Literature DB >> 23284506

2-Amino-5-methyl-pyridinium 3-chloro-benzoate.

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

Abstract

The 3-chloro-benzoate anion of the title salt, C(6)H(9)N(2) (+)·C(7)H(4)ClO(2) (-), is nearly planar with a dihedral angle of 2.44 (13)° 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 of the anion via a pair of N-H⋯O hydrogen bonds with an R(2) (2)(8) ring motif, forming an approximately planar ion pair with a dihedral angle of 7.92 (5)° between the pyridinium and benzene rings. The ion pairs are further connected via N-H⋯O and C-H⋯O hydrogen bonds, forming a two-dimensional network parallel to the bc plane.

Entities:  

Year:  2012        PMID: 23284506      PMCID: PMC3515286          DOI: 10.1107/S1600536812043231

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 details of hydrogen bonding, see: Jeffrey (1997 ▶); Scheiner (1997 ▶). 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 the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C6H9N2C7H4ClO2 M = 264.70 Monoclinic, a = 9.0318 (11) Å b = 11.6590 (14) Å c = 12.1166 (15) Å β = 101.521 (2)° V = 1250.2 (3) Å3 Z = 4 Mo Kα radiation μ = 0.30 mm−1 T = 100 K 0.53 × 0.31 × 0.22 mm

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.856, T max = 0.936 13594 measured reflections 3629 independent reflections 3201 reflections with I > 2σ(I) R int = 0.031

