| Literature DB >> 30443388 |
Yousef Hijji1, Ellis Benjamin2, Jerry P Jasinski3, Ray J Butcher4.
Abstract
The title compound, C13H16N2O4, crystallizes in the monoclinic centrosymmetric space group,Entities:
Keywords: crystal structure; pseudomerohedral twinning; thalidomide analogs
Year: 2018 PMID: 30443388 PMCID: PMC6218906 DOI: 10.1107/S2056989018014317
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of the title compound 4, with the atom-numbering scheme. Atomic displacement parameters are drawn at the 30% probability level.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| N2—H2 | 0.88 (5) | 2.07 (5) | 2.928 (3) | 165 (4) |
| C7—H7 | 1.00 | 2.42 | 3.150 (3) | 129 |
| C9—H9 | 1.00 | 2.65 | 3.385 (3) | 130 |
| C12—H12 | 0.99 | 2.53 | 3.143 (3) | 120 |
| C13—H13 | 0.99 | 2.56 | 3.142 (3) | 118 |
| C13—H13 | 0.99 | 2.52 | 3.163 (3) | 122 |
Symmetry codes: (i) ; (ii) ; (iii) .
Figure 2Packing diagram viewed along the a axis showing the extensive N—H⋯O and C—H⋯O interactions (drawn as dashed lines) linking the molecules into a complex three-dimensional array.
Experimental details
| Crystal data | |
| Chemical formula | C13H16N2O4 |
|
| 264.28 |
| Crystal system, space group | Monoclinic, |
| Temperature (K) | 123 |
|
| 11.4519 (3), 9.2370 (3), 11.8727 (4) |
| β (°) | 90.475 (3) |
|
| 1255.87 (7) |
|
| 4 |
| Radiation type | Cu |
| μ (mm−1) | 0.87 |
| Crystal size (mm) | 0.42 × 0.34 × 0.18 |
| Data collection | |
| Diffractometer | Rigaku Oxford Diffraction Xcalibur, Ruby, Gemini |
| Absorption correction | Multi-scan ( |
|
| 0.822, 1.000 |
| No. of measured, independent and observed [ | 9733, 2626, 2572 |
|
| 0.024 |
| (sin θ/λ)max (Å−1) | 0.633 |
| Refinement | |
|
| 0.066, 0.208, 1.19 |
| No. of reflections | 2626 |
| No. of parameters | 177 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.33, −0.35 |
Computer programs: CrysAlis PRO (Rigaku OD, 2012 ▸), SHELXS97 and SHELXTL (Sheldrick, 2008 ▸) and SHELXL2018/3 (Sheldrick, 2015 ▸).
| C13H16N2O4 | |
| Monoclinic, | Cu |
| Cell parameters from 7629 reflections | |
| θ = 3.7–77.3° | |
| µ = 0.87 mm−1 | |
| β = 90.475 (3)° | |
| Prism, colorless | |
| 0.42 × 0.34 × 0.18 mm |
| Rigaku Oxford Diffraction Xcalibur, Ruby, Gemini diffractometer | 2572 reflections with |
| Detector resolution: 10.5081 pixels mm-1 | |
| ω scans | θmax = 77.5°, θmin = 3.7° |
| Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2012) | |
| 9733 measured reflections | |
| 2626 independent reflections |
| Refinement on | Primary atom site location: structure-invariant direct methods |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| Hydrogen site location: mixed | |
