| Literature DB >> 31523473 |
Dang Tran Buu1, Vu Duong Ba1, Minh Khoi Nguyen Hoang2, Trung Vu Quoc3, Linh Duong Khanh3, Yen Oanh Doan Thi4, Luc Van Meervelt5.
Abstract
The structure of the title compound (systematic name: N-{[(2-hy-droxy-phen-yl)methyl-idene]amino}-morpholine-4-carbo-thio-amide), C12H15N3O2S, was prev-iously determined (Koo et al., 1977 ▸) using multiple-film equi-inclination Weissenberg data, but has been redetermined with higher precision to explore its conformation and the hydrogen-bonding patterns and supra-molecular inter-actions. The mol-ecular structure shows intra-molecular O-H⋯N and C-H⋯S inter-actions. The configuration of the C=N bond is E. The mol-ecule is slightly twisted about the central N-N bond. The best planes through the phenyl ring and the morpholino ring make an angle of 43.44 (17)°. In the crystal, the mol-ecules are connected into chains by N-H⋯O and C-H⋯O hydrogen bonds, which combine to generate sheets lying parallel to (002). The most prominent contribution to the surface contacts are H⋯H contacts (51.6%), as concluded from a Hirshfeld surface analysis.Entities:
Keywords: Hirshfeld analysis; crystal structure; hydrogen bonding; thiosemicarbazone
Year: 2019 PMID: 31523473 PMCID: PMC6727042 DOI: 10.1107/S2056989019011812
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1A view of the molecular structure of (3), with atom labels and displacement ellipsoids drawn at the 50% probability level. H atoms are shown as small circles of arbitrary radii and the intramolecular O—H⋯N and C—H⋯S interactions, respectively, by blue and grey dashed lines.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| N9—H9⋯O4i | 0.86 (3) | 2.33 (3) | 3.141 (3) | 157 (3) |
| O18—H18⋯N10 | 0.80 (4) | 1.91 (5) | 2.597 (3) | 145 (4) |
| C6—H6 | 0.97 | 2.62 | 3.121 (3) | 112 |
| C15—H15⋯O18ii | 0.93 | 2.48 | 3.404 (4) | 176 |
Symmetry codes: (i) ; (ii) .
Figure 2Partial crystal packing of (3), showing the N—H⋯O interactions (red dashed lines) resulting in chain formation in the a-axis direction [see Table 1 ▸; symmetry code: (i) x + , −y + , z].
Figure 3Partial crystal packing of (3), showing the C—H⋯O interactions (red dashed lines) resulting in chain formation in the a-direction [see Table 1 ▸; symmetry code: (ii) x + , −y + , z].
Figure 4The Hirshfeld surface mapped over d norm for (3) in the range −0.3153 to 1.2662 a.u.
Figure 5Full two-dimensional fingerprint plots for (3), showing (a) all interactions, and delineated into (b) H⋯H, (c) O⋯H/H⋯O, (d) S⋯H/H⋯S, (e) C⋯H/H⋯C and (f) N⋯C/C⋯N interactions. The d i and d e values are the closest internal and external distances (in Å) from a given point on the Hirshfeld surface.
Figure 6(a) Fragment used for a search in the CSD. (b),(c) Histograms of torsion angles τ1 and τ2. The vertical pink lines show the torsion angle observed in (3).
Figure 7Reaction scheme for the synthesis of (3).
Experimental details
| Crystal data | |
| Chemical formula | C12H15N3O2S |
|
| 265.33 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 293 |
|
| 11.7579 (4), 15.0584 (5), 7.1103 (3) |
|
| 1258.92 (8) |
|
| 4 |
| Radiation type | Mo |
| μ (mm−1) | 0.26 |
| Crystal size (mm) | 0.5 × 0.2 × 0.1 |
| Data collection | |
| Diffractometer | Rigaku Oxford Diffraction SuperNova, Single source at offset/far, Eos |
| Absorption correction | Multi-scan ( |
|
| 0.483, 1.000 |
| No. of measured, independent and observed [ | 12278, 2565, 2314 |
|
| 0.025 |
| (sin θ/λ)max (Å−1) | 0.625 |
| Refinement | |
|
| 0.034, 0.087, 1.07 |
| No. of reflections | 2565 |
| No. of parameters | 171 |
| No. of restraints | 1 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.17, −0.17 |
| Absolute structure | Flack |
| Absolute structure parameter | 0.02 (3) |
Computer programs: CrysAlis PRO (Rigaku OD, 2018 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL (Sheldrick, 2015b ▸) and OLEX2 (Dolomanov et al., 2009 ▸).
