| Literature DB >> 26870396 |
Ísmail Çelik1, Mehmet Akkurt2, Hüseyin Akşit3, Ramazan Erenler3, Santiago García-Granda4.
Abstract
In the mol-ecule of title compound, C15H20O6, also known as cynarinin A, the cyclo-pentane ring having twist conformation and a γ-lactone ring assuming an envelope conformation are trans- and cis-fused, respectively, to a cyclo-heptane ring adopting a twist-chair conformation. In the crystal, O-H⋯O hydrogen bonds link neighbouring mol-ecules, forming a three-dimensional network. Theoretical calculations of the mol-ecular structure using the CNDO approximation and MOPAC PM3 geometry optimization are in satisfactory agreement with the results of the X-ray structure analysis.Entities:
Keywords: CNDO; Centaurea polypodiifolia; HOMO; LUMO; PM3; crystal structure; cynarinin A; theoretical investigation
Year: 2015 PMID: 26870396 PMCID: PMC4719805 DOI: 10.1107/S2056989015019623
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of the title compound, with displacement ellipsoids drawn at the 50% probability level.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| O3—H3 | 0.78 (5) | 2.06 (4) | 2.818 (3) | 168 (4) |
| O4—H4 | 0.95 (5) | 2.14 (5) | 2.956 (3) | 144 (4) |
| O4—H4 | 0.95 (5) | 2.45 (5) | 3.156 (3) | 132 (4) |
| O5—H5 | 0.90 (4) | 2.45 (4) | 2.877 (3) | 109 (3) |
| O5—H5 | 0.90 (4) | 2.22 (4) | 3.096 (2) | 164 (4) |
Symmetry codes: (i) ; (ii) ; (iii) .
Figure 2The crystal packing of the title compound, viewed down the b axis, showing the three-dimensional hydrogen-bonding network (dashed lines).
Figure 3Spatial view of the molecule of the title compound calculated using the PM3 method.
Experimental details
| Crystal data | |
| Chemical formula | C15H20O6 |
|
| 296.31 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 293 |
|
| 8.1980 (1), 10.0290 (2), 16.7720 (3) |
|
| 1378.96 (4) |
|
| 4 |
| Radiation type | Cu |
| μ (mm−1) | 0.92 |
| Crystal size (mm) | 0.65 × 0.47 × 0.30 |
| Data collection | |
| Diffractometer | Agilent Xcalibur Ruby Gemini |
| Absorption correction | Multi-scan ( |
|
| 0.773, 1.000 |
| No. of measured, independent and observed [ | 12778, 2623, 2502 |
|
| 0.040 |
| (sin θ/λ)max (Å−1) | 0.613 |
| Refinement | |
|
| 0.035, 0.096, 1.05 |
| No. of reflections | 2623 |
| No. of parameters | 200 |
| Δρmax, Δρmin (e Å−3) | 0.27, −0.17 |
| Absolute structure | Flack (1983 |
| Absolute structure parameter | −0.09 (9) |
Computer programs: CrysAlis PRO (Agilent, 2013 ▸), SHELXS97 and SHELXL97 (Sheldrick, 2008 ▸), ORTEP-3 for Windows (Farrugia, 2012 ▸) and PLATON (Spek, 2009 ▸).
