| Literature DB >> 28529789 |
Julio Zukerman-Schpector1, Angélica V Moro2,3, Marcelo R Dos Santos2,4, Carlos Roque D Correia2, Mukesh M Jotani5, Edward R T Tiekink6.
Abstract
The title isoaltholactone derivative, C13H13NO3, has an NH group in place of the ether-O atom in the five-membered ring of the natural product. The five-membered ring is twisted about the N-C bond linking it to the six-membered ring, which has a half-chair conformation with the O atom connected to the ether-O atom lying above the plane defined by the remaining atoms. The dihedral angle between the mean planes of the rings comprising the fused-ring system is 75.10 (8)°. In the crystal, hy-droxy-O-H⋯N(amine) hydrogen bonding sustains linear supra-molecular chains along the a axis. Chains are linked into a three-dimensional architecture via amine-N-H⋯π(phen-yl) and phenyl-C-H⋯O(hy-droxy) inter-actions. The influence of the amine-N-H⋯π(phen-yl) contact on the mol-ecular packing is revealed by an analysis of the Hirshfeld surface.Entities:
Keywords: Hirshfeld surface analysis; aza-isoaltholactone; crystal structure; hydrogen bonding
Year: 2017 PMID: 28529789 PMCID: PMC5418797 DOI: 10.1107/S2056989017005680
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of (I), showing the atom-labelling scheme and displacement ellipsoids at the 50% probability level.
Figure 2Molecular packing in (I): (a) a view of the supramolecular chain sustained by hydroxy-O—H⋯N(amine) hydrogen bonding and (b) a view of the unit-cell contents shown in projection down the a axis. The O—H⋯N, N—H⋯π and C—H⋯O interactions are shown as orange, purple and blue dashed lines, respectively.
Hydrogen-bond geometry (Å, °)
Cg1 is the centroid of the C8–C13 ring.
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| O3—H3 | 0.86 (2) | 2.07 (2) | 2.920 (3) | 174 (4) |
| N1—H1 | 0.87 (1) | 2.88 (2) | 3.705 (3) | 160 (2) |
| C11—H11⋯O1iii | 0.95 | 2.60 | 3.280 (3) | 129 |
Symmetry codes: (i) ; (ii) ; (iii) .
Figure 3Two views of the Hirshfeld surface for (I) mapped over d norm over the range −0.435 to 1.180 au.
Figure 4Two views of the Hirshfeld surfaces for (I) mapped over the calculated electrostatic potential over the range ±0.116 au. The red and blue regions represent negative and positive electrostatic potentials, respectively.
Figure 5Views of Hirshfeld surface for a reference molecule in (I) mapped over the shape-index property highlighting: (a) O—H⋯N hydrogen bonds (black dashed lines), (b) C—H⋯O interactions (black dashed lines) and (c) N—H⋯ π–π⋯H—N interactions as red- and white- dotted lines, respectively.
Figure 6(a) The full two-dimensional fingerprint plots for (I) and fingerprint plots delineated into (b) H⋯H, (c) O⋯H/H⋯O, (d) N⋯H/H⋯H and (e) C⋯H/H⋯C contacts.
Percentage contributions of inter-atomic contacts to the Hirshfeld surface for (I)
| Contact | percentage contribution |
|---|---|
| H⋯H | 50.4 |
| O⋯H/H⋯O | 25.1 |
| C⋯H/H⋯C | 18.9 |
| N⋯H/H⋯N | 3.0 |
| C⋯O/O⋯C | 1.3 |
| O⋯O | 1.3 |
Summary of short inter-atomic contacts (Å) in (I)
| Contact | distance | symmetry operation |
|---|---|---|
| H1 | 2.888 (18) | 1 − |
| H1 | 2.875 (19) | 1 − |
| H5⋯C10 | 2.89 | 1 − |
| H7⋯C9 | 2.84 | 1 − |
| H7⋯C10 | 2.80 | 1 − |
| H2⋯O2 | 2.64 | 2 − |
| H3⋯O1 | 2.62 | −1 + |
| C3⋯O1 | 3.209 (3) | −1 + |
Figure 7Molecular overlay diagram of (I) and (+)-isoaltholactone shown as red and blue images, respectively.
