organic compounds
2-(3-Aminopyridinium-1-yl)-3-carboxypropanoate monohydrate
aFacultad de Ingeniería Mochis, Universidad Autónoma de Sinaloa, Fuente de Poseidón y Prol. Angel Flores, CP 81223, Los Mochis, Sinaloa, Mexico, and bInstituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacan, CP 04510, México, DF, Mexico
*Correspondence e-mail: cenriqueza@yahoo.com.mx
The title compound, C9H10N2O4·H2O, was obtained as a zwitterion derived from the nucleophilic attack of 3-aminopyridine on the fumaric α,β-system. Within the molecule, the aminopyridine moiety and the carboxylate and carboxylic acid fragments form dihedral angles of 68.6 (2) and 62.8 (2)°, respectively. The geometry adopted by the molecule does not allow the formation of centrosymmetric dimeric hydrogen-bonded units; instead chains along the a axis are linked by COO—H⋯OOC motifs. These chains are interconnected by N—H⋯O and O—H⋯O hydrogen bonds involving the carboxylic acid and carboxylate units and the solvent water molecules.
Related literature
For background to the synthesis, see: Kavuru et al. (2010). For structures and applications of zwitterion derivatives, see: Bis & Zaworotko (2005); Hill et al. (2001); Sarma et al. (2009). For fundamental hydrogen-bond interactions, see: Desiraju (1995); Etter (1990, 1991).
Experimental
Crystal data
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Data collection
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Refinement
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Data collection: SMART (Bruker, 2007); cell SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and SHELXL97 (Sheldrick, 2008); software used to prepare material for publication: SHELXL97.
Supporting information
10.1107/S1600536812006897/fj2513sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812006897/fj2513Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812006897/fj2513Isup3.cml
A solution of fumaric acid (0.05 g, 430 mmol) in MeOH (5 ml) was mixed at room temperature for 10 min. After this time 3-aminopyridine (0.04 g, 430 mmol) was added and mixed for further 30 minutes. Crystals suitable for single-crystal X ray diffraction studies were grown by slow evaporation at room temperature from a
of compound (I) in methanol (yield: 60%) m.p. 417 K. IR (KBr): 3414, 3347, 3235, 2581, 2147, 1722, 1652, 1173 y 1090 cm-1.H atoms on O and N atoms,were located in the Fourier map and refined isotropically (O—H 0.85 Å, N—H, 0.90 Å). All H atoms were included in calculated positions (C—H = 0.93Å for arom, 0.98Å for methine, 0.97Å for methylene), and refined using a riding model,with Uiso(H) = 1.2Ueq of the
The was not determined by difraction experiment and the refined was fixed arbitrary. 852 Friedel pairs were merged.Data collection: SMART (Bruker, 2007); cell
SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and SHELXL97 (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).Fig. 1. The molecular structure of the title compound (I), with atom labels and displacement ellipsoids drawn at the 40% probability level. | |
Fig. 2. Crystal packing of the title compound (I). Only H atoms involved in interactions were drawn. |
C9H10N2O4·H2O | F(000) = 480 |
Mr = 228.21 | Dx = 1.481 Mg m−3 |
Orthorhombic, Pna21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2c -2n | Cell parameters from 5172 reflections |
a = 7.4939 (8) Å | θ = 2.9–25.3° |
b = 19.446 (2) Å | µ = 0.12 mm−1 |
