| Literature DB >> 26870423 |
Shobanbabu Bommagani1, Narsimha R Penthala1, Sean Parkin2, Peter A Crooks1.
Abstract
The title compound, C19H22N2O3, {systematic name (1aR,4E,7aS,8E,10aS,10bR)-1a,5-dimethyl-8-[(pyrimidin-5-yl)-methylid-ene]-2,3,6,7,7a,8,10a,10b-octa-hydro-oxireno[2',3':9,10]cyclo-deca-[1,2-b]furan-9(1aH)-one} was obtained from the reaction of parthenolide [systematic name (1aR,7aS,10aS,10bR,E)-1a,5-dimethyl-8-methyl-ene-2,3,6,7,7a,8,10a,10b-octa-hydro-oxireno[2',3':9,10]cyclodeca-[1,2-b]furan-9(1aH)-one] with 5-bromo-pyrimidine under Heck reaction conditions, and was identified as an E isomer. The mol-ecule possesses ten-, five- (lactone) and three-membered (epoxide) rings with a pyrimidine group as a substituent. The ten-membered ring displays an approximate chair-chair conformation, while the lactone ring shows a flattened envelope-type conformation. The dihedral angle between the pyrimidine moiety and the lactone ring system is 29.43 (7)°.Entities:
Keywords: Heck product; crystal structure; parthenolide; pyrimidine
Year: 2015 PMID: 26870423 PMCID: PMC4719832 DOI: 10.1107/S2056989015021507
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of the title compound with probability ellipsoids drawn at the 50% probability level.
Experimental details
| Crystal data | |
| Chemical formula | C19H22N2O3 |
|
| 326.38 |
| Crystal system, space group | Monoclinic, |
| Temperature (K) | 90 |
|
| 10.3526 (2), 7.2612 (1), 11.9198 (2) |
| β (°) | 108.1210 (6) |
|
| 851.60 (2) |
|
| 2 |
| Radiation type | Cu |
| μ (mm−1) | 0.70 |
| Crystal size (mm) | 0.25 × 0.13 × 0.10 |
| Data collection | |
| Diffractometer | Bruker X8 Proteum |
| Absorption correction | Multi-scan ( |
|
| 0.850, 0.942 |
| No. of measured, independent and observed [ | 11370, 3020, 3013 |
|
| 0.032 |
| (sin θ/λ)max (Å−1) | 0.602 |
| Refinement | |
|
| 0.027, 0.068, 1.05 |
| No. of reflections | 3020 |
| No. of parameters | 220 |
| No. of restraints | 1 |
| H-atom treatment | H-atom parameters constrained |
| Δρmax, Δρmin (e Å−3) | 0.15, −0.14 |
| Absolute structure | Flack |
| Absolute structure parameter | −0.04 (3) |
Computer programs: APEX2 and SAINT (Bruker, 2006 ▸), SHELXS97, SHELXTL and XP in SHELXTL (Sheldrick, 2008 ▸), SHELXL2014 (Sheldrick, 2015 ▸) and CIFFIX (Parkin, 2013 ▸).
| C19H22N2O3 | |
| Monoclinic, | Cu |
| Cell parameters from 9908 reflections | |
| θ = 4.5–68.2° | |
| µ = 0.70 mm−1 | |
| β = 108.1210 (6)° | |
| Solvent-rounded block, colourless | |
| 0.25 × 0.13 × 0.10 mm |
| Bruker X8 Proteum diffractometer | 3020 independent reflections |
| Radiation source: fine-focus rotating anode | 3013 reflections with |
| Detector resolution: 5.6 pixels mm-1 | |
| φ and ω scans | θmax = 68.2°, θmin = 4.5° |
