| Literature DB >> 32939297 |
Tamira Eckhardt1, Richard Goddard2, Ines Rudolph1, Adrian Richter1, Christoph Lehmann1, Peter Imming1, Rüdiger W Seidel1.
Abstract
1,3-Benzo-thia-zin-4-ones (BTZs) are a promising new class of anti-tuberculosis drug candidates, some of which have reached clinical trials. The title compound, the benzamide derivative [2-chloro-3-nitro-5-(tri-fluoro-meth-yl)phen-yl](piper-id-in-1-yl)methanone, C13H12ClF3N2O3, occurs as a side product as a result of competitive reaction pathways in the nucleophilic attack during the synthesis of the BTZ 8-nitro-2-(piperidin-1-yl)-6-(tri-fluoro-meth-yl)-1,3-benzo-thia-zin-4-one, following the original synthetic route, whereby the corresponding benzoyl iso-thio-cyanate is reacted with piperidine as secondary amine. In the title compound, the nitro group and the nearly planar amide group are significantly twisted out of the plane of the benzene ring. The piperidine ring adopts a chair conformation. The tri-fluoro-methyl group exhibits slight rotational disorder with a refined ratio of occupancies of 0.972 (2):0.028 (2). There is structural evidence for inter-molecular weak C-H⋯O hydrogen bonds. © Eckhardt et al. 2020.Entities:
Keywords: anti-tuberculosis drugs; benzothiazinones; crystal structure; nitrobenzamides; reaction mechanism
Year: 2020 PMID: 32939297 PMCID: PMC7472761 DOI: 10.1107/S2056989020010658
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1Synthetic pathway from 2-chloro-3-nitro-5-(trifluoromethyl)benzoic acid (1) to BTZ 3 and side product 4, illustrating the two different points of nucleophilic attack of piperidine at the intermediate 2-chloro-3-nitro-5-(trifluoromethyl)benzoyl isothiocyanate (2), resulting in 3 and 4 (Rudolph, 2014 ▸).
Figure 2Molecular structure of 4. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented by small spheres of arbitrary radii. The minor occupancy component of the disordered trifluoromethyl group is depicted by empty ellipsoids.
Selected geometric parameters (Å, °)
| C1—C8 | 1.510 (3) | C7—F3 | 1.328 (3) |
| C2—Cl1 | 1.725 (2) | C7—F2 | 1.336 (3) |
| C3—N1 | 1.468 (3) | C8—O3 | 1.234 (2) |
| C5—C7 | 1.497 (3) | C8—N2 | 1.342 (3) |
| C7—F1 | 1.325 (3) | ||
| C4—C3—N1 | 116.41 (17) | N2—C9—C10 | 110.59 (18) |
| C2—C3—N1 | 122.35 (18) | C9—C10—C11 | 110.61 (19) |
| F1—C7—F3 | 107.69 (19) | C12—C11—C10 | 109.74 (18) |
| F1—C7—F2 | 105.98 (19) | C13—C12—C11 | 111.01 (18) |
| F3—C7—F2 | 105.59 (17) | N2—C13—C12 | 111.35 (17) |
| F1—C7—C5 | 112.43 (17) | O2—N1—O1 | 124.48 (17) |
| F3—C7—C5 | 112.80 (18) | O2—N1—C3 | 117.04 (17) |
| F2—C7—C5 | 111.86 (17) | O1—N1—C3 | 118.44 (16) |
| O3—C8—N2 | 124.72 (18) | C8—N2—C13 | 120.26 (16) |
| O3—C8—C1 | 118.43 (18) | C8—N2—C9 | 124.74 (16) |
| N2—C8—C1 | 116.85 (17) | C13—N2—C9 | 114.89 (16) |
| C4—C3—N1—O2 | 36.6 (2) | O3—C8—N2—C13 | 3.0 (3) |
| C2—C3—N1—O2 | −143.29 (19) | C1—C8—N2—C13 | −176.62 (17) |
| C4—C3—N1—O1 | −141.34 (18) | O3—C8—N2—C9 | 179.0 (2) |
| C2—C3—N1—O1 | 38.8 (3) | C1—C8—N2—C9 | −0.6 (3) |
Figure 3Short contacts (dashed lines) between adjacent molecules in the crystal structure of 4. The minor component of the disordered trifluoromethyl group is omitted for clarity. Symmetry codes: (i) −x + 1, y + , −z + ; (ii) −x + , y + , z; (iii) x, y + 1, z; (iv) x + , −y + , −z.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| C6—H6⋯O3i | 0.95 | 2.59 | 3.526 (3) | 169 |
| C9—H9 | 0.99 | 2.45 | 3.361 (3) | 154 |
| C9—H9 | 0.99 | 2.58 | 3.369 (3) | 137 |
| C13—H13 | 0.99 | 2.92 | 3.447 (2) | 114 |
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .
