| Literature DB >> 28932421 |
John Nicolson Low1, Ligia R Gomes2,3, Alexandra Gaspar4, Fernanda Borges4.
Abstract
Herein, the synthesis and crystal structure of 7-hy-droxy-3-(2-meth-oxy-phen-yl)-2-tri-fluoro-meth-yl-4H-chromen-4-one, C17H11F3O4, are reported. This isoflavone is used as a starting material in the preparation an array of potent and competitive FPR antagonists. The pyran ring significantly deviates from planarity and the dihedral angle between the benzo-pyran mean plane and that of the exocyclic benzene ring is 88.18 (4)°. In the crystal, O-H⋯O hydrogen bonds connect the mol-ecules into C(8) chains propagating in the [010] direction.Entities:
Keywords: chromone; crystal structure; isoflavone
Year: 2017 PMID: 28932421 PMCID: PMC5598833 DOI: 10.1107/S2056989017009896
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of 1 (left) and (right)the rotation of the exocyclic benzene relative to the benzopyran best plane [dihedral angle = 88.18 (4)°]. Displacement ellipsoids are drawn at the 70% probability level.
Deviations (in Å) of the pyran ring atoms and attached atoms from the mean plane of the chromone benzene ring
| Atom | O1 | C2 | C3′ | C4 | C21 | C31 | O4 |
|---|---|---|---|---|---|---|---|
| Distance | −0.0092 (18) | −0.243 (2) | −0.380 (2) | −0.155 (2) | −0.372 (3) | −0.805 (3) | −0.1267 (16) |
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| O7—H7⋯O4i | 0.87 (2) | 1.79 (2) | 2.6416 (13) | 166 (2) |
| C6—H6⋯O3ii | 0.95 | 2.59 | 3.4309 (16) | 148 |
| C36—H36⋯O7iii | 0.95 | 2.49 | 3.3886 (18) | 157 |
| C8—H8⋯ | 0.95 | 2.93 | 3.5972 (14) | 128 |
| C321—H32b⋯ | 0.98 | 2.75 | 3.6348 (17) | 150 |
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .
Figure 2Compound 1, the simple C8 chain formed by the O7—H7⋯O4i hydrogen bond. This chain extends along the b axis. Symmetry codes: (i) −x + , y − , z; (ii) −x + , y + , z). Hydrogen atoms not involved in the hydrogen bonding have been omitted.
Figure 3Compound 1, view of the ladder of alternating linked (18) and (20) structures formed by the interaction of centrosymmetrically related pairs of C6—H6⋯O3ii hydrogen bonds across the centre of symmetry at (0, , ) and centrosymmetrically related pairs of C36—H36⋯O7iii hydrogen bonds across the centre of symmetry at (, , ). This chain extends by unit translation along the a axis. Hydrogen atoms not involved in the hydrogen bonding have been omitted.
Percentages for the most relevant atom–atom contacts in 1
| H⋯H’ | H⋯O/O⋯H | H⋯F/F⋯H | H⋯C/C⋯H | C⋯C | C⋯O/O⋯C | O⋯F/F⋯C | O⋯O | F⋯O/O⋯F | F⋯F |
|---|---|---|---|---|---|---|---|---|---|
| 22.1 | 18.3 | 25.1 | 18.3 | 6.1 | 2.3 | 0.2 | 3.0 | 0.8 | 3.4 |
Figure 4Views of the Hirshfeld surface mapped over d norm for 1 and the corresponding FP plot. The highlighted red spots with large area on the top left image indicate O⋯H contact points involving the carbonyl oxygen atom of the chromone core and the hydrogen atom of the hydroxyl substituent while the pair of superposed light-red spots indicate C⋯H and O⋯H close contacts. The small red-spot areas on the concave and convex face of the right image are due to C⋯H close contacts. The bottom of the figure presents the FP plot for molecule 1 The light-blue area in the middle of the FP plot at d e/d i ∼ 1.9 Å shows a higher frequency of the pixels that are due to C⋯C contacts. The sharp spikes pointing to southwest are due to O⋯H contacts: the inner one on the right is related to O⋯H contacts and the short wings due to C⋯H close contacts (see Fig. 5 ▸ for details).
Figure 5Detail of the FP plot for 1 highlighting the H⋯C contacts (blue) and the corresponding areas in the Hirshfeld surface; The blue area covers the C⋯H/ H⋯C close contacts and displays two small wings as well as a pair of short spikes pointing to southwest ending at (d e/ d i)/(1.5/1.0) Å and vice versa that reflect the C36—H36⋯C7 contact area.