c = 7.0227 (7) Å | T = 298 K |
V = 1023.39 (19) Å3 | Prism, orange |
Z = 4 | 0.30 × 0.12 × 0.10 mm |
Bruker SMART APEX CCD area-detector diffractometer | 1642 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.037 |
Graphite monochromator | θmax = 25.3°, θmin = 2.1° |
Detector resolution: 0.83 pixels mm-1 | h = −9→9 |
ω scans | k = −23→23 |
10663 measured reflections | l = −8→8 |
1868 independent reflections |
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)] = 0.028 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.058 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.96 | w = 1/[σ2(Fo2) + (0.028P)2] where P = (Fo2 + 2Fc2)/3 |
1868 reflections | (Δ/σ)max < 0.001 |
160 parameters | Δρmax = 0.11 e Å−3 |
6 restraints | Δρmin = −0.12 e Å−3 |
C9H10N2O4·H2O | V = 1023.39 (19) Å3 |
Mr = 228.21 | Z = 4 |
Orthorhombic, Pna21 | Mo Kα radiation |
a = 7.4939 (8) Å | µ = 0.12 mm−1 |
b = 19.446 (2) Å | T = 298 K |
c = 7.0227 (7) Å | 0.30 × 0.12 × 0.10 mm |
Bruker SMART APEX CCD area-detector diffractometer | 1642 reflections with I > 2σ(I) |
10663 measured reflections | Rint = 0.037 |
1868 independent reflections |
R[F2 > 2σ(F2)] = 0.028 | 6 restraints |
wR(F2) = 0.058 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.96 | Δρmax = 0.11 e Å−3 |
1868 reflections | Δρmin = −0.12 e Å−3 |
160 parameters |
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 | ||
O1 | 1.04824 (15) | 0.51597 (6) | 0.4732 (2) | 0.0417 (3) | |
O2 | 1.13193 (13) | 0.41287 (5) | 0.36700 (19) | 0.0395 (3) | |
O3 | 0.44407 (15) | 0.45071 (7) | 0.4070 (2) | 0.0565 (4) | |
H3 | 0.3347 (15) | 0.4376 (9) | 0.389 (3) | 0.068* | |
O4 | 0.45279 (16) | 0.39455 (7) | 0.67937 (19) | 0.0528 (4) | |
O5 | 0.59669 (18) | 0.13525 (7) | 0.8132 (2) | 0.0557 (4) | |
H5A | 0.6976 (17) | 0.1248 (11) | 0.767 (3) | 0.067* | |
H5B | 0.559 (3) | 0.0989 (7) | 0.870 (3) | 0.067* | |
N1 | 0.79643 (15) | 0.36728 (7) | 0.3184 (2) | 0.0291 (3) | |
N2 | 0.6301 (2) | 0.28176 (8) | −0.1026 (2) | 0.0554 (4) | |
H2A | 0.605 (2) | 0.2377 (6) | −0.137 (3) | 0.066* | |
H2B | 0.581 (2) | 0.3184 (8) | −0.163 (3) | 0.066* | |
C1 | 1.0183 (2) | 0.45789 (8) | 0.4126 (2) | 0.0307 (4) | |
C2 | 0.81973 (19) | 0.43883 (7) | 0.3871 (2) | 0.0299 (4) | |
H2 | 0.7699 | 0.4696 | 0.2902 | 0.036* | |
C3 | 0.7156 (2) | 0.45043 (9) | 0.5703 (3) | 0.0363 (4) | |
H3A | 0.7718 | 0.4246 | 0.6721 | 0.044* | |
H3B | 0.7217 | 0.4988 | 0.6036 | 0.044* | |
C4 | 0.5235 (2) | 0.42955 (8) | 0.5568 (3) | 0.0341 (4) | |
C5 | 0.7281 (2) | 0.35719 (8) | 0.1437 (2) | 0.0325 (4) | |
H5 | 0.6999 | 0.3950 | 0.0682 | 0.039* | |
C6 | 0.6988 (2) | 0.29126 (9) | 0.0739 (3) | 0.0359 (4) | |
C7 | 0.7427 (2) | 0.23635 (9) | 0.1932 (3) | 0.0411 (5) | |
H7 | 0.7242 | 0.1914 | 0.1522 | 0.049* | |
C8 | 0.8125 (2) | 0.24828 (8) | 0.3696 (3) | 0.0412 (4) | |
H8 | 0.8415 | 0.2114 | 0.4481 | 0.049* | |
C9 | 0.8403 (2) | 0.31445 (8) | 0.4320 (3) | 0.0376 (4) | |
H9 | 0.8891 | 0.3225 | 0.5517 | 0.045* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0332 (7) | 0.0403 (7) | 0.0515 (8) | −0.0082 (5) | −0.0007 (6) | −0.0106 (6) |
O2 | 0.0239 (6) | 0.0369 (6) | 0.0577 (8) | 0.0034 (5) | 0.0002 (6) | −0.0013 (6) |
O3 | 0.0244 (7) | 0.0849 (10) | 0.0600 (9) | −0.0104 (6) | −0.0076 (8) | 0.0293 (8) |
O4 | 0.0381 (8) | 0.0673 (9) | 0.0530 (9) | −0.0094 (6) | −0.0001 (7) | 0.0195 (8) |
O5 | 0.0528 (8) | 0.0420 (7) | 0.0724 (11) | 0.0014 (7) | 0.0116 (8) | −0.0036 (8) |