Experimental details
| Crystal data | |
| Chemical formula | C13H12ClF3N2O3 |
|
| 336.70 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 100 |
|
| 18.0904 (7), 7.8971 (3), 19.8043 (8) |
|
| 2829.28 (19) |
|
| 8 |
| Radiation type | Cu |
| μ (mm−1) | 2.88 |
| Crystal size (mm) | 0.59 × 0.50 × 0.44 |
| Data collection | |
| Diffractometer | Bruker Kappa Mach3 APEXII |
| Absorption correction | Gaussian ( |
|
| 0.297, 0.586 |
| No. of measured, independent and observed [ | 49954, 2784, 2699 |
|
| 0.041 |
| (sin θ/λ)max (Å−1) | 0.617 |
| Refinement | |
|
| 0.043, 0.115, 1.15 |
| No. of reflections | 2784 |
| No. of parameters | 209 |
| No. of restraints | 45 |
| H-atom treatment | H-atom parameters constrained |
| Δρmax, Δρmin (e Å−3) | 0.32, −0.32 |
Computer programs: APEX3 (Bruker, 2017 ▸), SAINT (Bruker, 2004 ▸), SHELXT2014/4 (Sheldrick, 2015a ▸), SHELXL2018/3 (Sheldrick, 2015b ▸), DIAMOND (Brandenburg, 2018 ▸), enCIFer (Allen et al., 2004 ▸) and publCIF (Westrip, 2010 ▸).
| C13H12ClF3N2O3 | |
| Cu | |
| Orthorhombic, | Cell parameters from 9968 reflections |
| θ = 4.9–71.6° | |
| µ = 2.88 mm−1 | |
| Block, colourless | |
| 0.59 × 0.50 × 0.44 mm | |
| Bruker Kappa Mach3 APEXII diffractometer | 2784 independent reflections |
| Radiation source: 0.2 × 2 mm2 focus rotating anode | 2699 reflections with |
| MONTEL graded multilayer optics monochromator | |
| Detector resolution: 66.67 pixels mm-1 | θmax = 72.2°, θmin = 4.9° |
| φ– and ω–scans | |
| Absorption correction: gaussian (SADABS; Krause | |
| 49954 measured reflections |
| Refinement on | Primary atom site location: dual |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| Hydrogen site location: inferred from neighbouring sites | |
| H-atom parameters constrained | |
| 2784 reflections | (Δ/σ)max < 0.001 |
| 209 parameters | Δρmax = 0.32 e Å−3 |
| 45 restraints | Δρmin = −0.32 e Å−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. |
| Occ. (<1) | |||||
| C1 | 0.41556 (10) | 0.3250 (3) | 0.23581 (10) | 0.0230 (4) | |
| C2 | 0.38370 (10) | 0.1651 (3) | 0.23833 (10) | 0.0224 (4) | |