| H atoms treated by a mixture of independent and constrained refinement | |
| 2626 reflections | (Δ/σ)max < 0.001 |
| 177 parameters | Δρmax = 0.33 e Å−3 |
| 0 restraints | Δρmin = −0.35 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. |
| Refinement. Refined as a two-component twin |
| O1 | 0.66960 (17) | 0.4309 (2) | 0.56402 (17) | 0.0291 (4) | |
| O2 | 0.67111 (18) | 0.8499 (2) | 0.76606 (18) | 0.0305 (5) | |
| O3 | 0.58392 (17) | 0.8448 (2) | 0.51862 (17) | 0.0299 (5) | |
| O4 | 0.21720 (17) | 0.9000 (2) | 0.64578 (19) | 0.0339 (5) | |
| N1 | 0.64254 (19) | 0.6373 (2) | 0.66901 (18) | 0.0228 (5) | |
| N2 | 0.4008 (2) | 0.8685 (2) | 0.58537 (19) | 0.0263 (5) | |
| H2N | 0.393 (4) | 0.952 (5) | 0.550 (3) | 0.043 (10)* | |
| C1 | 0.7100 (2) | 0.5317 (3) | 0.6160 (2) | 0.0233 (5) | |
| C2 | 0.8368 (2) | 0.5762 (3) | 0.6283 (2) | 0.0240 (5) | |
| H2A | 0.886927 | 0.491448 | 0.648892 | 0.029* | |
| C3 | 0.8713 (2) | 0.6388 (3) | 0.5124 (2) | 0.0288 (6) | |
| H3A | 0.893112 | 0.558146 | 0.461791 | 0.035* | |
| H3B | 0.802837 | 0.688401 | 0.478581 | 0.035* | |
| C4 | 0.9729 (2) | 0.7454 (3) | 0.5201 (2) | 0.0311 (6) | |
| H4A | 1.043151 | 0.695475 | 0.549779 | 0.037* | |
| H4B | 0.990952 | 0.783222 | 0.444218 | 0.037* | |
| C5 | 0.9407 (2) | 0.8704 (3) | 0.5979 (2) | 0.0295 (6) | |
| H5A | 1.003226 | 0.944367 | 0.597275 | 0.035* | |
| H5B | 0.867389 | 0.916344 | 0.571200 | 0.035* | |
| C6 | 0.9248 (2) | 0.8128 (3) | 0.7171 (2) | 0.0278 (6) | |
| H6A | 0.899178 | 0.893048 | 0.766341 | 0.033* | |
| H6B | 1.001037 | 0.777727 | 0.746054 | 0.033* | |
| C7 | 0.8356 (2) | 0.6895 (3) | 0.7240 (2) | 0.0236 (5) | |
| H7A | 0.850009 | 0.636936 | 0.796398 | 0.028* | |
| C8 | 0.7103 (2) | 0.7412 (3) | 0.7241 (2) | 0.0235 (5) | |
| C9 | 0.5186 (2) | 0.6584 (3) | 0.6460 (2) | 0.0236 (5) | |
| H9A | 0.491323 | 0.576348 | 0.597625 | 0.028* | |
| C10 | 0.5061 (2) | 0.7980 (3) | 0.5776 (2) | 0.0239 (5) | |
| C11 | 0.3047 (2) | 0.8261 (3) | 0.6481 (2) | 0.0264 (5) | |
| C12 | 0.3171 (2) | 0.6889 (3) | 0.7153 (2) | 0.0285 (6) | |
| H12A | 0.288711 | 0.606388 | 0.669460 | 0.034* | |
| H12B | 0.267804 | 0.695498 | 0.783153 | 0.034* | |
| C13 | 0.4435 (2) | 0.6608 (3) | 0.7512 (2) | 0.0260 (5) | |
| H13A | 0.470638 | 0.737979 | 0.802975 | 0.031* | |
| H13B | 0.449314 | 0.566826 | 0.790999 | 0.031* |
| O1 | 0.0298 (9) | 0.0199 (9) | 0.0374 (10) | −0.0011 (7) | −0.0051 (8) | −0.0043 (7) |
| O2 | 0.0306 (10) | 0.0200 (9) | 0.0407 (11) | 0.0001 (7) | −0.0028 (8) | −0.0059 (7) |
| O3 | 0.0280 (10) | 0.0269 (10) | 0.0347 (10) | 0.0042 (7) | 0.0006 (8) | 0.0055 (7) |
| O4 | 0.0266 (9) | 0.0273 (10) | 0.0478 (12) | 0.0052 (8) | −0.0031 (8) | −0.0019 (9) |
