Literature DB >> 23476517

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

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

Abstract

In the title salt, C6H9N2(+)·C7H4ClO2(-), the 3-chloro-benzoate anion shows a whole-mol-ecule disorder over two positions with a refined occupancy ratio of 0.505 (4):0.495 (4). In the crystal, the cations and anions are linked via N-H⋯O hydrogen bonds, forming a centrosymmetric 2 + 2 aggregate with R2(2)(8) and R4(2)(8) ring motifs. The crystal structure also features a π-π stacking inter-action between the pyridinium rings with a centroid-centroid distance of 3.8339 (9) Å.

Entities:  

Year:  2013        PMID: 23476517      PMCID: PMC3588495          DOI: 10.1107/S1600536813002559

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: Hemamalini & Fun (2010 ▶); Thanigaimani et al. (2012 ▶); Draguta et al. (2012 ▶). 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

C6H9N2 +·C7H4ClO2 M = 264.70 Monoclinic, a = 22.3118 (15) Å b = 15.2053 (10) Å c = 7.4166 (5) Å β = 100.924 (1)° V = 2470.5 (3) Å3 Z = 8 Mo Kα radiation μ = 0.30 mm−1 T = 100 K 0.36 × 0.06 × 0.05 mm

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.898, T max = 0.985 24731 measured reflections 3575 independent reflections 2446 reflections with I > 2σ(I) R int = 0.053

