| Literature DB >> 27308035 |
Takeshi Oishi1, Shun Tsuzaki2, Tomoya Sugai2, Takaaki Sato2, Noritaka Chida2.
Abstract
In the title compound, C12H19NO6, the six-membered 1,3-dioxane ring adopts a chair-like conformation. The seat of this chair, containing two O atoms, is essentially planar, with a maximum deviation of 0.0021 (12) Å. The five-membered oxolane ring cis-fused to the 1,3-dioxane ring adopts an envelope form. The bridgehead C atom at the flap, which is bonded to the tetra-substituted C atom of the oxolane ring, deviates from the mean plane of other ring atoms by 0.539 (4) Å. In the crystal, classical O-H⋯O and N-H⋯O hydrogen bonds link the mol-ecules into a sheet structure enclosing an R 4 (4)(24) graph-set motif. Weak inter-molecular C-H⋯O inter-actions support the sheet formation.Entities:
Keywords: 1,3-dioxane; bicyclic compound; crystal structure; hydrogen bond; hydroxy group; oxolane
Year: 2016 PMID: 27308035 PMCID: PMC4908510 DOI: 10.1107/S2056989016006800
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of the title compound, showing the atom labeling. Displacement ellipsoids are drawn at the 50% probability level. Only H atoms connected to N, O and chiral C atoms are shown for clarity.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| O16—H16⋯O14i | 0.84 | 1.91 | 2.742 (2) | 168 |
| N11—H11⋯O16ii | 0.88 | 2.28 | 2.928 (3) | 131 |
| C5—H5⋯O10iii | 1.00 | 2.42 | 3.289 (3) | 145 |
| C19—H19 | 0.98 | 2.52 | 3.386 (3) | 147 |
| C13—H13 | 0.98 | 2.55 | 3.433 (3) | 150 |
| C13—H13 | 0.98 | 2.62 | 3.424 (3) | 140 |
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .
Figure 2A partial packing diagram, viewed down the b axis, showing the chain structure running along the c axis. Yellow lines indicate the intermolecular O—H⋯O hydrogen bonds. Black dashed lines indicate weak intermolecular C—H⋯O interactions. Only H atoms involved in the hydrogen bonds are shown for clarity. [Symmetry codes: (i) x, y, z + 1; (iv) x, y, z − 1.]
Figure 3Another partial packing diagram, viewed down the c axis, showing the sheet structure parallel to (100). Yellow lines indicate the intermolecular N—H⋯O hydrogen bonds. Black dashed lines indicate weak intermolecular C—H⋯O interactions. Only H atoms involved in the hydrogen bonds are shown for clarity. [Symmetry codes: (ii) −x + 2, y − , −z + 1; (iii) −x + 2, y + , −z + 1; (vi) x, y + 1, z + 1.]
Figure 4A packing diagram, viewed down the a axis, showing the hydrogen bonds in the sheet structure parallel to (100). Yellow lines indicate intermolecular O—H⋯O and N—H⋯O hydrogen bonds. Black dashed lines indicate weak intermolecular C—H⋯O interactions. Only H atoms involved in the hydrogen bonds are shown for clarity.
Figure 5The core structures for database survey: (a) 2,4,7-trioxabicyclo[4.3.0]nonan-8-one, and its derivatives with (b) 3,3-dimethyl, (c) 5-hydroxymethyl and (d) 9-methyl-9-N-substituents.
Experimental details
| Crystal data | |
| Chemical formula | C12H19NO6 |
|
| 273.28 |
| Crystal system, space group | Monoclinic, |
| Temperature (K) | 90 |
|
| 8.2102 (3), 9.9513 (3), 8.7480 (3) |
| β (°) | 108.142 (2) |
|
| 679.20 (4) |
|
| 2 |
| Radiation type | Cu |
| μ (mm−1) | 0.91 |
| Crystal size (mm) | 0.14 × 0.14 × 0.07 |
| Data collection | |
| Diffractometer | Bruker D8 Venture |
| Absorption correction | Multi-scan ( |
|
| 0.88, 0.94 |
| No. of measured, independent and observed [ | 8304, 2386, 2235 |
|
| 0.039 |
| (sin θ/λ)max (Å−1) | 0.596 |
| Refinement | |
|
| 0.032, 0.068, 1.00 |
| No. of reflections | 2386 |
| No. of parameters | 177 |
| No. of restraints | 1 |
| H-atom treatment | H-atom parameters constrained |
| Δρmax, Δρmin (e Å−3) | 0.20, −0.18 |
| Absolute structure | Flack |
| Absolute structure parameter | 0.13 (11) |
Computer programs: APEX2 and SAINT (Bruker, 2014 ▸), SHELXS2013 (Sheldrick, 2008 ▸), SHELXL2014 (Sheldrick, 2015 ▸), Mercury (Macrae et al., 2006 ▸), publCIF (Westrip, 2010 ▸) and PLATON (Spek, 2009 ▸).
