organic compounds
2-Amino-5-methylpyridinium 3-chlorobenzoate
aSchool of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: arazaki@usm.my
The 3-chlorobenzoate anion of the title salt, C6H9N2+·C7H4ClO2−, is nearly planar with a dihedral angle of 2.44 (13)° between the benzene ring and the carboxylate group. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxylate O atoms of the anion via a pair of N—H⋯O hydrogen bonds with an R22(8) ring motif, forming an approximately planar 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.
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
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Refinement
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Data collection: APEX2 (Bruker, 2009); cell 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).
Supporting information
10.1107/S1600536812043231/is5201sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812043231/is5201Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812043231/is5201Isup3.cml
Hot methanol solutions (20 ml) of 2-amino5-methylpyridine (54 mg, Aldrich) and 3-chlorobenzoic acid (39 mg, Merck) were mixed and warmed over a heating magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature and crystals of the title compound (I) appeared after a few days.
N-bound H atoms were located in a difference Fourier maps and refined freely [refined N—H distances 1.00 (2), 0.949 (19) and 0.90 (2) Å]. The remaining H atoms were positioned geometrically (C—H= 0.95 and 0.98 Å) and were refined using a riding model, with Uiso(H) = 1.2 Ueq(C) or 1.5Ueq(methyl C). A rotating-group model was used for the methyl group. In the final
four outliers were omitted (1 1 8, 1 0 8, 2 3 1 and -1 4 8).Data collection: APEX2 (Bruker, 2009); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).C6H9N2+·C7H4ClO2− | F(000) = 552 |
Mr = 264.70 | Dx = 1.406 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 6768 reflections |
a = 9.0318 (11) Å | θ = 2.3–30.1° |
b = 11.6590 (14) Å | µ = 0.30 mm−1 |
c = 12.1166 (15) Å | T = 100 K |
β = 101.521 (2)° | Block, colourless |
V = 1250.2 (3) Å3 | 0.53 × 0.31 × 0.22 mm |
Z = 4 |
Bruker SMART APEXII DUO CCD area-detector diffractometer | 3629 independent reflections |
Radiation source: fine-focus sealed tube | 3201 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.031 |
ϕ and ω scans | θmax = 30.1°, θmin = 2.3° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −12→12 |
Tmin = 0.856, Tmax = 0.936 | k = −16→16 |
13594 measured reflections | l = −17→17 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.038 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.115 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | w = 1/[σ2(Fo2) + (0.070P)2 + 0.2814P] where P = (Fo2 + 2Fc2)/3 |
3629 reflections | (Δ/σ)max < 0.001 |
176 parameters | Δρmax = 0.48 e Å−3 |
0 restraints | Δρmin = −0.33 e Å−3 |
C6H9N2+·C7H4ClO2− | V = 1250.2 (3) Å3 |
Mr = 264.70 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.0318 (11) Å | µ = 0.30 mm−1 |
b = 11.6590 (14) Å | T = 100 K |