Figure 6The electrostatic potential surfaces for 1 (ranging from −0.0920 to 0.2582 a.u.). The surfaces show the complementary of electropositive area (blue) near the hydrogen atom of the hydroxyl substituent and red electronegative area surrounding the vicinity of the lone pairs of the oxo oxygen atom O4.
Experimental details
| Crystal data | |
| Chemical formula | C17H11F3O4 |
|
| 336.27 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 100 |
|
| 7.9147 (5), 16.2171 (11), 22.5254 (16) |
|
| 2891.2 (3) |
|
| 8 |
| Radiation type | Mo |
| μ (mm−1) | 0.14 |
| Crystal size (mm) | 0.21 × 0.07 × 0.01 |
| Data collection | |
| Diffractometer | Rigaku AFC12 |
| Absorption correction | Multi-scan ( |
|
| 0.775, 1.000 |
| No. of measured, independent and observed [ | 35487, 3314, 2777 |
|
| 0.058 |
| (sin θ/λ)max (Å−1) | 0.649 |
| Refinement | |
|
| 0.036, 0.103, 1.02 |
| No. of reflections | 3314 |
| No. of parameters | 222 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.34, −0.21 |
Computer programs: CrystalClear-SM Expert (Rigaku, 2012 ▸), SHELXT (Sheldrick, 2015a ▸), OSCAIL (McArdle et al., 2004 ▸), ShelXle (Hübschle et al., 2011 ▸), SHELXL2014 (Sheldrick, 2015b ▸), Mercury (Macrae et al., 2006 ▸) and PLATON (Spek, 2009 ▸).
| C17H11F3O4 | |
| Mo | |
| Orthorhombic, | Cell parameters from 31907 reflections |
| θ = 2.5–27.5° | |
| µ = 0.14 mm−1 | |
| Plate, colourless | |
| 0.21 × 0.07 × 0.01 mm | |
| Rigaku AFC12 diffractometer | 3314 independent reflections |
| Radiation source: Rotating Anode | 2777 reflections with |
| Detector resolution: 28.5714 pixels mm-1 | |
| profile data from ω–scans | θmax = 27.5°, θmin = 2.5° |
| Absorption correction: multi-scan ( | |
| 35487 measured reflections |
| Refinement on | 0 restraints |
| Least-squares matrix: full | Hydrogen site location: mixed |
| H atoms treated by a mixture of independent and constrained refinement | |
| (Δ/σ)max < 0.001 | |
| 3314 reflections | Δρmax = 0.34 e Å−3 |
| 222 parameters | Δρmin = −0.21 e Å−3 |
| 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. |
| F21 | 0.37922 (12) | 0.49225 (7) | 0.27664 (4) | 0.0476 (3) | |
| F22 | 0.59157 (13) | 0.56872 (5) | 0.29861 (4) | 0.0459 (3) | |
| F23 | 0.59737 (12) | 0.43950 (5) | 0.31761 (4) | 0.0416 (2) | |
| O1 | 0.38627 (12) | 0.44652 (5) | 0.40256 (4) | 0.0248 (2) | |
| O3 | 0.13208 (12) | 0.65679 (5) | 0.33431 (4) | 0.0276 (2) | |
| O4 | 0.29964 (14) | 0.66084 (5) | 0.49162 (4) | 0.0323 (2) | |
| O7 | 0.08054 (13) | 0.29227 (6) | 0.54664 (4) | 0.0293 (2) | |
| H7 | 0.114 (3) | 0.2531 (13) | 0.5233 (9) | 0.055 (6)* | |
| C2 | 0.42085 (16) | 0.52119 (7) | 0.37796 (6) | 0.0235 (3) | |
