 (19) | −0.0046 (15) | −0.0005 (15) | −0.0051 (15) |
C10 | 0.0198 (17) | 0.016 (3) | 0.0199 (17) | 0.0029 (14) | 0.0022 (14) | −0.0014 (14) |
C11 | 0.0192 (18) | 0.018 (2) | 0.0130 (16) | −0.0001 (15) | −0.0019 (14) | −0.0011 (14) |
C12 | 0.0198 (16) | 0.019 (2) | 0.0171 (15) | 0.0002 (17) | −0.0022 (12) | 0.0006 (17) |
Br1—C4 | 1.893 (4) | C3—C4 | 1.399 (5) |
Cl1—C10 | 1.754 (4) | C3—H3A | 0.9500 |
O1—C12 | 1.252 (4) | C4—C5 | 1.350 (5) |
O2—C12 | 1.284 (5) | C5—H5A | 0.9500 |
O3—C7 | 1.359 (5) | C6—C7 | 1.396 (5) |
O3—H1O3 | 0.77 (8) | C6—C11 | 1.398 (5) |
N1—C1 | 1.346 (4) | C6—C12 | 1.483 (6) |
N1—C5 | 1.357 (5) | C7—C8 | 1.393 (5) |
N1—H1N1 | 0.86 (5) | C8—C9 | 1.382 (6) |
N2—C1 | 1.321 (6) | C8—H8A | 0.9500 |
N2—H1N2 | 0.96 (6) | C9—C10 | 1.389 (5) |
N2—H2N2 | 0.88 (5) | C9—H9A | 0.9500 |
C1—C2 | 1.412 (6) | C10—C11 | 1.375 (5) |
C2—C3 | 1.372 (6) | C11—H11A | 0.9500 |
C2—H2A | 0.9500 | ||
C7—O3—H1O3 | 123 (4) | C7—C6—C11 | 118.7 (4) |
C1—N1—C5 | 122.5 (4) | C7—C6—C12 | 122.1 (3) |
C1—N1—H1N1 | 119 (3) | C11—C6—C12 | 119.2 (3) |
C5—N1—H1N1 | 118 (3) | O3—C7—C8 | 117.7 (3) |
C1—N2—H1N2 | 120 (3) | O3—C7—C6 | 121.9 (4) |
C1—N2—H2N2 | 117 (3) | C8—C7—C6 | 120.3 (4) |
H1N2—N2—H2N2 | 122 (4) | C9—C8—C7 | 120.6 (4) |
N2—C1—N1 | 118.4 (4) | C9—C8—H8A | 119.7 |
N2—C1—C2 | 123.1 (3) | C7—C8—H8A | 119.7 |
N1—C1—C2 | 118.5 (4) | C8—C9—C10 | 118.7 (4) |
C3—C2—C1 | 119.3 (4) | C8—C9—H9A | 120.6 |
C3—C2—H2A | 120.4 | C10—C9—H9A | 120.6 |
C1—C2—H2A | 120.4 | C11—C10—C9 | 121.5 (4) |
C2—C3—C4 | 120.0 (4) | C11—C10—Cl1 | 119.6 (3) |
C2—C3—H3A | 120.0 | C9—C10—Cl1 | 118.9 (3) |
C4—C3—H3A | 120.0 | C10—C11—C6 | 120.1 (3) |
C5—C4—C3 | 119.6 (4) | C10—C11—H11A | 120.0 |
C5—C4—Br1 | 120.3 (3) | C6—C11—H11A | 120.0 |
C3—C4—Br1 | 120.1 (3) | O1—C12—O2 | 122.9 (4) |
C4—C5—N1 | 120.2 (4) | O1—C12—C6 | 119.7 (4) |
C4—C5—H5A | 119.9 | O2—C12—C6 | 117.4 (3) |
N1—C5—H5A | 119.9 | ||
C5—N1—C1—N2 | 179.6 (4) | O3—C7—C8—C9 | 177.9 (4) |
C5—N1—C1—C2 | 0.6 (6) | C6—C7—C8—C9 | 0.0 (6) |
N2—C1—C2—C3 | −179.6 (4) | C7—C8—C9—C10 | 0.9 (6) |
N1—C1—C2—C3 | −0.5 (6) | C8—C9—C10—C11 | −0.9 (6) |
C1—C2—C3—C4 | 0.7 (6) | C8—C9—C10—Cl1 | 178.9 (3) |
C2—C3—C4—C5 | −1.0 (6) | C9—C10—C11—C6 | 0.1 (5) |
C2—C3—C4—Br1 | 179.8 (3) | Cl1—C10—C11—C6 | −179.7 (3) |
C3—C4—C5—N1 | 1.0 (6) | C7—C6—C11—C10 | 0.8 (5) |
Br1—C4—C5—N1 | −179.7 (3) | C12—C6—C11—C10 | −179.4 (3) |
C1—N1—C5—C4 | −0.8 (6) | C7—C6—C12—O1 | −178.9 (4) |
C11—C6—C7—O3 | −178.6 (3) | C11—C6—C12—O1 | 1.3 (6) |
C12—C6—C7—O3 | 1.6 (6) | C7—C6—C12—O2 | 1.1 (5) |
C11—C6—C7—C8 | −0.8 (6) | C11—C6—C12—O2 | −178.7 (3) |
C12—C6—C7—C8 | 179.4 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H1O3···O2 | 0.77 (8) | 2.02 (5) | 2.553 (4) | 127 (6) |
N1—H1N1···O2i | 0.86 (5) | 1.82 (5) | 2.666 (4) | 172 (4) |
N2—H1N2···O1i | 0.96 (6) | 1.81 (6) | 2.770 (5) | 175 (4) |
N2—H2N2···O1ii | 0.88 (5) | 1.95 (5) | 2.799 (5) | 164 (3) |
C8—H8A···O3iii | 0.95 | 2.53 | 3.410 (5) | 154 |
Symmetry codes: (i) −x+2, y−3/2, −z+1; (ii) x, y−1, z−1; (iii) −x+1, y−1/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C5H6BrN2+·C7H4ClO3− |
Mr | 345.58 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 100 |
