| Literature DB >> 29765766 |
Takeshi Oishi1, Makoto Yoritate2, Takaaki Sato2, Noritaka Chida2.
Abstract
The title compound, C17H23NO4·H2O, is an epimer of the natural tetra-cyclic alkaloid isosaxorumamide which consists of a fused 5-7-5 tricyclic core and a di-hydro-furan-one substituent. The terminal di-hydro-furan ring is essentially planar with a maximum deviation of 0.0273 (14) Å from the mean plane and oxolane, azepane and pyrrolidine rings in the tricyclic ring system adopt twist, twist-chair and envelope forms, respectively. In the crystal, the amide and water mol-ecules are linked by O-H⋯O hydrogen bonds, forming a tape structure running along the b-axis direction. The tapes are further connected by C-H⋯O inter-actions into a three-dimensional architecture.Entities:
Keywords: azepane; crystal structure; fused tricyclic core; hydrogen bond; isosaxorumamide; oxolane; pyrrolidine; tetracyclic compound
Year: 2018 PMID: 29765766 PMCID: PMC5946988 DOI: 10.1107/S2056989018004425
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1Structures of two natural products, saxorumamide and isosaxorumamide, and the title compound. Differences in the relative stereochemistries of these three diastereomers are shown in red.
Figure 2The asymmetric unit of the title compound, showing the atom labelling. Displacement ellipsoids are drawn at the 50% probability level. Only H atoms connected to O and chiral C atoms are shown for clarity.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| O1 | 0.86 (2) | 2.02 (2) | 2.874 (3) | 173 (3) |
| O1 | 0.86 (2) | 1.99 (2) | 2.835 (3) | 167 (3) |
| C7—H7⋯O21iii | 1.00 | 2.47 | 3.254 (3) | 135 |
| C22—H22 | 0.98 | 2.58 | 3.407 (3) | 142 |
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .
Figure 3A partial packing diagram viewed down the a axis, showing the tape structure running along the b-axis direction. Yellow lines indicate the O—H⋯O hydrogen bonds. Black dashed lines indicate C—H⋯O interactions. Only H atoms involved in the hydrogen bonds are shown for clarity. [Symmetry codes: (i) x − 1, y, z; (ii) −x + 2, y − , −z + ; (v) x − 1, y + 1, z.]
Figure 4The crystal packing of the title compound, viewed down the b axis, showing wavy architectures which consist of the tape structures running along the b-axis direction. Yellow lines indicate the O—H⋯O hydrogen bonds. Black dashed lines indicate C—H⋯O interactions. Only H atoms involved in the hydrogen bonds are shown for clarity. [Symmetry code: (iv) x + , −y + , −z.]
Figure 5The core structures for database survey; (a) 8-methyl-1-aza-6-oxatricyclo[8.3.0.05,9]tridecane, and its (b) −13-one and (c) 7-(3-methyl-2-oxo-oxolan-3-en-5-ylidene) derivatives. Structures of the title compound and (–)-stemoamide are also shown for comparison.
Experimental details
| Crystal data | |
| Chemical formula | C17H23NO4·H2O |
|
| 323.38 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 90 |
|
| 6.6180 (3), 7.1197 (3), 34.7351 (15) |
|
| 1636.65 (12) |
|
| 4 |
| Radiation type | Mo |
| μ (mm−1) | 0.10 |
| Crystal size (mm) | 0.23 × 0.20 × 0.18 |
| Data collection | |
| Diffractometer | Bruker D8 Venture |
| Absorption correction | Multi-scan ( |
|
| 0.98, 0.98 |
| No. of measured, independent and observed [ | 29644, 2879, 2759 |
|
| 0.047 |
| (sin θ/λ)max (Å−1) | 0.595 |
| Refinement | |
|
| 0.033, 0.069, 1.00 |
| No. of reflections | 2879 |
| No. of parameters | 216 |
| No. of restraints | 3 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.21, −0.19 |
Computer programs: APEX3 (Bruker, 2016 ▸), SAINT (Bruker, 2016 ▸), SHELXT2014/5 (Sheldrick, 2015a ▸), SHELXL2014/7 (Sheldrick, 2015b ▸), Mercury (Macrae et al., 2008 ▸), publCIF (Westrip, 2010 ▸) and PLATON (Spek, 2009 ▸).