| C3 | 0.38708 (16) | 0.59517 (7) | 0.40248 (6) | 0.0232 (3) | |
| C4 | 0.31834 (16) | 0.59616 (7) | 0.46352 (6) | 0.0243 (3) | |
| C5 | 0.17944 (17) | 0.50964 (7) | 0.54149 (6) | 0.0253 (3) | |
| H5 | 0.1607 | 0.5575 | 0.5649 | 0.030* | |
| C4A | 0.26922 (16) | 0.51638 (7) | 0.48767 (5) | 0.0230 (3) | |
| C6 | 0.11873 (17) | 0.43488 (7) | 0.56045 (6) | 0.0256 (3) | |
| H6 | 0.0579 | 0.4311 | 0.5967 | 0.031* | |
| C7 | 0.14709 (17) | 0.36333 (7) | 0.52579 (6) | 0.0248 (3) | |
| C8 | 0.24070 (17) | 0.36720 (7) | 0.47361 (6) | 0.0244 (3) | |
| H8 | 0.2647 | 0.3190 | 0.4512 | 0.029* | |
| C8A | 0.29805 (16) | 0.44429 (7) | 0.45536 (5) | 0.0224 (3) | |
| C21 | 0.49789 (19) | 0.50614 (7) | 0.31732 (6) | 0.0277 (3) | |
| C31 | 0.40573 (17) | 0.67677 (7) | 0.37198 (6) | 0.0244 (3) | |
| C32 | 0.26803 (16) | 0.70816 (7) | 0.33969 (5) | 0.0237 (3) | |
| C33 | 0.27695 (18) | 0.78732 (8) | 0.31499 (6) | 0.0274 (3) | |
| H33 | 0.1837 | 0.8090 | 0.2935 | 0.033* | |
| C34 | 0.42290 (19) | 0.83407 (8) | 0.32209 (6) | 0.0303 (3) | |
| H34 | 0.4285 | 0.8878 | 0.3055 | 0.036* | |
| C35 | 0.56005 (19) | 0.80327 (8) | 0.35305 (6) | 0.0314 (3) | |
| H35 | 0.6600 | 0.8352 | 0.3571 | 0.038* | |
| C36 | 0.55002 (18) | 0.72477 (8) | 0.37832 (6) | 0.0290 (3) | |
| H36 | 0.6433 | 0.7039 | 0.4002 | 0.035* | |
| C321 | −0.01472 (19) | 0.69009 (9) | 0.30555 (7) | 0.0343 (3) | |
| H32A | −0.1047 | 0.6486 | 0.3052 | 0.051* | |
| H32B | 0.0137 | 0.7053 | 0.2647 | 0.051* | |
| H32C | −0.0533 | 0.7391 | 0.3271 | 0.051* |
| F21 | 0.0446 (6) | 0.0703 (7) | 0.0280 (5) | 0.0018 (5) | −0.0036 (4) | −0.0067 (4) |
| F22 | 0.0623 (6) | 0.0276 (4) | 0.0478 (5) | −0.0090 (4) | 0.0258 (5) | −0.0027 (4) |
| F23 | 0.0549 (6) | 0.0325 (4) | 0.0373 (5) | 0.0188 (4) | 0.0129 (4) | 0.0034 (3) |
| O1 | 0.0320 (5) | 0.0160 (4) | 0.0265 (5) | 0.0010 (3) | 0.0023 (4) | −0.0003 (3) |
| O3 | 0.0260 (5) | 0.0259 (4) | 0.0308 (5) | 0.0002 (4) | −0.0032 (4) | 0.0043 (4) |
| O4 | 0.0432 (6) | 0.0178 (4) | 0.0357 (5) | −0.0001 (4) | 0.0037 (4) | −0.0044 (4) |
| O7 | 0.0375 (6) | 0.0178 (4) | 0.0327 (5) | −0.0016 (4) | 0.0040 (4) | 0.0008 (4) |
| C2 | 0.0248 (6) | 0.0188 (6) | 0.0269 (6) | 0.0001 (5) | −0.0016 (5) | 0.0017 (4) |
| C3 | 0.0228 (6) | 0.0189 (5) | 0.0280 (6) | 0.0008 (4) | −0.0030 (5) | 0.0005 (5) |
| C4 | 0.0251 (6) | 0.0184 (5) | 0.0294 (6) | 0.0017 (5) | −0.0031 (5) | −0.0006 (5) |
| C5 | 0.0307 (7) | 0.0191 (5) | 0.0262 (6) | 0.0022 (5) | −0.0019 (5) | −0.0027 (5) |
| C4A | 0.0257 (6) | 0.0174 (5) | 0.0258 (6) | 0.0016 (5) | −0.0030 (5) | −0.0012 (4) |
