research communications
Synthesis and tert-butyl 1-(2-iodobenzoyl)cyclopent-3-ene-1-carboxylate
ofaSchool of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi in Jiangsu Province, People's Republic of China
*Correspondence e-mail: ydjszlg@163.com
1-(2-Iodobenzoyl)-cyclopent-3-ene-1-carboxylates are novel substrates to construct bicyclo[3.2.1]octanes with antibacterial and antithrombotic activities. In this context, tert-butyl 1-(2-iodobenzoyl)-cyclopent-3-ene-1-carboxylate, C17H19IO3, was synthesized and structurally characterized. The 2-iodobenzoyl group is attached to the tertiary C atom of the cyclopent-3-ene ring. The dihedral angle between the benzene ring and the mean plane of the envelope-type cyclopent-3-ene ring is 26.0 (3)°. In the crystal, pairs of C-H⋯O hydrogen bonds link the molecules to form inversion dimers.
Keywords: crystal structure; substrate; cyclopentene ring; hydrogen bonding.
CCDC reference: 1899475
1. Chemical context
1-(2-Iodobenzoyl)cyclopent-3-ene-1-carboxylates were recently employed as novel substrates to construct bicyclo[3.2.1]octanes that are widely found in natural products and bioactive molecules with antibacterial and antithrombotic activities (Yuan et al., 2019). Although the authors carried out some control experiments to reveal the crystal structures of the substrates have not been reported yet. Moreover, 1-(2-iodobenzoyl)cyclopent-3-ene is crucial to the reductive Heck reaction and thus may provide more direct information on this if more detailed structural data are available. Herein, the synthesis and of tert-butyl 1-(2-iodobenzoyl)cyclopent-3-ene-1-carboxylate are reported.
2. Structural commentary
The molecular structure of the title compound is shown in Fig. 1. The 2-iodobenzoyl group is attached to the tertiary C atom (C8) of the cyclopent-3-ene ring, with the tert-butyl carboxylate group as the other substituent. The five-membered C8–C12 ring adopts an with atom C8 as the flap, and with puckering parameters (Cremer & Pople, 1975) Q = 0.1526 Å and φ = 0.5354°, and pseudo-rotation parameters (Rao et al., 1981) P = 162.5 (1)° and τ(M) = 15.2 (3)°. The deviation of C8 from the mean plane defined by atoms C9–C12 is 0.097 (4) Å. The dihedral angle between the benzene ring and the alkene plane (C9–C12) of the cyclopent-3-ene ring is 26.51 (19)°.
3. Supramolecular features
In the crystal, molecules are linked by a pair of C—H⋯O hydrogen bonds forming inversion dimers (Table 1 and Fig. 2). They stack up the b axis and form layers parallel to the bc plane. There are no other significant intermolecular interactions present in the crystal.
4. Database survey
A search of the Cambridge Structural Database (CSD, Version 5.39, update of August 2018; Groom et al., 2016) for entities containing (1-methylcyclopent-3-en-1-yl)(phenyl)methanone yielded 27 hits. Only two of these compounds involve no other substituents at the cyclopent-3-ene ring as in the title compound, viz. methyl 4-[(1-methylcyclopent-3-en-1-yl)carbonyl]benzoate in the Pnma (CSD refcode CIQHAM; Yang et al., 2007), and 4-benzoyl-4-(methoxycarbonyl)cyclopentene in the P21/c, with four independent molecules in the (CSD refcode KOGSIJ; Jiang et al., 2008). In the structures of these two compounds, the folding angles of the cyclopent-3-ene ring are 17.00 (13) and 11.91 (12)°, respectively, while in the title compound it is 15.0 (3)°. The benzene ring in each structure is inclined to the alkene plane of the cyclopent-3-ene ring by 90.00 (8) and 61.40 (6)°, respectively, while the corresponding dihedral angle in the title compound is 26.51 (19)°. Apparently, different kinds of intermolecular C—H⋯O hydrogen bonds and the presence or not of weak π–π contacts in the three structures lead to different molecular packing and dihedral angles between the benzene ring and the cyclopent-3-ene ring.
