Literature DB >> 23284507

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

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

Abstract

In the 2-amino-benzoate anion of the title salt, C(6)H(9)N(2) (+)·C(7)H(6)NO(2) (-), an intra-molecular N-H⋯O hydrogen bond is observed. The dihedral angle between the ring and the CO(2) group is 8.41 (13)°. 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 ion pairs are further connected via N-H⋯O hydrogen bonds, resulting in a donor-donor-acceptor-acceptor (DDAA) array of quadruple hydrogen bonds. The crystal structure also features a weak N-H⋯O hydrogen bond and a C-H⋯π inter-action, resulting in a three-dimensional network.

Entities:  

Year:  2012        PMID: 23284507      PMCID: PMC3515287          DOI: 10.1107/S1600536812043243

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 related structures, see: Nahringbauer & Kvick (1977 ▶); Hemamalini & Fun (2010a ▶,b ▶); Bis & Zaworotko (2005 ▶); Thanigaimani et al. (2012 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For hydrogen-bonding patterns in organic salts, see: Baskar Raj et al. (2003 ▶). 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

C6H9N2C7H6NO2 M = 245.28 Monoclinic, a = 9.2394 (8) Å b = 13.9200 (11) Å c = 12.1514 (8) Å β = 129.850 (4)° V = 1199.82 (16) Å3 Z = 4 Mo Kα radiation μ = 0.09 mm−1 T = 100 K 0.35 × 0.33 × 0.14 mm

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.968, T max = 0.987 11650 measured reflections 2707 independent reflections 2361 reflections with I > 2σ(I) R int = 0.031