c = 12.1166 (15) Å | 0.53 × 0.31 × 0.22 mm |
β = 101.521 (2)° |
Bruker SMART APEXII DUO CCD area-detector diffractometer | 3629 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 3201 reflections with I > 2σ(I) |
Tmin = 0.856, Tmax = 0.936 | Rint = 0.031 |
13594 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 0 restraints |
wR(F2) = 0.115 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.48 e Å−3 |
3629 reflections | Δρmin = −0.33 e Å−3 |
176 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Cl1 | 1.05016 (3) | 0.25195 (2) | 0.66489 (3) | 0.02535 (11) | |
O1 | 0.60056 (10) | 0.65207 (8) | 0.46906 (7) | 0.02385 (19) | |
O2 | 0.72588 (10) | 0.62484 (8) | 0.64581 (7) | 0.02350 (19) | |
N1 | 0.45310 (10) | 0.81988 (8) | 0.55172 (8) | 0.01776 (19) | |
N2 | 0.55220 (12) | 0.77783 (10) | 0.73908 (9) | 0.0219 (2) | |
C1 | 0.46396 (12) | 0.84318 (9) | 0.66248 (10) | 0.0179 (2) | |
C2 | 0.37858 (13) | 0.93693 (10) | 0.69173 (10) | 0.0210 (2) | |
H2A | 0.3833 | 0.9561 | 0.7686 | 0.025* | |
C3 | 0.28968 (13) | 0.99913 (10) | 0.60827 (11) | 0.0218 (2) | |
H3A | 0.2327 | 1.0615 | 0.6283 | 0.026* | |
C4 | 0.27996 (12) | 0.97334 (10) | 0.49275 (10) | 0.0204 (2) | |
C5 | 0.36421 (12) | 0.88246 (10) | 0.46891 (10) | 0.0190 (2) | |
H5A | 0.3607 | 0.8624 | 0.3924 | 0.023* | |
C6 | 0.18156 (14) | 1.04262 (11) | 0.40224 (11) | 0.0262 (3) | |
H6A | 0.1968 | 1.0170 | 0.3283 | 0.039* | |
H6B | 0.2084 | 1.1239 | 0.4124 | 0.039* | |
H6C | 0.0754 | 1.0321 | 0.4070 | 0.039* | |
C7 | 0.69320 (12) | 0.59788 (9) | 0.54401 (9) | 0.0175 (2) | |
C8 | 0.76799 (11) | 0.49160 (9) | 0.50805 (9) | 0.0159 (2) | |
C9 | 0.86515 (12) | 0.42923 (9) | 0.59063 (9) | 0.0172 (2) | |
H9A | 0.8840 | 0.4537 | 0.6670 | 0.021* | |
C10 | 0.93380 (12) | 0.33117 (9) | 0.55982 (10) | 0.0180 (2) | |
C11 | 0.91118 (13) | 0.29472 (10) | 0.44867 (10) | 0.0212 (2) | |
H11A | 0.9603 | 0.2280 | 0.4288 | 0.025* | |
C12 | 0.81496 (13) | 0.35797 (10) | 0.36693 (10) | 0.0224 (2) | |
H12A | 0.7987 | 0.3345 | 0.2904 | 0.027* | |
C13 | 0.74215 (12) | 0.45553 (10) | 0.39638 (9) | 0.0198 (2) | |
H13A | 0.6750 | 0.4973 | 0.3402 | 0.024* | |
H1N1 | 0.511 (3) | 0.7554 (18) | 0.526 (2) | 0.055 (7)* | |
H1N2 | 0.617 (2) | 0.7251 (16) | 0.7129 (17) | 0.037 (5)* | |
H2N2 | 0.574 (2) | 0.8015 (16) | 0.8114 (16) | 0.035 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.02441 (17) | 0.02607 (17) | 0.02424 (17) | 0.00991 (9) | 0.00168 (12) | 0.00262 (10) |
O1 | 0.0302 (4) | 0.0259 (4) | 0.0161 (4) | 0.0125 (3) | 0.0061 (3) | 0.0030 (3) |
O2 | 0.0285 (4) | 0.0253 (4) | 0.0163 (4) | 0.0075 (3) | 0.0034 (3) | −0.0021 (3) |
N1 | 0.0183 (4) | 0.0195 (4) | 0.0156 (4) | 0.0034 (3) | 0.0037 (3) | −0.0019 (3) |
N2 | 0.0240 (5) | 0.0262 (5) | 0.0150 (5) | 0.0050 (4) | 0.0025 (4) | −0.0025 (4) |
C1 | 0.0168 (5) | 0.0201 (5) | 0.0173 (5) | −0.0003 (4) | 0.0047 (4) | −0.0028 (4) |
C2 | 0.0206 (5) | 0.0231 (5) | 0.0203 (5) | 0.0005 (4) | 0.0066 (4) | −0.0061 (4) |
C3 | 0.0193 (5) | 0.0207 (5) | 0.0263 (6) | 0.0030 (4) | 0.0064 (4) | −0.0047 (4) |
C4 | 0.0183 (5) | 0.0202 (5) | 0.0230 (5) | 0.0024 (4) | 0.0045 (4) | 0.0000 (4) |