| C15H20O6 | |
| Orthorhombic, | Cu |
| Hall symbol: P 2ac 2ab | Cell parameters from 7099 reflections |
| θ = 4.4–70.5° | |
| µ = 0.92 mm−1 | |
| Prism, colourless | |
| 0.65 × 0.47 × 0.30 mm |
| Agilent Xcalibur Ruby Gemini diffractometer | 2623 independent reflections |
| Radiation source: Enhance (Cu) X-ray Source | 2502 reflections with |
| Graphite monochromator | |
| Detector resolution: 10.2673 pixels mm-1 | θmax = 70.9°, θmin = 5.1° |
| ω scans | |
| Absorption correction: multi-scan ( | |
| 12778 measured reflections |
| Refinement on | |
| Least-squares matrix: full | (Δ/σ)max < 0.001 |
| Δρmax = 0.27 e Å−3 | |
| Δρmin = −0.17 e Å−3 | |
| Extinction correction: | |
| 2623 reflections | Extinction coefficient: 0.0184 (14) |
| 200 parameters | Absolute structure: Flack (1983), 1073 Friedel pairs |
| 0 restraints | Absolute structure parameter: −0.09 (9) |
| Hydrogen site location: mixed |
| Geometry. Bond distances, angles |
| Refinement. Refinement on |
| O1 | 0.2767 (2) | 0.42340 (18) | 0.94867 (10) | 0.0363 (5) | |
| O2 | 0.5458 (2) | 0.3191 (2) | 1.23883 (10) | 0.0417 (6) | |
| O3 | 0.6704 (3) | 0.7021 (2) | 0.83279 (12) | 0.0430 (6) | |
| O4 | 0.4798 (3) | 0.3608 (2) | 0.79632 (13) | 0.0583 (8) | |
| O5 | 0.2968 (2) | 0.68723 (17) | 0.81640 (11) | 0.0385 (5) | |
| O6 | 0.0874 (2) | 0.4674 (2) | 0.85721 (12) | 0.0526 (7) | |
| C1 | 0.6584 (3) | 0.5976 (2) | 0.89063 (13) | 0.0298 (7) | |
| C2 | 0.7676 (3) | 0.6329 (3) | 0.96189 (15) | 0.0371 (7) | |
| C3 | 0.7539 (3) | 0.5438 (2) | 1.03466 (14) | 0.0324 (7) | |
| C4 | 0.6038 (3) | 0.5670 (2) | 1.08525 (13) | 0.0294 (7) | |
| C5 | 0.4523 (3) | 0.4859 (2) | 1.05600 (13) | 0.0259 (6) | |
| C6 | 0.4448 (3) | 0.4643 (2) | 0.96656 (13) | 0.0266 (6) | |
| C7 | 0.4782 (3) | 0.5846 (2) | 0.91215 (13) | 0.0255 (6) | |
| C8 | 0.3588 (3) | 0.5632 (2) | 0.84275 (13) | 0.0284 (6) | |
| C9 | 0.2237 (3) | 0.4813 (2) | 0.88134 (14) | 0.0331 (7) | |
| C10 | 0.4595 (3) | 0.3538 (2) | 1.10233 (13) | 0.0280 (6) | |
| C11 | 0.5437 (3) | 0.3898 (2) | 1.17991 (13) | 0.0301 (7) | |
| C12 | 0.6183 (3) | 0.5262 (3) | 1.17351 (14) | 0.0347 (7) | |
| C13 | 0.8685 (3) | 0.4549 (3) | 1.05183 (18) | 0.0476 (9) | |
| C14 | 0.4213 (4) | 0.4848 (3) | 0.77071 (15) | 0.0384 (8) | |
| C15 | 0.3005 (3) | 0.2790 (3) | 1.11343 (15) | 0.0389 (8) | |
| H1 | 0.69630 | 0.51390 | 0.86680 | 0.0360* | |
| H2A | 0.88010 | 0.63170 | 0.94400 | 0.0450* | |
| H2B | 0.74270 | 0.72350 | 0.97810 | 0.0450* | |
| H3O | 0.755 (6) | 0.703 (4) | 0.812 (2) | 0.0650* | |