| Absorption correction: multi-scan ( | |
| 11370 measured reflections |
| Refinement on | Hydrogen site location: difference Fourier map |
| Least-squares matrix: full | H-atom parameters constrained |
| (Δ/σ)max < 0.001 | |
| Δρmax = 0.15 e Å−3 | |
| 3020 reflections | Δρmin = −0.14 e Å−3 |
| 220 parameters | Extinction correction: |
| 1 restraint | Extinction coefficient: 0.010 (2) |
| Primary atom site location: structure-invariant direct methods | Absolute structure: Flack x determined using 1354 quotients
[( |
| Secondary atom site location: difference Fourier map | Absolute structure parameter: −0.04 (3) |
| Experimental. The crystal was mounted with polyisobutene oil on the tip of a fine glass fibre, which was fastened in a copper mounting pin with electrical solder. It was placed directly into the cold gas stream of a liquid nitrogen based cryostat, according to published methods. Diffraction data were collected with the crystal at 90 K, which is standard practice in this laboratory for the majority of flash-cooled crystals.The crystals were large, and could not be cut to size without inducing damage by crushing, leading to shattered, frayed ends. These damaged parts could easily be dissolved away, however, to give solvent-rounded undamaged pieces of optimal size for data collection. |
| Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
| Refinement. Refinement progress was checked using |
| O1 | 0.59428 (12) | 0.24072 (19) | 0.48957 (10) | 0.0228 (3) | |
| O2 | 0.30633 (12) | 0.25486 (17) | 0.43887 (10) | 0.0195 (3) | |
| O3 | 0.12397 (13) | 0.29255 (19) | 0.49855 (11) | 0.0266 (3) | |
| C1 | 0.57679 (17) | 0.5285 (2) | 0.19945 (14) | 0.0185 (4) | |
| H1A | 0.5833 | 0.6439 | 0.2384 | 0.022* | |
| C2 | 0.70386 (17) | 0.4134 (3) | 0.23289 (16) | 0.0208 (4) | |
| H2A | 0.7809 | 0.4881 | 0.2257 | 0.025* | |
| H2B | 0.6915 | 0.3076 | 0.1781 | 0.025* | |
| C3 | 0.73676 (17) | 0.3417 (3) | 0.36116 (15) | 0.0202 (4) | |
| H3A | 0.8146 | 0.2554 | 0.3792 | 0.024* | |
| H3B | 0.7615 | 0.4460 | 0.4173 | 0.024* | |
| C4 | 0.61322 (17) | 0.2447 (2) | 0.37345 (14) | 0.0178 (4) | |
| C5 | 0.51035 (16) | 0.3615 (2) | 0.40010 (13) | 0.0165 (3) | |
| H5A | 0.5353 | 0.4948 | 0.4118 | 0.020* | |
| C6 | 0.35977 (16) | 0.3252 (2) | 0.34753 (14) | 0.0159 (3) | |
| H6A | 0.3445 | 0.2321 | 0.2829 | 0.019* | |
| C7 | 0.27894 (16) | 0.5036 (2) | 0.29783 (13) | 0.0149 (3) | |
| H7A | 0.3396 | 0.6113 | 0.3292 | 0.018* | |
| C8 | 0.22800 (16) | 0.5184 (3) | 0.16174 (14) | 0.0176 (4) | |
| H8A | 0.1434 | 0.5923 | 0.1376 | 0.021* | |
| H8B | 0.2058 | 0.3936 | 0.1278 | 0.021* | |
| C9 | 0.33322 (17) | 0.6078 (3) | 0.11062 (14) | 0.0185 (4) | |
| H9A | 0.2884 | 0.6358 | 0.0261 | 0.022* | |