C5 | 0.0189 (5) | 0.0215 (5) | 0.0166 (5) | 0.0021 (4) | 0.0038 (4) | −0.0006 (4) |
C6 | 0.0253 (6) | 0.0258 (6) | 0.0269 (6) | 0.0084 (4) | 0.0038 (5) | 0.0024 (5) |
C7 | 0.0195 (5) | 0.0181 (5) | 0.0163 (5) | 0.0023 (4) | 0.0069 (4) | 0.0013 (4) |
C8 | 0.0156 (4) | 0.0169 (4) | 0.0159 (5) | 0.0012 (3) | 0.0049 (4) | 0.0000 (4) |
C9 | 0.0166 (4) | 0.0187 (5) | 0.0164 (5) | 0.0011 (4) | 0.0037 (4) | 0.0000 (4) |
C10 | 0.0146 (4) | 0.0188 (5) | 0.0205 (5) | 0.0019 (3) | 0.0030 (4) | 0.0016 (4) |
C11 | 0.0197 (5) | 0.0203 (5) | 0.0238 (6) | 0.0029 (4) | 0.0046 (4) | −0.0039 (4) |
C12 | 0.0242 (5) | 0.0246 (5) | 0.0182 (5) | 0.0032 (4) | 0.0036 (4) | −0.0047 (4) |
C13 | 0.0208 (5) | 0.0223 (5) | 0.0160 (5) | 0.0033 (4) | 0.0029 (4) | −0.0003 (4) |
Cl1—C10 | 1.7447 (11) | C5—H5A | 0.9500 |
O1—C7 | 1.2729 (13) | C6—H6A | 0.9800 |
O2—C7 | 1.2498 (14) | C6—H6B | 0.9800 |
N1—C1 | 1.3535 (14) | C6—H6C | 0.9800 |
N1—C5 | 1.3645 (14) | C7—C8 | 1.5163 (15) |
N1—H1N1 | 1.00 (2) | C8—C13 | 1.3914 (15) |
N2—C1 | 1.3348 (15) | C8—C9 | 1.3961 (15) |
N2—H1N2 | 0.949 (19) | C9—C10 | 1.3870 (15) |
N2—H2N2 | 0.90 (2) | C9—H9A | 0.9500 |
C1—C2 | 1.4227 (15) | C10—C11 | 1.3878 (16) |
C2—C3 | 1.3671 (17) | C11—C12 | 1.3914 (16) |
C2—H2A | 0.9500 | C11—H11A | 0.9500 |
C3—C4 | 1.4171 (17) | C12—C13 | 1.3955 (16) |
C3—H3A | 0.9500 | C12—H12A | 0.9500 |
C4—C5 | 1.3686 (15) | C13—H13A | 0.9500 |
C4—C6 | 1.5019 (16) | ||
C1—N1—C5 | 122.50 (10) | C4—C6—H6C | 109.5 |
C1—N1—H1N1 | 121.5 (14) | H6A—C6—H6C | 109.5 |
C5—N1—H1N1 | 116.0 (14) | H6B—C6—H6C | 109.5 |
C1—N2—H1N2 | 117.5 (12) | O2—C7—O1 | 124.84 (10) |
C1—N2—H2N2 | 119.1 (12) | O2—C7—C8 | 117.27 (9) |
H1N2—N2—H2N2 | 119.4 (17) | O1—C7—C8 | 117.88 (10) |
N2—C1—N1 | 119.33 (10) | C13—C8—C9 | 119.93 (10) |
N2—C1—C2 | 122.91 (11) | C13—C8—C7 | 121.91 (9) |
N1—C1—C2 | 117.75 (10) | C9—C8—C7 | 118.16 (9) |
C3—C2—C1 | 119.39 (11) | C10—C9—C8 | 119.15 (10) |
C3—C2—H2A | 120.3 | C10—C9—H9A | 120.4 |
C1—C2—H2A | 120.3 | C8—C9—H9A | 120.4 |
C2—C3—C4 | 121.97 (10) | C9—C10—C11 | 121.77 (10) |
C2—C3—H3A | 119.0 | C9—C10—Cl1 | 118.45 (9) |
C4—C3—H3A | 119.0 | C11—C10—Cl1 | 119.77 (8) |
C5—C4—C3 | 116.45 (10) | C10—C11—C12 | 118.59 (10) |
C5—C4—C6 | 122.35 (11) | C10—C11—H11A | 120.7 |
C3—C4—C6 | 121.20 (10) | C12—C11—H11A | 120.7 |
N1—C5—C4 | 121.94 (10) | C11—C12—C13 | 120.61 (11) |
N1—C5—H5A | 119.0 | C11—C12—H12A | 119.7 |
C4—C5—H5A | 119.0 | C13—C12—H12A | 119.7 |
C4—C6—H6A | 109.5 | C8—C13—C12 | 119.93 (10) |
C4—C6—H6B | 109.5 | C8—C13—H13A | 120.0 |
H6A—C6—H6B | 109.5 | C12—C13—H13A | 120.0 |
C5—N1—C1—N2 | 179.47 (10) | O2—C7—C8—C9 | 1.54 (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—C3 | 0.12 (16) | C7—C8—C9—C10 | 179.45 (9) |
C1—C2—C3—C4 | −0.16 (18) | C8—C9—C10—C11 | 1.46 (16) |
C2—C3—C4—C5 | 0.13 (17) | C8—C9—C10—Cl1 | −178.02 (8) |
C2—C3—C4—C6 | 179.96 (11) | C9—C10—C11—C12 | −1.01 (17) |
C1—N1—C5—C4 | 0.03 (17) | Cl1—C10—C11—C12 | 178.47 (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—C12 | 179.19 (10) |