| C12H19NO6 | |
| Melting point = 497–498 K | |
| Monoclinic, | Cu |
| Cell parameters from 5609 reflections | |
| θ = 5.3–66.5° | |
| µ = 0.91 mm−1 | |
| β = 108.142 (2)° | |
| Prism, colorless | |
| 0.14 × 0.14 × 0.07 mm | |
| Bruker D8 Venture diffractometer | 2386 independent reflections |
| Radiation source: fine-focus sealed tube | 2235 reflections with |
| Multilayered confocal mirror monochromator | |
| Detector resolution: 10.4167 pixels mm-1 | θmax = 66.8°, θmin = 5.3° |
| φ and ω scans | |
| Absorption correction: multi-scan ( | |
| 8304 measured reflections |
| Refinement on | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| H-atom parameters constrained | |
| (Δ/σ)max < 0.001 | |
| 2386 reflections | Δρmax = 0.20 e Å−3 |
| 177 parameters | Δρmin = −0.18 e Å−3 |
| 1 restraint | Absolute structure: Flack |
| Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.13 (11) |
| Experimental. IR (KBr): 3311, 2967, 2896, 1785, 1658, 1539, 1170, 1117, 1057 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 |
| C1 | 0.9761 (3) | 0.3025 (3) | 0.3147 (3) | 0.0188 (6) | |
| H1 | 0.9423 | 0.3845 | 0.2459 | 0.023* | |
| O2 | 0.8860 (2) | 0.18536 (19) | 0.2398 (2) | 0.0201 (4) | |
| C3 | 0.7125 (3) | 0.1762 (3) | 0.2378 (3) | 0.0206 (6) | |
| O4 | 0.7068 (2) | 0.17674 (19) | 0.3987 (2) | 0.0210 (4) | |
| C5 | 0.7792 (3) | 0.2941 (3) | 0.4887 (3) | 0.0204 (6) | |
| H5 | 0.7051 | 0.3729 | 0.4412 | 0.024* | |
| C6 | 0.9578 (3) | 0.3214 (3) | 0.4822 (3) | 0.0199 (6) | |
| H6 | 0.9921 | 0.4151 | 0.5201 | 0.024* | |
| O7 | 1.0816 (2) | 0.22653 (18) | 0.5827 (2) | 0.0209 (4) | |
| C8 | 1.2000 (3) | 0.1928 (3) | 0.5118 (3) | 0.0197 (6) | |
| C9 | 1.1663 (3) | 0.2685 (3) | 0.3525 (3) | 0.0188 (6) | |
| O10 | 1.3137 (2) | 0.1152 (2) | 0.5716 (2) | 0.0250 (5) | |
| N11 | 1.2014 (3) | 0.1803 (2) | 0.2341 (2) | 0.0189 (5) | |
| H11 | 1.2597 | 0.1056 | 0.2656 | 0.023* | |
| C12 | 1.1456 (3) | 0.2118 (3) | 0.0764 (3) | 0.0199 (6) | |
| C13 | 1.1567 (4) | 0.1008 (3) | −0.0361 (3) | 0.0243 (6) | |
| H13A | 1.2479 | 0.0382 | 0.0198 | 0.037* | |
| H13B | 1.1822 | 0.139 | −0.1294 | 0.037* | |
| H13C | 1.0471 | 0.0528 | −0.0722 | 0.037* | |
| O14 | 1.0868 (2) | 0.32336 (19) | 0.0272 (2) | 0.0232 (4) | |