| C17H23NO4·H2O | |
| Melting point = 466–467 K | |
| Orthorhombic, | Mo |
| Cell parameters from 9946 reflections | |
| θ = 2.4–25.1° | |
| µ = 0.10 mm−1 | |
| Prism, pale yellow | |
| 0.23 × 0.20 × 0.18 mm |
| Bruker D8 Venture diffractometer | 2879 independent reflections |
| Radiation source: fine-focus sealed tube | 2759 reflections with |
| Multilayered confocal mirror monochromator | |
| Detector resolution: 7.4074 pixels mm-1 | θmax = 25.0°, θmin = 2.4° |
| φ and ω scans | |
| Absorption correction: multi-scan ( | |
| 29644 measured 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 | |
| 2879 reflections | (Δ/σ)max < 0.001 |
| 216 parameters | Δρmax = 0.21 e Å−3 |
| 3 restraints | Δρmin = −0.19 e Å−3 |
| Experimental. IR (film):
2925, 2855, 1756, 1667, 1455, 1261, 1083, 802 cm-1;
1H NMR (500 MHz, CDCl3): |
| 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. Refinement of |
| N1 | 1.0068 (3) | 0.5967 (3) | 0.18662 (5) | 0.0148 (4) | |
| C2 | 1.0057 (4) | 0.4003 (3) | 0.17441 (6) | 0.0163 (5) | |
| H2A | 0.8647 | 0.3539 | 0.1739 | 0.02* | |
| H2B | 1.0817 | 0.3241 | 0.1933 | 0.02* | |
| C3 | 1.0999 (4) | 0.3752 (4) | 0.13469 (7) | 0.0174 (5) | |
| H3A | 1.2346 | 0.4357 | 0.1346 | 0.021* | |
| H3B | 1.1204 | 0.2393 | 0.13 | 0.021* | |
| C4 | 0.9764 (4) | 0.4558 (3) | 0.10156 (7) | 0.0160 (5) | |
| H4A | 1.0537 | 0.4403 | 0.0774 | 0.019* | |
| H4B | 0.8499 | 0.3825 | 0.099 | 0.019* | |
| C5 | 0.9231 (4) | 0.6613 (3) | 0.10638 (6) | 0.0138 (5) | |
| H5 | 1.0485 | 0.7338 | 0.1126 | 0.017* | |
| O6 | 0.8410 (3) | 0.7277 (2) | 0.07027 (4) | 0.0169 (4) | |
| C7 | 0.6625 (4) | 0.8368 (3) | 0.07655 (7) | 0.0165 (5) | |
| H7 | 0.678 | 0.9594 | 0.0628 | 0.02* | |
| C8 | 0.6556 (4) | 0.8755 (3) | 0.11996 (7) | 0.0156 (5) | |
| H8 | 0.7432 | 0.9872 | 0.1251 | 0.019* | |
| C9 | 0.7626 (4) | 0.7031 (3) | 0.13668 (6) | 0.0129 (5) | |
| H9 | 0.6641 | 0.5966 | 0.1368 | 0.015* | |
| C10 | 0.8418 (4) | 0.7289 (3) | 0.17783 (6) | 0.0144 (5) | |
| H10 | 0.7283 | 0.7068 | 0.1963 | 0.017* | |
| C11 | 0.9401 (4) | 0.9177 (3) | 0.18706 (7) | 0.0171 (5) | |
| H11A | 0.8389 | 1.0086 | 0.1967 | 0.021* | |
