Literature DB >> 23634078

2-Amino-5-bromo-pyridinium 5-chloro-2-hy-droxy-benzoate.

Kaliyaperumal Thanigaimani1, Nuridayanti Che Khalib, Suhana Arshad, Ibrahim Abdul Razak.   

Abstract

In the 5-chloro-salicylate anion of the title salt, C5H6BrN2 (+)·C7H4ClO3 (-), an intra-molecular 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 carboxyl-ate group. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl-ate O atoms via a pair of N-H⋯O hydrogen bonds, forming an R 2 (2)(8) ring motif. The crystal structure also features N-H⋯O and weak C-H⋯O inter-actions, resulting in a layer parallel to the (10-1) plane.

Entities:  

Year:  2013        PMID: 23634078      PMCID: PMC3629591          DOI: 10.1107/S160053681300665X

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


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

C5H6BrN2C7H4ClO3 M = 345.58 Monoclinic, a = 8.9769 (17) Å b = 5.6601 (12) Å c = 12.753 (2) Å β = 90.662 (5)° V = 647.9 (2) Å3 Z = 2 Mo Kα radiation μ = 3.38 mm−1 T = 100 K 0.31 × 0.04 × 0.03 mm

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.417, T max = 0.894 8030 measured reflections 4233 independent reflections 3014 reflections with I > 2σ(I) R int = 0.087