O1—C7—C8—C13 | 2.43 (16) | C11—C12—C13—C8 | 1.32 (18) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O1 | 1.00 (2) | 1.68 (2) | 2.6716 (13) | 174 (2) |
N2—H1N2···O2 | 0.946 (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 | 0.95 | 2.52 | 3.2104 (15) | 130 |
Symmetry codes: (i) x, −y+3/2, z+1/2; (ii) −x+1, y+1/2, −z+3/2. |
Experimental details
Crystal data | |
Chemical formula | C6H9N2+·C7H4ClO2− |
Mr | 264.70 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 9.0318 (11), 11.6590 (14), 12.1166 (15) |
β (°) | 101.521 (2) |
V (Å3) | 1250.2 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.30 |
Crystal size (mm) | 0.53 × 0.31 × 0.22 |
Data collection | |
Diffractometer | Bruker SMART APEXII DUO CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.856, 0.936 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 13594, 3629, 3201 |
Rint | 0.031 |
(sin θ/λ)max (Å−1) | 0.705 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.115, 1.06 |
No. of reflections | 3629 |
No. of parameters | 176 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.48, −0.33 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O1 | 1.00 (2) | 1.68 (2) | 2.6716 (13) | 174 (2) |
N2—H1N2···O2 | 0.946 (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 | 0.95 | 2.52 | 3.2104 (15) | 130 |
Symmetry codes: (i) x, −y+3/2, z+1/2; (ii) −x+1, y+1/2, −z+3/2. |
Footnotes
‡Thomson Reuters ResearcherID: A-5599-2009.
Acknowledgements
The authors thank the Malaysian Government and Universiti Sains Malaysia (USM) for the research facilities and Fundamental Research Grant Scheme (FRGS) No. 203/PFIZIK/6711171 to conduct this work. KT thanks The Academy of Sciences for the Developing World and USM for a TWAS–USM fellowship.
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Pyridine and its derivatives play an important role in heterocyclic chemistry (Pozharski et al., 1997; Katritzky et al., 1996). They are often involved in hydrogen-bond interactions (Jeffrey, 1997; Scheiner, 1997). In order to study some interesting hydrogen bonding interactions, the synthesis and structure of the title compound, (I), is presented here.
The asymmetric unit of the title compound contains a protonated 2-amino-5-methylpyridinium cation and a 3-chlorobenzoate anion (Fig. 1). In the 2-amino-5-methylpyridinium cation, a wider than normal angle [C1—N1—C5 = 122.50 (10)°] is subtended at the protonated N1 atom. The 2-amino-5-methylpyridinium cation is planar with a maximum deviation of 0.001 (1) Å for atom C2. The dihedral angle between the pyridine (N1/C1–C5) and benzene (C8–C13) rings is 7.92 (5)°. The bond lengths (Allen et al., 1987) and angles are normal. In the crystal packing (Fig. 2), the protonated N1 atom and a nitrogen atom of the 2-amino group (N2) are hydrogen-bonded to the carboxylate oxygen atoms (O1 and O2) via a pair of N—H···O hydrogen bonds (Table 1), forming a ring motif R22(8) (Bernstein et al., 1995). Furthermore, these motifs are connected via N2—H2N2···O1i and C2—H2A···O2ii hydrogen bonds to form a two-dimensional network parallel to the bc plane.