| Literature DB >> 31709080 |
V Siva1,2, M Suresh3, S Athimoolam4, S Asath Bahadur1,2.
Abstract
Amino-pyridine and phthalic acid are well known synthons for supra-molecular architectures for the synthesis of new materials for optical applications. The 2-amino-pyridinium hydrogen phthalate title salt, C5H7N2 +·C8H5O4 -, crystallizes in the non-centrosymmetric space group P21. The nitro-gen atom of the -NH2 group in the cation deviates from the fitted pyridine plane by 0.035 (7) Å. The plane of the pyridinium ring and phenyl ring of the anion are oriented at an angle of 80.5 (3)° to each other in the asymmetric unit. The anion features a strong intra-molecular O-H⋯O hydrogen bond, forming a self-associated S(7) ring motif. The crystal packing is dominated by inter-molecular N-H⋯O hydrogen bonds leading to the formation of 21 helices, with a C(11) chain motif. They propagate along the b axis and enclose R 2 2(8) ring motifs. The helices are linked by C-H⋯O hydrogen bonds, forming layers parallel to the ab plane. Hirshfeld surface analysis and two-dimensional fingerprint plots were used to investigate and qu-antify the inter-molecular inter-actions in the crystal. © Siva et al. 2019.Entities:
Keywords: Hirshfeld surface analysis; NLO; crystal structure; hetero-synthon; hydrogen bonding; organic salt
Year: 2019 PMID: 31709080 PMCID: PMC6829739 DOI: 10.1107/S2056989019012957
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The asymmetric unit of the title salt, with atom labelling and 50% probability displacement ellipsoids.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| O22—H22 | 1.08 (10) | 1.32 (10) | 2.402 (7) | 173 (9) |
| N11—H1 | 0.93 (7) | 1.78 (7) | 2.705 (7) | 180 (7) |
| N12—H12 | 0.86 | 2.11 | 2.965 (7) | 174 |
| N12—H12 | 0.86 | 2.31 | 3.003 (8) | 138 |
| C12—H12⋯O23iii | 0.93 | 2.53 | 3.374 (8) | 151 |
| C14—H14⋯O21iv | 0.93 | 2.50 | 3.203 (9) | 132 |
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .
Figure 2The crystal packing of the title salt viewed along the a axis. Hydrogen bonds are shown as dashed lines (Table 1 ▸). For clarity, the C-bound H atoms have been omitted.
Figure 3Packing of the title salt viewed along the c axis. Hydrogen bonds are shown as dashed lines (Table 1 ▸). For clarity, H atoms not involved in hydrogen bonding have been omitted.
Figure 4Hirshfeld surface for the title salt mapped over d norm, in the colour range −0.7098 to 1.1914 au.
Figure 5(a) The full two-dimensional fingerprint plot and the fingerprint plots delineated into H⋯H, O⋯H/H⋯O, C⋯H/H⋯C and C⋯O contacts for the title salt, (b) the full two-dimensional fingerprint plot and fingerprint plots delineated into H⋯H, O⋯H/H⋯O, C⋯H/H⋯C and C⋯O contacts for the cation, and (c) the full two-dimensional fingerprint plot and fingerprint plots delineated into H⋯H, O⋯H/H⋯O, C⋯H/H⋯C and C⋯O contacts for the anion (see Table 2 ▸ for further details).
Relative percentage contributions of close contacts to the Hirshfeld surface for the title salt, the cation and the anion
| Contact | cation+anion | cation | anion |
|---|---|---|---|
| H⋯H | 32.0 | 40.4 | 30.6 |
| O⋯H/H⋯O | 31.0 | 26.3 | 31.6 |
| C⋯H/H⋯C | 22.0 | 18.2 | 24.0 |
| C⋯O | 7.3 | 4.6 | 8.8 |
| N⋯H/H⋯N | 2.5 | 5.1 | 0.4 |
| C⋯C | 2.5 | 2.2 | 2.6 |
Experimental details
| Crystal data | |
| Chemical formula | C5H7N2 +·C8H5O4 − |
|
| 260.25 |
| Crystal system, space group | Monoclinic, |
| Temperature (K) | 293 |
|
| 5.1593 (6), 8.6124 (9), 13.5745 (19) |
| β (°) | 97.087 (4) |
|
| 598.56 (13) |
|
| 2 |
| Radiation type | Mo |
| μ (mm−1) | 0.11 |
| Crystal size (mm) | 0.26 × 0.24 × 0.20 |
| Data collection | |
| Diffractometer | Bruker SMART APEX CCD area-detector |
| No. of measured, independent and observed [ | 6704, 2099, 1972 |
|
| 0.023 |
| (sin θ/λ)max (Å−1) | 0.595 |
| Refinement | |
|
| 0.059, 0.186, 1.24 |
| No. of reflections | 2099 |
| No. of parameters | 180 |
| No. of restraints | 1 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.35, −0.24 |
| Absolute structure | Flack |
| Absolute structure parameter | 0.1 (4) |
Computer programs: SMART and SAINT (Bruker, 2001 ▸), SHELXT2014 (Sheldrick, 2015a ▸), SHELXL2014 (Sheldrick, 2015b ▸), Mercury (Macrae et al., 2008 ▸) and PLATON (Spek, 2009 ▸).
