organic compounds
2-Amino-5-methylpyridinium 4-carboxybutanoate
aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my
In the title salt, C6H9N2+·C5H7O4−, the 2-amino-5-methylpyridinium cation is essentially planar, with a maximum deviation of 0.008 (1) Å. In the crystal, the protonated N atom and the 2-amino group are hydrogen bonded to the carboxylate O atoms via a pair of N—H⋯O hydrogen bonds, forming an R22(8) ring motif. The 4-carboxybutanoate anions are linked via O—H⋯O hydrogen bonds. The is further stabilized by weak C—H⋯O interactions.
Related literature
For background to the chemistry of substituted pyridines, see: Pozharski et al. (1997); Katritzky et al. (1996). For applications of glutaric acid, see: Windholz (1976); Saraswathi et al. (2001). For details of hydrogen bonding, see: Jeffrey & Saenger (1991); Jeffrey (1997); Scheiner (1997). For related structures, see: Hemamalini & Fun (2010a,b); Fun et al. (2010). 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 in 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/S1600536810024451/bv2141sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536810024451/bv2141Isup2.hkl
A hot methanol solution (20 ml) of 2-amino-5-methylpyridine (27 mg, Aldrich) and glutaric acid (33 mg, Merck) were mixed and warmed over a heating magnetic stirrer for a few minutes. The resulting solution was allowed to cool slowly at room temperature and crystals of the title compound appeared after a few days.
All hydrogen atoms were positioned geometrically [C–H = 0.93–0.97 Å, N–H = 0.86 Å and O–H = 0.82 Å] and were refined using a riding model, with Uiso(H) = 1.2 Ueq(C, N) or 1.5 Ueq(O). The methyl H atoms were positioned geometrically and were refined using a riding model, with Uiso(H) = 1.5Ueq(C). A rotating group model was used for the methyl group. In the absence of significant
effects, 1457 Friedel pairs were merged.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+·C5H7O4− | F(000) = 512 |
Mr = 240.26 | Dx = 1.336 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 2351 reflections |
a = 5.3159 (10) Å | θ = 3.1–29.9° |
b = 14.383 (3) Å | µ = 0.10 mm−1 |
c = 15.625 (3) Å | T = 100 K |
V = 1194.7 (4) Å3 | Block, colourless |
Z = 4 | 0.29 × 0.17 × 0.10 mm |
Bruker APEXII DUO CCD area-detector diffractometer | 2028 independent reflections |
Radiation source: fine-focus sealed tube | 1752 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.037 |
ϕ and ω scans | θmax = 30.1°, θmin = 2.8° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −7→7 |
Tmin = 0.971, Tmax = 0.990 | k = −13→20 |
7996 measured reflections | l = −21→21 |
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)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.109 | H-atom parameters constrained |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0703P)2 + 0.0024P] where P = (Fo2 + 2Fc2)/3 |
2028 reflections | (Δ/σ)max = 0.001 |
156 parameters | Δρmax = 0.23 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
C6H9N2+·C5H7O4− | V = 1194.7 (4) Å3 |
Mr = 240.26 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 5.3159 (10) Å | µ = 0.10 mm−1 |
b = 14.383 (3) Å | T = 100 K |
c = 15.625 (3) Å | 0.29 × 0.17 × 0.10 mm |
Bruker APEXII DUO CCD area-detector diffractometer | 2028 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 1752 reflections with I > 2σ(I) |