Experimental details
| Crystal data | |
| Chemical formula | C13H13NO3 |
|
| 231.24 |
| Crystal system, space group | Monoclinic, |
| Temperature (K) | 100 |
|
| 5.9638 (2), 8.4266 (3), 11.0246 (4) |
| β (°) | 92.779 (3) |
|
| 553.39 (3) |
|
| 2 |
| Radiation type | Mo |
| μ (mm−1) | 0.10 |
| Crystal size (mm) | 0.40 × 0.40 × 0.20 |
| Data collection | |
| Diffractometer | Bruker SMART APEXII |
| Absorption correction | Multi-scan ( |
|
| 0.914, 1.000 |
| No. of measured, independent and observed [ | 4550, 2377, 2149 |
|
| 0.017 |
| (sin θ/λ)max (Å−1) | 0.650 |
| Refinement | |
|
| 0.036, 0.094, 1.03 |
| No. of reflections | 2377 |
| No. of parameters | 160 |
| No. of restraints | 3 |
| H-atom treatment | H-atom parameters not refined |
| Δρmax, Δρmin (e Å−3) | 0.14, −0.19 |
| Absolute structure | Flack |
| Absolute structure parameter | 0.7 (5) |
Computer programs: APEX2 and SAINT (Bruker, 2007 ▸), SHELXS97 (Sheldrick, 2008 ▸), SHELXL2014 (Sheldrick, 2015 ▸), ORTEP-3 for Windows (Farrugia, 2012 ▸), QMol (Gans & Shalloway, 2001 ▸), DIAMOND (Brandenburg, 2006 ▸) and publCIF (Westrip, 2010 ▸).
| C13H13NO3 | |
| Monoclinic, | Mo |
| Cell parameters from 2450 reflections | |
| θ = 2.4–27.3° | |
| µ = 0.10 mm−1 | |
| β = 92.779 (3)° | |
| Block, colourless | |
| 0.40 × 0.40 × 0.20 mm |
| Bruker SMART APEXII diffractometer | 2377 independent reflections |
| Radiation source: sealed tube | 2149 reflections with |
| Graphite monochromator | |
| φ and ω scans | θmax = 27.5°, θmin = 1.9° |
| Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | |
| 4550 measured reflections |
| Refinement on | H-atom parameters not refined |
| Least-squares matrix: full | |
| (Δ/σ)max < 0.001 | |
| Δρmax = 0.14 e Å−3 | |
| Δρmin = −0.19 e Å−3 | |
| 2377 reflections | Absolute structure: Flack |
| 160 parameters | Absolute structure parameter: 0.7 (5) |
| 3 restraints |
| 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. |
| O1 | 1.1372 (3) | 0.1225 (4) | 0.51075 (18) | 0.0772 (7) | |
| O2 | 1.0038 (3) | −0.0413 (2) | 0.37308 (15) | 0.0519 (5) | |
| O3 | 1.0370 (3) | 0.1267 (2) | 0.16741 (16) | 0.0474 (4) | |
| H3O | 1.171 (3) | 0.091 (5) | 0.176 (3) | 0.071* | |
| N1 | 0.4839 (3) | −0.0156 (3) | 0.18328 (16) | 0.0399 (4) | |
| H1N | 0.463 (4) | −0.1113 (19) | 0.156 (2) | 0.048* | |
| C1 | 0.9838 (4) | 0.0886 (4) | 0.44096 (19) | 0.0497 (6) | |
| C2 | 0.7749 (4) | 0.1800 (3) | 0.4292 (2) | 0.0499 (6) | |
| H2 | 0.7692 | 0.2817 | 0.4661 | 0.060* | |
| C3 | 0.5947 (4) | 0.1256 (4) | 0.3691 (2) | 0.0452 (5) | |
| H3 | 0.4612 | 0.1873 | 0.3664 | 0.054* | |
| C4 | 0.5952 (4) | −0.0302 (3) | 0.3053 (2) | 0.0424 (5) | |
| H4 | 0.5202 | −0.1133 | 0.3538 | 0.051* | |
| C5 | 0.8350 (4) | −0.0795 (3) | 0.2802 (2) | 0.0427 (5) | |
| H5 | 0.8361 | −0.1971 | 0.2683 | 0.051* | |