5. Synthesis and crystallization
The title compound was prepared according to a general literature protocol (Yuan et al., 2019). 1H NMR (300 MHz, CDCl3): δ 8.0 (dd, J = 7.9, 1.2 Hz, 1H), 7.4 (dd, J = 7.8, 1.8 Hz, 1H), 7.3 (td, J = 7.5, 1.2 Hz, 1H), 7.1 (td, J = 7.8, 1.8 Hz, 1H), 5.6 (s, 2H), 3.1 (s, 4H), 1.2 (s, 9H). HRMS (ESI) calcd for [C17H19IO3+Na]+ 421.0271, found 421.0272. Crystallization from a 5:1 mixture (v/v) of dichloromethane and n-hexane by slow evaporation at room temperature for about 7 d gave block-shaped crystals of the title compound.
6. Refinement
Crystal data, data collection and structure . H atoms attached to C atoms were included in calculated positions and refined using a riding model: C—H = 0.93-0.97 Å with Uiso(H) = 1.5Ueq(C-methyl) and 1.2Ueq(C) for other H atoms.
details are summarized in Table 2Supporting information
CCDC reference: 1899475
https://doi.org/10.1107/S2056989019011514/wm5513sup1.cif
contains datablocks global, I. DOI:Supporting information file. DOI: https://doi.org/10.1107/S2056989019011514/wm5513Isup2.cml
Structure factors: contains datablock 20180530A_0m_a. DOI: https://doi.org/10.1107/S2056989019011514/wm5513Isup3.hkl
Data collection: APEX3 (Bruker, 2014); cell
SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015b), PLATON (Spek, 2009) and publCIF (Westrip, 2010).C17H19IO3 | F(000) = 792 |
Mr = 398.22 | Dx = 1.533 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54178 Å |
a = 9.4977 (2) Å | Cell parameters from 5961 reflections |
b = 9.3635 (2) Å | θ = 4.6–69.9° |
c = 19.8978 (4) Å | µ = 14.64 mm−1 |
β = 102.752 (1)° | T = 299 K |
V = 1725.90 (6) Å3 | Block, colourless |
Z = 4 | 0.3 × 0.2 × 0.1 mm |
Bruker APEXII CCD diffractometer | 2612 reflections with I > 2σ(I) |
φ and ω scans | Rint = 0.066 |
Absorption correction: multi-scan (SADABS; Bruker, 2014) | θmax = 70.1°, θmin = 4.6° |
Tmin = 0.262, Tmax = 0.753 | h = −10→11 |
16056 measured reflections | k = −11→11 |
3278 independent reflections | l = −24→22 |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.051 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.131 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0548P)2 + 2.0895P] where P = (Fo2 + 2Fc2)/3 |
3278 reflections | (Δ/σ)max < 0.001 |
193 parameters | Δρmax = 0.61 e Å−3 |
0 restraints | Δρmin = −1.22 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. |
x | y | z | Uiso*/Ueq | ||
I1 | 0.22879 (4) | 0.41049 (5) | 0.17053 (2) | 0.0858 (2) | |
O1 | 0.1852 (4) | 0.6510 (4) | 0.28314 (19) | 0.0681 (9) | |
C1 | 0.3928 (4) | 0.5060 (4) | 0.3155 (2) | 0.0425 (8) | |
O2 | 0.2177 (3) | 0.3021 (3) | 0.37481 (14) | 0.0444 (6) | |
C2 | 0.5151 (4) | 0.5150 (5) | 0.3679 (2) | 0.0489 (9) | |
H2 | 0.509986 | 0.562449 | 0.408373 | 0.059* | |
O3 | 0.3190 (4) | 0.3762 (3) | 0.48200 (17) | 0.0596 (8) | |
C3 | 0.6447 (5) | 0.4554 (6) | 0.3617 (3) | 0.0581 (12) | |
H3 | 0.726078 | 0.463818 | 0.397392 | 0.07* | |
C4 | 0.6522 (5) | 0.3836 (6) | 0.3024 (3) | 0.0647 (13) | |