| H9B | 0.3638 | 0.7258 | 0.1519 | 0.022* | |
| C10 | 0.45591 (17) | 0.4887 (2) | 0.12176 (14) | 0.0179 (4) | |
| C11 | 0.16862 (16) | 0.5027 (2) | 0.35605 (14) | 0.0159 (3) | |
| C12 | 0.19100 (17) | 0.3425 (3) | 0.43718 (14) | 0.0184 (4) | |
| C13 | 0.06867 (17) | 0.6212 (3) | 0.35248 (14) | 0.0179 (4) | |
| H13A | 0.0096 | 0.5872 | 0.3961 | 0.021* | |
| C14 | 0.42876 (19) | 0.3267 (3) | 0.03864 (16) | 0.0269 (4) | |
| H14A | 0.5140 | 0.2609 | 0.0473 | 0.040* | |
| H14B | 0.3908 | 0.3705 | −0.0428 | 0.040* | |
| H14C | 0.3639 | 0.2434 | 0.0573 | 0.040* | |
| C15 | 0.57578 (18) | 0.0643 (2) | 0.30934 (18) | 0.0239 (4) | |
| H15A | 0.5012 | 0.0072 | 0.3311 | 0.036* | |
| H15B | 0.6548 | −0.0179 | 0.3312 | 0.036* | |
| H15C | 0.5470 | 0.0861 | 0.2240 | 0.036* | |
| C16 | 0.03901 (16) | 0.7977 (2) | 0.28928 (14) | 0.0180 (4) | |
| C17 | 0.13568 (18) | 0.9097 (3) | 0.26601 (18) | 0.0244 (4) | |
| H17A | 0.2281 | 0.8719 | 0.2933 | 0.029* | |
| N18 | 0.10538 (16) | 1.0688 (2) | 0.20684 (16) | 0.0293 (4) | |
| C19 | −0.02533 (19) | 1.1156 (3) | 0.17269 (17) | 0.0252 (4) | |
| H19A | −0.0485 | 1.2265 | 0.1287 | 0.030* | |
| N20 | −0.12697 (15) | 1.0248 (2) | 0.19312 (14) | 0.0256 (4) | |
| C21 | −0.09291 (18) | 0.8673 (3) | 0.25279 (15) | 0.0219 (4) | |
| H21A | −0.1621 | 0.7994 | 0.2713 | 0.026* |
| O1 | 0.0188 (6) | 0.0306 (7) | 0.0176 (6) | 0.0061 (5) | 0.0035 (5) | 0.0092 (5) |
| O2 | 0.0187 (6) | 0.0200 (6) | 0.0221 (6) | 0.0038 (5) | 0.0098 (5) | 0.0064 (5) |
| O3 | 0.0242 (6) | 0.0305 (8) | 0.0303 (7) | 0.0031 (6) | 0.0162 (5) | 0.0097 (6) |
| C1 | 0.0218 (8) | 0.0163 (8) | 0.0197 (8) | −0.0006 (7) | 0.0100 (7) | 0.0024 (7) |
| C2 | 0.0184 (8) | 0.0208 (9) | 0.0254 (9) | −0.0018 (7) | 0.0101 (7) | −0.0001 (7) |
| C3 | 0.0157 (8) | 0.0216 (9) | 0.0228 (8) | 0.0016 (7) | 0.0053 (6) | −0.0004 (7) |
| C4 | 0.0163 (8) | 0.0184 (8) | 0.0174 (8) | 0.0036 (7) | 0.0031 (6) | 0.0040 (7) |
| C5 | 0.0175 (8) | 0.0173 (8) | 0.0141 (7) | 0.0020 (7) | 0.0043 (6) | 0.0031 (6) |
| C6 | 0.0173 (8) | 0.0162 (8) | 0.0154 (7) | 0.0002 (6) | 0.0068 (6) | 0.0012 (6) |
| C7 | 0.0155 (7) | 0.0147 (8) | 0.0142 (7) | −0.0011 (6) | 0.0041 (6) | −0.0008 (6) |
| C8 | 0.0172 (8) | 0.0201 (8) | 0.0143 (8) | 0.0005 (7) | 0.0034 (6) | 0.0003 (7) |
| C9 | 0.0209 (8) | 0.0195 (8) | 0.0147 (7) | 0.0018 (7) | 0.0051 (6) | 0.0044 (7) |
| C10 | 0.0221 (8) | 0.0190 (9) | 0.0150 (7) | 0.0003 (7) | 0.0092 (7) | 0.0026 (7) |
| C11 | 0.0153 (7) | 0.0170 (8) | 0.0143 (7) | −0.0021 (7) | 0.0031 (6) | −0.0010 (7) |
| C12 | 0.0166 (8) | 0.0206 (9) | 0.0187 (8) | 0.0004 (7) | 0.0065 (6) | 0.0014 (7) |
| C13 | 0.0144 (8) | 0.0213 (9) | 0.0175 (8) | −0.0011 (7) | 0.0044 (6) | −0.0018 (7) |
| C14 | 0.0258 (9) | 0.0321 (11) | 0.0219 (8) | 0.0041 (8) | 0.0061 (7) | −0.0061 (8) |