| H11B | 1.0069 | 0.9711 | 0.164 | 0.021* | |
| C12 | 1.0951 (4) | 0.8701 (4) | 0.21821 (7) | 0.0186 (6) | |
| H12A | 1.2148 | 0.9531 | 0.2164 | 0.022* | |
| H12B | 1.0354 | 0.8817 | 0.2442 | 0.022* | |
| C13 | 1.1500 (4) | 0.6692 (3) | 0.20942 (7) | 0.0165 (5) | |
| O14 | 1.2991 (3) | 0.5844 (3) | 0.22177 (5) | 0.0233 (4) | |
| C15 | 0.4482 (4) | 0.9164 (4) | 0.13680 (7) | 0.0218 (6) | |
| H15A | 0.382 | 1.0147 | 0.1216 | 0.033* | |
| H15B | 0.4629 | 0.9589 | 0.1635 | 0.033* | |
| H15C | 0.366 | 0.802 | 0.1362 | 0.033* | |
| C16 | 0.4817 (4) | 0.7338 (3) | 0.05958 (6) | 0.0180 (5) | |
| H16 | 0.3564 | 0.8095 | 0.0639 | 0.022* | |
| O17 | 0.4601 (3) | 0.5530 (2) | 0.07769 (5) | 0.0184 (4) | |
| C18 | 0.4827 (4) | 0.4170 (4) | 0.05060 (7) | 0.0196 (5) | |
| C19 | 0.5050 (4) | 0.5060 (4) | 0.01261 (7) | 0.0207 (6) | |
| C20 | 0.5018 (4) | 0.6892 (4) | 0.01778 (7) | 0.0203 (6) | |
| H20 | 0.5109 | 0.7799 | −0.0022 | 0.024* | |
| O21 | 0.4813 (3) | 0.2530 (3) | 0.05902 (5) | 0.0289 (5) | |
| C22 | 0.5281 (4) | 0.3907 (4) | −0.02303 (7) | 0.0292 (7) | |
| H22A | 0.5321 | 0.4736 | −0.0455 | 0.044* | |
| H22B | 0.4134 | 0.3044 | −0.0253 | 0.044* | |
| H22C | 0.654 | 0.3185 | −0.0216 | 0.044* | |
| O1W | 0.5010 (4) | 0.2300 (3) | 0.21248 (6) | 0.0424 (6) | |
| H1WA | 0.440 (5) | 0.334 (4) | 0.2174 (10) | 0.064* | |
| H1WB | 0.549 (6) | 0.198 (5) | 0.2345 (7) | 0.064* |
| N1 | 0.0184 (10) | 0.0129 (10) | 0.0131 (9) | 0.0011 (10) | −0.0012 (9) | 0.0001 (8) |
| C2 | 0.0202 (12) | 0.0116 (11) | 0.0170 (11) | −0.0013 (12) | −0.0012 (11) | 0.0025 (9) |
| C3 | 0.0188 (13) | 0.0137 (12) | 0.0197 (13) | 0.0027 (11) | −0.0005 (11) | −0.0013 (10) |
| C4 | 0.0149 (13) | 0.0179 (13) | 0.0152 (11) | 0.0027 (11) | 0.0027 (11) | −0.0030 (10) |
| C5 | 0.0147 (12) | 0.0168 (12) | 0.0098 (11) | −0.0005 (10) | −0.0003 (10) | 0.0009 (9) |
| O6 | 0.0151 (9) | 0.0225 (9) | 0.0133 (8) | 0.0052 (8) | 0.0010 (7) | 0.0030 (7) |
| C7 | 0.0147 (12) | 0.0161 (12) | 0.0186 (12) | 0.0030 (11) | 0.0018 (10) | 0.0049 (10) |
| C8 | 0.0164 (12) | 0.0120 (12) | 0.0184 (12) | 0.0001 (11) | −0.0021 (10) | 0.0000 (10) |
| C9 | 0.0123 (11) | 0.0130 (12) | 0.0134 (11) | 0.0000 (10) | 0.0018 (10) | −0.0001 (10) |