a, b, c (Å) | 8.9769 (17), 5.6601 (12), 12.753 (2) |
β (°) | 90.662 (5) |
V (Å3) | 647.9 (2) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 3.38 |
Crystal size (mm) | 0.31 × 0.04 × 0.03 |
Data collection | |
Diffractometer | Bruker SMART APEXII DUO CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.417, 0.894 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8030, 4233, 3014 |
Rint | 0.087 |
(sin θ/λ)max (Å−1) | 0.760 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.046, 0.091, 0.91 |
No. of reflections | 4233 |
No. of parameters | 188 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.84, −0.98 |
Absolute structure | Flack (1983), 1558 Friedel pairs |
Absolute structure parameter | 0.037 (11) |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H1O3···O2 | 0.77 (8) | 2.02 (5) | 2.553 (4) | 127 (6) |
N1—H1N1···O2i | 0.86 (5) | 1.82 (5) | 2.666 (4) | 172 (4) |
N2—H1N2···O1i | 0.96 (6) | 1.81 (6) | 2.770 (5) | 175 (4) |
N2—H2N2···O1ii | 0.88 (5) | 1.95 (5) | 2.799 (5) | 164 (3) |
C8—H8A···O3iii | 0.95 | 2.53 | 3.410 (5) | 154 |
Symmetry codes: (i) −x+2, y−3/2, −z+1; (ii) x, y−1, z−1; (iii) −x+1, y−1/2, −z+1. |
Footnotes
‡Thomson Reuters ResearcherID: A-5599-2009.
Acknowledgements
The authors thank the Malaysian Government and Universiti Sains Malaysia (USM) for research facilities and a 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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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-bonding interactions. Related crystal structures of 2-amino-5-bromopyridine (Goubitz et al., 2001), 2-amino-5-bromopyridinium 2-hydroxybenzoate (Quah et al., 2010) and 2-amino-5-methylpyridinium 2-hydroxy-5-chlorobenzoate (Thanigaimani et al., 2013) have been 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-amino-5-bromopyridinium cation and one 5-chlorosalicylate anion. An intramolecular O3–H1O3···O2 hydrogen bond in the 5-chlorosalicylate anion generates an S(6) ring motif (Bernstein et al., 1995). This motif is also observed in the crystal structures of 5-chloro-2-hydroxybenzoic acid (Raza et al., 2010). In the 2-amino-5-bromopyridinium cation, a wide angle [122.5 (4)°] is subtended at the protonated N1 atom. The 2-amino-5-bromopyridinium cation and 5-chlorosalicylate anion are essentially planar, with a maximum deviation of 0.008 (4) Å for atom N2 and 0.026 (4) Å for atom O1, respectively. The bond lengths (Allen et al., 1987) and angles are normal.
In the crystal packing (Fig. 2), the protonated N1 atom and a nitrogen atom of the 2-amino group (N2) are hydrogen-bonded to the carboxylate oxygen atoms (O1 and O2) via a pair of intermolecular N1—H1N1···O2i and N2—H1N2···O1i hydrogen bonds (symmetry code in Table 1), forming a ring motif R22(8) (Bernstein et al., 1995). The crystal structure is further stabilized by N2—H2N2···O1ii and C8—H8A···O3iii (symmetry codes in Table 1) intermolecular interactions. These interactions have resulted in a molecular layer parallel to the (101) plane. This crystal structure is isomorphous to the crystal structure of 2-amino-5-methylpyridinium 2-hydroxy-5-chlorobenzoate (Thanigaimani et al., 2013).