| C3 | 0.35007 (10) | 0.1004 (3) | 0.18023 (10) | 0.0227 (4) | |
| C4 | 0.34763 (10) | 0.1927 (3) | 0.12111 (10) | 0.0243 (4) | |
| H4 | 0.325215 | 0.146458 | 0.081847 | 0.029* | |
| C5 | 0.37831 (10) | 0.3541 (3) | 0.11961 (10) | 0.0242 (4) | |
| C6 | 0.41190 (11) | 0.4206 (3) | 0.17666 (10) | 0.0250 (4) | |
| H6 | 0.432417 | 0.531321 | 0.175487 | 0.030* | |
| C7 | 0.37425 (12) | 0.4549 (3) | 0.05572 (11) | 0.0298 (5) | |
| C8 | 0.45848 (10) | 0.3906 (2) | 0.29575 (10) | 0.0232 (4) | |
| C9 | 0.34929 (13) | 0.5683 (3) | 0.32422 (11) | 0.0327 (5) | |
| H9A | 0.325497 | 0.503425 | 0.287381 | 0.039* | |
| H9B | 0.351745 | 0.688568 | 0.310277 | 0.039* | |
| C10 | 0.30335 (12) | 0.5528 (3) | 0.38813 (13) | 0.0404 (6) | |
| H10A | 0.296350 | 0.431647 | 0.399304 | 0.048* | |
| H10B | 0.254021 | 0.603627 | 0.380559 | 0.048* | |
| C11 | 0.34134 (13) | 0.6421 (3) | 0.44689 (11) | 0.0373 (5) | |
| H11A | 0.344826 | 0.764952 | 0.437412 | 0.045* | |
| H11B | 0.311898 | 0.626777 | 0.488581 | 0.045* | |
| C12 | 0.41843 (12) | 0.5691 (3) | 0.45695 (10) | 0.0294 (5) | |
| H12A | 0.443955 | 0.632047 | 0.493365 | 0.035* | |
| H12B | 0.414464 | 0.449164 | 0.470978 | 0.035* | |
| C13 | 0.46343 (11) | 0.5807 (3) | 0.39245 (10) | 0.0277 (4) | |
| H13A | 0.473754 | 0.701122 | 0.382205 | 0.033* | |
| H13B | 0.511333 | 0.522352 | 0.398982 | 0.033* | |
| N1 | 0.31581 (9) | −0.0681 (2) | 0.17845 (9) | 0.0253 (4) | |
| N2 | 0.42423 (9) | 0.5038 (2) | 0.33544 (8) | 0.0249 (4) | |
| O1 | 0.28104 (8) | −0.1161 (2) | 0.22819 (8) | 0.0324 (4) | |
| O2 | 0.32229 (8) | −0.1493 (2) | 0.12611 (8) | 0.0341 (4) | |
| O3 | 0.52198 (7) | 0.33806 (19) | 0.30471 (7) | 0.0288 (3) | |
| F1 | 0.38438 (14) | 0.3603 (2) | 0.00122 (7) | 0.0711 (7) | 0.972 (2) |
| F2 | 0.30831 (8) | 0.52847 (19) | 0.04797 (8) | 0.0418 (4) | 0.972 (2) |
| F3 | 0.42321 (8) | 0.5801 (2) | 0.05379 (8) | 0.0470 (4) | 0.972 (2) |
| F1' | 0.352 (3) | 0.612 (3) | 0.0688 (18) | 0.0711 (7) | 0.028 (2) |
| F2' | 0.4387 (11) | 0.472 (6) | 0.0269 (18) | 0.0418 (4) | 0.028 (2) |
| F3' | 0.325 (2) | 0.397 (5) | 0.0129 (15) | 0.0470 (4) | 0.028 (2) |