N1 | 0.0218 (6) | 0.0325 (7) | 0.0330 (8) | −0.0018 (6) | 0.0001 (6) | −0.0012 (6) |
N2 | 0.0796 (12) | 0.0400 (9) | 0.0466 (11) | −0.0056 (9) | −0.0157 (10) | −0.0030 (9) |
C1 | 0.0278 (9) | 0.0351 (9) | 0.0293 (9) | −0.0034 (7) | −0.0018 (8) | 0.0034 (8) |
C2 | 0.0243 (8) | 0.0306 (8) | 0.0349 (10) | −0.0011 (6) | −0.0011 (8) | −0.0015 (8) |
C3 | 0.0266 (9) | 0.0443 (10) | 0.0380 (10) | −0.0004 (8) | −0.0001 (8) | −0.0074 (8) |
C4 | 0.0261 (9) | 0.0367 (9) | 0.0394 (11) | 0.0021 (8) | 0.0020 (9) | −0.0027 (9) |
C5 | 0.0304 (9) | 0.0339 (9) | 0.0330 (11) | −0.0031 (7) | 0.0021 (8) | 0.0031 (8) |
C6 | 0.0346 (9) | 0.0382 (10) | 0.0351 (11) | −0.0071 (8) | −0.0010 (9) | −0.0009 (9) |
C7 | 0.0414 (11) | 0.0306 (9) | 0.0512 (13) | −0.0046 (8) | 0.0031 (10) | −0.0005 (9) |
C8 | 0.0428 (10) | 0.0336 (9) | 0.0472 (12) | −0.0006 (8) | −0.0036 (10) | 0.0065 (9) |
C9 | 0.0327 (9) | 0.0421 (10) | 0.0380 (11) | −0.0026 (8) | −0.0042 (9) | 0.0030 (8) |
O1—C1 | 1.2276 (18) | C2—C3 | 1.522 (2) |
O2—C1 | 1.2623 (19) | C2—H2 | 0.9800 |
O3—C4 | 1.277 (2) | C3—C4 | 1.499 (2) |
O3—H3 | 0.868 (9) | C3—H3A | 0.9700 |
O4—C4 | 1.2183 (19) | C3—H3B | 0.9700 |
O5—H5A | 0.848 (9) | C5—C6 | 1.390 (2) |
O5—H5B | 0.861 (9) | C5—H5 | 0.9300 |
N1—C9 | 1.341 (2) | C6—C7 | 1.396 (2) |
N1—C5 | 1.344 (2) | C7—C8 | 1.365 (3) |
N1—C2 | 1.4830 (18) | C7—H7 | 0.9300 |
N2—C6 | 1.355 (2) | C8—C9 | 1.375 (2) |
N2—H2A | 0.909 (9) | C8—H8 | 0.9300 |
N2—H2B | 0.907 (9) | C9—H9 | 0.9300 |
C1—C2 | 1.544 (2) | ||
C4—O3—H3 | 117.7 (16) | C2—C3—H3B | 108.9 |
H5A—O5—H5B | 106 (2) | H3A—C3—H3B | 107.7 |
C9—N1—C5 | 121.62 (14) | O4—C4—O3 | 124.03 (15) |
C9—N1—C2 | 119.75 (14) | O4—C4—C3 | 121.62 (16) |
C5—N1—C2 | 118.62 (13) | O3—C4—C3 | 114.34 (16) |
C6—N2—H2A | 116.6 (14) | N1—C5—C6 | 121.11 (15) |
C6—N2—H2B | 118.2 (14) | N1—C5—H5 | 119.4 |
H2A—N2—H2B | 122.2 (18) | C6—C5—H5 | 119.4 |
O1—C1—O2 | 127.07 (14) | N2—C6—C5 | 120.55 (16) |
O1—C1—C2 | 115.91 (14) | N2—C6—C7 | 122.28 (17) |
O2—C1—C2 | 117.02 (14) | C5—C6—C7 | 117.17 (17) |
N1—C2—C3 | 110.72 (13) | C8—C7—C6 | 120.32 (16) |
N1—C2—C1 | 112.11 (12) | C8—C7—H7 | 119.8 |
C3—C2—C1 | 111.15 (13) | C6—C7—H7 | 119.8 |
N1—C2—H2 | 107.5 | C7—C8—C9 | 120.42 (17) |
C3—C2—H2 | 107.5 | C7—C8—H8 | 119.8 |
C1—C2—H2 | 107.5 | C9—C8—H8 | 119.8 |
C4—C3—C2 | 113.52 (14) | N1—C9—C8 | 119.35 (16) |
C4—C3—H3A | 108.9 | N1—C9—H9 | 120.3 |
C2—C3—H3A | 108.9 | C8—C9—H9 | 120.3 |
C4—C3—H3B | 108.9 | ||
C9—N1—C2—C3 | −57.28 (17) | C2—C3—C4—O3 | −46.5 (2) |
C5—N1—C2—C3 | 121.47 (14) | C9—N1—C5—C6 | 0.5 (2) |
C9—N1—C2—C1 | 67.48 (17) | C2—N1—C5—C6 | −178.25 (13) |
C5—N1—C2—C1 | −113.77 (15) | N1—C5—C6—N2 | −179.88 (16) |
O1—C1—C2—N1 | −178.48 (14) | N1—C5—C6—C7 | 0.3 (2) |
O2—C1—C2—N1 | 2.4 (2) | N2—C6—C7—C8 | 179.63 (17) |
O1—C1—C2—C3 | −53.95 (19) | C5—C6—C7—C8 | −0.5 (3) |
O2—C1—C2—C3 | 126.92 (16) | C6—C7—C8—C9 | 0.1 (3) |
N1—C2—C3—C4 | −51.92 (18) | C5—N1—C9—C8 | −0.9 (2) |
C1—C2—C3—C4 | −177.22 (13) | C2—N1—C9—C8 | 177.77 (14) |
C2—C3—C4—O4 | 132.57 (18) | C7—C8—C9—N1 | 0.7 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···O2i | 0.87 (1) | 1.60 (1) | 2.4681 (15) | 177 (2) |
O5—H5A···O4ii | 0.85 (1) | 2.04 (1) | 2.8879 (18) | 174 (2) |
O5—H5B···O1iii | 0.86 (1) | 1.94 (1) | 2.7968 (19) | 173 (2) |
N2—H2A···O5iv | 0.91 (1) | 2.02 (1) | 2.920 (2) | 168 (2) |
N2—H2B···O4iv | 0.91 (1) | 2.08 (1) | 2.987 (2) | 173 (2) |
Symmetry codes: (i) x−1, y, z; (ii) x+1/2, −y+1/2, z; (iii) −x+3/2, y−1/2, z+1/2; (iv) x, y, z−1. |
