Literature DB >> 23476391

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

Kaliyaperumal Thanigaimani1, Abbas Farhadikoutenaei, Suhana Arshad, Ibrahim Abdul Razak.   

Abstract

In the 5-chloro-salicylate anion of the title salt, C6H9N2(+)·C7H4ClO3(-), an intra-molecular O-H⋯O hydrogen bond with an S(6) graph-set motif is observed and the dihedral angle between the benzene ring and the -CO2 group is 1.6 (6)°. 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 R2(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 (10-1).

Entities:  

Year:  2012        PMID: 23476391      PMCID: PMC3588363          DOI: 10.1107/S160053681205101X

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


Related literature

For details of non-covalent inter­actions, see: Desiraju (2007 ▶); Aakeroy & Seddon (1993 ▶). For background to the chemistry of substituted pyridines, see: Pozharski et al. (1997 ▶); Katritzky et al. (1996 ▶). For related structures, see: Nahringbauer & Kvick (1977 ▶); Raza et al. (2010 ▶); Thanigaimani et al. (2012a ▶,b ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For bond-length data, see: Allen et al. (1987 ▶). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C6H9N2C7H4ClO3 M = 280.70 Monoclinic, a = 9.004 (7) Å b = 5.767 (5) Å c = 12.617 (10) Å β = 90.415 (16)° V = 655.2 (9) Å3 Z = 2 Mo Kα radiation μ = 0.30 mm−1 T = 100 K 0.46 × 0.18 × 0.07 mm

Data collection

Bruker SMART APEXII Duo CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.877, T max = 0.979 4785 measured reflections 2204 independent reflections 1539 reflections with I > 2σ(I) R int = 0.061