| C15 | 0.7705 (4) | 0.2708 (3) | 0.6581 (3) | 0.0223 (6) | |
| H15A | 0.6511 | 0.2505 | 0.6536 | 0.027* | |
| H15B | 0.8432 | 0.1931 | 0.7074 | 0.027* | |
| O16 | 0.8286 (2) | 0.3877 (2) | 0.7522 (2) | 0.0251 (4) | |
| H16 | 0.9172 | 0.3693 | 0.8284 | 0.038* | |
| C17 | 0.6531 (4) | 0.0385 (3) | 0.1716 (3) | 0.0265 (6) | |
| H17A | 0.735 | −0.0292 | 0.2314 | 0.04* | |
| H17B | 0.6455 | 0.035 | 0.0577 | 0.04* | |
| H17C | 0.54 | 0.0202 | 0.1828 | 0.04* | |
| C18 | 0.6035 (4) | 0.2878 (3) | 0.1367 (3) | 0.0248 (6) | |
| H18A | 0.646 | 0.3752 | 0.1842 | 0.037* | |
| H18B | 0.484 | 0.2765 | 0.1339 | 0.037* | |
| H18C | 0.6104 | 0.2834 | 0.027 | 0.037* | |
| C19 | 1.2807 (3) | 0.3934 (3) | 0.3836 (3) | 0.0225 (6) | |
| H19A | 1.2492 | 0.4528 | 0.4593 | 0.034* | |
| H19B | 1.2653 | 0.4411 | 0.2821 | 0.034* | |
| H19C | 1.4009 | 0.3663 | 0.4295 | 0.034* |
| C1 | 0.0219 (13) | 0.0169 (14) | 0.0158 (12) | −0.0014 (11) | 0.0034 (10) | 0.0009 (11) |
| O2 | 0.0200 (9) | 0.0209 (10) | 0.0178 (8) | −0.0027 (8) | 0.0033 (7) | −0.0019 (8) |
| C3 | 0.0201 (13) | 0.0240 (14) | 0.0163 (12) | −0.0004 (12) | 0.0036 (10) | 0.0020 (13) |
| O4 | 0.0253 (10) | 0.0196 (10) | 0.0165 (9) | −0.0042 (8) | 0.0044 (7) | −0.0005 (8) |
| C5 | 0.0235 (14) | 0.0174 (14) | 0.0190 (13) | 0.0008 (11) | 0.0049 (10) | −0.0018 (12) |
| C6 | 0.0247 (15) | 0.0149 (14) | 0.0179 (13) | 0.0023 (11) | 0.0035 (11) | −0.0008 (11) |
| O7 | 0.0227 (10) | 0.0232 (11) | 0.0155 (9) | 0.0015 (8) | 0.0038 (7) | 0.0010 (8) |
| C8 | 0.0202 (13) | 0.0199 (14) | 0.0162 (12) | −0.0041 (11) | 0.0016 (10) | −0.0031 (12) |
| C9 | 0.0217 (14) | 0.0185 (14) | 0.0150 (12) | 0.0001 (10) | 0.0039 (10) | −0.0021 (11) |
| O10 | 0.0265 (11) | 0.0251 (11) | 0.0199 (10) | 0.0042 (9) | 0.0021 (8) | 0.0016 (9) |
| N11 | 0.0204 (11) | 0.0182 (11) | 0.0168 (11) | 0.0034 (9) | 0.0040 (8) | −0.0010 (10) |
| C12 | 0.0160 (12) | 0.0230 (15) | 0.0196 (13) | −0.0034 (11) | 0.0043 (10) | −0.0029 (12) |
| C13 | 0.0298 (16) | 0.0242 (15) | 0.0185 (13) | 0.0026 (12) | 0.0069 (11) | −0.0003 (12) |
| O14 | 0.0292 (10) | 0.0189 (11) | 0.0190 (9) | 0.0018 (8) | 0.0040 (8) | 0.0024 (8) |