Refinement

R[F 2 > 2σ(F 2)] = 0.045 wR(F 2) = 0.128 S = 1.06 3575 reflections 267 parameters 5 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.29 e Å−3 Δρmin = −0.28 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/S1600536813002559/is5234sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813002559/is5234Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813002559/is5234Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C6H9N2+·C7H4ClO2F(000) = 1104
Mr = 264.70Dx = 1.423 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 4651 reflections
a = 22.3118 (15) Åθ = 2.7–29.3°
b = 15.2053 (10) ŵ = 0.30 mm1
c = 7.4166 (5) ÅT = 100 K
β = 100.924 (1)°Needle, colourless
V = 2470.5 (3) Å30.36 × 0.06 × 0.05 mm
Z = 8
Bruker SMART APEXII DUO CCD area-detector diffractometer3575 independent reflections
Radiation source: fine-focus sealed tube2446 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.053
φ and ω scansθmax = 30.0°, θmin = 1.6°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −30→31
Tmin = 0.898, Tmax = 0.985k = −21→21
24731 measured reflectionsl = −10→10
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.045Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.128H atoms treated by a mixture of independent and constrained refinement
S = 1.06w = 1/[σ2(Fo2) + (0.0584P)2 + 1.2878P] where P = (Fo2 + 2Fc2)/3
3575 reflections(Δ/σ)max < 0.001
267 parametersΔρmax = 0.29 e Å3
5 restraintsΔρmin = −0.28 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*/UeqOcc. (<1)
Cl10.51442 (12)0.09433 (16)0.5251 (4)0.0377 (5)0.505 (4)
O10.3604 (3)0.4344 (4)0.2546 (10)0.0298 (12)0.505 (4)
O20.3335 (7)0.2966 (7)0.1833 (12)0.0279 (16)0.505 (4)
C70.3716 (3)0.3536 (4)0.2547 (8)0.0223 (11)0.505 (4)
C80.43409 (15)0.3242 (2)0.3507 (6)0.0224 (7)0.505 (4)
C90.4472 (5)0.2368 (8)0.3839 (11)0.0217 (13)0.505 (4)
H9A0.41660.19450.33940.026*0.505 (4)
C100.5042 (5)0.2072 (5)0.4815 (14)0.0368 (18)0.505 (4)
C110.54930 (16)0.2695 (3)0.5297 (6)0.0348 (9)0.505 (4)
H11A0.58900.25150.58850.042*0.505 (4)
C120.53779 (14)0.3580 (3)0.4939 (5)0.0345 (9)0.505 (4)
H12A0.56930.40000.53010.041*0.505 (4)
C130.48029 (14)0.3853 (2)0.4052 (5)0.0286 (8)0.505 (4)
H13A0.47250.44600.38160.034*0.505 (4)
Cl1X0.52750 (12)0.11634 (16)0.5138 (4)0.0336 (4)0.495 (4)
O1X0.3491 (3)0.4332 (4)0.3044 (10)0.0294 (11)0.495 (4)
O2X0.3302 (7)0.2910 (8)0.2304 (12)0.0273 (15)0.495 (4)
C7X0.3620 (3)0.3525 (4)0.3103 (9)0.0225 (11)0.495 (4)
C8X0.42352 (17)0.3289 (2)0.4266 (6)0.0222 (8)0.495 (4)
C9X0.4418 (5)0.2415 (8)0.4305 (11)0.0223 (14)0.495 (4)
H9XA0.41520.19630.37480.027*0.495 (4)
C10X0.5005 (5)0.2239 (4)0.5195 (13)0.0314 (16)0.495 (4)
C11X0.53950 (16)0.2854 (3)0.6185 (6)0.0319 (9)0.495 (4)
H11B0.57870.26910.68440.038*0.495 (4)
C12X0.51893 (15)0.3713 (2)0.6175 (5)0.0303 (8)0.495 (4)
H12B0.54450.41550.68200.036*0.495 (4)
C13X0.46134 (15)0.3931 (2)0.5228 (5)0.0272 (8)0.495 (4)
H13B0.44740.45220.52330.033*0.495 (4)
N10.25283 (5)0.49267 (8)0.09853 (17)0.0197 (3)
N20.21460 (7)0.35423 (9)0.0235 (2)0.0337 (4)
C10.20717 (6)0.44124 (10)0.0094 (2)0.0211 (3)