Tmin = 0.971, Tmax = 0.990 | Rint = 0.037 |
7996 measured reflections |
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.109 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.23 e Å−3 |
2028 reflections | Δρmin = −0.20 e Å−3 |
156 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 s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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 | ||
N1 | 0.1366 (3) | 0.23633 (10) | 0.72155 (9) | 0.0178 (3) | |
H1 | 0.2568 | 0.1970 | 0.7149 | 0.021* | |
N2 | 0.2291 (4) | 0.29299 (12) | 0.58707 (9) | 0.0238 (4) | |
H2A | 0.3451 | 0.2516 | 0.5828 | 0.029* | |
H2B | 0.2030 | 0.3313 | 0.5457 | 0.029* | |
C1 | 0.0899 (4) | 0.29783 (12) | 0.65773 (10) | 0.0187 (4) | |
C2 | −0.1037 (4) | 0.36383 (13) | 0.67157 (11) | 0.0232 (4) | |
H2 | −0.1392 | 0.4084 | 0.6301 | 0.028* | |
C3 | −0.2378 (4) | 0.36172 (14) | 0.74603 (12) | 0.0237 (4) | |
H3 | −0.3653 | 0.4051 | 0.7543 | 0.028* | |
C4 | −0.1888 (4) | 0.29528 (12) | 0.81139 (11) | 0.0198 (4) | |
C5 | 0.0019 (4) | 0.23393 (12) | 0.79573 (10) | 0.0184 (3) | |
H5 | 0.0408 | 0.1894 | 0.8368 | 0.022* | |
C6 | −0.3412 (4) | 0.29045 (14) | 0.89247 (13) | 0.0266 (4) | |
H6A | −0.5064 | 0.2673 | 0.8797 | 0.040* | |
H6B | −0.3544 | 0.3514 | 0.9170 | 0.040* | |
H6C | −0.2601 | 0.2495 | 0.9324 | 0.040* | |
O1 | −0.0252 (3) | 0.40052 (9) | 0.28998 (7) | 0.0196 (3) | |
O2 | 0.0882 (3) | 0.35424 (10) | 0.42007 (7) | 0.0238 (3) | |
O3 | 0.7031 (3) | 0.57159 (10) | 0.58440 (8) | 0.0245 (3) | |
O4 | 0.3325 (3) | 0.54500 (10) | 0.64750 (8) | 0.0240 (3) | |
H4 | 0.4108 | 0.5588 | 0.6909 | 0.036* | |
C7 | 0.1204 (4) | 0.40279 (12) | 0.35520 (10) | 0.0160 (3) | |
C8 | 0.3451 (4) | 0.46878 (12) | 0.34924 (10) | 0.0172 (3) | |
H8A | 0.4587 | 0.4460 | 0.3054 | 0.021* | |
H8B | 0.2852 | 0.5294 | 0.3311 | 0.021* | |
C9 | 0.4914 (4) | 0.48016 (12) | 0.43228 (10) | 0.0177 (3) | |
H9A | 0.6509 | 0.5102 | 0.4205 | 0.021* | |
H9B | 0.5261 | 0.4194 | 0.4565 | 0.021* | |
C10 | 0.3435 (4) | 0.53813 (13) | 0.49684 (10) | 0.0191 (4) | |
H10A | 0.3062 | 0.5982 | 0.4717 | 0.023* | |
H10B | 0.1847 | 0.5074 | 0.5086 | 0.023* | |
C11 | 0.4815 (4) | 0.55288 (11) | 0.58018 (10) | 0.0167 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0184 (8) | 0.0183 (7) | 0.0169 (6) | 0.0033 (6) | −0.0006 (6) | 0.0006 (5) |
N2 | 0.0275 (9) | 0.0264 (8) | 0.0176 (6) | 0.0062 (7) | −0.0001 (7) | 0.0053 (5) |
C1 | 0.0203 (9) | 0.0176 (7) | 0.0181 (7) | −0.0002 (7) | −0.0050 (7) | 0.0006 (6) |
C2 | 0.0236 (9) | 0.0193 (8) | 0.0268 (8) | 0.0038 (8) | −0.0040 (8) | 0.0049 (7) |
C3 | 0.0194 (9) | 0.0179 (8) | 0.0339 (9) | 0.0052 (8) | −0.0008 (9) | −0.0002 (7) |
C4 | 0.0185 (9) | 0.0177 (7) | 0.0233 (8) | −0.0028 (7) | 0.0012 (8) | −0.0017 (6) |
C5 | 0.0206 (9) | 0.0175 (7) | 0.0170 (7) | −0.0001 (7) | −0.0010 (7) | −0.0002 (5) |
C6 | 0.0259 (10) | 0.0230 (9) | 0.0308 (9) | −0.0021 (9) | 0.0070 (9) | −0.0045 (7) |
O1 | 0.0215 (7) | 0.0246 (6) | 0.0126 (5) | −0.0056 (6) | −0.0017 (5) | 0.0022 (4) |
O2 | 0.0298 (8) | 0.0269 (6) | 0.0146 (5) | −0.0080 (6) | −0.0044 (6) | 0.0058 (5) |
O3 | 0.0200 (7) | 0.0339 (7) | 0.0195 (6) | −0.0022 (6) | −0.0026 (6) | −0.0033 (5) |
O4 | 0.0230 (7) | 0.0354 (7) | 0.0136 (5) | −0.0054 (6) | −0.0003 (6) | −0.0058 (5) |