| C5H7N2+·C8H5O4− | |
| Monoclinic, | Mo |
| Cell parameters from 2425 reflections | |
| θ = 2.2–24.7° | |
| µ = 0.11 mm−1 | |
| β = 97.087 (4)° | |
| Block, colourless | |
| 0.26 × 0.24 × 0.20 mm |
| Bruker SMART APEX CCD area-detector diffractometer | |
| Radiation source: fine-focus sealed tube | θmax = 25.0°, θmin = 1.5° |
| ω scans | |
| 6704 measured reflections | |
| 2099 independent reflections | |
| 1972 reflections with |
| Refinement on | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: mixed |
| H atoms treated by a mixture of independent and constrained refinement | |
| (Δ/σ)max < 0.001 | |
| 2099 reflections | Δρmax = 0.35 e Å−3 |
| 180 parameters | Δρmin = −0.24 e Å−3 |
| 1 restraint | Absolute structure: Flack |
| Primary atom site location: dual | Absolute structure parameter: 0.1 (4) |
| Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
| C11 | 0.5973 (12) | 0.4659 (7) | 0.8983 (5) | 0.0401 (14) | |
| C12 | 0.7974 (14) | 0.3719 (9) | 0.9463 (6) | 0.0545 (19) | |
| H12 | 0.8233 | 0.3657 | 1.0152 | 0.065* | |
| C13 | 0.9516 (13) | 0.2908 (8) | 0.8913 (7) | 0.056 (2) | |
| H13 | 1.0809 | 0.2268 | 0.9232 | 0.067* | |
| C14 | 0.9221 (15) | 0.3005 (8) | 0.7882 (7) | 0.057 (2) | |
| H14 | 1.0323 | 0.2466 | 0.7510 | 0.069* | |
| C15 | 0.7263 (13) | 0.3915 (8) | 0.7440 (5) | 0.0489 (16) | |
| H15 | 0.7002 | 0.3992 | 0.6751 | 0.059* | |
| N11 | 0.5683 (10) | 0.4714 (6) | 0.7988 (4) | 0.0370 (12) | |
| N12 | 0.4392 (12) | 0.5509 (8) | 0.9461 (4) | 0.0532 (16) | |
| H12A | 0.3216 | 0.6079 | 0.9134 | 0.064* | |
| H12B | 0.4542 | 0.5492 | 1.0099 | 0.064* | |
| H1N | 0.448 (13) | 0.538 (8) | 0.764 (5) | 0.031 (15)* | |
| C21 | 0.1288 (10) | 0.3445 (6) | 0.3331 (4) | 0.0302 (12) | |
| C22 | 0.0707 (13) | 0.3464 (8) | 0.4303 (4) | 0.0421 (15) | |
| H22 | −0.0615 | 0.2820 | 0.4472 | 0.050* | |
| C23 | 0.1998 (15) | 0.4394 (9) | 0.5026 (5) | 0.0534 (18) | |
| H23 | 0.1531 | 0.4385 | 0.5666 | 0.064* | |
| C24 | 0.3968 (15) | 0.5326 (9) | 0.4797 (5) | 0.0514 (17) | |
| H24 | 0.4850 | 0.5969 | 0.5278 | 0.062* | |
| C25 | 0.4648 (13) | 0.5309 (8) | 0.3840 (5) | 0.0465 (15) | |
| H25 | 0.6035 | 0.5925 | 0.3697 | 0.056* | |
| C26 | 0.3347 (10) | 0.4413 (7) | 0.3089 (4) | 0.0333 (13) | |
| C27 | 0.4332 (12) | 0.4634 (9) | 0.2093 (5) | 0.0431 (15) | |
| C28 | −0.0455 (11) | 0.2378 (7) | 0.2648 (4) | 0.0335 (13) | |
| O21 | 0.6142 (12) | 0.5515 (7) | 0.2021 (4) | 0.0696 (16) | |