| C15 | 0.0244 (15) | 0.0226 (15) | 0.0191 (13) | −0.0023 (11) | 0.0057 (11) | −0.0022 (12) |
| O16 | 0.0310 (11) | 0.0215 (10) | 0.0188 (10) | 0.0032 (9) | 0.0018 (8) | −0.0035 (9) |
| C17 | 0.0260 (15) | 0.0288 (16) | 0.0223 (14) | −0.0040 (12) | 0.0040 (12) | −0.0041 (13) |
| C18 | 0.0223 (14) | 0.0299 (17) | 0.0195 (13) | −0.0006 (12) | 0.0028 (11) | 0.0035 (13) |
| C19 | 0.0229 (14) | 0.0216 (14) | 0.0219 (14) | −0.0021 (11) | 0.0053 (11) | −0.0020 (13) |
| C1—O2 | 1.426 (3) | N11—H11 | 0.88 |
| C1—C6 | 1.530 (4) | C12—O14 | 1.233 (3) |
| C1—C9 | 1.530 (4) | C12—C13 | 1.501 (4) |
| C1—H1 | 1.0 | C13—H13A | 0.98 |
| O2—C3 | 1.422 (3) | C13—H13B | 0.98 |
| C3—O4 | 1.423 (3) | C13—H13C | 0.98 |
| C3—C17 | 1.509 (4) | C15—O16 | 1.419 (3) |
| C3—C18 | 1.525 (4) | C15—H15A | 0.99 |
| O4—C5 | 1.431 (3) | C15—H15B | 0.99 |
| C5—C6 | 1.510 (4) | O16—H16 | 0.84 |
| C5—C15 | 1.523 (4) | C17—H17A | 0.98 |
| C5—H5 | 1.0 | C17—H17B | 0.98 |
| C6—O7 | 1.463 (3) | C17—H17C | 0.98 |
| C6—H6 | 1.0 | C18—H18A | 0.98 |
| O7—C8 | 1.349 (3) | C18—H18B | 0.98 |
| C8—O10 | 1.199 (3) | C18—H18C | 0.98 |
| C8—C9 | 1.532 (4) | C19—H19A | 0.98 |
| C9—N11 | 1.453 (3) | C19—H19B | 0.98 |
| C9—C19 | 1.530 (4) | C19—H19C | 0.98 |
| N11—C12 | 1.348 (3) | ||
| O2—C1—C6 | 110.4 (2) | C12—N11—H11 | 119.7 |
| O2—C1—C9 | 105.5 (2) | C9—N11—H11 | 119.7 |
| C6—C1—C9 | 102.6 (2) | O14—C12—N11 | 122.6 (3) |
| O2—C1—H1 | 112.6 | O14—C12—C13 | 122.0 (2) |
| C6—C1—H1 | 112.6 | N11—C12—C13 | 115.4 (2) |
| C9—C1—H1 | 112.6 | C12—C13—H13A | 109.5 |
| C3—O2—C1 | 115.6 (2) | C12—C13—H13B | 109.5 |
| O2—C3—O4 | 109.22 (18) | H13A—C13—H13B | 109.5 |
| O2—C3—C17 | 105.4 (2) | C12—C13—H13C | 109.5 |
| O4—C3—C17 | 106.1 (2) | H13A—C13—H13C | 109.5 |
| O2—C3—C18 | 111.4 (2) | H13B—C13—H13C | 109.5 |
| O4—C3—C18 | 112.1 (2) | O16—C15—C5 | 109.3 (2) |
| C17—C3—C18 | 112.2 (2) | O16—C15—H15A | 109.8 |
| C3—O4—C5 | 114.3 (2) | C5—C15—H15A | 109.8 |
| O4—C5—C6 | 111.6 (2) | O16—C15—H15B | 109.8 |
| O4—C5—C15 | 105.8 (2) | C5—C15—H15B | 109.8 |
| C6—C5—C15 | 113.9 (2) | H15A—C15—H15B | 108.3 |
| O4—C5—H5 | 108.5 | C15—O16—H16 | 109.5 |
| C6—C5—H5 | 108.5 | C3—C17—H17A | 109.5 |
| C15—C5—H5 | 108.5 | C3—C17—H17B | 109.5 |
| O7—C6—C5 | 111.2 (2) | H17A—C17—H17B | 109.5 |