| Cl1 | 0.38924 (3) | 0.05417 (6) | 0.31320 (2) | 0.02635 (16) |
| C1 | 0.0194 (9) | 0.0250 (9) | 0.0246 (9) | 0.0021 (7) | 0.0012 (7) | −0.0019 (8) |
| C2 | 0.0186 (8) | 0.0246 (9) | 0.0239 (9) | 0.0021 (7) | 0.0011 (7) | 0.0002 (8) |
| C3 | 0.0166 (8) | 0.0219 (9) | 0.0296 (10) | 0.0011 (7) | 0.0009 (7) | −0.0021 (8) |
| C4 | 0.0202 (9) | 0.0288 (10) | 0.0239 (9) | 0.0050 (8) | −0.0004 (7) | −0.0031 (8) |
| C5 | 0.0219 (9) | 0.0261 (10) | 0.0247 (10) | 0.0056 (8) | 0.0021 (7) | 0.0011 (8) |
| C6 | 0.0248 (10) | 0.0226 (9) | 0.0277 (10) | 0.0006 (8) | 0.0004 (8) | 0.0002 (8) |
| C7 | 0.0350 (11) | 0.0292 (11) | 0.0251 (10) | 0.0056 (9) | 0.0005 (8) | −0.0002 (8) |
| C8 | 0.0225 (9) | 0.0226 (9) | 0.0245 (9) | −0.0035 (8) | −0.0003 (7) | 0.0033 (8) |
| C9 | 0.0335 (11) | 0.0298 (11) | 0.0347 (11) | 0.0094 (9) | −0.0117 (9) | −0.0088 (9) |
| C10 | 0.0200 (10) | 0.0517 (15) | 0.0495 (14) | 0.0058 (9) | −0.0038 (9) | −0.0188 (11) |
| C11 | 0.0324 (11) | 0.0474 (14) | 0.0322 (11) | 0.0039 (10) | −0.0011 (9) | −0.0114 (10) |
| C12 | 0.0308 (11) | 0.0327 (11) | 0.0247 (10) | −0.0010 (9) | −0.0013 (8) | 0.0002 (8) |
| C13 | 0.0267 (10) | 0.0306 (10) | 0.0257 (10) | −0.0070 (8) | −0.0028 (8) | −0.0018 (8) |
| N1 | 0.0190 (8) | 0.0260 (9) | 0.0310 (9) | −0.0009 (6) | −0.0037 (7) | −0.0016 (7) |
| N2 | 0.0213 (8) | 0.0277 (9) | 0.0257 (8) | −0.0010 (7) | −0.0042 (7) | −0.0030 (7) |
| O1 | 0.0267 (7) | 0.0334 (8) | 0.0371 (8) | −0.0062 (6) | 0.0010 (6) | 0.0028 (7) |
| O2 | 0.0348 (8) | 0.0320 (8) | 0.0356 (8) | −0.0010 (6) | −0.0045 (6) | −0.0098 (7) |
| O3 | 0.0204 (7) | 0.0324 (8) | 0.0337 (8) | 0.0005 (6) | −0.0017 (6) | −0.0003 (6) |
| F1 | 0.151 (2) | 0.0382 (9) | 0.0239 (7) | 0.0278 (10) | 0.0154 (9) | −0.0002 (6) |
| F2 | 0.0336 (7) | 0.0457 (8) | 0.0460 (8) | 0.0053 (6) | −0.0056 (6) | 0.0175 (7) |
| F3 | 0.0389 (8) | 0.0567 (10) | 0.0453 (8) | −0.0142 (7) | −0.0052 (6) | 0.0251 (7) |
| F1' | 0.151 (2) | 0.0382 (9) | 0.0239 (7) | 0.0278 (10) | 0.0154 (9) | −0.0002 (6) |
| F2' | 0.0336 (7) | 0.0457 (8) | 0.0460 (8) | 0.0053 (6) | −0.0056 (6) | 0.0175 (7) |