| C12H15N3O2S | |
| Mo | |
| Orthorhombic, | Cell parameters from 5842 reflections |
| θ = 3.2–27.3° | |
| µ = 0.26 mm−1 | |
| Block, colourless | |
| 0.5 × 0.2 × 0.1 mm | |
| Rigaku Oxford Diffraction SuperNova, Single source at offset/far, Eos diffractometer | 2565 independent reflections |
| Radiation source: micro-focus sealed X-ray tube, SuperNova (Mo) X-ray Source | 2314 reflections with |
| Mirror monochromator | |
| Detector resolution: 15.9631 pixels mm-1 | θmax = 26.4°, θmin = 2.7° |
| ω scans | |
| Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018) | |
| 12278 measured reflections |
| 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 | |
| 2565 reflections | Δρmax = 0.17 e Å−3 |
| 171 parameters | Δρmin = −0.17 e Å−3 |
| 1 restraint | Absolute structure: Flack |
| Primary atom site location: dual space | Absolute structure parameter: 0.02 (3) |
| 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. |
| N1 | 0.12956 (17) | 0.37994 (13) | 0.5311 (5) | 0.0441 (5) | |
| C2 | 0.1602 (2) | 0.28850 (18) | 0.4815 (5) | 0.0438 (7) | |
| H2A | 0.174911 | 0.254390 | 0.594672 | 0.053* | |
| H2B | 0.228621 | 0.288274 | 0.405192 | 0.053* | |
| C3 | 0.0625 (3) | 0.2474 (2) | 0.3728 (5) | 0.0552 (8) | |
| H3A | 0.050961 | 0.280351 | 0.257136 | 0.066* | |
| H3B | 0.081833 | 0.186795 | 0.339747 | 0.066* | |
| O4 | −0.04027 (17) | 0.24774 (14) | 0.4794 (3) | 0.0545 (6) | |
| C5 | −0.0710 (2) | 0.3379 (2) | 0.5178 (7) | 0.0615 (9) | |
| H5A | −0.141436 | 0.338728 | 0.588879 | 0.074* | |
| H5B | −0.084419 | 0.368531 | 0.399814 | 0.074* | |
| C6 | 0.0177 (3) | 0.3860 (2) | 0.6249 (6) | 0.0597 (9) | |
| H6A | −0.003873 | 0.447934 | 0.636901 | 0.072* | |
| H6B | 0.023218 | 0.361089 | 0.750398 | 0.072* | |
| C7 | 0.2028 (2) | 0.44909 (15) | 0.5299 (5) | 0.0388 (6) | |
| S8 | 0.16206 (6) | 0.55578 (4) | 0.54532 (17) | 0.0552 (2) | |
| N9 | 0.31482 (18) | 0.42656 (14) | 0.5168 (4) | 0.0406 (6) | |
| H9 | 0.337 (2) | 0.3724 (19) | 0.521 (6) | 0.044 (8)* | |
| N10 | 0.39379 (18) | 0.49289 (14) | 0.4965 (3) | 0.0384 (6) | |
| C11 | 0.4978 (2) | 0.47549 (15) | 0.5317 (5) | 0.0366 (5) | |
| H11 | 0.519030 | 0.418814 | 0.569994 | 0.044* | |
| C12 | 0.5829 (2) | 0.54502 (15) | 0.5115 (4) | 0.0353 (6) | |
| C13 | 0.5532 (2) | 0.63316 (17) | 0.4666 (4) | 0.0394 (6) | |
| C14 | 0.6374 (3) | 0.69733 (19) | 0.4546 (5) | 0.0512 (8) | |
| H14 | 0.617815 | 0.755628 | 0.426000 | 0.061* | |
| C15 | 0.7497 (3) | 0.6758 (2) | 0.4845 (4) | 0.0542 (8) | |
| H15 | 0.805097 | 0.719608 | 0.475521 | 0.065* | |