Refinement

R[F 2 > 2σ(F 2)] = 0.073 wR(F 2) = 0.201 S = 1.01 2204 reflections 189 parameters 2 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.47 e Å−3 Δρmin = −0.44 e Å−3 Absolute structure: Flack (1983 ▶), 941 Friedel pairs Flack parameter: 0.09 (16) 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/S160053681205101X/is5232sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681205101X/is5232Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S160053681205101X/is5232Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C6H9N2+·C7H4ClO3F(000) = 292
Mr = 280.70Dx = 1.423 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 1722 reflections
a = 9.004 (7) Åθ = 2.8–29.7°
b = 5.767 (5) ŵ = 0.30 mm1
c = 12.617 (10) ÅT = 100 K
β = 90.415 (16)°Block, colourless
V = 655.2 (9) Å30.46 × 0.18 × 0.07 mm
Z = 2
Bruker SMART APEXII Duo CCD area-detector diffractometer2204 independent reflections
Radiation source: fine-focus sealed tube1539 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.061
φ and ω scansθmax = 25.0°, θmin = 1.6°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −10→10
Tmin = 0.877, Tmax = 0.979k = −6→6
4785 measured reflectionsl = −14→15
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.073H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.201w = 1/[σ2(Fo2) + (0.1249P)2] where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max = 0.001
2204 reflectionsΔρmax = 0.47 e Å3
189 parametersΔρmin = −0.44 e Å3
2 restraintsAbsolute structure: Flack (1983), 941 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.09 (16)
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
Cl10.49320 (17)0.7884 (3)0.59756 (12)0.0882 (6)
O10.1352 (4)0.0724 (8)0.6317 (2)0.0718 (11)
O20.1487 (4)−0.0555 (7)0.7972 (2)0.0665 (10)
O30.3088 (5)0.1483 (9)0.9319 (3)0.0809 (13)
N10.9568 (5)0.6055 (9)0.7468 (3)0.0581 (11)
N20.9360 (7)0.7221 (10)0.5745 (4)0.0730 (15)
C10.8976 (5)0.5709 (10)0.6496 (3)0.0555 (13)
C20.8031 (5)0.3909 (10)0.6344 (4)0.0613 (15)
H2A0.75930.36460.56670.074*
C30.7716 (6)0.2485 (12)0.7170 (4)0.0724 (17)
H3A0.70490.12320.70560.087*
C40.8336 (6)0.2786 (13)0.8183 (4)0.0683 (14)
C50.9247 (6)0.4608 (11)0.8286 (4)0.0622 (14)
H5A0.96880.49020.89590.075*
C60.8003 (8)0.1215 (15)0.9103 (5)0.093 (2)
H6A0.84510.18540.97500.139*
H6B0.8416−0.03280.89660.139*
H6C0.69250.10960.91910.139*
C70.3500 (5)0.2962 (12)0.8536 (3)0.0604 (13)
C80.4479 (6)0.4684 (11)0.8751 (4)0.0681 (16)
H8A0.48650.48340.94500.082*
C90.4933 (6)0.6238 (11)0.7977 (4)0.0666 (15)
H9A0.56150.74460.81380.080*
C100.4360 (5)0.5971 (11)0.6960 (4)0.0620 (13)
C110.3378 (6)0.4262 (11)0.6724 (4)0.0581 (13)
H11A0.30050.41160.60210.070*
C120.2916 (5)0.2732 (11)0.7495 (3)0.0507 (11)
C130.1848 (5)0.0861 (11)0.7244 (3)0.0579 (13)
H1N11.019 (6)0.735 (11)0.754 (4)0.070 (17)*
H1N20.985 (6)0.846 (7)0.587 (5)0.09 (3)*
H2N20.888 (7)0.705 (14)0.517 (5)0.09 (2)*
H1O30.225 (7)0.071 (13)0.909 (5)0.083 (19)*
U11U22U33U12U13U23
Cl10.0888 (9)0.0908 (11)0.0850 (10)−0.0173 (9)0.0112 (7)0.0067 (10)
O10.076 (2)0.099 (3)0.0404 (16)−0.016 (2)−0.0140 (14)−0.001 (2)
O20.076 (2)0.080 (3)0.0430 (16)−0.011 (2)−0.0066 (14)0.0066 (19)
O30.103 (3)0.103 (4)0.0371 (17)−0.013 (3)−0.0145 (17)0.0037 (19)
N10.066 (2)0.068 (3)0.0402 (19)−0.005 (2)−0.0016 (16)−0.002 (2)
N20.095 (3)0.082 (4)0.042 (2)−0.012 (3)−0.009 (2)−0.009 (2)