| C10 | 0.0157 (12) | 0.0146 (12) | 0.0130 (11) | 0.0009 (11) | 0.0038 (10) | 0.0002 (10) |
| C11 | 0.0204 (13) | 0.0133 (12) | 0.0177 (12) | 0.0015 (11) | 0.0027 (10) | −0.0031 (10) |
| C12 | 0.0230 (13) | 0.0186 (13) | 0.0141 (12) | −0.0010 (11) | 0.0010 (11) | −0.0045 (10) |
| C13 | 0.0220 (14) | 0.0183 (13) | 0.0092 (11) | −0.0005 (12) | 0.0011 (10) | 0.0023 (10) |
| O14 | 0.0257 (10) | 0.0215 (9) | 0.0227 (9) | 0.0035 (9) | −0.0099 (8) | −0.0002 (8) |
| C15 | 0.0203 (13) | 0.0235 (13) | 0.0217 (13) | 0.0057 (12) | −0.0004 (11) | −0.0050 (11) |
| C16 | 0.0171 (13) | 0.0193 (12) | 0.0177 (11) | 0.0038 (11) | 0.0002 (11) | 0.0030 (10) |
| O17 | 0.0194 (9) | 0.0202 (9) | 0.0157 (8) | −0.0035 (8) | −0.0002 (7) | 0.0015 (7) |
| C18 | 0.0139 (12) | 0.0230 (14) | 0.0220 (13) | 0.0017 (12) | −0.0053 (11) | −0.0009 (11) |
| C19 | 0.0133 (12) | 0.0297 (14) | 0.0190 (12) | 0.0060 (13) | −0.0038 (11) | −0.0020 (11) |
| C20 | 0.0143 (13) | 0.0297 (14) | 0.0169 (12) | 0.0007 (13) | −0.0022 (11) | 0.0058 (10) |
| O21 | 0.0334 (11) | 0.0210 (10) | 0.0324 (10) | 0.0006 (10) | −0.0099 (10) | 0.0010 (8) |
| C22 | 0.0267 (15) | 0.0374 (16) | 0.0234 (14) | 0.0100 (15) | −0.0053 (12) | −0.0085 (12) |
| O1W | 0.0562 (15) | 0.0365 (12) | 0.0345 (11) | 0.0201 (13) | −0.0228 (12) | −0.0136 (10) |
| N1—C13 | 1.338 (3) | C10—H10 | 1.0 |
| N1—C2 | 1.461 (3) | C11—C12 | 1.529 (3) |
| N1—C10 | 1.474 (3) | C11—H11A | 0.99 |
| C2—C3 | 1.525 (3) | C11—H11B | 0.99 |
| C2—H2A | 0.99 | C12—C13 | 1.507 (3) |
| C2—H2B | 0.99 | C12—H12A | 0.99 |
| C3—C4 | 1.524 (3) | C12—H12B | 0.99 |
| C3—H3A | 0.99 | C13—O14 | 1.234 (3) |
| C3—H3B | 0.99 | C15—H15A | 0.98 |
| C4—C5 | 1.515 (3) | C15—H15B | 0.98 |
| C4—H4A | 0.99 | C15—H15C | 0.98 |
| C4—H4B | 0.99 | C16—O17 | 1.440 (3) |
| C5—O6 | 1.446 (3) | C16—C20 | 1.492 (3) |
| C5—C9 | 1.525 (3) | C16—H16 | 1.0 |
| C5—H5 | 1.0 | O17—C18 | 1.359 (3) |
| O6—C7 | 1.431 (3) | C18—O21 | 1.204 (3) |
| C7—C16 | 1.522 (4) | C18—C19 | 1.471 (3) |
| C7—C8 | 1.534 (3) | C19—C20 | 1.317 (4) |
| C7—H7 | 1.0 | C19—C22 | 1.493 (3) |
| C8—C15 | 1.521 (3) | C20—H20 | 0.95 |