| H4 | 0.57660 | 0.66200 | 1.08300 | 0.0350* | |
| H4O | 0.480 (6) | 0.298 (5) | 0.754 (3) | 0.0880* | |
| H5 | 0.35370 | 0.53380 | 1.07230 | 0.0310* | |
| H5O | 0.200 (5) | 0.668 (4) | 0.794 (2) | 0.0580* | |
| H6 | 0.51910 | 0.39170 | 0.95210 | 0.0320* | |
| H7 | 0.44530 | 0.66550 | 0.94070 | 0.0310* | |
| H10 | 0.53330 | 0.29460 | 1.07310 | 0.0340* | |
| H12A | 0.73190 | 0.52400 | 1.18980 | 0.0420* | |
| H12B | 0.56050 | 0.58900 | 1.20720 | 0.0420* | |
| H13A | 0.85900 | 0.40230 | 1.09730 | 0.0570* | |
| H13B | 0.95820 | 0.44510 | 1.01840 | 0.0570* | |
| H14A | 0.33360 | 0.47210 | 0.73260 | 0.0460* | |
| H14B | 0.50810 | 0.53410 | 0.74470 | 0.0460* | |
| H15A | 0.25390 | 0.25940 | 1.06220 | 0.0580* | |
| H15B | 0.32090 | 0.19720 | 1.14150 | 0.0580* | |
| H15C | 0.22600 | 0.33280 | 1.14360 | 0.0580* |
| O1 | 0.0354 (9) | 0.0441 (9) | 0.0295 (8) | −0.0134 (7) | −0.0076 (7) | 0.0066 (8) |
| O2 | 0.0504 (11) | 0.0463 (10) | 0.0285 (9) | −0.0056 (9) | −0.0076 (8) | 0.0089 (8) |
| O3 | 0.0399 (10) | 0.0489 (11) | 0.0403 (10) | −0.0025 (9) | 0.0115 (8) | 0.0163 (9) |
| O4 | 0.0839 (17) | 0.0463 (12) | 0.0448 (11) | 0.0247 (12) | −0.0133 (11) | −0.0176 (9) |
| O5 | 0.0447 (10) | 0.0302 (8) | 0.0407 (9) | 0.0053 (8) | −0.0094 (8) | 0.0039 (8) |
| O6 | 0.0391 (11) | 0.0711 (15) | 0.0477 (11) | −0.0126 (10) | −0.0136 (9) | 0.0099 (10) |
| C1 | 0.0314 (12) | 0.0314 (12) | 0.0266 (10) | −0.0001 (10) | 0.0055 (9) | 0.0032 (10) |
| C2 | 0.0306 (12) | 0.0426 (13) | 0.0380 (13) | −0.0097 (11) | 0.0022 (10) | 0.0041 (11) |
| C3 | 0.0280 (12) | 0.0377 (12) | 0.0316 (12) | −0.0081 (10) | −0.0029 (9) | 0.0002 (10) |
| C4 | 0.0336 (12) | 0.0265 (11) | 0.0280 (11) | −0.0041 (9) | −0.0003 (10) | −0.0019 (9) |
| C5 | 0.0263 (10) | 0.0268 (10) | 0.0245 (10) | −0.0014 (8) | 0.0010 (9) | −0.0005 (8) |
| C6 | 0.0271 (11) | 0.0273 (11) | 0.0254 (11) | −0.0027 (9) | −0.0011 (8) | 0.0001 (8) |
| C7 | 0.0294 (11) | 0.0239 (10) | 0.0232 (10) | 0.0018 (9) | 0.0020 (9) | −0.0017 (8) |
| C8 | 0.0341 (12) | 0.0255 (11) | 0.0256 (10) | 0.0043 (9) | −0.0024 (9) | −0.0004 (9) |
| C9 | 0.0339 (13) | 0.0363 (12) | 0.0290 (11) | −0.0009 (10) | −0.0050 (10) | −0.0016 (10) |
| C10 | 0.0322 (11) | 0.0280 (11) | 0.0239 (10) | −0.0019 (9) | 0.0002 (9) | −0.0003 (8) |
| C11 | 0.0285 (11) | 0.0360 (12) | 0.0257 (11) | 0.0012 (10) | −0.0001 (10) | −0.0007 (9) |
| C12 | 0.0390 (13) | 0.0385 (13) | 0.0266 (11) | −0.0052 (11) | −0.0022 (10) | −0.0040 (10) |