| C6 | 0.0299 (7) | 0.0223 (6) | 0.0245 (6) | 0.0027 (5) | 0.0006 (5) | −0.0003 (5) |
| C7 | 0.0270 (7) | 0.0188 (5) | 0.0286 (6) | 0.0008 (5) | −0.0037 (5) | 0.0018 (5) |
| C8 | 0.0296 (7) | 0.0161 (5) | 0.0275 (6) | 0.0012 (5) | −0.0022 (5) | −0.0018 (4) |
| C8A | 0.0246 (6) | 0.0197 (6) | 0.0231 (6) | 0.0016 (5) | −0.0017 (5) | −0.0007 (4) |
| C21 | 0.0336 (7) | 0.0202 (6) | 0.0294 (6) | 0.0015 (5) | 0.0020 (5) | 0.0004 (5) |
| C31 | 0.0296 (7) | 0.0176 (5) | 0.0258 (6) | 0.0016 (5) | 0.0017 (5) | 0.0001 (4) |
| C32 | 0.0276 (6) | 0.0203 (5) | 0.0231 (6) | 0.0016 (5) | 0.0025 (5) | −0.0006 (4) |
| C33 | 0.0339 (7) | 0.0223 (6) | 0.0259 (6) | 0.0055 (5) | 0.0028 (5) | 0.0019 (5) |
| C34 | 0.0426 (8) | 0.0196 (6) | 0.0287 (7) | 0.0007 (5) | 0.0081 (6) | 0.0019 (5) |
| C35 | 0.0361 (7) | 0.0220 (6) | 0.0361 (7) | −0.0056 (5) | 0.0043 (6) | −0.0028 (5) |
| C36 | 0.0301 (7) | 0.0222 (6) | 0.0346 (7) | 0.0000 (5) | −0.0015 (5) | −0.0007 (5) |
| C321 | 0.0292 (7) | 0.0375 (7) | 0.0362 (7) | 0.0034 (6) | −0.0058 (6) | 0.0056 (6) |
| F21—C21 | 1.3314 (17) | C6—C7 | 1.4164 (17) |
| F22—C21 | 1.3256 (15) | C6—H6 | 0.9500 |
| F23—C21 | 1.3371 (15) | C7—C8 | 1.3908 (19) |
| O1—C2 | 1.3594 (15) | C8—C8A | 1.3921 (17) |
| O1—C8A | 1.3796 (15) | C8—H8 | 0.9500 |
| O3—C32 | 1.3662 (15) | C31—C36 | 1.3895 (19) |
| O3—C321 | 1.4356 (16) | C31—C32 | 1.4057 (18) |
| O4—C4 | 1.2340 (15) | C32—C33 | 1.4008 (17) |
| O7—C7 | 1.3514 (15) | C33—C34 | 1.391 (2) |
| O7—H7 | 0.87 (2) | C33—H33 | 0.9500 |
| C2—C3 | 1.3475 (17) | C34—C35 | 1.384 (2) |
| C2—C21 | 1.5158 (18) | C34—H34 | 0.9500 |
| C3—C4 | 1.4788 (18) | C35—C36 | 1.3967 (18) |
| C3—C31 | 1.4983 (17) | C35—H35 | 0.9500 |
| C4—C4A | 1.4564 (16) | C36—H36 | 0.9500 |
| C5—C6 | 1.3723 (17) | C321—H32A | 0.9800 |
| C5—C4A | 1.4094 (18) | C321—H32B | 0.9800 |
| C5—H5 | 0.9500 | C321—H32C | 0.9800 |
| C4A—C8A | 1.3960 (16) | ||
| C2—O1—C8A | 118.46 (9) | F22—C21—F21 | 107.78 (11) |
| C32—O3—C321 | 116.62 (10) | F22—C21—F23 | 106.92 (12) |
| C7—O7—H7 | 107.1 (13) | F21—C21—F23 | 106.39 (11) |
| C3—C2—O1 | 125.88 (12) | F22—C21—C2 | 112.84 (10) |
| C3—C2—C21 | 126.33 (11) | F21—C21—C2 | 111.33 (12) |
| O1—C2—C21 | 107.75 (10) | F23—C21—C2 | 111.26 (10) |
| C2—C3—C4 | 117.63 (11) | C36—C31—C32 | 119.18 (11) |
| C2—C3—C31 | 125.38 (12) | C36—C31—C3 | 121.91 (12) |
| C4—C3—C31 | 116.93 (10) | C32—C31—C3 | 118.73 (11) |
| O4—C4—C4A | 122.10 (12) | O3—C32—C33 | 124.28 (12) |
| O4—C4—C3 | 122.03 (11) | O3—C32—C31 | 115.83 (10) |
| C4A—C4—C3 | 115.84 (10) | C33—C32—C31 | 119.89 (12) |
| C6—C5—C4A | 120.84 (11) | C34—C33—C32 | 119.71 (13) |
| C6—C5—H5 | 119.6 | C34—C33—H33 | 120.1 |