| C6 | 0.8844 (3) | −0.0009 (3) | 0.15679 (18) | 0.0371 (5) | |
| H6 | 0.9389 | −0.0821 | 0.0990 | 0.044* | |
| C7 | 0.6538 (3) | 0.0636 (3) | 0.11123 (18) | 0.0325 (4) | |
| H7 | 0.6510 | 0.1788 | 0.1330 | 0.039* | |
| C8 | 0.6046 (3) | 0.0531 (3) | −0.02427 (19) | 0.0343 (4) | |
| C9 | 0.3983 (4) | 0.0059 (3) | −0.0742 (2) | 0.0429 (5) | |
| H9 | 0.2824 | −0.0227 | −0.0222 | 0.051* | |
| C10 | 0.3576 (4) | −0.0004 (3) | −0.1992 (2) | 0.0483 (6) | |
| H10 | 0.2153 | −0.0342 | −0.2319 | 0.058* | |
| C11 | 0.5227 (4) | 0.0422 (3) | −0.2758 (2) | 0.0495 (6) | |
| H11 | 0.4947 | 0.0384 | −0.3614 | 0.059* | |
| C12 | 0.7296 (4) | 0.0904 (4) | −0.2272 (2) | 0.0513 (6) | |
| H12 | 0.8446 | 0.1197 | −0.2796 | 0.062* | |
| C13 | 0.7697 (4) | 0.0962 (3) | −0.1027 (2) | 0.0457 (6) | |
| H13 | 0.9122 | 0.1302 | −0.0703 | 0.055* |
| O1 | 0.0479 (11) | 0.130 (2) | 0.0521 (10) | 0.0000 (13) | −0.0175 (9) | −0.0153 (14) |
| O2 | 0.0411 (9) | 0.0693 (12) | 0.0437 (8) | 0.0104 (8) | −0.0133 (7) | 0.0077 (9) |
| O3 | 0.0286 (7) | 0.0602 (10) | 0.0528 (9) | −0.0071 (7) | −0.0035 (7) | 0.0029 (9) |
| N1 | 0.0318 (9) | 0.0502 (11) | 0.0374 (9) | −0.0081 (9) | −0.0018 (7) | 0.0015 (9) |
| C1 | 0.0378 (12) | 0.0800 (19) | 0.0307 (10) | −0.0039 (12) | −0.0044 (9) | 0.0034 (12) |
| C2 | 0.0434 (13) | 0.0707 (17) | 0.0356 (11) | 0.0002 (12) | 0.0022 (10) | −0.0095 (11) |
| C3 | 0.0333 (11) | 0.0673 (15) | 0.0351 (10) | 0.0030 (11) | 0.0037 (8) | −0.0010 (11) |
| C4 | 0.0341 (11) | 0.0546 (14) | 0.0383 (11) | −0.0068 (10) | −0.0009 (8) | 0.0079 (11) |
| C5 | 0.0398 (12) | 0.0440 (12) | 0.0433 (12) | 0.0033 (10) | −0.0084 (10) | 0.0047 (10) |
| C6 | 0.0278 (9) | 0.0451 (12) | 0.0379 (10) | 0.0038 (9) | −0.0027 (8) | −0.0032 (10) |
| C7 | 0.0258 (9) | 0.0366 (10) | 0.0348 (10) | 0.0011 (8) | −0.0010 (8) | 0.0003 (9) |
| C8 | 0.0309 (10) | 0.0354 (10) | 0.0363 (10) | 0.0033 (8) | −0.0025 (9) | 0.0000 (8) |
| C9 | 0.0322 (10) | 0.0561 (14) | 0.0400 (11) | −0.0028 (10) | −0.0014 (9) | −0.0019 (11) |
| C10 | 0.0391 (11) | 0.0620 (15) | 0.0426 (12) | −0.0018 (12) | −0.0098 (10) | −0.0040 (12) |
| C11 | 0.0535 (14) | 0.0582 (14) | 0.0363 (11) | 0.0033 (12) | −0.0036 (11) | 0.0019 (11) |
| C12 | 0.0468 (13) | 0.0663 (18) | 0.0410 (12) | −0.0055 (12) | 0.0039 (10) | 0.0090 (12) |
| C13 | 0.0373 (12) | 0.0560 (14) | 0.0433 (12) | −0.0076 (10) | −0.0032 (9) | 0.0050 (11) |
| O1—C1 | 1.201 (3) | C5—H5 | 1.0000 |
| O2—C1 | 1.334 (4) | C6—C7 | 1.540 (3) |
| O2—C5 | 1.437 (3) | C6—H6 | 1.0000 |
| O3—C6 | 1.409 (3) | C7—C8 | 1.511 (3) |
| O3—H3O | 0.852 (13) | C7—H7 | 1.0000 |
| N1—C4 | 1.476 (3) | C8—C9 | 1.382 (3) |
| N1—C7 | 1.477 (3) | C8—C13 | 1.390 (3) |
| N1—H1N | 0.869 (13) | C9—C10 | 1.388 (3) |
| C1—C2 | 1.465 (4) | C9—H9 | 0.9500 |