Experimental details
Crystal data | |
Chemical formula | C9H10N2O4·H2O |
Mr | 228.21 |
Crystal system, space group | Orthorhombic, Pna21 |
Temperature (K) | 298 |
a, b, c (Å) | 7.4939 (8), 19.446 (2), 7.0227 (7) |
V (Å3) | 1023.39 (19) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.30 × 0.12 × 0.10 |
Data collection | |
Diffractometer | Bruker SMART APEX CCD area-detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10663, 1868, 1642 |
Rint | 0.037 |
(sin θ/λ)max (Å−1) | 0.602 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.028, 0.058, 0.96 |
No. of reflections | 1868 |
No. of parameters | 160 |
No. of restraints | 6 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.11, −0.12 |
Computer programs: SMART (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and SHELXL97 (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···O2i | 0.868 (9) | 1.601 (10) | 2.4681 (15) | 177 (2) |
O5—H5A···O4ii | 0.848 (9) | 2.043 (10) | 2.8879 (18) | 174 (2) |
O5—H5B···O1iii | 0.861 (9) | 1.941 (10) | 2.7968 (19) | 173 (2) |
N2—H2A···O5iv | 0.909 (9) | 2.024 (10) | 2.920 (2) | 168.3 (18) |
N2—H2B···O4iv | 0.907 (9) | 2.084 (10) | 2.987 (2) | 173 (2) |
Symmetry codes: (i) x−1, y, z; (ii) x+1/2, −y+1/2, z; (iii) −x+3/2, y−1/2, z+1/2; (iv) x, y, z−1. |
Acknowledgements
This work was supported by the Secretaria de Educación Pública (PROMEP, PTC-035) and Universidad Autónoma de Sinaloa (DGIP, PROFAPI-048). Support of this research by CONACyT (grant No. 154732) is gratefully acknowledged.
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.
Crystal engineering is defined in terms of structural geometry and topology (Desiraju, 1995) and hydrogen's rules (Etter, 1990, 1991) are described for predicting hydrogen-bond patterns. Recently, zwitterion derivatives have been of particular interest as building blocks for the synthesis of salts, co-crystals (Kavuru et al. 2010) and polymeric compounds (Hill et al. 2001). For this purpose, hydrogen bonded supramolecular synthons are commonly used to build co-crystals or organic-based self-assembled structures because of their strength and directionality. In this context, aminopyridines and carboxylic acids have been employed for the generation of multicomponent crystals (Bis & Zaworotko, 2005; Sarma et al., 2009). Thus, in this opportunity we would like to describe the molecular and crystal structure of 2-(3-aminopyridinium) succinate acid monohydrate (I).
The asymmetric unit of I contains one 2-(3-aminopyridinium) succinic acid and one water molecule (Figure 1). The 3-aminopyridinium and the di-acid fragment are not coplanar, and are forming dihedral angles of 68.6 (2)° between the aminopyridinium and the carboxylate anion and of 62.8 (2)° between the 3-aminopyridinium fragment and the carboxylic acid group. The carboxylate anion and carboxylic acid fragments are rotated around C2 and C3 respectively, forming an almost perpendicular dihedral angle of 80.6 (1)°. This adopted geometry does not allow the classical dimers as patterns, and form chains along the a axis, via O3—H3—O2. These chains are linked by intermolecular interactions of N2—H2B—O4 thus generating a two-dimensional network along the c axis (Figure 2). The two-dimensional network is interconnected through O5—H5A—O4, O5—H5B—O1 and N2—HA—O5 hydrogen bonds to give an overall three-dimensional hydrogen bonded network (Table 1 and Fig. 2).