| O22 | 0.3306 (11) | 0.3890 (8) | 0.1326 (4) | 0.0627 (15) | |
| O23 | −0.0154 (9) | 0.2241 (6) | 0.1742 (3) | 0.0469 (11) | |
| O24 | −0.2148 (10) | 0.1635 (6) | 0.3020 (3) | 0.0488 (12) | |
| H22A | 0.17 (2) | 0.320 (11) | 0.149 (7) | 0.08 (3)* |
| C11 | 0.039 (3) | 0.039 (3) | 0.043 (3) | −0.011 (3) | 0.004 (3) | 0.009 (3) |
| C12 | 0.052 (4) | 0.052 (4) | 0.055 (4) | −0.006 (3) | −0.014 (3) | 0.020 (3) |
| C13 | 0.034 (3) | 0.046 (4) | 0.083 (6) | 0.000 (3) | −0.008 (4) | 0.016 (4) |
| C14 | 0.046 (4) | 0.044 (4) | 0.084 (6) | 0.009 (3) | 0.014 (4) | −0.003 (4) |
| C15 | 0.046 (3) | 0.048 (4) | 0.052 (4) | 0.001 (3) | 0.002 (3) | −0.007 (3) |
| N11 | 0.034 (2) | 0.038 (3) | 0.038 (3) | −0.002 (2) | 0.002 (2) | 0.006 (2) |
| N12 | 0.059 (4) | 0.066 (4) | 0.036 (3) | 0.016 (3) | 0.010 (3) | 0.011 (3) |
| C21 | 0.029 (3) | 0.031 (3) | 0.030 (3) | 0.004 (2) | 0.003 (2) | 0.001 (2) |
| C22 | 0.046 (3) | 0.048 (4) | 0.032 (3) | −0.006 (3) | 0.006 (3) | −0.003 (3) |
| C23 | 0.068 (4) | 0.058 (4) | 0.033 (3) | 0.000 (4) | 0.001 (3) | −0.009 (3) |
| C24 | 0.056 (4) | 0.053 (4) | 0.042 (4) | −0.003 (3) | −0.006 (3) | −0.016 (3) |
| C25 | 0.039 (3) | 0.047 (4) | 0.051 (4) | −0.006 (3) | −0.001 (3) | −0.001 (3) |
| C26 | 0.031 (3) | 0.032 (3) | 0.036 (3) | 0.004 (2) | 0.003 (2) | 0.002 (2) |
| C27 | 0.040 (3) | 0.046 (3) | 0.044 (4) | −0.001 (3) | 0.007 (3) | 0.011 (3) |
| C28 | 0.038 (3) | 0.031 (3) | 0.031 (3) | 0.003 (3) | 0.001 (2) | 0.003 (2) |
| O21 | 0.067 (3) | 0.073 (4) | 0.075 (4) | −0.023 (3) | 0.033 (3) | −0.001 (3) |
| O22 | 0.065 (3) | 0.093 (4) | 0.033 (2) | −0.016 (3) | 0.015 (2) | 0.001 (3) |
| O23 | 0.056 (3) | 0.056 (3) | 0.028 (2) | −0.009 (2) | 0.0030 (19) | −0.006 (2) |
| O24 | 0.056 (3) | 0.055 (3) | 0.035 (2) | −0.021 (2) | 0.002 (2) | −0.004 (2) |
| C11—N12 | 1.325 (9) | C21—C28 | 1.519 (8) |
| C11—N11 | 1.341 (8) | C22—C23 | 1.374 (10) |
| C11—C12 | 1.407 (9) | C22—H22 | 0.9300 |
| C12—C13 | 1.351 (11) | C23—C24 | 1.361 (11) |
| C12—H12 | 0.9300 | C23—H23 | 0.9300 |
| C13—C14 | 1.391 (12) | C24—C25 | 1.387 (10) |
| C13—H13 | 0.9300 | C24—H24 | 0.9300 |
| C14—C15 | 1.359 (10) | C25—C26 | 1.385 (9) |
| C14—H14 | 0.9300 | C25—H25 | 0.9300 |
| C15—N11 | 1.357 (9) | C26—C27 | 1.514 (9) |
| C15—H15 | 0.9300 | C27—O21 | 1.216 (9) |
| N11—H1N | 0.93 (7) | C27—O22 | 1.280 (9) |
| N12—H12A | 0.8600 | C28—O24 | 1.239 (7) |
| N12—H12B | 0.8600 | C28—O23 | 1.264 (7) |