C10.058 (3)0.070 (4)0.038 (2)0.004 (3)0.0016 (19)−0.005 (3)
C20.067 (3)0.073 (4)0.044 (2)−0.004 (3)−0.003 (2)−0.010 (3)
C30.070 (3)0.077 (5)0.070 (3)−0.010 (3)0.004 (2)−0.014 (3)
C40.067 (3)0.079 (4)0.059 (3)0.004 (3)0.007 (2)−0.002 (3)
C50.076 (3)0.072 (4)0.038 (2)0.003 (3)0.001 (2)0.002 (2)
C60.108 (5)0.098 (5)0.072 (3)−0.003 (4)0.014 (3)0.017 (4)
C70.058 (3)0.083 (4)0.040 (2)0.003 (3)−0.0017 (18)−0.006 (3)
C80.070 (3)0.087 (5)0.047 (2)−0.002 (3)−0.007 (2)−0.016 (3)
C90.063 (3)0.068 (4)0.069 (3)0.000 (3)0.003 (2)−0.018 (3)
C100.053 (2)0.075 (4)0.058 (3)−0.005 (3)0.005 (2)−0.004 (3)
C110.064 (3)0.069 (3)0.042 (2)0.003 (3)0.0054 (19)−0.008 (2)
C120.048 (2)0.068 (3)0.036 (2)0.010 (3)−0.0010 (15)−0.009 (3)
C130.060 (3)0.069 (4)0.044 (2)0.000 (3)−0.0012 (19)0.005 (3)
Cl1—C101.742 (6)C4—C51.339 (9)
O1—C131.251 (5)C4—C61.504 (9)
O2—C131.273 (6)C5—H5A0.9500
O3—C71.359 (7)C6—H6A0.9800
O3—H1O30.92 (7)C6—H6B0.9800
N1—C11.349 (6)C6—H6C0.9800
N1—C51.359 (7)C7—C81.354 (9)
N1—H1N10.94 (6)C7—C121.417 (6)
N2—C11.335 (7)C8—C91.389 (8)
N2—H1N20.853 (10)C8—H8A0.9500
N2—H2N20.85 (7)C9—C101.388 (7)
C1—C21.355 (8)C9—H9A0.9500
C2—C31.358 (8)C10—C111.356 (8)
C2—H2A0.9500C11—C121.380 (8)
C3—C41.403 (8)C11—H11A0.9500
C3—H3A0.9500C12—C131.478 (8)
C7—O3—H1O3107 (4)C4—C6—H6C109.5
C1—N1—C5120.9 (5)H6A—C6—H6C109.5
C1—N1—H1N1116 (3)H6B—C6—H6C109.5
C5—N1—H1N1123 (3)C8—C7—O3119.7 (4)
C1—N2—H1N2124 (4)C8—C7—C12119.4 (5)
C1—N2—H2N2114 (5)O3—C7—C12120.9 (5)
H1N2—N2—H2N2121 (7)C7—C8—C9121.8 (4)
N2—C1—N1116.5 (5)C7—C8—H8A119.1
N2—C1—C2124.5 (4)C9—C8—H8A119.1
N1—C1—C2119.0 (5)C10—C9—C8118.0 (5)
C1—C2—C3119.3 (5)C10—C9—H9A121.0
C1—C2—H2A120.4C8—C9—H9A121.0
C3—C2—H2A120.4C11—C10—C9121.4 (5)
C2—C3—C4122.7 (6)C11—C10—Cl1120.0 (4)
C2—C3—H3A118.6C9—C10—Cl1118.6 (5)
C4—C3—H3A118.6C10—C11—C12120.6 (4)
C5—C4—C3115.1 (5)C10—C11—H11A119.7
C5—C4—C6121.6 (5)C12—C11—H11A119.7
C3—C4—C6123.3 (6)C11—C12—C7118.8 (5)
C4—C5—N1122.9 (5)C11—C12—C13121.0 (4)
C4—C5—H5A118.6C7—C12—C13120.2 (5)
N1—C5—H5A118.6O1—C13—O2122.9 (5)
C4—C6—H6A109.5O1—C13—C12118.3 (4)
C4—C6—H6B109.5O2—C13—C12118.8 (4)
H6A—C6—H6B109.5
C5—N1—C1—N2−179.9 (5)C8—C9—C10—Cl1−179.3 (4)
C5—N1—C1—C21.0 (7)C9—C10—C11—C120.2 (8)
N2—C1—C2—C3−179.7 (5)Cl1—C10—C11—C12179.9 (4)
N1—C1—C2—C3−0.7 (8)C10—C11—C12—C7−0.8 (7)
C1—C2—C3—C4−0.3 (9)C10—C11—C12—C13−179.9 (5)
C2—C3—C4—C51.0 (9)C8—C7—C12—C110.8 (7)
C2—C3—C4—C6−179.7 (6)O3—C7—C12—C11−179.4 (5)
C3—C4—C5—N1−0.7 (8)C8—C7—C12—C13179.9 (5)
C6—C4—C5—N1180.0 (5)O3—C7—C12—C13−0.3 (7)
C1—N1—C5—C4−0.3 (8)C11—C12—C13—O1−1.3 (7)
O3—C7—C8—C9180.0 (5)C7—C12—C13—O1179.6 (5)
C12—C7—C8—C9−0.2 (8)C11—C12—C13—O2177.8 (4)
C7—C8—C9—C10−0.4 (8)C7—C12—C13—O2−1.2 (7)
C8—C9—C10—C110.4 (8)
D—H···AD—HH···AD···AD—H···A
O3—H1O3···O20.92 (6)1.73 (7)2.512 (6)141 (6)
N1—H1N1···O2i0.94 (6)1.76 (6)2.683 (7)166 (5)
N2—H1N2···O1i0.85 (5)1.96 (5)2.793 (8)165 (4)
N2—H2N2···O1ii0.85 (6)2.04 (7)2.811 (6)152 (7)
C8—H8A···O3iii0.952.583.425 (7)148
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
O3—H1O3⋯O20.92 (6)1.73 (7)2.512 (6)141 (6)
N1—H1N1⋯O2i 0.94 (6)1.76 (6)2.683 (7)166 (5)
N2—H1N2⋯O1i 0.85 (5)1.96 (5)2.793 (8)165 (4)
N2—H2N2⋯O1ii 0.85 (6)2.04 (7)2.811 (6)152 (7)
C8—H8A⋯O3iii 0.952.583.425 (7)148

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

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