| C8—C9 | 1.531 (3) | C22—H22A | 0.98 |
| C8—H8 | 1.0 | C22—H22B | 0.98 |
| C9—C10 | 1.533 (3) | C22—H22C | 0.98 |
| C9—H9 | 1.0 | O1W—H1WA | 0.86 (2) |
| C10—C11 | 1.528 (3) | O1W—H1WB | 0.86 (2) |
| C13—N1—C2 | 123.0 (2) | C11—C10—C9 | 116.5 (2) |
| C13—N1—C10 | 113.62 (19) | N1—C10—H10 | 108.9 |
| C2—N1—C10 | 123.2 (2) | C11—C10—H10 | 108.9 |
| N1—C2—C3 | 111.90 (19) | C9—C10—H10 | 108.9 |
| N1—C2—H2A | 109.2 | C10—C11—C12 | 103.9 (2) |
| C3—C2—H2A | 109.2 | C10—C11—H11A | 111.0 |
| N1—C2—H2B | 109.2 | C12—C11—H11A | 111.0 |
| C3—C2—H2B | 109.2 | C10—C11—H11B | 111.0 |
| H2A—C2—H2B | 107.9 | C12—C11—H11B | 111.0 |
| C4—C3—C2 | 114.8 (2) | H11A—C11—H11B | 109.0 |
| C4—C3—H3A | 108.6 | C13—C12—C11 | 103.2 (2) |
| C2—C3—H3A | 108.6 | C13—C12—H12A | 111.1 |
| C4—C3—H3B | 108.6 | C11—C12—H12A | 111.1 |
| C2—C3—H3B | 108.6 | C13—C12—H12B | 111.1 |
| H3A—C3—H3B | 107.5 | C11—C12—H12B | 111.1 |
| C5—C4—C3 | 113.9 (2) | H12A—C12—H12B | 109.1 |
| C5—C4—H4A | 108.8 | O14—C13—N1 | 125.7 (2) |
| C3—C4—H4A | 108.8 | O14—C13—C12 | 125.9 (2) |
| C5—C4—H4B | 108.8 | N1—C13—C12 | 108.4 (2) |
| C3—C4—H4B | 108.8 | C8—C15—H15A | 109.5 |
| H4A—C4—H4B | 107.7 | C8—C15—H15B | 109.5 |
| O6—C5—C4 | 107.90 (18) | H15A—C15—H15B | 109.5 |
| O6—C5—C9 | 105.84 (19) | C8—C15—H15C | 109.5 |
| C4—C5—C9 | 115.3 (2) | H15A—C15—H15C | 109.5 |
| O6—C5—H5 | 109.2 | H15B—C15—H15C | 109.5 |
| C4—C5—H5 | 109.2 | O17—C16—C20 | 104.1 (2) |
| C9—C5—H5 | 109.2 | O17—C16—C7 | 109.86 (19) |
| C7—O6—C5 | 110.83 (17) | C20—C16—C7 | 114.2 (2) |
| O6—C7—C16 | 109.18 (19) | O17—C16—H16 | 109.5 |
| O6—C7—C8 | 105.77 (19) | C20—C16—H16 | 109.5 |
| C16—C7—C8 | 116.4 (2) | C7—C16—H16 | 109.5 |
| O6—C7—H7 | 108.4 | C18—O17—C16 | 108.90 (17) |
| C16—C7—H7 | 108.4 | O21—C18—O17 | 121.5 (2) |
| C8—C7—H7 | 108.4 | O21—C18—C19 | 129.5 (2) |
| C15—C8—C9 | 115.1 (2) | O17—C18—C19 | 109.0 (2) |
| C15—C8—C7 | 116.1 (2) | C20—C19—C18 | 107.6 (2) |
| C9—C8—C7 | 102.43 (19) | C20—C19—C22 | 131.2 (2) |
| C15—C8—H8 | 107.6 | C18—C19—C22 | 121.2 (2) |
| C9—C8—H8 | 107.6 | C19—C20—C16 | 110.2 (2) |
| C7—C8—H8 | 107.6 | C19—C20—H20 | 124.9 |
| C5—C9—C8 | 102.52 (19) | C16—C20—H20 | 124.9 |