C20.15454 (7)0.48210 (10)−0.0898 (2)0.0238 (3)
H2A0.12230.4479−0.15720.029*
C30.15048 (7)0.57153 (11)−0.0877 (2)0.0307 (4)
H3A0.11490.5996−0.15330.037*
C40.19795 (8)0.62255 (11)0.0095 (3)0.0363 (4)
H4A0.19440.68480.01210.044*
C50.24940 (7)0.58195 (10)0.1006 (2)0.0257 (3)
C60.30466 (8)0.62859 (11)0.2048 (3)0.0372 (4)
H6A0.29550.69130.21360.056*
H6B0.33880.62130.14020.056*
H6C0.31570.60360.32840.056*
H1N10.1883 (11)0.3210 (14)−0.050 (3)0.046 (6)*
H2N20.2887 (10)0.4672 (15)0.165 (3)0.050 (6)*
H1N20.2487 (11)0.3311 (14)0.077 (3)0.044 (6)*
U11U22U33U12U13U23
Cl10.0260 (10)0.0318 (11)0.0523 (8)0.0162 (6)0.0001 (7)0.0009 (8)
O10.016 (2)0.0172 (13)0.051 (4)−0.0007 (13)−0.0063 (17)−0.0018 (18)
O20.020 (2)0.0134 (18)0.043 (4)0.0000 (14)−0.014 (3)0.000 (3)
C70.012 (2)0.0175 (16)0.035 (3)−0.0021 (13)−0.0015 (19)0.0004 (19)
C80.0103 (15)0.0277 (16)0.027 (2)0.0008 (11)−0.0011 (13)−0.0050 (15)
C90.014 (2)0.0240 (19)0.028 (4)0.0072 (15)0.006 (3)−0.005 (3)
C100.013 (2)0.037 (3)0.055 (4)0.016 (2)−0.006 (2)−0.016 (2)
C110.0138 (16)0.059 (3)0.029 (2)0.0094 (15)−0.0032 (14)−0.0084 (17)
C120.0134 (15)0.054 (2)0.0331 (19)−0.0063 (14)−0.0032 (12)−0.0057 (15)
C130.0182 (15)0.0351 (17)0.0299 (18)−0.0033 (12)−0.0019 (12)−0.0044 (13)
Cl1X0.0247 (9)0.0289 (10)0.0442 (7)0.0119 (6)−0.0011 (6)0.0025 (7)
O1X0.021 (3)0.0190 (14)0.043 (3)−0.0005 (14)−0.0066 (16)−0.0035 (17)
O2X0.0172 (18)0.020 (2)0.038 (4)−0.0025 (14)−0.011 (3)0.002 (2)
C7X0.013 (2)0.0213 (18)0.032 (3)−0.0016 (14)0.0023 (18)0.002 (2)
C8X0.0144 (16)0.0268 (17)0.0247 (19)−0.0003 (12)0.0018 (14)−0.0018 (15)
C9X0.010 (2)0.035 (3)0.023 (3)0.0040 (18)0.005 (2)−0.003 (3)
C10X0.021 (2)0.022 (3)0.051 (4)0.016 (2)0.007 (3)0.001 (3)
C11X0.0132 (15)0.052 (2)0.0276 (19)0.0019 (14)−0.0032 (14)−0.0008 (17)
C12X0.0193 (15)0.0391 (19)0.0294 (18)−0.0090 (13)−0.0031 (13)−0.0029 (14)
C13X0.0243 (16)0.0254 (16)0.0302 (18)−0.0062 (12)0.0011 (13)−0.0025 (12)
N10.0155 (6)0.0161 (6)0.0264 (6)0.0011 (4)0.0012 (5)0.0000 (4)
N20.0220 (7)0.0179 (6)0.0526 (9)0.0009 (5)−0.0147 (6)−0.0074 (6)
C10.0171 (7)0.0200 (7)0.0251 (7)0.0015 (5)0.0012 (5)−0.0020 (5)
C20.0165 (7)0.0285 (8)0.0253 (7)0.0031 (6)0.0008 (5)−0.0008 (6)
C30.0232 (8)0.0318 (9)0.0356 (9)0.0091 (6)0.0016 (6)0.0068 (7)
C40.0313 (9)0.0191 (7)0.0563 (11)0.0053 (6)0.0030 (8)0.0057 (7)
C50.0231 (8)0.0179 (7)0.0366 (8)−0.0001 (6)0.0068 (6)0.0006 (6)
C60.0254 (9)0.0189 (7)0.0652 (12)−0.0044 (6)0.0036 (8)−0.0039 (7)
Cl1—C101.753 (7)C11X—C12X1.385 (5)
O1—C71.253 (6)C11X—H11B0.9500
O2—C71.258 (14)C12X—C13X1.383 (4)
C7—C81.509 (8)C12X—H12B0.9500
C8—C91.372 (12)C13X—H13B0.9500
C8—C131.390 (5)N1—C11.3530 (18)
C9—C101.413 (16)N1—C51.3599 (19)
C9—H9A0.9500N1—H2N20.94 (2)
C10—C111.379 (11)N2—C11.335 (2)
C11—C121.385 (6)N2—H1N10.88 (2)
C11—H11A0.9500N2—H1N20.86 (2)
C12—C131.390 (4)C1—C21.4067 (19)
C12—H12A0.9500C2—C31.363 (2)
C13—H13A0.9500C2—H2A0.9500
Cl1X—C10X1.747 (6)C3—C41.398 (2)
O1X—C7X1.259 (7)C3—H3A0.9500
O2X—C7X1.253 (14)C4—C51.365 (2)
C7X—C8X1.519 (8)C4—H4A0.9500
C8X—C9X1.389 (13)C5—C61.503 (2)
C8X—C13X1.395 (5)C6—H6A0.9800
C9X—C10X1.377 (17)C6—H6B0.9800