C7 | 0.0175 (8) | 0.0166 (7) | 0.0138 (6) | −0.0002 (7) | 0.0006 (7) | −0.0015 (5) |
C8 | 0.0176 (8) | 0.0204 (8) | 0.0136 (6) | −0.0029 (7) | 0.0003 (7) | −0.0017 (6) |
C9 | 0.0172 (8) | 0.0196 (7) | 0.0163 (7) | 0.0013 (7) | −0.0008 (7) | −0.0027 (6) |
C10 | 0.0182 (9) | 0.0236 (8) | 0.0155 (7) | 0.0037 (7) | −0.0045 (7) | −0.0054 (6) |
C11 | 0.0198 (8) | 0.0154 (7) | 0.0150 (6) | 0.0028 (7) | −0.0022 (7) | −0.0012 (5) |
N1—C1 | 1.356 (2) | C6—H6C | 0.9600 |
N1—C5 | 1.363 (2) | O1—C7 | 1.280 (2) |
N1—H1 | 0.8600 | O2—C7 | 1.243 (2) |
N2—C1 | 1.331 (2) | O3—C11 | 1.210 (2) |
N2—H2A | 0.8600 | O4—C11 | 1.321 (2) |
N2—H2B | 0.8600 | O4—H4 | 0.8200 |
C1—C2 | 1.417 (3) | C7—C8 | 1.528 (3) |
C2—C3 | 1.365 (3) | C8—C9 | 1.522 (2) |
C2—H2 | 0.9300 | C8—H8A | 0.9700 |
C3—C4 | 1.423 (3) | C8—H8B | 0.9700 |
C3—H3 | 0.9300 | C9—C10 | 1.527 (2) |
C4—C5 | 1.366 (3) | C9—H9A | 0.9700 |
C4—C6 | 1.505 (3) | C9—H9B | 0.9700 |
C5—H5 | 0.9300 | C10—C11 | 1.509 (2) |
C6—H6A | 0.9600 | C10—H10A | 0.9700 |
C6—H6B | 0.9600 | C10—H10B | 0.9700 |
C1—N1—C5 | 123.09 (16) | H6B—C6—H6C | 109.5 |
C1—N1—H1 | 118.5 | C11—O4—H4 | 109.5 |
C5—N1—H1 | 118.5 | O2—C7—O1 | 123.48 (17) |
C1—N2—H2A | 120.0 | O2—C7—C8 | 120.42 (15) |
C1—N2—H2B | 120.0 | O1—C7—C8 | 116.09 (14) |
H2A—N2—H2B | 120.0 | C9—C8—C7 | 114.48 (13) |
N2—C1—N1 | 118.31 (16) | C9—C8—H8A | 108.6 |
N2—C1—C2 | 124.45 (16) | C7—C8—H8A | 108.6 |
N1—C1—C2 | 117.24 (16) | C9—C8—H8B | 108.6 |
C3—C2—C1 | 119.66 (16) | C7—C8—H8B | 108.6 |
C3—C2—H2 | 120.2 | H8A—C8—H8B | 107.6 |
C1—C2—H2 | 120.2 | C8—C9—C10 | 111.04 (15) |
C2—C3—C4 | 122.08 (18) | C8—C9—H9A | 109.4 |
C2—C3—H3 | 119.0 | C10—C9—H9A | 109.4 |
C4—C3—H3 | 119.0 | C8—C9—H9B | 109.4 |
C5—C4—C3 | 116.18 (16) | C10—C9—H9B | 109.4 |
C5—C4—C6 | 121.36 (16) | H9A—C9—H9B | 108.0 |
C3—C4—C6 | 122.44 (17) | C11—C10—C9 | 113.37 (15) |
N1—C5—C4 | 121.73 (16) | C11—C10—H10A | 108.9 |
N1—C5—H5 | 119.1 | C9—C10—H10A | 108.9 |
C4—C5—H5 | 119.1 | C11—C10—H10B | 108.9 |
C4—C6—H6A | 109.5 | C9—C10—H10B | 108.9 |
C4—C6—H6B | 109.5 | H10A—C10—H10B | 107.7 |
H6A—C6—H6B | 109.5 | O3—C11—O4 | 123.98 (16) |
C4—C6—H6C | 109.5 | O3—C11—C10 | 123.45 (17) |
H6A—C6—H6C | 109.5 | O4—C11—C10 | 112.56 (15) |
C5—N1—C1—N2 | −178.57 (16) | C3—C4—C5—N1 | −0.2 (3) |
C5—N1—C1—C2 | 2.0 (3) | C6—C4—C5—N1 | 178.30 (16) |
N2—C1—C2—C3 | 178.99 (19) | O2—C7—C8—C9 | −9.4 (2) |
N1—C1—C2—C3 | −1.7 (3) | O1—C7—C8—C9 | 171.50 (15) |
C1—C2—C3—C4 | 0.4 (3) | C7—C8—C9—C10 | −72.74 (19) |
C2—C3—C4—C5 | 0.5 (3) | C8—C9—C10—C11 | −179.18 (14) |
C2—C3—C4—C6 | −177.97 (18) | C9—C10—C11—O3 | 42.8 (2) |
C1—N1—C5—C4 | −1.1 (3) | C9—C10—C11—O4 | −138.56 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.86 | 1.82 | 2.672 (2) | 170 |
N2—H2A···O2i | 0.86 | 2.00 | 2.853 (3) | 174 |
N2—H2B···O2 | 0.86 | 2.08 | 2.854 (2) | 149 |
O4—H4···O1ii | 0.82 | 1.76 | 2.5729 (19) | 169 |
C2—H2···O3iii | 0.93 | 2.59 | 3.441 (2) | 152 |
C5—H5···O3iv | 0.93 | 2.50 | 3.379 (2) | 158 |
Symmetry codes: (i) x+1/2, −y+1/2, −z+1; (ii) −x+1/2, −y+1, z+1/2; (iii) x−1, y, z; (iv) −x+1, y−1/2, −z+3/2. |
Experimental details
Crystal data | |
Chemical formula | C6H9N2+·C5H7O4− |
Mr | 240.26 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 5.3159 (10), 14.383 (3), 15.625 (3) |