| F3' | 0.0389 (8) | 0.0567 (10) | 0.0453 (8) | −0.0142 (7) | −0.0052 (6) | 0.0251 (7) |
| Cl1 | 0.0267 (3) | 0.0273 (3) | 0.0250 (3) | −0.00271 (18) | 0.00002 (17) | 0.00364 (17) |
| C1—C2 | 1.389 (3) | C8—N2 | 1.342 (3) |
| C1—C6 | 1.395 (3) | C9—N2 | 1.465 (3) |
| C1—C8 | 1.510 (3) | C9—C10 | 1.519 (3) |
| C2—C3 | 1.398 (3) | C9—H9A | 0.9900 |
| C2—Cl1 | 1.725 (2) | C9—H9B | 0.9900 |
| C3—C4 | 1.380 (3) | C10—C11 | 1.525 (3) |
| C3—N1 | 1.468 (3) | C10—H10A | 0.9900 |
| C4—C5 | 1.390 (3) | C10—H10B | 0.9900 |
| C4—H4 | 0.9500 | C11—C12 | 1.522 (3) |
| C5—C6 | 1.386 (3) | C11—H11A | 0.9900 |
| C5—C7 | 1.497 (3) | C11—H11B | 0.9900 |
| C6—H6 | 0.9500 | C12—C13 | 1.518 (3) |
| C7—F2' | 1.304 (14) | C12—H12A | 0.9900 |
| C7—F3' | 1.314 (14) | C12—H12B | 0.9900 |
| C7—F1 | 1.325 (3) | C13—N2 | 1.465 (2) |
| C7—F3 | 1.328 (3) | C13—H13A | 0.9900 |
| C7—F1' | 1.332 (14) | C13—H13B | 0.9900 |
| C7—F2 | 1.336 (3) | N1—O2 | 1.225 (2) |
| C8—O3 | 1.234 (2) | N1—O1 | 1.229 (2) |
| C2—C1—C6 | 120.16 (18) | C10—C9—H9A | 109.5 |
| C2—C1—C8 | 119.82 (17) | N2—C9—H9B | 109.5 |
| C6—C1—C8 | 119.90 (17) | C10—C9—H9B | 109.5 |
| C1—C2—C3 | 118.92 (18) | H9A—C9—H9B | 108.1 |
| C1—C2—Cl1 | 117.93 (15) | C9—C10—C11 | 110.61 (19) |
| C3—C2—Cl1 | 123.13 (16) | C9—C10—H10A | 109.5 |
| C4—C3—C2 | 121.24 (18) | C11—C10—H10A | 109.5 |
| C4—C3—N1 | 116.41 (17) | C9—C10—H10B | 109.5 |
| C2—C3—N1 | 122.35 (18) | C11—C10—H10B | 109.5 |
| C3—C4—C5 | 119.32 (18) | H10A—C10—H10B | 108.1 |
| C3—C4—H4 | 120.3 | C12—C11—C10 | 109.74 (18) |
| C5—C4—H4 | 120.3 | C12—C11—H11A | 109.7 |
| C6—C5—C4 | 120.33 (18) | C10—C11—H11A | 109.7 |
| C6—C5—C7 | 120.58 (19) | C12—C11—H11B | 109.7 |
| C4—C5—C7 | 119.09 (18) | C10—C11—H11B | 109.7 |
| C5—C6—C1 | 119.98 (19) | H11A—C11—H11B | 108.2 |
| C5—C6—H6 | 120.0 | C13—C12—C11 | 111.01 (18) |
| C1—C6—H6 | 120.0 | C13—C12—H12A | 109.4 |
| F2'—C7—F3' | 111.1 (19) | C11—C12—H12A | 109.4 |
| F1—C7—F3 | 107.69 (19) | C13—C12—H12B | 109.4 |
| F2'—C7—F1' | 105.2 (19) | C11—C12—H12B | 109.4 |
| F3'—C7—F1' | 104.0 (19) | H12A—C12—H12B | 108.0 |
| F1—C7—F2 | 105.98 (19) | N2—C13—C12 | 111.35 (17) |