| N1 | 0.0226 (10) | 0.0164 (9) | 0.0294 (10) | 0.0004 (8) | −0.0062 (8) | 0.0003 (8) |
| N2 | 0.0260 (11) | 0.0189 (10) | 0.0337 (11) | 0.0043 (8) | −0.0044 (9) | 0.0023 (9) |
| C1 | 0.0265 (12) | 0.0173 (11) | 0.0259 (11) | 0.0017 (9) | −0.0049 (9) | 0.0024 (9) |
| C2 | 0.0245 (11) | 0.0177 (11) | 0.0297 (12) | 0.0005 (9) | −0.0039 (9) | 0.0002 (9) |
| C3 | 0.0297 (13) | 0.0276 (13) | 0.0291 (13) | −0.0027 (10) | −0.0008 (10) | −0.0019 (10) |
| C4 | 0.0306 (13) | 0.0319 (14) | 0.0309 (13) | −0.0046 (11) | −0.0008 (10) | 0.0011 (10) |
| C5 | 0.0286 (13) | 0.0252 (13) | 0.0345 (14) | −0.0050 (10) | −0.0035 (10) | 0.0027 (10) |
| C6 | 0.0250 (12) | 0.0275 (12) | 0.0309 (13) | −0.0053 (10) | −0.0045 (10) | −0.0006 (10) |
| C7 | 0.0240 (11) | 0.0216 (11) | 0.0253 (11) | −0.0020 (9) | −0.0039 (9) | 0.0014 (9) |
| C8 | 0.0250 (11) | 0.0195 (11) | 0.0258 (11) | −0.0010 (9) | −0.0043 (9) | 0.0017 (9) |
| C9 | 0.0219 (11) | 0.0170 (11) | 0.0319 (12) | 0.0015 (8) | −0.0070 (9) | −0.0005 (9) |
| C10 | 0.0253 (11) | 0.0180 (11) | 0.0283 (11) | 0.0021 (9) | −0.0054 (9) | −0.0006 (9) |
| C11 | 0.0242 (12) | 0.0213 (12) | 0.0336 (13) | 0.0007 (9) | −0.0054 (10) | −0.0053 (10) |
| C12 | 0.0245 (12) | 0.0217 (12) | 0.0393 (14) | −0.0016 (9) | −0.0017 (10) | 0.0001 (10) |
| C13 | 0.0239 (12) | 0.0218 (12) | 0.0322 (13) | −0.0007 (9) | −0.0034 (10) | 0.0030 (9) |
| O1—C1 | 1.207 (3) | C4—H4B | 0.9900 |
| O2—C8 | 1.208 (3) | C5—C6 | 1.525 (4) |
| O3—C10 | 1.217 (3) | C5—H5A | 0.9900 |
| O4—C11 | 1.213 (3) | C5—H5B | 0.9900 |
| N1—C8 | 1.394 (3) | C6—C7 | 1.532 (3) |
| N1—C1 | 1.397 (3) | C6—H6A | 0.9900 |
| N1—C9 | 1.456 (3) | C6—H6B | 0.9900 |
| N2—C10 | 1.374 (3) | C7—C8 | 1.513 (3) |
| N2—C11 | 1.390 (4) | C7—H7A | 1.0000 |
| N2—H2N | 0.88 (5) | C9—C13 | 1.522 (4) |
| C1—C2 | 1.515 (3) | C9—C10 | 1.531 (3) |
| C2—C7 | 1.544 (3) | C9—H9A | 1.0000 |
| C2—C3 | 1.548 (4) | C11—C12 | 1.503 (4) |
| C2—H2A | 1.0000 | C12—C13 | 1.528 (4) |
| C3—C4 | 1.527 (4) | C12—H12A | 0.9900 |
| C3—H3A | 0.9900 | C12—H12B | 0.9900 |
| C3—H3B | 0.9900 | C13—H13A | 0.9900 |
| C4—C5 | 1.525 (4) | C13—H13B | 0.9900 |
| C4—H4A | 0.9900 | ||
| C8—N1—C1 | 112.6 (2) | C5—C6—H6B | 108.9 |
| C8—N1—C9 | 122.3 (2) | C7—C6—H6B | 108.9 |
| C1—N1—C9 | 123.4 (2) | H6A—C6—H6B | 107.8 |
| C10—N2—C11 | 127.0 (2) | C8—C7—C6 | 113.4 (2) |
| C10—N2—H2N | 118 (3) | C8—C7—C2 | 103.24 (19) |
| C11—N2—H2N | 115 (3) | C6—C7—C2 | 117.1 (2) |
| O1—C1—N1 | 123.9 (2) | C8—C7—H7A | 107.5 |
| O1—C1—C2 | 128.4 (2) | C6—C7—H7A | 107.5 |
| N1—C1—C2 | 107.5 (2) | C2—C7—H7A | 107.5 |
| C1—C2—C7 | 103.9 (2) | O2—C8—N1 | 123.9 (2) |
| C1—C2—C3 | 105.49 (19) | O2—C8—C7 | 128.2 (2) |