C9X—H9XA0.9500C6—H6C0.9800
C10X—C11X1.388 (12)
O1—C7—O2123.8 (9)C10X—C11X—H11B121.4
O1—C7—C8117.2 (6)C13X—C12X—C11X120.3 (3)
O2—C7—C8118.9 (8)C13X—C12X—H12B119.9
C9—C8—C13118.3 (6)C11X—C12X—H12B119.9
C9—C8—C7121.2 (6)C12X—C13X—C8X120.4 (3)
C13—C8—C7120.5 (4)C12X—C13X—H13B119.8
C8—C9—C10122.8 (10)C8X—C13X—H13B119.8
C8—C9—H9A118.6C1—N1—C5122.95 (13)
C10—C9—H9A118.6C1—N1—H2N2120.4 (14)
C11—C10—C9117.1 (7)C5—N1—H2N2116.7 (14)
C11—C10—Cl1124.2 (7)C1—N2—H1N1117.5 (14)
C9—C10—Cl1118.7 (8)C1—N2—H1N2121.7 (14)
C10—C11—C12121.2 (4)H1N1—N2—H1N2119 (2)
C10—C11—H11A119.4N2—C1—N1117.63 (13)
C12—C11—H11A119.4N2—C1—C2123.89 (14)
C11—C12—C13120.1 (3)N1—C1—C2118.48 (13)
C11—C12—H12A119.9C3—C2—C1119.04 (14)
C13—C12—H12A119.9C3—C2—H2A120.5
C8—C13—C12120.3 (3)C1—C2—H2A120.5
C8—C13—H13A119.8C2—C3—C4120.93 (14)
C12—C13—H13A119.8C2—C3—H3A119.5
O2X—C7X—O1X127.3 (10)C4—C3—H3A119.5
O2X—C7X—C8X117.5 (8)C5—C4—C3119.24 (15)
O1X—C7X—C8X115.2 (7)C5—C4—H4A120.4
C9X—C8X—C13X120.8 (6)C3—C4—H4A120.4
C9X—C8X—C7X117.9 (6)N1—C5—C4119.32 (15)
C13X—C8X—C7X121.3 (4)N1—C5—C6115.76 (13)
C10X—C9X—C8X116.4 (9)C4—C5—C6124.91 (15)
C10X—C9X—H9XA121.8C5—C6—H6A109.5
C8X—C9X—H9XA121.8C5—C6—H6B109.5
C9X—C10X—C11X124.5 (7)H6A—C6—H6B109.5
C9X—C10X—Cl1X118.1 (8)C5—C6—H6C109.5
C11X—C10X—Cl1X117.3 (7)H6A—C6—H6C109.5
C12X—C11X—C10X117.3 (4)H6B—C6—H6C109.5
C12X—C11X—H11B121.4
O1—C7—C8—C9169.3 (5)C7X—C8X—C9X—C10X172.7 (6)
O2—C7—C8—C9−9.3 (8)C8X—C9X—C10X—C11X6.5 (12)
O1—C7—C8—C13−11.7 (7)C8X—C9X—C10X—Cl1X−175.4 (5)
O2—C7—C8—C13169.7 (6)C9X—C10X—C11X—C12X−4.3 (11)
C13—C8—C9—C104.3 (9)Cl1X—C10X—C11X—C12X177.7 (4)
C7—C8—C9—C10−176.7 (6)C10X—C11X—C12X—C13X1.0 (7)
C8—C9—C10—C11−5.7 (11)C11X—C12X—C13X—C8X−0.4 (6)
C8—C9—C10—Cl1177.0 (5)C9X—C8X—C13X—C12X2.8 (7)
C9—C10—C11—C123.9 (10)C7X—C8X—C13X—C12X−175.5 (3)
Cl1—C10—C11—C12−178.8 (5)C5—N1—C1—N2−177.15 (15)
C10—C11—C12—C13−1.1 (7)C5—N1—C1—C21.9 (2)
C9—C8—C13—C12−1.2 (6)N2—C1—C2—C3176.80 (16)
C7—C8—C13—C12179.9 (4)N1—C1—C2—C3−2.2 (2)
C11—C12—C13—C8−0.4 (6)C1—C2—C3—C40.7 (3)
O2X—C7X—C8X—C9X2.7 (9)C2—C3—C4—C51.2 (3)
O1X—C7X—C8X—C9X−176.6 (5)C1—N1—C5—C40.0 (2)
O2X—C7X—C8X—C13X−178.9 (6)C1—N1—C5—C6−179.36 (14)
O1X—C7X—C8X—C13X1.8 (6)C3—C4—C5—N1−1.5 (3)
C13X—C8X—C9X—C10X−5.7 (9)C3—C4—C5—C6177.75 (17)
D—H···AD—HH···AD···AD—H···A
N1—H2N2···O10.94 (2)1.69 (2)2.614 (7)168 (2)
N2—H1N2···O20.86 (2)1.98 (3)2.832 (14)170 (2)
N2—H1N1···O2i0.88 (2)2.06 (2)2.853 (11)150 (2)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N1—H2N2⋯O10.94 (2)1.69 (2)2.614 (7)168 (2)
N2—H1N2⋯O20.86 (2)1.98 (3)2.832 (14)170 (2)
N2—H1N1⋯O2i 0.88 (2)2.06 (2)2.853 (11)150 (2)

Symmetry code: (i) .

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Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

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

4.  6-Methyl-pyridin-2-amine.

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5.  Structure validation in chemical crystallography.

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1.  2-Amino-5-methyl-pyridinium 3-hy-droxy-pyridine-2-carboxyl-ate.

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