| C15 | 0.0206 (8) | 0.0177 (9) | 0.0346 (10) | 0.0023 (7) | 0.0105 (8) | 0.0005 (7) |
| C16 | 0.0175 (8) | 0.0190 (9) | 0.0161 (7) | 0.0009 (7) | 0.0032 (6) | −0.0044 (7) |
| C17 | 0.0156 (8) | 0.0189 (9) | 0.0350 (10) | 0.0005 (7) | 0.0024 (8) | 0.0019 (8) |
| N18 | 0.0209 (8) | 0.0216 (9) | 0.0409 (10) | −0.0014 (6) | 0.0030 (7) | 0.0062 (7) |
| C19 | 0.0240 (9) | 0.0183 (9) | 0.0288 (9) | 0.0021 (8) | 0.0016 (7) | 0.0019 (8) |
| N20 | 0.0206 (8) | 0.0232 (8) | 0.0304 (8) | 0.0042 (6) | 0.0043 (6) | 0.0003 (7) |
| C21 | 0.0194 (8) | 0.0219 (9) | 0.0253 (9) | 0.0026 (7) | 0.0084 (7) | −0.0024 (7) |
| O1—C5 | 1.444 (2) | C8—H8B | 0.9900 |
| O1—C4 | 1.457 (2) | C9—C10 | 1.508 (2) |
| O2—C12 | 1.348 (2) | C9—H9A | 0.9900 |
| O2—C6 | 1.4585 (19) | C9—H9B | 0.9900 |
| O3—C12 | 1.210 (2) | C10—C14 | 1.507 (3) |
| C1—C10 | 1.337 (2) | C11—C13 | 1.336 (2) |
| C1—C2 | 1.504 (2) | C11—C12 | 1.484 (2) |
| C1—H1A | 0.9500 | C13—C16 | 1.470 (2) |
| C2—C3 | 1.549 (2) | C13—H13A | 0.9500 |
| C2—H2A | 0.9900 | C14—H14A | 0.9800 |
| C2—H2B | 0.9900 | C14—H14B | 0.9800 |
| C3—C4 | 1.507 (2) | C14—H14C | 0.9800 |
| C3—H3A | 0.9900 | C15—H15A | 0.9800 |
| C3—H3B | 0.9900 | C15—H15B | 0.9800 |
| C4—C5 | 1.471 (2) | C15—H15C | 0.9800 |
| C4—C15 | 1.505 (3) | C16—C17 | 1.383 (3) |
| C5—C6 | 1.511 (2) | C16—C21 | 1.393 (2) |
| C5—H5A | 1.0000 | C17—N18 | 1.339 (2) |
| C6—C7 | 1.556 (2) | C17—H17A | 0.9500 |
| C6—H6A | 1.0000 | N18—C19 | 1.330 (2) |
| C7—C11 | 1.510 (2) | C19—N20 | 1.327 (3) |
| C7—C8 | 1.546 (2) | C19—H19A | 0.9500 |
| C7—H7A | 1.0000 | N20—C21 | 1.335 (3) |
| C8—C9 | 1.547 (2) | C21—H21A | 0.9500 |
| C8—H8A | 0.9900 | ||
| C5—O1—C4 | 60.94 (10) | H8A—C8—H8B | 107.8 |
| C12—O2—C6 | 111.31 (12) | C10—C9—C8 | 113.70 (14) |
| C10—C1—C2 | 128.05 (17) | C10—C9—H9A | 108.8 |
| C10—C1—H1A | 116.0 | C8—C9—H9A | 108.8 |
| C2—C1—H1A | 116.0 | C10—C9—H9B | 108.8 |
| C1—C2—C3 | 110.73 (14) | C8—C9—H9B | 108.8 |
| C1—C2—H2A | 109.5 | H9A—C9—H9B | 107.7 |
| C3—C2—H2A | 109.5 | C1—C10—C14 | 124.58 (16) |
| C1—C2—H2B | 109.5 | C1—C10—C9 | 121.22 (16) |
| C3—C2—H2B | 109.5 | C14—C10—C9 | 114.20 (15) |
| H2A—C2—H2B | 108.1 | C13—C11—C12 | 119.20 (15) |
| C4—C3—C2 | 108.68 (14) | C13—C11—C7 | 132.19 (16) |
| C4—C3—H3A | 110.0 | C12—C11—C7 | 108.42 (13) |
| C2—C3—H3A | 110.0 | O3—C12—O2 | 121.43 (16) |
| C4—C3—H3B | 110.0 | O3—C12—C11 | 128.78 (16) |
| C2—C3—H3B | 110.0 | O2—C12—C11 | 109.75 (13) |
| H3A—C3—H3B | 108.3 | C11—C13—C16 | 127.89 (16) |
| O1—C4—C5 | 59.08 (10) | C11—C13—H13A | 116.1 |
| O1—C4—C15 | 112.05 (15) | C16—C13—H13A | 116.1 |
| C5—C4—C15 | 121.46 (15) | C10—C14—H14A | 109.5 |
| O1—C4—C3 | 118.08 (14) | C10—C14—H14B | 109.5 |
| C5—C4—C3 | 116.40 (15) | H14A—C14—H14B | 109.5 |