| C21—C22 | 1.389 (8) | O22—H22A | 1.08 (10) |
| C21—C26 | 1.421 (8) | O23—H22A | 1.32 (11) |
| N12—C11—N11 | 118.4 (6) | C23—C22—C21 | 122.9 (6) |
| N12—C11—C12 | 123.5 (6) | C23—C22—H22 | 118.5 |
| N11—C11—C12 | 118.1 (7) | C21—C22—H22 | 118.5 |
| C13—C12—C11 | 119.3 (7) | C24—C23—C22 | 119.4 (7) |
| C13—C12—H12 | 120.3 | C24—C23—H23 | 120.3 |
| C11—C12—H12 | 120.3 | C22—C23—H23 | 120.3 |
| C12—C13—C14 | 121.8 (7) | C23—C24—C25 | 119.3 (6) |
| C12—C13—H13 | 119.1 | C23—C24—H24 | 120.3 |
| C14—C13—H13 | 119.1 | C25—C24—H24 | 120.3 |
| C15—C14—C13 | 117.5 (7) | C26—C25—C24 | 122.7 (7) |
| C15—C14—H14 | 121.2 | C26—C25—H25 | 118.7 |
| C13—C14—H14 | 121.2 | C24—C25—H25 | 118.7 |
| N11—C15—C14 | 120.9 (7) | C25—C26—C21 | 117.8 (6) |
| N11—C15—H15 | 119.5 | C25—C26—C27 | 113.7 (6) |
| C14—C15—H15 | 119.5 | C21—C26—C27 | 128.5 (5) |
| C11—N11—C15 | 122.3 (6) | O21—C27—O22 | 119.4 (6) |
| C11—N11—H1N | 121 (4) | O21—C27—C26 | 119.7 (6) |
| C15—N11—H1N | 117 (4) | O22—C27—C26 | 120.8 (6) |
| C11—N12—H12A | 120.0 | O24—C28—O23 | 121.7 (5) |
| C11—N12—H12B | 120.0 | O24—C28—C21 | 117.2 (5) |
| H12A—N12—H12B | 120.0 | O23—C28—C21 | 121.1 (5) |
| C22—C21—C26 | 117.9 (5) | C27—O22—H22A | 112 (5) |
| C22—C21—C28 | 114.0 (5) | C28—O23—H22A | 112 (4) |
| C26—C21—C28 | 128.1 (5) | ||
| N12—C11—C12—C13 | −179.0 (6) | C24—C25—C26—C27 | 177.2 (7) |
| N11—C11—C12—C13 | −0.2 (9) | C22—C21—C26—C25 | 0.2 (8) |
| C11—C12—C13—C14 | 1.6 (11) | C28—C21—C26—C25 | 179.0 (6) |
| C12—C13—C14—C15 | −1.9 (11) | C22—C21—C26—C27 | −178.7 (6) |
| C13—C14—C15—N11 | 0.9 (10) | C28—C21—C26—C27 | 0.1 (9) |
| N12—C11—N11—C15 | 178.1 (6) | C25—C26—C27—O21 | 1.4 (9) |
| C12—C11—N11—C15 | −0.8 (9) | C21—C26—C27—O21 | −179.7 (6) |
| C14—C15—N11—C11 | 0.5 (10) | C25—C26—C27—O22 | −179.5 (7) |
| C26—C21—C22—C23 | 1.2 (10) | C21—C26—C27—O22 | −0.6 (10) |
| C28—C21—C22—C23 | −177.7 (6) | C22—C21—C28—O24 | −1.0 (7) |
| C21—C22—C23—C24 | −1.1 (11) | C26—C21—C28—O24 | −179.9 (6) |
| C22—C23—C24—C25 | −0.6 (11) | C22—C21—C28—O23 | −179.9 (6) |
| C23—C24—C25—C26 | 2.1 (11) | C26—C21—C28—O23 | 1.2 (8) |
| C24—C25—C26—C21 | −1.9 (9) |
| H··· | ||||
| O22—H22 | 1.08 (10) | 1.32 (10) | 2.402 (7) | 173 (9) |
| N11—H1 | 0.93 (7) | 1.78 (7) | 2.705 (7) | 180 (7) |
| N12—H12 | 0.86 | 2.11 | 2.965 (7) | 174 |
| N12—H12 | 0.86 | 2.31 | 3.003 (8) | 138 |
| C12—H12···O23iii | 0.93 | 2.53 | 3.374 (8) | 151 |
| C14—H14···O21iv | 0.93 | 2.50 | 3.203 (9) | 132 |