| C16 | 0.7811 (2) | 0.5896 (2) | 0.5277 (6) | 0.0537 (7) | |
| H16 | 0.857037 | 0.575138 | 0.547403 | 0.064* | |
| C17 | 0.6977 (2) | 0.52566 (18) | 0.5408 (6) | 0.0466 (6) | |
| H17 | 0.718495 | 0.467720 | 0.570242 | 0.056* | |
| O18 | 0.44378 (18) | 0.65822 (14) | 0.4336 (4) | 0.0513 (6) | |
| H18 | 0.402 (3) | 0.617 (3) | 0.446 (6) | 0.073 (13)* |
| N1 | 0.0326 (10) | 0.0409 (10) | 0.0590 (14) | −0.0031 (9) | 0.0038 (14) | −0.0046 (15) |
| C2 | 0.0354 (13) | 0.0407 (13) | 0.0551 (19) | −0.0024 (11) | 0.0056 (13) | −0.0046 (13) |
| C3 | 0.0576 (18) | 0.0553 (18) | 0.0528 (19) | −0.0181 (15) | 0.0075 (16) | −0.0038 (15) |
| O4 | 0.0436 (11) | 0.0530 (11) | 0.0670 (16) | −0.0148 (9) | 0.0020 (11) | 0.0020 (11) |
| C5 | 0.0376 (14) | 0.0584 (17) | 0.088 (3) | −0.0044 (13) | −0.0064 (19) | 0.014 (2) |
| C6 | 0.0370 (16) | 0.0545 (17) | 0.088 (3) | −0.0016 (14) | 0.0139 (17) | −0.0090 (18) |
| C7 | 0.0360 (12) | 0.0418 (12) | 0.0387 (14) | −0.0009 (10) | −0.0011 (15) | 0.0015 (15) |
| S8 | 0.0481 (4) | 0.0396 (3) | 0.0780 (6) | 0.0056 (3) | 0.0010 (5) | −0.0010 (5) |
| N9 | 0.0333 (11) | 0.0329 (10) | 0.0556 (16) | −0.0031 (8) | 0.0009 (12) | 0.0040 (12) |
| N10 | 0.0336 (11) | 0.0359 (10) | 0.0458 (15) | −0.0050 (9) | −0.0004 (10) | 0.0032 (10) |
| C11 | 0.0388 (13) | 0.0329 (10) | 0.0380 (13) | −0.0003 (9) | −0.0010 (14) | 0.0021 (14) |
| C12 | 0.0353 (12) | 0.0354 (11) | 0.0353 (16) | −0.0029 (9) | 0.0002 (12) | −0.0007 (12) |
| C13 | 0.0418 (14) | 0.0356 (12) | 0.0408 (15) | 0.0001 (11) | 0.0026 (12) | −0.0019 (12) |
| C14 | 0.0605 (19) | 0.0351 (13) | 0.0581 (19) | −0.0111 (13) | 0.0005 (16) | 0.0001 (14) |
| C15 | 0.0534 (17) | 0.0585 (17) | 0.0507 (19) | −0.0249 (15) | −0.0003 (15) | −0.0007 (15) |
| C16 | 0.0363 (14) | 0.0681 (17) | 0.0567 (18) | −0.0104 (13) | −0.0022 (17) | 0.0016 (19) |
| C17 | 0.0389 (14) | 0.0465 (13) | 0.0545 (16) | −0.0001 (11) | −0.0039 (18) | 0.0019 (18) |
| O18 | 0.0448 (11) | 0.0349 (10) | 0.0744 (15) | 0.0042 (9) | −0.0019 (11) | 0.0049 (10) |
| N1—C2 | 1.466 (3) | N9—H9 | 0.86 (3) |
| N1—C6 | 1.478 (4) | N9—N10 | 1.371 (3) |
| N1—C7 | 1.351 (3) | N10—C11 | 1.275 (3) |
| C2—H2A | 0.9700 | C11—H11 | 0.9300 |
| C2—H2B | 0.9700 | C11—C12 | 1.456 (3) |
| C2—C3 | 1.516 (4) | C12—C13 | 1.409 (3) |
| C3—H3A | 0.9700 | C12—C17 | 1.396 (4) |
| C3—H3B | 0.9700 | C13—C14 | 1.386 (4) |
| C3—O4 | 1.426 (3) | C13—O18 | 1.361 (3) |
| O4—C5 | 1.432 (4) | C14—H14 | 0.9300 |
| C5—H5A | 0.9700 | C14—C15 | 1.376 (4) |
| C5—H5B | 0.9700 | C15—H15 | 0.9300 |
| C5—C6 | 1.481 (5) | C15—C16 | 1.383 (4) |
| C6—H6A | 0.9700 | C16—H16 | 0.9300 |