Refinement

R[F 2 > 2σ(F 2)] = 0.046 wR(F 2) = 0.091 S = 0.91 4233 reflections 188 parameters 1 restraint H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.84 e Å−3 Δρmin = −0.98 e Å−3 Absolute structure: Flack (1983 ▶), 1558 Friedel pairs Flack parameter: 0.037 (11) Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: 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 ▶). Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S160053681300665X/is5251sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681300665X/is5251Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S160053681300665X/is5251Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H6BrN2+·C7H4ClO3F(000) = 344
Mr = 345.58Dx = 1.771 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 1541 reflections
a = 8.9769 (17) Åθ = 3.9–25.8°
b = 5.6601 (12) ŵ = 3.38 mm1
c = 12.753 (2) ÅT = 100 K
β = 90.662 (5)°Needle, colourless
V = 647.9 (2) Å30.31 × 0.04 × 0.03 mm
Z = 2
Bruker SMART APEXII DUO CCD area-detector diffractometer4233 independent reflections
Radiation source: fine-focus sealed tube3014 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.087
φ and ω scansθmax = 32.7°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −13→13
Tmin = 0.417, Tmax = 0.894k = −7→8
8030 measured reflectionsl = −19→19
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.046H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.091w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3
S = 0.91(Δ/σ)max < 0.001
4233 reflectionsΔρmax = 0.84 e Å3
188 parametersΔρmin = −0.98 e Å3
1 restraintAbsolute structure: Flack (1983), 1558 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.037 (11)
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.
xyzUiso*/Ueq
Br10.79689 (4)0.54521 (9)0.42592 (3)0.02463 (10)
Cl10.50091 (11)0.29983 (19)0.90762 (8)0.0253 (2)
O10.8634 (3)1.0293 (8)0.87224 (17)0.0248 (6)
O20.8465 (3)1.1615 (5)0.7080 (2)0.0205 (6)
O30.6812 (3)0.9496 (7)0.5736 (2)0.0239 (7)
N10.9596 (4)0.0044 (6)0.2466 (2)0.0190 (8)
N20.9338 (4)−0.1193 (7)0.0762 (3)0.0209 (8)
C10.8982 (4)0.0324 (11)0.1506 (2)0.0177 (7)
C20.8005 (4)0.2245 (7)0.1337 (3)0.0196 (8)
H2A0.75610.24950.06660.024*
C30.7703 (4)0.3746 (7)0.2152 (3)0.0196 (8)
H3A0.70390.50340.20500.024*
C40.8375 (4)0.3379 (7)0.3134 (3)0.0188 (8)
C50.9301 (4)0.1523 (7)0.3275 (3)0.0207 (8)
H5A0.97480.12520.39430.025*
C60.7012 (4)0.8297 (7)0.7544 (3)0.0162 (7)
C70.6406 (4)0.8057 (8)0.6536 (3)0.0177 (7)
C80.5392 (4)0.6258 (7)0.6314 (3)0.0223 (9)
H8A0.49860.61100.56260.027*
C90.4971 (4)0.4687 (7)0.7085 (3)0.0210 (8)
H9A0.42900.34470.69320.025*
C100.5563 (4)0.4956 (7)0.8089 (3)0.0187 (9)
C110.6566 (4)0.6721 (7)0.8323 (3)0.0169 (8)
H11A0.69570.68680.90160.020*
C120.8105 (4)1.0173 (9)0.7811 (3)0.0188 (8)
H1O30.721 (5)1.068 (16)0.582 (4)0.025 (16)*
H1N11.027 (5)−0.101 (9)0.256 (4)0.023 (12)*
H1N21.000 (6)−0.248 (12)0.092 (4)0.039 (15)*
H2N20.898 (4)−0.093 (8)0.013 (4)0.021 (11)*
U11U22U33U12U13U23
Br10.02863 (18)0.02674 (19)0.01847 (16)0.0061 (3)−0.00223 (12)−0.0056 (2)
Cl10.0287 (5)0.0241 (5)0.0232 (5)−0.0076 (4)−0.0007 (4)0.0025 (4)
O10.0301 (12)0.0291 (17)0.0151 (11)−0.0079 (18)−0.0073 (9)0.0053 (16)
O20.0256 (14)0.0202 (14)0.0158 (13)−0.0045 (12)−0.0028 (11)0.0015 (11)