Refinement

R[F 2 > 2σ(F 2)] = 0.038 wR(F 2) = 0.115 S = 1.06 3629 reflections 176 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.48 e Å−3 Δρmin = −0.33 e Å−3 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/S1600536812043231/is5201sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812043231/is5201Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536812043231/is5201Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C6H9N2+·C7H4ClO2F(000) = 552
Mr = 264.70Dx = 1.406 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 6768 reflections
a = 9.0318 (11) Åθ = 2.3–30.1°
b = 11.6590 (14) ŵ = 0.30 mm1
c = 12.1166 (15) ÅT = 100 K
β = 101.521 (2)°Block, colourless
V = 1250.2 (3) Å30.53 × 0.31 × 0.22 mm
Z = 4
Bruker SMART APEXII DUO CCD area-detector diffractometer3629 independent reflections
Radiation source: fine-focus sealed tube3201 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.031
φ and ω scansθmax = 30.1°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −12→12
Tmin = 0.856, Tmax = 0.936k = −16→16
13594 measured reflectionsl = −17→17
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.115H atoms treated by a mixture of independent and constrained refinement
S = 1.06w = 1/[σ2(Fo2) + (0.070P)2 + 0.2814P] where P = (Fo2 + 2Fc2)/3
3629 reflections(Δ/σ)max < 0.001
176 parametersΔρmax = 0.48 e Å3
0 restraintsΔρmin = −0.33 e Å3
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
Cl11.05016 (3)0.25195 (2)0.66489 (3)0.02535 (11)
O10.60056 (10)0.65207 (8)0.46906 (7)0.02385 (19)
O20.72588 (10)0.62484 (8)0.64581 (7)0.02350 (19)
N10.45310 (10)0.81988 (8)0.55172 (8)0.01776 (19)
N20.55220 (12)0.77783 (10)0.73908 (9)0.0219 (2)
C10.46396 (12)0.84318 (9)0.66248 (10)0.0179 (2)
C20.37858 (13)0.93693 (10)0.69173 (10)0.0210 (2)
H2A0.38330.95610.76860.025*
C30.28968 (13)0.99913 (10)0.60827 (11)0.0218 (2)
H3A0.23271.06150.62830.026*
C40.27996 (12)0.97334 (10)0.49275 (10)0.0204 (2)
C50.36421 (12)0.88246 (10)0.46891 (10)0.0190 (2)
H5A0.36070.86240.39240.023*
C60.18156 (14)1.04262 (11)0.40224 (11)0.0262 (3)
H6A0.19681.01700.32830.039*
H6B0.20841.12390.41240.039*
H6C0.07541.03210.40700.039*
C70.69320 (12)0.59788 (9)0.54401 (9)0.0175 (2)
C80.76799 (11)0.49160 (9)0.50805 (9)0.0159 (2)
C90.86515 (12)0.42923 (9)0.59063 (9)0.0172 (2)
H9A0.88400.45370.66700.021*
C100.93380 (12)0.33117 (9)0.55982 (10)0.0180 (2)
C110.91118 (13)0.29472 (10)0.44867 (10)0.0212 (2)
H11A0.96030.22800.42880.025*
C120.81496 (13)0.35797 (10)0.36693 (10)0.0224 (2)
H12A0.79870.33450.29040.027*
C130.74215 (12)0.45553 (10)0.39638 (9)0.0198 (2)
H13A0.67500.49730.34020.024*
H1N10.511 (3)0.7554 (18)0.526 (2)0.055 (7)*
H1N20.617 (2)0.7251 (16)0.7129 (17)0.037 (5)*
H2N20.574 (2)0.8015 (16)0.8114 (16)0.035 (4)*
U11U22U33U12U13U23
Cl10.02441 (17)0.02607 (17)0.02424 (17)0.00991 (9)0.00168 (12)0.00262 (10)
O10.0302 (4)0.0259 (4)0.0161 (4)0.0125 (3)0.0061 (3)0.0030 (3)
O20.0285 (4)0.0253 (4)0.0163 (4)0.0075 (3)0.0034 (3)−0.0021 (3)
N10.0183 (4)0.0195 (4)0.0156 (4)0.0034 (3)0.0037 (3)−0.0019 (3)
N20.0240 (5)0.0262 (5)0.0150 (5)0.0050 (4)0.0025 (4)−0.0025 (4)
C10.0168 (5)0.0201 (5)0.0173 (5)−0.0003 (4)0.0047 (4)−0.0028 (4)
C20.0206 (5)0.0231 (5)0.0203 (5)0.0005 (4)0.0066 (4)−0.0061 (4)
C30.0193 (5)0.0207 (5)0.0263 (6)0.0030 (4)0.0064 (4)−0.0047 (4)
C40.0183 (5)0.0202 (5)0.0230 (5)0.0024 (4)0.0045 (4)0.0000 (4)
C50.0189 (5)0.0215 (5)0.0166 (5)0.0021 (4)0.0038 (4)−0.0006 (4)
C60.0253 (6)0.0258 (6)0.0269 (6)0.0084 (4)0.0038 (5)0.0024 (5)
C70.0195 (5)0.0181 (5)0.0163 (5)0.0023 (4)0.0069 (4)0.0013 (4)
C80.0156 (4)0.0169 (4)0.0159 (5)0.0012 (3)0.0049 (4)0.0000 (4)
C90.0166 (4)0.0187 (5)0.0164 (5)0.0011 (4)0.0037 (4)0.0000 (4)