| C7—C2—C3 | 113.9 (2) | N1—C8—C7 | 107.8 (2) |
| C1—C2—H2A | 111.1 | N1—C9—C13 | 113.9 (2) |
| C7—C2—H2A | 111.1 | N1—C9—C10 | 107.4 (2) |
| C3—C2—H2A | 111.1 | C13—C9—C10 | 111.9 (2) |
| C4—C3—C2 | 112.8 (2) | N1—C9—H9A | 107.8 |
| C4—C3—H3A | 109.0 | C13—C9—H9A | 107.8 |
| C2—C3—H3A | 109.0 | C10—C9—H9A | 107.8 |
| C4—C3—H3B | 109.0 | O3—C10—N2 | 121.2 (2) |
| C2—C3—H3B | 109.0 | O3—C10—C9 | 122.6 (2) |
| H3A—C3—H3B | 107.8 | N2—C10—C9 | 116.2 (2) |
| C5—C4—C3 | 109.7 (2) | O4—C11—N2 | 119.1 (2) |
| C5—C4—H4A | 109.7 | O4—C11—C12 | 124.1 (3) |
| C3—C4—H4A | 109.7 | N2—C11—C12 | 116.8 (2) |
| C5—C4—H4B | 109.7 | C11—C12—C13 | 112.1 (2) |
| C3—C4—H4B | 109.7 | C11—C12—H12A | 109.2 |
| H4A—C4—H4B | 108.2 | C13—C12—H12A | 109.2 |
| C6—C5—C4 | 109.2 (2) | C11—C12—H12B | 109.2 |
| C6—C5—H5A | 109.8 | C13—C12—H12B | 109.2 |
| C4—C5—H5A | 109.8 | H12A—C12—H12B | 107.9 |
| C6—C5—H5B | 109.8 | C9—C13—C12 | 108.3 (2) |
| C4—C5—H5B | 109.8 | C9—C13—H13A | 110.0 |
| H5A—C5—H5B | 108.3 | C12—C13—H13A | 110.0 |
| C5—C6—C7 | 113.2 (2) | C9—C13—H13B | 110.0 |
| C5—C6—H6A | 108.9 | C12—C13—H13B | 110.0 |
| C7—C6—H6A | 108.9 | H13A—C13—H13B | 108.4 |
| C8—N1—C1—O1 | 179.5 (2) | C9—N1—C8—C7 | −174.9 (2) |
| C9—N1—C1—O1 | −15.2 (4) | C6—C7—C8—O2 | −34.8 (4) |
| C8—N1—C1—C2 | −5.3 (3) | C2—C7—C8—O2 | −162.5 (3) |
| C9—N1—C1—C2 | 160.0 (2) | C6—C7—C8—N1 | 147.1 (2) |
| O1—C1—C2—C7 | −167.9 (2) | C2—C7—C8—N1 | 19.4 (3) |
| N1—C1—C2—C7 | 17.2 (2) | C8—N1—C9—C13 | −67.6 (3) |
| O1—C1—C2—C3 | 72.0 (3) | C1—N1—C9—C13 | 128.4 (2) |
| N1—C1—C2—C3 | −102.9 (2) | C8—N1—C9—C10 | 56.9 (3) |
| C1—C2—C3—C4 | 155.2 (2) | C1—N1—C9—C10 | −107.1 (3) |
| C7—C2—C3—C4 | 41.9 (3) | C11—N2—C10—O3 | 179.1 (2) |
| C2—C3—C4—C5 | −58.7 (3) | C11—N2—C10—C9 | −0.4 (4) |
| C3—C4—C5—C6 | 64.9 (3) | N1—C9—C10—O3 | 25.9 (3) |
| C4—C5—C6—C7 | −55.2 (3) | C13—C9—C10—O3 | 151.6 (2) |
| C5—C6—C7—C8 | −80.1 (3) | N1—C9—C10—N2 | −154.6 (2) |
| C5—C6—C7—C2 | 40.0 (3) | C13—C9—C10—N2 | −28.9 (3) |
| C1—C2—C7—C8 | −21.7 (2) | C10—N2—C11—O4 | −179.6 (2) |
| C3—C2—C7—C8 | 92.6 (2) | C10—N2—C11—C12 | 0.4 (4) |
| C1—C2—C7—C6 | −147.1 (2) | O4—C11—C12—C13 | −151.1 (3) |
| C3—C2—C7—C6 | −32.8 (3) | N2—C11—C12—C13 | 28.9 (3) |
| C1—N1—C8—O2 | 172.5 (2) | N1—C9—C13—C12 | 178.0 (2) |
| C9—N1—C8—O2 | 6.9 (4) | C10—C9—C13—C12 | 55.9 (3) |
| C1—N1—C8—C7 | −9.4 (3) | C11—C12—C13—C9 | −56.1 (3) |
| H··· | ||||
| N2—H2 | 0.88 (5) | 2.07 (5) | 2.928 (3) | 165 (4) |
| C7—H7 | 1.00 | 2.42 | 3.150 (3) | 129 |
| C9—H9 | 1.00 | 2.65 | 3.385 (3) | 130 |
| C12—H12 | 0.99 | 2.53 | 3.143 (3) | 120 |
| C13—H13 | 0.99 | 2.56 | 3.142 (3) | 118 |
| C13—H13 | 0.99 | 2.52 | 3.163 (3) | 122 |