O30.0306 (18)0.0268 (18)0.0141 (14)−0.0079 (15)−0.0061 (12)0.0035 (12)
N10.0225 (15)0.020 (2)0.0148 (13)0.0051 (15)−0.0014 (11)−0.0013 (13)
N20.0232 (18)0.027 (2)0.0128 (16)0.0059 (15)−0.0048 (13)−0.0038 (14)
C10.0196 (15)0.0188 (19)0.0147 (14)0.001 (2)0.0000 (11)0.005 (2)
C20.023 (2)0.021 (2)0.0151 (17)0.0002 (16)−0.0060 (15)0.0048 (15)
C30.0193 (19)0.019 (2)0.0204 (19)0.0038 (16)−0.0021 (15)0.0031 (15)
C40.0206 (19)0.022 (2)0.0136 (17)0.0026 (16)0.0004 (14)−0.0021 (15)
C50.027 (2)0.022 (2)0.0129 (17)−0.0013 (17)−0.0025 (15)0.0010 (15)
C60.0192 (18)0.0173 (19)0.0119 (16)0.0013 (15)−0.0006 (13)−0.0022 (14)
C70.0157 (17)0.021 (2)0.0158 (17)−0.0011 (16)−0.0032 (13)−0.0027 (16)
C80.0209 (18)0.027 (2)0.0188 (18)−0.0023 (16)−0.0037 (15)−0.0038 (15)
C90.0183 (18)0.023 (2)0.0218 (19)−0.0046 (15)−0.0005 (15)−0.0051 (15)
C100.0198 (17)0.016 (3)0.0199 (17)0.0029 (14)0.0022 (14)−0.0014 (14)
C110.0192 (18)0.018 (2)0.0130 (16)−0.0001 (15)−0.0019 (14)−0.0011 (14)
C120.0198 (16)0.019 (2)0.0171 (15)0.0002 (17)−0.0022 (12)0.0006 (17)
Br1—C41.893 (4)C3—C41.399 (5)
Cl1—C101.754 (4)C3—H3A0.9500
O1—C121.252 (4)C4—C51.350 (5)
O2—C121.284 (5)C5—H5A0.9500
O3—C71.359 (5)C6—C71.396 (5)
O3—H1O30.77 (8)C6—C111.398 (5)
N1—C11.346 (4)C6—C121.483 (6)
N1—C51.357 (5)C7—C81.393 (5)
N1—H1N10.86 (5)C8—C91.382 (6)
N2—C11.321 (6)C8—H8A0.9500
N2—H1N20.96 (6)C9—C101.389 (5)
N2—H2N20.88 (5)C9—H9A0.9500
C1—C21.412 (6)C10—C111.375 (5)
C2—C31.372 (6)C11—H11A0.9500
C2—H2A0.9500
C7—O3—H1O3123 (4)C7—C6—C11118.7 (4)
C1—N1—C5122.5 (4)C7—C6—C12122.1 (3)
C1—N1—H1N1119 (3)C11—C6—C12119.2 (3)
C5—N1—H1N1118 (3)O3—C7—C8117.7 (3)
C1—N2—H1N2120 (3)O3—C7—C6121.9 (4)
C1—N2—H2N2117 (3)C8—C7—C6120.3 (4)
H1N2—N2—H2N2122 (4)C9—C8—C7120.6 (4)
N2—C1—N1118.4 (4)C9—C8—H8A119.7
N2—C1—C2123.1 (3)C7—C8—H8A119.7
N1—C1—C2118.5 (4)C8—C9—C10118.7 (4)
C3—C2—C1119.3 (4)C8—C9—H9A120.6
C3—C2—H2A120.4C10—C9—H9A120.6
C1—C2—H2A120.4C11—C10—C9121.5 (4)
C2—C3—C4120.0 (4)C11—C10—Cl1119.6 (3)
C2—C3—H3A120.0C9—C10—Cl1118.9 (3)
C4—C3—H3A120.0C10—C11—C6120.1 (3)
C5—C4—C3119.6 (4)C10—C11—H11A120.0
C5—C4—Br1120.3 (3)C6—C11—H11A120.0
C3—C4—Br1120.1 (3)O1—C12—O2122.9 (4)
C4—C5—N1120.2 (4)O1—C12—C6119.7 (4)
C4—C5—H5A119.9O2—C12—C6117.4 (3)
N1—C5—H5A119.9
C5—N1—C1—N2179.6 (4)O3—C7—C8—C9177.9 (4)
C5—N1—C1—C20.6 (6)C6—C7—C8—C90.0 (6)
N2—C1—C2—C3−179.6 (4)C7—C8—C9—C100.9 (6)
N1—C1—C2—C3−0.5 (6)C8—C9—C10—C11−0.9 (6)
C1—C2—C3—C40.7 (6)C8—C9—C10—Cl1178.9 (3)
C2—C3—C4—C5−1.0 (6)C9—C10—C11—C60.1 (5)
C2—C3—C4—Br1179.8 (3)Cl1—C10—C11—C6−179.7 (3)
C3—C4—C5—N11.0 (6)C7—C6—C11—C100.8 (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—O11.3 (6)
C12—C6—C7—O31.6 (6)C7—C6—C12—O21.1 (5)
C11—C6—C7—C8−0.8 (6)C11—C6—C12—O2−178.7 (3)
C12—C6—C7—C8179.4 (3)
D—H···AD—HH···AD···AD—H···A
O3—H1O3···O20.77 (8)2.02 (5)2.553 (4)127 (6)
N1—H1N1···O2i0.86 (5)1.82 (5)2.666 (4)172 (4)
N2—H1N2···O1i0.96 (6)1.81 (6)2.770 (5)175 (4)
N2—H2N2···O1ii0.88 (5)1.95 (5)2.799 (5)164 (3)
C8—H8A···O3iii0.952.533.410 (5)154
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
O3—H1O3⋯O20.77 (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 0.952.533.410 (5)154

Symmetry codes: (i) ; (ii) ; (iii) .

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