Refinement

R[F 2 > 2σ(F 2)] = 0.037 wR(F 2) = 0.101 S = 1.07 2707 reflections 184 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.27 e Å−3 Δρmin = −0.24 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/S1600536812043243/is5202sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812043243/is5202Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536812043243/is5202Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C6H9N2+·C7H6NO2F(000) = 520
Mr = 245.28Dx = 1.358 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4117 reflections
a = 9.2394 (8) Åθ = 2.6–32.5°
b = 13.9200 (11) ŵ = 0.09 mm1
c = 12.1514 (8) ÅT = 100 K
β = 129.850 (4)°Block, pink
V = 1199.82 (16) Å30.35 × 0.33 × 0.14 mm
Z = 4
Bruker SMART APEXII DUO CCD area-detector diffractometer2707 independent reflections
Radiation source: fine-focus sealed tube2361 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.031
φ and ω scansθmax = 27.5°, θmin = 2.9°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −12→12
Tmin = 0.968, Tmax = 0.987k = −18→18
11650 measured reflectionsl = −15→15
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.101H atoms treated by a mixture of independent and constrained refinement
S = 1.07w = 1/[σ2(Fo2) + (0.0457P)2 + 0.4478P] where P = (Fo2 + 2Fc2)/3
2707 reflections(Δ/σ)max < 0.001
184 parametersΔρmax = 0.27 e Å3
0 restraintsΔρmin = −0.24 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
N1−0.05463 (13)0.58465 (7)0.37647 (10)0.0151 (2)
N2−0.25399 (14)0.50164 (8)0.16340 (12)0.0204 (2)
C10.11839 (16)0.60745 (8)0.50265 (12)0.0151 (2)
H1A0.12740.65490.56290.018*
C20.27885 (15)0.56356 (8)0.54419 (12)0.0155 (2)
C30.25605 (16)0.49221 (8)0.45170 (13)0.0171 (2)
H3A0.36390.45860.47840.020*
C40.08252 (16)0.47011 (9)0.32426 (13)0.0177 (3)
H4A0.07110.42250.26310.021*
C5−0.07917 (16)0.51858 (8)0.28449 (12)0.0159 (2)
C60.47064 (16)0.59045 (9)0.68135 (13)0.0196 (3)
H6A0.45740.61810.74870.029*
H6B0.52890.63780.66070.029*
H6C0.55020.53300.72380.029*
O10.43909 (11)0.88549 (6)0.58761 (9)0.0185 (2)
O20.63811 (11)0.83318 (6)0.81350 (9)0.0196 (2)
N30.50078 (14)0.75894 (8)0.93299 (11)0.0194 (2)
C70.12951 (16)0.86387 (9)0.57403 (13)0.0182 (2)
H7A0.11690.89840.50080.022*
C8−0.03024 (16)0.84480 (9)0.55754 (13)0.0205 (3)
H8A−0.15070.86580.47470.025*
C9−0.01034 (16)0.79390 (9)0.66560 (13)0.0194 (3)
H9A−0.11900.77880.65500.023*
C100.16495 (16)0.76523 (9)0.78755 (13)0.0171 (2)
H10A0.17510.73100.85990.021*
C110.32976 (15)0.78581 (8)0.80692 (12)0.0149 (2)
C120.31006 (15)0.83401 (8)0.69541 (12)0.0147 (2)
C130.47372 (15)0.85226 (8)0.69945 (12)0.0150 (2)
H1−0.280 (2)0.4597 (12)0.0936 (19)0.032 (4)*
H20.500 (2)0.7164 (12)0.9882 (18)0.027 (4)*
H30.605 (2)0.7676 (13)0.9397 (18)0.034 (4)*
H4−0.165 (2)0.6175 (13)0.3487 (19)0.038 (5)*
H5−0.354 (2)0.5383 (12)0.1417 (18)0.031 (4)*
U11U22U33U12U13U23
N10.0141 (5)0.0158 (5)0.0159 (5)0.0000 (4)0.0099 (4)−0.0003 (4)
N20.0149 (5)0.0239 (5)0.0183 (5)−0.0009 (4)0.0088 (4)−0.0060 (4)
C10.0171 (5)0.0140 (5)0.0147 (5)−0.0024 (4)0.0104 (5)−0.0017 (4)
C20.0150 (5)0.0156 (5)0.0153 (5)−0.0013 (4)0.0094 (5)0.0012 (4)
C30.0158 (5)0.0169 (5)0.0201 (6)0.0007 (4)0.0123 (5)0.0013 (5)
C40.0190 (6)0.0167 (5)0.0191 (6)−0.0009 (4)0.0130 (5)−0.0028 (5)
C50.0163 (5)0.0162 (5)0.0156 (5)−0.0018 (4)0.0105 (5)−0.0002 (4)
C60.0156 (5)0.0200 (6)0.0184 (6)−0.0007 (4)0.0087 (5)−0.0018 (5)
O10.0187 (4)0.0220 (4)0.0151 (4)−0.0006 (3)0.0109 (4)0.0014 (3)