C100.0146 (4)0.0188 (5)0.0205 (5)0.0019 (3)0.0030 (4)0.0016 (4)
C110.0197 (5)0.0203 (5)0.0238 (6)0.0029 (4)0.0046 (4)−0.0039 (4)
C120.0242 (5)0.0246 (5)0.0182 (5)0.0032 (4)0.0036 (4)−0.0047 (4)
C130.0208 (5)0.0223 (5)0.0160 (5)0.0033 (4)0.0029 (4)−0.0003 (4)
Cl1—C101.7447 (11)C5—H5A0.9500
O1—C71.2729 (13)C6—H6A0.9800
O2—C71.2498 (14)C6—H6B0.9800
N1—C11.3535 (14)C6—H6C0.9800
N1—C51.3645 (14)C7—C81.5163 (15)
N1—H1N11.00 (2)C8—C131.3914 (15)
N2—C11.3348 (15)C8—C91.3961 (15)
N2—H1N20.949 (19)C9—C101.3870 (15)
N2—H2N20.90 (2)C9—H9A0.9500
C1—C21.4227 (15)C10—C111.3878 (16)
C2—C31.3671 (17)C11—C121.3914 (16)
C2—H2A0.9500C11—H11A0.9500
C3—C41.4171 (17)C12—C131.3955 (16)
C3—H3A0.9500C12—H12A0.9500
C4—C51.3686 (15)C13—H13A0.9500
C4—C61.5019 (16)
C1—N1—C5122.50 (10)C4—C6—H6C109.5
C1—N1—H1N1121.5 (14)H6A—C6—H6C109.5
C5—N1—H1N1116.0 (14)H6B—C6—H6C109.5
C1—N2—H1N2117.5 (12)O2—C7—O1124.84 (10)
C1—N2—H2N2119.1 (12)O2—C7—C8117.27 (9)
H1N2—N2—H2N2119.4 (17)O1—C7—C8117.88 (10)
N2—C1—N1119.33 (10)C13—C8—C9119.93 (10)
N2—C1—C2122.91 (11)C13—C8—C7121.91 (9)
N1—C1—C2117.75 (10)C9—C8—C7118.16 (9)
C3—C2—C1119.39 (11)C10—C9—C8119.15 (10)
C3—C2—H2A120.3C10—C9—H9A120.4
C1—C2—H2A120.3C8—C9—H9A120.4
C2—C3—C4121.97 (10)C9—C10—C11121.77 (10)
C2—C3—H3A119.0C9—C10—Cl1118.45 (9)
C4—C3—H3A119.0C11—C10—Cl1119.77 (8)
C5—C4—C3116.45 (10)C10—C11—C12118.59 (10)
C5—C4—C6122.35 (11)C10—C11—H11A120.7
C3—C4—C6121.20 (10)C12—C11—H11A120.7
N1—C5—C4121.94 (10)C11—C12—C13120.61 (11)
N1—C5—H5A119.0C11—C12—H12A119.7
C4—C5—H5A119.0C13—C12—H12A119.7
C4—C6—H6A109.5C8—C13—C12119.93 (10)
C4—C6—H6B109.5C8—C13—H13A120.0
H6A—C6—H6B109.5C12—C13—H13A120.0
C5—N1—C1—N2179.47 (10)O2—C7—C8—C91.54 (15)
C5—N1—C1—C2−0.06 (16)O1—C7—C8—C9−177.53 (10)
N2—C1—C2—C3−179.39 (11)C13—C8—C9—C10−0.51 (16)
N1—C1—C2—C30.12 (16)C7—C8—C9—C10179.45 (9)
C1—C2—C3—C4−0.16 (18)C8—C9—C10—C111.46 (16)
C2—C3—C4—C50.13 (17)C8—C9—C10—Cl1−178.02 (8)
C2—C3—C4—C6179.96 (11)C9—C10—C11—C12−1.01 (17)
C1—N1—C5—C40.03 (17)Cl1—C10—C11—C12178.47 (9)
C3—C4—C5—N1−0.06 (16)C10—C11—C12—C13−0.39 (18)
C6—C4—C5—N1−179.89 (10)C9—C8—C13—C12−0.85 (17)
O2—C7—C8—C13−178.50 (10)C7—C8—C13—C12179.19 (10)
O1—C7—C8—C132.43 (16)C11—C12—C13—C81.32 (18)
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O11.00 (2)1.68 (2)2.6716 (13)174 (2)
N2—H1N2···O20.946 (19)1.820 (19)2.7618 (15)173.0 (19)
N2—H2N2···O1i0.90 (2)1.95 (2)2.8526 (14)174.0 (17)
C2—H2A···O2ii0.952.523.2104 (15)130
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N1—H1N1⋯O11.00 (2)1.68 (2)2.6716 (13)174 (2)
N2—H1N2⋯O20.946 (19)1.820 (19)2.7618 (15)173.0 (19)
N2—H2N2⋯O1i 0.90 (2)1.95 (2)2.8526 (14)174.0 (17)
C2—H2A⋯O2ii 0.952.523.2104 (15)130

Symmetry codes: (i) ; (ii) .

  2 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  2 in total
  4 in total

1.  2-Amino-5-methyl-pyridinium 2-amino-benzoate.

Authors:  Kaliyaperumal Thanigaimani; Abbas Farhadikoutenaei; Nuridayanti Che Khalib; Suhana Arshad; Ibrahim Abdul Razak
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-10-24

2.  2-Amino-5-methyl-pyridinium 4-chloro-benzoate.

Authors:  Kaliyaperumal Thanigaimani; Abbas Farhadikoutenaei; Suhana Arshad; Ibrahim Abdul Razak
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-12-22

3.  2-Amino-5-methyl-pyridinium 4-methyl-benzoate.

Authors:  Kaliyaperumal Thanigaimani; Abbas Farhadikoutenaei; Suhana Arshad; Ibrahim Abdul Razak
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-12-15

4.  2-Amino-6-methyl-pyridinium 3-chloro-benzoate.

Authors:  Kaliyaperumal Thanigaimani; Nuridayanti Che Khalib; Suhana Arshad; Ibrahim Abdul Razak
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2013-02-02
  4 in total

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