| C15—C4—C3 | 116.73 (15) | C10—C14—H14C | 109.5 |
| O1—C5—C4 | 59.97 (10) | H14A—C14—H14C | 109.5 |
| O1—C5—C6 | 120.41 (14) | H14B—C14—H14C | 109.5 |
| C4—C5—C6 | 122.16 (14) | C4—C15—H15A | 109.5 |
| O1—C5—H5A | 114.5 | C4—C15—H15B | 109.5 |
| C4—C5—H5A | 114.5 | H15A—C15—H15B | 109.5 |
| C6—C5—H5A | 114.5 | C4—C15—H15C | 109.5 |
| O2—C6—C5 | 109.48 (12) | H15A—C15—H15C | 109.5 |
| O2—C6—C7 | 106.97 (12) | H15B—C15—H15C | 109.5 |
| C5—C6—C7 | 112.07 (13) | C17—C16—C21 | 115.11 (16) |
| O2—C6—H6A | 109.4 | C17—C16—C13 | 124.52 (15) |
| C5—C6—H6A | 109.4 | C21—C16—C13 | 120.31 (15) |
| C7—C6—H6A | 109.4 | N18—C17—C16 | 123.19 (16) |
| C11—C7—C8 | 115.01 (13) | N18—C17—H17A | 118.4 |
| C11—C7—C6 | 102.45 (13) | C16—C17—H17A | 118.4 |
| C8—C7—C6 | 115.15 (13) | C19—N18—C17 | 115.52 (17) |
| C11—C7—H7A | 107.9 | N20—C19—N18 | 127.34 (18) |
| C8—C7—H7A | 107.9 | N20—C19—H19A | 116.3 |
| C6—C7—H7A | 107.9 | N18—C19—H19A | 116.3 |
| C7—C8—C9 | 112.99 (13) | C19—N20—C21 | 115.48 (15) |
| C7—C8—H8A | 109.0 | N20—C21—C16 | 123.23 (17) |
| C9—C8—H8A | 109.0 | N20—C21—H21A | 118.4 |
| C7—C8—H8B | 109.0 | C16—C21—H21A | 118.4 |
| C9—C8—H8B | 109.0 | ||
| C10—C1—C2—C3 | −110.99 (19) | C2—C1—C10—C14 | −8.9 (3) |
| C1—C2—C3—C4 | 53.54 (19) | C2—C1—C10—C9 | 171.47 (16) |
| C5—O1—C4—C15 | −114.44 (16) | C8—C9—C10—C1 | −107.23 (18) |
| C5—O1—C4—C3 | 105.54 (17) | C8—C9—C10—C14 | 73.07 (19) |
| C2—C3—C4—O1 | −152.28 (15) | C8—C7—C11—C13 | −56.5 (2) |
| C2—C3—C4—C5 | −84.95 (18) | C6—C7—C11—C13 | 177.78 (17) |
| C2—C3—C4—C15 | 69.54 (18) | C8—C7—C11—C12 | 128.73 (15) |
| C4—O1—C5—C6 | 111.94 (17) | C6—C7—C11—C12 | 3.06 (16) |
| C15—C4—C5—O1 | 98.43 (17) | C6—O2—C12—O3 | 172.90 (16) |
| C3—C4—C5—O1 | −108.37 (16) | C6—O2—C12—C11 | −9.33 (18) |
| O1—C4—C5—C6 | −109.10 (17) | C13—C11—C12—O3 | 5.6 (3) |
| C15—C4—C5—C6 | −10.7 (2) | C7—C11—C12—O3 | −178.86 (18) |
| C3—C4—C5—C6 | 142.53 (15) | C13—C11—C12—O2 | −171.94 (15) |
| C12—O2—C6—C5 | 132.85 (14) | C7—C11—C12—O2 | 3.59 (18) |
| C12—O2—C6—C7 | 11.21 (17) | C12—C11—C13—C16 | 172.57 (15) |
| O1—C5—C6—O2 | 36.7 (2) | C7—C11—C13—C16 | −1.7 (3) |
| C4—C5—C6—O2 | 108.24 (17) | C11—C13—C16—C17 | −29.8 (3) |
| O1—C5—C6—C7 | 155.20 (14) | C11—C13—C16—C21 | 153.17 (17) |
| C4—C5—C6—C7 | −133.25 (15) | C21—C16—C17—N18 | −3.7 (3) |
| O2—C6—C7—C11 | −8.19 (16) | C13—C16—C17—N18 | 179.10 (17) |
| C5—C6—C7—C11 | −128.18 (14) | C16—C17—N18—C19 | 1.1 (3) |
| O2—C6—C7—C8 | −133.78 (14) | C17—N18—C19—N20 | 1.7 (3) |
| C5—C6—C7—C8 | 106.23 (15) | N18—C19—N20—C21 | −1.4 (3) |
| C11—C7—C8—C9 | 153.12 (15) | C19—N20—C21—C16 | −1.7 (3) |
| C6—C7—C8—C9 | −88.08 (18) | C17—C16—C21—N20 | 4.0 (2) |
| C7—C8—C9—C10 | 69.71 (19) | C13—C16—C21—N20 | −178.66 (16) |