| C4A—C5—H5 | 119.6 | C32—C33—H33 | 120.1 |
| C8A—C4A—C5 | 117.78 (11) | C35—C34—C33 | 120.85 (12) |
| C8A—C4A—C4 | 120.36 (11) | C35—C34—H34 | 119.6 |
| C5—C4A—C4 | 121.66 (11) | C33—C34—H34 | 119.6 |
| C5—C6—C7 | 119.78 (12) | C34—C35—C36 | 119.34 (13) |
| C5—C6—H6 | 120.1 | C34—C35—H35 | 120.3 |
| C7—C6—H6 | 120.1 | C36—C35—H35 | 120.3 |
| O7—C7—C8 | 122.67 (11) | C31—C36—C35 | 121.02 (13) |
| O7—C7—C6 | 116.44 (12) | C31—C36—H36 | 119.5 |
| C8—C7—C6 | 120.88 (11) | C35—C36—H36 | 119.5 |
| C7—C8—C8A | 117.63 (11) | O3—C321—H32A | 109.5 |
| C7—C8—H8 | 121.2 | O3—C321—H32B | 109.5 |
| C8A—C8—H8 | 121.2 | H32A—C321—H32B | 109.5 |
| O1—C8A—C8 | 116.31 (10) | O3—C321—H32C | 109.5 |
| O1—C8A—C4A | 120.69 (10) | H32A—C321—H32C | 109.5 |
| C8—C8A—C4A | 123.01 (12) | H32B—C321—H32C | 109.5 |
| C8A—O1—C2—C3 | 4.95 (19) | C4—C4A—C8A—O1 | 5.63 (18) |
| C8A—O1—C2—C21 | −172.99 (10) | C5—C4A—C8A—C8 | 0.76 (19) |
| O1—C2—C3—C4 | 5.0 (2) | C4—C4A—C8A—C8 | −174.13 (12) |
| C21—C2—C3—C4 | −177.39 (12) | C3—C2—C21—F22 | 25.4 (2) |
| O1—C2—C3—C31 | −171.91 (12) | O1—C2—C21—F22 | −156.64 (11) |
| C21—C2—C3—C31 | 5.7 (2) | C3—C2—C21—F21 | −95.91 (15) |
| C2—C3—C4—O4 | 172.60 (12) | O1—C2—C21—F21 | 82.03 (13) |
| C31—C3—C4—O4 | −10.19 (19) | C3—C2—C21—F23 | 145.61 (13) |
| C2—C3—C4—C4A | −9.24 (17) | O1—C2—C21—F23 | −36.46 (15) |
| C31—C3—C4—C4A | 167.97 (11) | C2—C3—C31—C36 | −95.96 (16) |
| C6—C5—C4A—C8A | −1.73 (19) | C4—C3—C31—C36 | 87.07 (16) |
| C6—C5—C4A—C4 | 173.08 (12) | C2—C3—C31—C32 | 88.86 (16) |
| O4—C4—C4A—C8A | −177.67 (12) | C4—C3—C31—C32 | −88.10 (14) |
| C3—C4—C4A—C8A | 4.17 (18) | C321—O3—C32—C33 | −5.40 (18) |
| O4—C4—C4A—C5 | 7.6 (2) | C321—O3—C32—C31 | 175.24 (11) |
| C3—C4—C4A—C5 | −170.51 (12) | C36—C31—C32—O3 | 178.68 (11) |
| C4A—C5—C6—C7 | 0.3 (2) | C3—C31—C32—O3 | −6.01 (17) |
| C5—C6—C7—O7 | −178.66 (12) | C36—C31—C32—C33 | −0.71 (18) |
| C5—C6—C7—C8 | 2.2 (2) | C3—C31—C32—C33 | 174.60 (11) |
| O7—C7—C8—C8A | 177.81 (12) | O3—C32—C33—C34 | −178.71 (12) |
| C6—C7—C8—C8A | −3.06 (19) | C31—C32—C33—C34 | 0.63 (18) |
| C2—O1—C8A—C8 | 169.42 (11) | C32—C33—C34—C35 | 0.3 (2) |
| C2—O1—C8A—C4A | −10.35 (17) | C33—C34—C35—C36 | −1.2 (2) |
| C7—C8—C8A—O1 | −178.16 (11) | C32—C31—C36—C35 | −0.2 (2) |
| C7—C8—C8A—C4A | 1.6 (2) | C3—C31—C36—C35 | −175.30 (12) |
| C5—C4A—C8A—O1 | −179.48 (11) | C34—C35—C36—C31 | 1.1 (2) |
| H··· | ||||
| O7—H7···O4i | 0.87 (2) | 1.79 (2) | 2.6416 (13) | 166 (2) |
| C6—H6···O3ii | 0.95 | 2.59 | 3.4309 (16) | 148 |
| C36—H36···O7iii | 0.95 | 2.49 | 3.3886 (18) | 157 |
| C8—H8··· | 0.95 | 2.93 | 3.5972 (14) | 128 |
| C321—H32b··· | 0.98 | 2.75 | 3.6348 (17) | 150 |