| C13 | 0.0364 (14) | 0.0650 (19) | 0.0413 (14) | 0.0038 (13) | −0.0002 (12) | 0.0033 (14) |
| C14 | 0.0478 (15) | 0.0404 (14) | 0.0269 (11) | 0.0048 (12) | −0.0004 (11) | −0.0054 (10) |
| C15 | 0.0414 (14) | 0.0425 (14) | 0.0328 (12) | −0.0135 (12) | −0.0028 (11) | 0.0052 (11) |
| O1—C6 | 1.469 (3) | C8—C9 | 1.523 (3) |
| O1—C9 | 1.342 (3) | C10—C11 | 1.517 (3) |
| O2—C11 | 1.216 (3) | C10—C15 | 1.515 (4) |
| O3—C1 | 1.432 (3) | C11—C12 | 1.502 (4) |
| O4—C14 | 1.400 (4) | C1—H1 | 0.9800 |
| O5—C8 | 1.415 (3) | C2—H2A | 0.9700 |
| O6—C9 | 1.197 (3) | C2—H2B | 0.9700 |
| O3—H3O | 0.78 (5) | C4—H4 | 0.9800 |
| O4—H4O | 0.95 (5) | C5—H5 | 0.9800 |
| O5—H5O | 0.90 (4) | C6—H6 | 0.9800 |
| C1—C2 | 1.535 (3) | C7—H7 | 0.9800 |
| C1—C7 | 1.526 (3) | C10—H10 | 0.9800 |
| C2—C3 | 1.517 (4) | C12—H12A | 0.9700 |
| C3—C4 | 1.513 (3) | C12—H12B | 0.9700 |
| C3—C13 | 1.327 (4) | C13—H13A | 0.9300 |
| C4—C5 | 1.564 (3) | C13—H13B | 0.9300 |
| C4—C12 | 1.540 (3) | C14—H14A | 0.9700 |
| C5—C6 | 1.517 (3) | C14—H14B | 0.9700 |
| C5—C10 | 1.537 (3) | C15—H15A | 0.9600 |
| C6—C7 | 1.537 (3) | C15—H15B | 0.9600 |
| C7—C8 | 1.536 (3) | C15—H15C | 0.9600 |
| C8—C14 | 1.530 (3) | ||
| C6—O1—C9 | 110.78 (17) | C2—C1—H1 | 109.00 |
| C1—O3—H3O | 112 (3) | C7—C1—H1 | 109.00 |
| C14—O4—H4O | 111 (3) | C1—C2—H2A | 108.00 |
| C8—O5—H5O | 105 (3) | C1—C2—H2B | 108.00 |
| O3—C1—C7 | 106.82 (19) | C3—C2—H2A | 108.00 |
| O3—C1—C2 | 108.59 (19) | C3—C2—H2B | 108.00 |
| C2—C1—C7 | 113.59 (19) | H2A—C2—H2B | 107.00 |
| C1—C2—C3 | 116.6 (2) | C3—C4—H4 | 108.00 |
| C2—C3—C4 | 114.90 (19) | C5—C4—H4 | 108.00 |
| C4—C3—C13 | 123.9 (2) | C12—C4—H4 | 108.00 |
| C2—C3—C13 | 121.2 (2) | C4—C5—H5 | 108.00 |
| C5—C4—C12 | 102.98 (18) | C6—C5—H5 | 108.00 |
| C3—C4—C5 | 112.96 (18) | C10—C5—H5 | 108.00 |
| C3—C4—C12 | 115.8 (2) | O1—C6—H6 | 109.00 |
| C4—C5—C6 | 114.63 (19) | C5—C6—H6 | 109.00 |
| C4—C5—C10 | 105.03 (18) | C7—C6—H6 | 109.00 |
| C6—C5—C10 | 112.24 (17) | C1—C7—H7 | 108.00 |
| O1—C6—C5 | 106.26 (18) | C6—C7—H7 | 108.00 |
| O1—C6—C7 | 105.37 (18) | C8—C7—H7 | 108.00 |
| C5—C6—C7 | 117.89 (17) | C5—C10—H10 | 107.00 |
| C1—C7—C8 | 116.72 (19) | C11—C10—H10 | 107.00 |
| C1—C7—C6 | 112.32 (18) | C15—C10—H10 | 107.00 |
| C6—C7—C8 | 103.10 (17) | C4—C12—H12A | 111.00 |
| O5—C8—C7 | 110.05 (17) | C4—C12—H12B | 110.00 |
| O5—C8—C9 | 110.22 (19) | C11—C12—H12A | 110.00 |
| C9—C8—C14 | 107.58 (19) | C11—C12—H12B | 111.00 |
| C7—C8—C14 | 117.2 (2) | H12A—C12—H12B | 109.00 |
| O5—C8—C14 | 109.00 (19) | C3—C13—H13A | 120.00 |