| C5—C9—C10 | 115.4 (2) | C19—C22—H22A | 109.5 |
| C8—C9—C10 | 114.6 (2) | C19—C22—H22B | 109.5 |
| C5—C9—H9 | 108.0 | H22A—C22—H22B | 109.5 |
| C8—C9—H9 | 108.0 | C19—C22—H22C | 109.5 |
| C10—C9—H9 | 108.0 | H22A—C22—H22C | 109.5 |
| N1—C10—C11 | 101.69 (19) | H22B—C22—H22C | 109.5 |
| N1—C10—C9 | 111.73 (18) | H1WA—O1W—H1WB | 103 (3) |
| C13—N1—C2—C3 | −96.5 (3) | C5—C9—C10—C11 | 77.7 (3) |
| C10—N1—C2—C3 | 89.0 (3) | C8—C9—C10—C11 | −41.0 (3) |
| N1—C2—C3—C4 | −69.5 (3) | N1—C10—C11—C12 | −28.7 (2) |
| C2—C3—C4—C5 | 54.7 (3) | C9—C10—C11—C12 | −150.4 (2) |
| C3—C4—C5—O6 | 169.37 (19) | C10—C11—C12—C13 | 28.6 (2) |
| C3—C4—C5—C9 | −72.6 (3) | C2—N1—C13—O14 | 2.5 (4) |
| C4—C5—O6—C7 | 134.6 (2) | C10—N1—C13—O14 | 177.4 (2) |
| C9—C5—O6—C7 | 10.7 (3) | C2—N1—C13—C12 | −176.1 (2) |
| C5—O6—C7—C16 | −113.8 (2) | C10—N1—C13—C12 | −1.1 (3) |
| C5—O6—C7—C8 | 12.1 (3) | C11—C12—C13—O14 | 163.8 (2) |
| O6—C7—C8—C15 | −155.9 (2) | C11—C12—C13—N1 | −17.7 (2) |
| C16—C7—C8—C15 | −34.4 (3) | O6—C7—C16—O17 | 59.7 (2) |
| O6—C7—C8—C9 | −29.6 (2) | C8—C7—C16—O17 | −59.9 (3) |
| C16—C7—C8—C9 | 91.8 (2) | O6—C7—C16—C20 | −56.8 (3) |
| O6—C5—C9—C8 | −28.7 (2) | C8—C7—C16—C20 | −176.4 (2) |
| C4—C5—C9—C8 | −147.9 (2) | C20—C16—O17—C18 | 4.8 (3) |
| O6—C5—C9—C10 | −153.92 (19) | C7—C16—O17—C18 | −117.8 (2) |
| C4—C5—C9—C10 | 86.9 (3) | C16—O17—C18—O21 | 176.1 (3) |
| C15—C8—C9—C5 | 161.9 (2) | C16—O17—C18—C19 | −4.3 (3) |
| C7—C8—C9—C5 | 35.0 (2) | O21—C18—C19—C20 | −178.6 (3) |
| C15—C8—C9—C10 | −72.4 (3) | O17—C18—C19—C20 | 1.9 (3) |
| C7—C8—C9—C10 | 160.7 (2) | O21—C18—C19—C22 | 0.8 (4) |
| C13—N1—C10—C11 | 19.3 (2) | O17—C18—C19—C22 | −178.7 (2) |
| C2—N1—C10—C11 | −165.7 (2) | C18—C19—C20—C16 | 1.2 (3) |
| C13—N1—C10—C9 | 144.3 (2) | C22—C19—C20—C16 | −178.1 (3) |
| C2—N1—C10—C9 | −40.7 (3) | O17—C16—C20—C19 | −3.7 (3) |
| C5—C9—C10—N1 | −38.5 (3) | C7—C16—C20—C19 | 116.1 (3) |
| C8—C9—C10—N1 | −157.2 (2) |
| H··· | ||||
| O1 | 0.86 (2) | 2.02 (2) | 2.874 (3) | 173 (3) |
| O1 | 0.86 (2) | 1.99 (2) | 2.835 (3) | 167 (3) |
| C7—H7···O21iii | 1.00 | 2.47 | 3.254 (3) | 135 |
| C22—H22 | 0.98 | 2.58 | 3.407 (3) | 142 |