O20.0132 (4)0.0241 (5)0.0180 (4)−0.0006 (3)0.0084 (4)0.0046 (3)
N30.0150 (5)0.0256 (5)0.0152 (5)−0.0005 (4)0.0085 (4)0.0043 (4)
C70.0179 (5)0.0189 (6)0.0146 (5)0.0009 (4)0.0090 (5)0.0006 (5)
C80.0135 (5)0.0250 (6)0.0164 (6)0.0020 (4)0.0065 (5)−0.0009 (5)
C90.0148 (5)0.0219 (6)0.0216 (6)−0.0031 (4)0.0117 (5)−0.0053 (5)
C100.0185 (5)0.0173 (6)0.0176 (6)−0.0032 (4)0.0125 (5)−0.0025 (4)
C110.0147 (5)0.0138 (5)0.0136 (5)−0.0010 (4)0.0079 (5)−0.0027 (4)
C120.0139 (5)0.0142 (5)0.0144 (5)−0.0017 (4)0.0084 (5)−0.0025 (4)
C130.0156 (5)0.0124 (5)0.0153 (5)−0.0010 (4)0.0091 (5)−0.0013 (4)
N1—C51.3498 (15)O1—C131.2672 (14)
N1—C11.3660 (14)O2—C131.2651 (14)
N1—H40.959 (18)N3—C111.3717 (15)
N2—C51.3356 (15)N3—H20.897 (17)
N2—H10.926 (18)N3—H30.923 (18)
N2—H50.933 (17)C7—C81.3821 (17)
C1—C21.3664 (16)C7—C121.4064 (16)
C1—H1A0.9500C7—H7A0.9500
C2—C31.4108 (17)C8—C91.3966 (18)
C2—C61.5077 (16)C8—H8A0.9500
C3—C41.3716 (16)C9—C101.3793 (16)
C3—H3A0.9500C9—H9A0.9500
C4—C51.4125 (16)C10—C111.4131 (16)
C4—H4A0.9500C10—H10A0.9500
C6—H6A0.9800C11—C121.4153 (16)
C6—H6B0.9800C12—C131.5029 (15)
C6—H6C0.9800
C5—N1—C1122.86 (10)H6B—C6—H6C109.5
C5—N1—H4117.1 (11)C11—N3—H2117.4 (10)
C1—N1—H4120.0 (11)C11—N3—H3117.0 (11)
C5—N2—H1122.7 (10)H2—N3—H3121.8 (15)
C5—N2—H5119.6 (10)C8—C7—C12122.28 (11)
H1—N2—H5117.2 (15)C8—C7—H7A118.9
N1—C1—C2121.54 (11)C12—C7—H7A118.9
N1—C1—H1A119.2C7—C8—C9118.44 (11)
C2—C1—H1A119.2C7—C8—H8A120.8
C1—C2—C3116.59 (10)C9—C8—H8A120.8
C1—C2—C6121.72 (11)C10—C9—C8120.90 (11)
C3—C2—C6121.68 (10)C10—C9—H9A119.6
C4—C3—C2121.81 (11)C8—C9—H9A119.6
C4—C3—H3A119.1C9—C10—C11121.22 (11)
C2—C3—H3A119.1C9—C10—H10A119.4
C3—C4—C5119.61 (11)C11—C10—H10A119.4
C3—C4—H4A120.2N3—C11—C10118.55 (11)
C5—C4—H4A120.2N3—C11—C12123.23 (10)
N2—C5—N1118.38 (10)C10—C11—C12118.22 (10)
N2—C5—C4124.05 (11)C7—C12—C11118.86 (10)
N1—C5—C4117.55 (10)C7—C12—C13118.47 (10)
C2—C6—H6A109.5C11—C12—C13122.65 (10)
C2—C6—H6B109.5O2—C13—O1123.53 (10)
H6A—C6—H6B109.5O2—C13—C12118.48 (10)
C2—C6—H6C109.5O1—C13—C12117.99 (10)
H6A—C6—H6C109.5
C5—N1—C1—C2−0.49 (17)C9—C10—C11—N3177.35 (11)
N1—C1—C2—C3−1.33 (17)C9—C10—C11—C12−2.10 (17)
N1—C1—C2—C6178.25 (11)C8—C7—C12—C11−2.35 (18)
C1—C2—C3—C42.07 (17)C8—C7—C12—C13175.98 (11)
C6—C2—C3—C4−177.52 (11)N3—C11—C12—C7−176.04 (11)
C2—C3—C4—C5−1.02 (18)C10—C11—C12—C73.38 (16)
C1—N1—C5—N2−179.68 (11)N3—C11—C12—C135.71 (18)
C1—N1—C5—C41.58 (16)C10—C11—C12—C13−174.87 (10)
C3—C4—C5—N2−179.47 (11)C7—C12—C13—O2173.86 (10)
C3—C4—C5—N1−0.81 (17)C11—C12—C13—O2−7.88 (17)
C12—C7—C8—C9−0.13 (18)C7—C12—C13—O1−6.58 (16)
C7—C8—C9—C101.51 (18)C11—C12—C13—O1171.69 (10)
C8—C9—C10—C11−0.38 (18)
D—H···AD—HH···AD···AD—H···A
N3—H3···O20.92 (2)1.97 (2)2.6734 (18)131.8 (15)
N2—H1···O1i0.926 (18)1.982 (18)2.8561 (14)157 (2)
N3—H2···O1ii0.897 (17)2.159 (18)3.0445 (14)168.7 (14)
N1—H4···O2iii0.959 (18)1.723 (18)2.6776 (13)172.7 (17)
N2—H5···O1iii0.933 (17)1.899 (18)2.8305 (14)176.8 (16)
C1—H1A···Cg10.952.583.5094 (13)165
Table 1

Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C7–C12 ring.

D—H⋯A D—HH⋯A DA D—H⋯A
N3—H3⋯O20.92 (2)1.97 (2)2.6734 (18)131.8 (15)
N2—H1⋯O1i 0.926 (18)1.982 (18)2.8561 (14)157 (2)
N3—H2⋯O1ii 0.897 (17)2.159 (18)3.0445 (14)168.7 (14)
N1—H4⋯O2iii 0.959 (18)1.723 (18)2.6776 (13)172.7 (17)
N2—H5⋯O1iii 0.933 (17)1.899 (18)2.8305 (14)176.8 (16)
C1—H1ACg10.952.583.5094 (13)165

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

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