| F3—C7—F2 | 105.59 (17) | N2—C13—H13A | 109.4 |
| F2'—C7—C5 | 112.3 (15) | C12—C13—H13A | 109.4 |
| F3'—C7—C5 | 113.2 (15) | N2—C13—H13B | 109.4 |
| F1—C7—C5 | 112.43 (17) | C12—C13—H13B | 109.4 |
| F3—C7—C5 | 112.80 (18) | H13A—C13—H13B | 108.0 |
| F1'—C7—C5 | 110.3 (15) | O2—N1—O1 | 124.48 (17) |
| F2—C7—C5 | 111.86 (17) | O2—N1—C3 | 117.04 (17) |
| O3—C8—N2 | 124.72 (18) | O1—N1—C3 | 118.44 (16) |
| O3—C8—C1 | 118.43 (18) | C8—N2—C13 | 120.26 (16) |
| N2—C8—C1 | 116.85 (17) | C8—N2—C9 | 124.74 (16) |
| N2—C9—C10 | 110.59 (18) | C13—N2—C9 | 114.89 (16) |
| N2—C9—H9A | 109.5 | ||
| C6—C1—C2—C3 | 1.9 (3) | C6—C5—C7—F1' | −47 (3) |
| C8—C1—C2—C3 | −174.16 (17) | C4—C5—C7—F1' | 133 (3) |
| C6—C1—C2—Cl1 | −179.32 (15) | C6—C5—C7—F2 | −99.4 (2) |
| C8—C1—C2—Cl1 | 4.6 (2) | C4—C5—C7—F2 | 80.3 (2) |
| C1—C2—C3—C4 | −0.5 (3) | C2—C1—C8—O3 | 77.8 (2) |
| Cl1—C2—C3—C4 | −179.22 (14) | C6—C1—C8—O3 | −98.3 (2) |
| C1—C2—C3—N1 | 179.37 (16) | C2—C1—C8—N2 | −102.6 (2) |
| Cl1—C2—C3—N1 | 0.6 (3) | C6—C1—C8—N2 | 81.4 (2) |
| C2—C3—C4—C5 | −0.9 (3) | N2—C9—C10—C11 | 55.5 (3) |
| N1—C3—C4—C5 | 179.25 (16) | C9—C10—C11—C12 | −56.9 (3) |
| C3—C4—C5—C6 | 0.9 (3) | C10—C11—C12—C13 | 55.8 (3) |
| C3—C4—C5—C7 | −178.87 (18) | C11—C12—C13—N2 | −53.4 (2) |
| C4—C5—C6—C1 | 0.5 (3) | C4—C3—N1—O2 | 36.6 (2) |
| C7—C5—C6—C1 | −179.75 (18) | C2—C3—N1—O2 | −143.29 (19) |
| C2—C1—C6—C5 | −1.9 (3) | C4—C3—N1—O1 | −141.34 (18) |
| C8—C1—C6—C5 | 174.13 (18) | C2—C3—N1—O1 | 38.8 (3) |
| C6—C5—C7—F2' | 70 (2) | O3—C8—N2—C13 | 3.0 (3) |
| C4—C5—C7—F2' | −110 (2) | C1—C8—N2—C13 | −176.62 (17) |
| C6—C5—C7—F3' | −163 (2) | O3—C8—N2—C9 | 179.0 (2) |
| C4—C5—C7—F3' | 17 (2) | C1—C8—N2—C9 | −0.6 (3) |
| C6—C5—C7—F1 | 141.5 (2) | C12—C13—N2—C8 | −130.0 (2) |
| C4—C5—C7—F1 | −38.8 (3) | C12—C13—N2—C9 | 53.6 (2) |
| C6—C5—C7—F3 | 19.5 (3) | C10—C9—N2—C8 | 129.2 (2) |
| C4—C5—C7—F3 | −160.82 (18) | C10—C9—N2—C13 | −54.6 (2) |
| H··· | ||||
| C6—H6···O3i | 0.95 | 2.59 | 3.526 (3) | 169 |
| C9—H9 | 0.99 | 2.45 | 3.361 (3) | 154 |
| C9—H9 | 0.99 | 2.58 | 3.369 (3) | 137 |
| C13—H13 | 0.99 | 2.92 | 3.447 (2) | 114 |