| C6—H6B | 0.9700 | C16—C17 | 1.377 (4) |
| C7—S8 | 1.680 (2) | C17—H17 | 0.9300 |
| C7—N9 | 1.364 (3) | O18—H18 | 0.80 (4) |
| C2—N1—C6 | 112.7 (2) | N1—C7—N9 | 115.1 (2) |
| C7—N1—C2 | 124.4 (2) | N9—C7—S8 | 121.17 (18) |
| C7—N1—C6 | 121.5 (2) | C7—N9—H9 | 121.8 (18) |
| N1—C2—H2A | 110.0 | C7—N9—N10 | 118.7 (2) |
| N1—C2—H2B | 110.0 | N10—N9—H9 | 119.5 (18) |
| N1—C2—C3 | 108.6 (2) | C11—N10—N9 | 118.6 (2) |
| H2A—C2—H2B | 108.4 | N10—C11—H11 | 120.3 |
| C3—C2—H2A | 110.0 | N10—C11—C12 | 119.5 (2) |
| C3—C2—H2B | 110.0 | C12—C11—H11 | 120.3 |
| C2—C3—H3A | 109.3 | C13—C12—C11 | 121.9 (2) |
| C2—C3—H3B | 109.3 | C17—C12—C11 | 120.0 (2) |
| H3A—C3—H3B | 107.9 | C17—C12—C13 | 118.1 (2) |
| O4—C3—C2 | 111.7 (3) | C14—C13—C12 | 119.5 (3) |
| O4—C3—H3A | 109.3 | O18—C13—C12 | 122.3 (2) |
| O4—C3—H3B | 109.3 | O18—C13—C14 | 118.1 (3) |
| C3—O4—C5 | 108.6 (2) | C13—C14—H14 | 119.6 |
| O4—C5—H5A | 109.1 | C15—C14—C13 | 120.7 (3) |
| O4—C5—H5B | 109.1 | C15—C14—H14 | 119.6 |
| O4—C5—C6 | 112.6 (2) | C14—C15—H15 | 119.6 |
| H5A—C5—H5B | 107.8 | C14—C15—C16 | 120.8 (3) |
| C6—C5—H5A | 109.1 | C16—C15—H15 | 119.6 |
| C6—C5—H5B | 109.1 | C15—C16—H16 | 120.6 |
| N1—C6—C5 | 111.4 (3) | C17—C16—C15 | 118.7 (3) |
| N1—C6—H6A | 109.4 | C17—C16—H16 | 120.6 |
| N1—C6—H6B | 109.4 | C12—C17—H17 | 118.9 |
| C5—C6—H6A | 109.4 | C16—C17—C12 | 122.1 (3) |
| C5—C6—H6B | 109.4 | C16—C17—H17 | 118.9 |
| H6A—C6—H6B | 108.0 | C13—O18—H18 | 110 (3) |
| N1—C7—S8 | 123.73 (19) | ||
| N1—C2—C3—O4 | −58.7 (4) | N9—N10—C11—C12 | −179.9 (3) |
| N1—C7—N9—N10 | 173.8 (3) | N10—C11—C12—C13 | 4.5 (5) |
| C2—N1—C6—C5 | −50.2 (4) | N10—C11—C12—C17 | −176.9 (3) |
| C2—N1—C7—S8 | 167.6 (3) | C11—C12—C13—C14 | 178.1 (3) |
| C2—N1—C7—N9 | −13.0 (5) | C11—C12—C13—O18 | −2.1 (4) |
| C2—C3—O4—C5 | 62.2 (4) | C11—C12—C17—C16 | −178.5 (4) |
| C3—O4—C5—C6 | −59.5 (4) | C12—C13—C14—C15 | 0.6 (5) |
| O4—C5—C6—N1 | 53.7 (4) | C13—C12—C17—C16 | 0.2 (5) |
| C6—N1—C2—C3 | 51.7 (4) | C13—C14—C15—C16 | −0.2 (5) |
| C6—N1—C7—S8 | −27.0 (5) | C14—C15—C16—C17 | −0.2 (5) |
| C6—N1—C7—N9 | 152.5 (3) | C15—C16—C17—C12 | 0.2 (6) |
| C7—N1—C2—C3 | −141.7 (3) | C17—C12—C13—C14 | −0.6 (4) |
| C7—N1—C6—C5 | 142.7 (3) | C17—C12—C13—O18 | 179.3 (3) |
| C7—N9—N10—C11 | 162.4 (3) | O18—C13—C14—C15 | −179.3 (3) |
| S8—C7—N9—N10 | −6.7 (4) |
| H··· | ||||
| N9—H9···O4i | 0.86 (3) | 2.33 (3) | 3.141 (3) | 157 (3) |
| O18—H18···N10 | 0.80 (4) | 1.91 (5) | 2.597 (3) | 145 (4) |
| C6—H6 | 0.97 | 2.62 | 3.121 (3) | 112 |
| C15—H15···O18ii | 0.93 | 2.48 | 3.404 (4) | 176 |