V (Å3) | 1194.7 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.29 × 0.17 × 0.10 |
Data collection | |
Diffractometer | Bruker APEXII DUO CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.971, 0.990 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7996, 2028, 1752 |
Rint | 0.037 |
(sin θ/λ)max (Å−1) | 0.705 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.109, 1.05 |
No. of reflections | 2028 |
No. of parameters | 156 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.23, −0.20 |
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—H1···O1i | 0.8600 | 1.8200 | 2.672 (2) | 170.00 |
N2—H2A···O2i | 0.8600 | 2.0000 | 2.853 (3) | 174.00 |
N2—H2B···O2 | 0.8600 | 2.0800 | 2.854 (2) | 149.00 |
O4—H4···O1ii | 0.8200 | 1.7600 | 2.5729 (19) | 169.00 |
C2—H2···O3iii | 0.9300 | 2.5900 | 3.441 (2) | 152.00 |
C5—H5···O3iv | 0.9300 | 2.5000 | 3.379 (2) | 158.00 |
Symmetry codes: (i) x+1/2, −y+1/2, −z+1; (ii) −x+1/2, −y+1, z+1/2; (iii) x−1, y, z; (iv) −x+1, y−1/2, −z+3/2. |
Footnotes
‡Thomson Reuters ResearcherID: A-3561-2009.
Acknowledgements
MH and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012. MH also thanks Universiti Sains Malaysia for a post-doctoral research fellowship.
References
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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 & Saenger, 1991; Jeffrey, 1997; Scheiner, 1997). Glutaric acid (pentanedioic acid) is a dicarboxylic acid with five carbon atoms, occurring in plant and animal tissues. Glutaric acid is found in the blood and urine. It is used in the synthesis of pharmaceuticals, surfactants and metal finishing compounds. Alpha-ketoglutaric acid is used in dietary supplements to improve protein synthesis (Windholz, 1976). We have recently reported the crystal structures of 2-amino-5-methylpyridinium 4-nitrobenzoate (Hemamalini & Fun, 2010a), 2-amino-5-methylpyridinium nicotinate (Fun et al., 2010) and 2-amino-5-methylpyridinium 3-aminobenzoate (Hemamalini & Fun, 2010b). In continuation of our studies of pyridinium derivatives, the crystal structure determination of the title compound has been undertaken.
The asymmetric unit (Fig. 1) contains a 2-amino-5-methylpyridinium cation and a 4-carboxybutanoate anion. The 2-amino-5-methylpyridinium cation is essentially planar, with a maximum deviation of 0.008 (1) Å for atom N1. In the 2-amino-5-methylpyridinium cation, a wide angle (123.09 (16)°) is subtended at the protonated N1 atom. The backbone conformation of the 4-carboxybutanoate anion can be described by the two torsion angles C11-C10-C9-C8 of -179.18 (14)° and C10-C9-C8-C7 of -72.74 (19)°. As evident from the torsion angles, the backbone is in a fully extended conformation (Saraswathi et al., 2001) of the two carboxyl groups, one is deprotonated while the other is not. The bond lengths (Allen et al., 1987) and angles are within normal ranges.
In the crystal packing (Fig. 2), the protonated N1 atom and the 2-amino group (N2) is hydrogen-bonded to the carboxylate oxygen atoms (O1 and O2) via a pair of intermolecular N1—H1···O1 and N2—H2A···O2 hydrogen bonds forming a ring motif R22(8) (Bernstein et al., 1995). The 4-carboxybutanoate anions self-assemble via O4—H4···O1 hydrogen bonds. The crystal structure is further stabilized by weak C2—H2···O3 and C5—H5···O3 (Table 1) hydrogen bonds.