| C7—C8—C9 | 102.52 (18) | C3—C13—H13B | 120.00 |
| O1—C9—O6 | 122.5 (2) | H13A—C13—H13B | 120.00 |
| O1—C9—C8 | 110.8 (2) | O4—C14—H14A | 110.00 |
| O6—C9—C8 | 126.7 (2) | O4—C14—H14B | 110.00 |
| C5—C10—C11 | 104.24 (17) | C8—C14—H14A | 110.00 |
| C5—C10—C15 | 117.1 (2) | C8—C14—H14B | 110.00 |
| C11—C10—C15 | 113.83 (19) | H14A—C14—H14B | 108.00 |
| O2—C11—C12 | 125.7 (2) | C10—C15—H15A | 109.00 |
| O2—C11—C10 | 124.4 (2) | C10—C15—H15B | 109.00 |
| C10—C11—C12 | 109.92 (18) | C10—C15—H15C | 110.00 |
| C4—C12—C11 | 106.21 (19) | H15A—C15—H15B | 109.00 |
| O4—C14—C8 | 109.2 (2) | H15A—C15—H15C | 109.00 |
| O3—C1—H1 | 109.00 | H15B—C15—H15C | 109.00 |
| C6—O1—C9—O6 | −176.4 (2) | C6—C5—C10—C15 | −79.1 (3) |
| C6—O1—C9—C8 | 3.7 (2) | C4—C5—C6—O1 | −163.79 (17) |
| C9—O1—C6—C5 | 139.66 (18) | O1—C6—C7—C1 | −151.38 (17) |
| C9—O1—C6—C7 | 13.8 (2) | C5—C6—C7—C8 | −143.2 (2) |
| O3—C1—C2—C3 | 171.8 (2) | O1—C6—C7—C8 | −24.9 (2) |
| O3—C1—C7—C8 | 54.4 (2) | C5—C6—C7—C1 | 90.3 (2) |
| C7—C1—C2—C3 | 53.2 (3) | C1—C7—C8—C14 | 32.2 (3) |
| O3—C1—C7—C6 | 173.17 (17) | C6—C7—C8—O5 | 143.33 (18) |
| C2—C1—C7—C6 | −67.1 (2) | C6—C7—C8—C9 | 26.1 (2) |
| C2—C1—C7—C8 | 174.11 (19) | C6—C7—C8—C14 | −91.4 (2) |
| C1—C2—C3—C13 | 104.8 (3) | C1—C7—C8—C9 | 149.70 (18) |
| C1—C2—C3—C4 | −76.4 (3) | C1—C7—C8—O5 | −93.1 (2) |
| C2—C3—C4—C5 | 86.5 (2) | O5—C8—C9—O6 | 43.5 (3) |
| C2—C3—C4—C12 | −155.1 (2) | O5—C8—C9—O1 | −136.56 (19) |
| C13—C3—C4—C5 | −94.8 (3) | C14—C8—C9—O1 | 104.7 (2) |
| C13—C3—C4—C12 | 23.7 (3) | C14—C8—C9—O6 | −75.2 (3) |
| C12—C4—C5—C10 | −34.5 (2) | O5—C8—C14—O4 | −178.8 (2) |
| C12—C4—C5—C6 | −158.11 (19) | C7—C8—C14—O4 | 55.4 (3) |
| C5—C4—C12—C11 | 26.5 (2) | C9—C8—C14—O4 | −59.3 (3) |
| C3—C4—C5—C10 | 91.2 (2) | C7—C8—C9—O1 | −19.4 (2) |
| C3—C4—C5—C6 | −32.5 (2) | C7—C8—C9—O6 | 160.6 (2) |
| C3—C4—C12—C11 | −97.3 (2) | C5—C10—C11—O2 | 165.6 (2) |
| C10—C5—C6—C7 | −165.7 (2) | C5—C10—C11—C12 | −12.6 (3) |
| C4—C5—C10—C15 | 155.79 (19) | C15—C10—C11—O2 | 36.8 (3) |
| C6—C5—C10—C11 | 154.2 (2) | C15—C10—C11—C12 | −141.4 (2) |
| C4—C5—C10—C11 | 29.1 (2) | O2—C11—C12—C4 | 172.8 (2) |
| C4—C5—C6—C7 | −46.0 (3) | C10—C11—C12—C4 | −9.1 (3) |
| C10—C5—C6—O1 | 76.5 (2) |
| H··· | ||||
| O3—H3 | 0.78 (5) | 2.06 (4) | 2.818 (3) | 168 (4) |
| O4—H4 | 0.95 (5) | 2.14 (5) | 2.956 (3) | 144 (4) |
| O4—H4 | 0.95 (5) | 2.45 (5) | 3.156 (3) | 132 (4) |
| O5—H5 | 0.90 (4) | 2.45 (4) | 2.877 (3) | 109 (3) |
| O5—H5 | 0.90 (4) | 2.22 (4) | 3.096 (2) | 164 (4) |