| C2—C3 | 1.317 (3) | C10—C11 | 1.376 (4) |
| C2—H2 | 0.9500 | C10—H10 | 0.9500 |
| C3—C4 | 1.490 (4) | C11—C12 | 1.383 (4) |
| C3—H3 | 0.9500 | C11—H11 | 0.9500 |
| C4—C5 | 1.527 (3) | C12—C13 | 1.383 (3) |
| C4—H4 | 1.0000 | C12—H12 | 0.9500 |
| C5—C6 | 1.554 (3) | C13—H13 | 0.9500 |
| C1—O2—C5 | 120.30 (18) | C7—C6—C5 | 103.38 (16) |
| C6—O3—H3O | 110 (3) | O3—C6—H6 | 110.3 |
| C4—N1—C7 | 103.78 (16) | C7—C6—H6 | 110.3 |
| C4—N1—H1N | 107.0 (17) | C5—C6—H6 | 110.3 |
| C7—N1—H1N | 108.7 (18) | N1—C7—C8 | 113.57 (17) |
| O1—C1—O2 | 117.9 (3) | N1—C7—C6 | 106.87 (16) |
| O1—C1—C2 | 123.3 (3) | C8—C7—C6 | 115.42 (17) |
| O2—C1—C2 | 118.7 (2) | N1—C7—H7 | 106.8 |
| C3—C2—C1 | 122.1 (3) | C8—C7—H7 | 106.8 |
| C3—C2—H2 | 119.0 | C6—C7—H7 | 106.8 |
| C1—C2—H2 | 119.0 | C9—C8—C13 | 118.11 (19) |
| C2—C3—C4 | 121.6 (2) | C9—C8—C7 | 122.51 (19) |
| C2—C3—H3 | 119.2 | C13—C8—C7 | 119.36 (19) |
| C4—C3—H3 | 119.2 | C8—C9—C10 | 121.1 (2) |
| N1—C4—C3 | 110.2 (2) | C8—C9—H9 | 119.5 |
| N1—C4—C5 | 103.95 (18) | C10—C9—H9 | 119.5 |
| C3—C4—C5 | 110.40 (19) | C11—C10—C9 | 120.3 (2) |
| N1—C4—H4 | 110.7 | C11—C10—H10 | 119.9 |
| C3—C4—H4 | 110.7 | C9—C10—H10 | 119.9 |
| C5—C4—H4 | 110.7 | C10—C11—C12 | 119.4 (2) |
| O2—C5—C4 | 116.09 (19) | C10—C11—H11 | 120.3 |
| O2—C5—C6 | 111.85 (19) | C12—C11—H11 | 120.3 |
| C4—C5—C6 | 105.18 (17) | C13—C12—C11 | 120.2 (2) |
| O2—C5—H5 | 107.8 | C13—C12—H12 | 119.9 |
| C4—C5—H5 | 107.8 | C11—C12—H12 | 119.9 |
| C6—C5—H5 | 107.8 | C12—C13—C8 | 121.0 (2) |
| O3—C6—C7 | 108.71 (18) | C12—C13—H13 | 119.5 |
| O3—C6—C5 | 113.67 (18) | C8—C13—H13 | 119.5 |
| C5—O2—C1—O1 | −174.2 (2) | C4—N1—C7—C8 | 164.56 (19) |
| C5—O2—C1—C2 | 7.4 (3) | C4—N1—C7—C6 | 36.1 (2) |
| O1—C1—C2—C3 | −167.4 (3) | O3—C6—C7—N1 | −137.08 (18) |
| O2—C1—C2—C3 | 10.9 (4) | C5—C6—C7—N1 | −16.0 (2) |
| C1—C2—C3—C4 | −2.3 (4) | O3—C6—C7—C8 | 95.6 (2) |
| C7—N1—C4—C3 | 76.7 (2) | C5—C6—C7—C8 | −143.36 (19) |
| C7—N1—C4—C5 | −41.6 (2) | N1—C7—C8—C9 | 13.6 (3) |
| C2—C3—C4—N1 | −135.3 (2) | C6—C7—C8—C9 | 137.5 (2) |
| C2—C3—C4—C5 | −21.0 (3) | N1—C7—C8—C13 | −168.2 (2) |
| C1—O2—C5—C4 | −32.2 (3) | C6—C7—C8—C13 | −44.3 (3) |
| C1—O2—C5—C6 | 88.5 (3) | C13—C8—C9—C10 | 0.8 (4) |
| N1—C4—C5—O2 | 155.49 (19) | C7—C8—C9—C10 | 179.1 (2) |
| C3—C4—C5—O2 | 37.3 (3) | C8—C9—C10—C11 | −0.7 (4) |
| N1—C4—C5—C6 | 31.3 (2) | C9—C10—C11—C12 | 0.3 (4) |
| C3—C4—C5—C6 | −86.9 (2) | C10—C11—C12—C13 | −0.2 (4) |
| O2—C5—C6—O3 | −18.5 (3) | C11—C12—C13—C8 | 0.4 (4) |
| C4—C5—C6—O3 | 108.4 (2) | C9—C8—C13—C12 | −0.7 (4) |
| O2—C5—C6—C7 | −136.12 (18) | C7—C8—C13—C12 | −179.0 (2) |
| C4—C5—C6—C7 | −9.3 (2) |
| H··· | ||||
| O3—H3 | 0.86 (2) | 2.07 (2) | 2.920 (3) | 174 (4) |
| N1—H1 | 0.87 (1) | 2.88 (2) | 3.705 (3) | 160 (2) |
| C11—H11···O1iii | 0.95 | 2.60 | 3.280 (3) | 129 |