| O7—C6—C1 | 103.9 (2) | C3—C17—H17C | 109.5 |
| C5—C6—C1 | 113.6 (2) | H17A—C17—H17C | 109.5 |
| O7—C6—H6 | 109.3 | H17B—C17—H17C | 109.5 |
| C5—C6—H6 | 109.3 | C3—C18—H18A | 109.5 |
| C1—C6—H6 | 109.3 | C3—C18—H18B | 109.5 |
| C8—O7—C6 | 110.5 (2) | H18A—C18—H18B | 109.5 |
| O10—C8—O7 | 122.3 (2) | C3—C18—H18C | 109.5 |
| O10—C8—C9 | 127.5 (2) | H18A—C18—H18C | 109.5 |
| O7—C8—C9 | 110.1 (2) | H18B—C18—H18C | 109.5 |
| N11—C9—C19 | 111.8 (2) | C9—C19—H19A | 109.5 |
| N11—C9—C1 | 113.3 (2) | C9—C19—H19B | 109.5 |
| C19—C9—C1 | 112.8 (2) | H19A—C19—H19B | 109.5 |
| N11—C9—C8 | 109.3 (2) | C9—C19—H19C | 109.5 |
| C19—C9—C8 | 108.1 (2) | H19A—C19—H19C | 109.5 |
| C1—C9—C8 | 100.9 (2) | H19B—C19—H19C | 109.5 |
| C12—N11—C9 | 120.6 (2) | ||
| C6—C1—O2—C3 | 51.4 (3) | C6—O7—C8—C9 | 1.5 (3) |
| C9—C1—O2—C3 | 161.5 (2) | O2—C1—C9—N11 | 33.6 (3) |
| C1—O2—C3—O4 | −59.9 (3) | C6—C1—C9—N11 | 149.3 (2) |
| C1—O2—C3—C17 | −173.5 (2) | O2—C1—C9—C19 | 161.8 (2) |
| C1—O2—C3—C18 | 64.6 (3) | C6—C1—C9—C19 | −82.5 (3) |
| O2—C3—O4—C5 | 59.4 (3) | O2—C1—C9—C8 | −83.1 (2) |
| C17—C3—O4—C5 | 172.6 (2) | C6—C1—C9—C8 | 32.6 (3) |
| C18—C3—O4—C5 | −64.6 (3) | O10—C8—C9—N11 | 39.2 (4) |
| C3—O4—C5—C6 | −52.2 (3) | O7—C8—C9—N11 | −141.7 (2) |
| C3—O4—C5—C15 | −176.5 (2) | O10—C8—C9—C19 | −82.7 (3) |
| O4—C5—C6—O7 | −74.1 (3) | O7—C8—C9—C19 | 96.4 (2) |
| C15—C5—C6—O7 | 45.7 (3) | O10—C8—C9—C1 | 158.7 (3) |
| O4—C5—C6—C1 | 42.7 (3) | O7—C8—C9—C1 | −22.2 (3) |
| C15—C5—C6—C1 | 162.4 (2) | C19—C9—N11—C12 | −75.4 (3) |
| O2—C1—C6—O7 | 79.1 (2) | C1—C9—N11—C12 | 53.3 (3) |
| C9—C1—C6—O7 | −32.9 (2) | C8—C9—N11—C12 | 164.9 (2) |
| O2—C1—C6—C5 | −41.8 (3) | C9—N11—C12—O14 | 11.3 (4) |
| C9—C1—C6—C5 | −153.9 (2) | C9—N11—C12—C13 | −167.6 (2) |
| C5—C6—O7—C8 | 142.6 (2) | O4—C5—C15—O16 | −175.7 (2) |
| C1—C6—O7—C8 | 20.1 (3) | C6—C5—C15—O16 | 61.4 (3) |
| C6—O7—C8—O10 | −179.4 (2) |
| H··· | ||||
| O16—H16···O14i | 0.84 | 1.91 | 2.742 (2) | 168 |
| N11—H11···O16ii | 0.88 | 2.28 | 2.928 (3) | 131 |
| C5—H5···O10iii | 1.00 | 2.42 | 3.289 (3) | 145 |
| C19—H19 | 0.98 | 2.52 | 3.386 (3) | 147 |
| C13—H13 | 0.98 | 2.55 | 3.433 (3) | 150 |
| C13—H13 | 0.98 | 2.62 | 3.424 (3) | 140 |