H4 | 0.738876 | 0.34243 | 0.298079 | 0.078* | |
C7 | 0.2544 (4) | 0.5741 (4) | 0.3257 (2) | 0.0442 (9) | |
C6 | 0.4034 (5) | 0.4366 (5) | 0.2548 (2) | 0.0496 (10) | |
C5 | 0.5325 (5) | 0.3725 (6) | 0.2497 (3) | 0.0613 (12) | |
H5 | 0.537768 | 0.321576 | 0.21015 | 0.074* | |
C8 | 0.2122 (4) | 0.5470 (4) | 0.3950 (2) | 0.0407 (8) | |
C9 | 0.0444 (4) | 0.5578 (5) | 0.3866 (3) | 0.0528 (11) | |
H9A | −0.000447 | 0.601873 | 0.342983 | 0.063* | |
H9B | 0.002167 | 0.464174 | 0.389089 | 0.063* | |
C10 | 0.0274 (5) | 0.6489 (5) | 0.4456 (3) | 0.0600 (12) | |
H10 | −0.060286 | 0.663186 | 0.458092 | 0.072* | |
C11 | 0.1492 (6) | 0.7068 (5) | 0.4781 (3) | 0.0612 (12) | |
H11 | 0.156817 | 0.766726 | 0.515951 | 0.073* | |
C12 | 0.2749 (5) | 0.6666 (5) | 0.4479 (2) | 0.0506 (10) | |
H12A | 0.354422 | 0.630768 | 0.483133 | 0.061* | |
H12B | 0.307966 | 0.747473 | 0.425131 | 0.061* | |
C13 | 0.2590 (4) | 0.4002 (4) | 0.4236 (2) | 0.0397 (8) | |
C14 | 0.2441 (5) | 0.1481 (5) | 0.3876 (3) | 0.0530 (10) | |
C15 | 0.1631 (9) | 0.0987 (6) | 0.4407 (4) | 0.091 (2) | |
H15A | 0.070819 | 0.145176 | 0.432802 | 0.137* | |
H15B | 0.217624 | 0.122419 | 0.485973 | 0.137* | |
H15C | 0.149492 | −0.002829 | 0.437233 | 0.137* | |
C16 | 0.1791 (7) | 0.0833 (6) | 0.3183 (3) | 0.0763 (16) | |
H16A | 0.079978 | 0.112254 | 0.304044 | 0.114* | |
H16B | 0.184221 | −0.018889 | 0.321627 | 0.114* | |
H16C | 0.231621 | 0.115416 | 0.285077 | 0.114* | |
C17 | 0.4050 (6) | 0.1218 (6) | 0.4074 (4) | 0.0851 (19) | |
H17A | 0.450457 | 0.165224 | 0.373923 | 0.128* | |
H17B | 0.423246 | 0.020849 | 0.408884 | 0.128* | |
H17C | 0.443561 | 0.16255 | 0.451908 | 0.128* |
U11 | U22 | U33 | U12 | U13 | U23 | |
I1 | 0.0721 (3) | 0.1182 (4) | 0.0569 (2) | −0.0009 (2) | −0.00751 (17) | −0.0218 (2) |
O1 | 0.0613 (19) | 0.078 (2) | 0.065 (2) | 0.0208 (17) | 0.0140 (17) | 0.0253 (18) |
C1 | 0.0403 (19) | 0.045 (2) | 0.042 (2) | −0.0023 (16) | 0.0093 (16) | 0.0044 (17) |
O2 | 0.0465 (14) | 0.0380 (14) | 0.0462 (15) | −0.0051 (11) | 0.0046 (12) | −0.0032 (12) |
C2 | 0.041 (2) | 0.059 (3) | 0.046 (2) | −0.0017 (18) | 0.0091 (17) | −0.002 (2) |
O3 | 0.074 (2) | 0.0489 (17) | 0.0468 (18) | 0.0025 (14) | −0.0058 (15) | 0.0017 (14) |
C3 | 0.036 (2) | 0.079 (3) | 0.058 (3) | −0.002 (2) | 0.0082 (19) | 0.004 (2) |
C4 | 0.046 (2) | 0.083 (4) | 0.068 (3) | 0.010 (2) | 0.019 (2) | 0.002 (3) |
C7 | 0.040 (2) | 0.046 (2) | 0.045 (2) | −0.0018 (17) | 0.0072 (17) | 0.0028 (18) |
C6 | 0.045 (2) | 0.058 (3) | 0.043 (2) | −0.0054 (18) | 0.0062 (17) | −0.0026 (19) |
C5 | 0.067 (3) | 0.069 (3) | 0.053 (3) | 0.003 (2) | 0.024 (2) | −0.010 (2) |
C8 | 0.0350 (18) | 0.043 (2) | 0.045 (2) | −0.0019 (15) | 0.0090 (15) | −0.0025 (17) |
C9 | 0.0351 (19) | 0.063 (3) | 0.062 (3) | 0.0045 (18) | 0.0126 (18) | 0.005 (2) |
C10 | 0.059 (3) | 0.061 (3) | 0.066 (3) | 0.020 (2) | 0.028 (2) | 0.014 (2) |
C11 | 0.084 (3) | 0.044 (2) | 0.062 (3) | 0.012 (2) | 0.029 (3) | 0.001 (2) |
C12 | 0.057 (2) | 0.043 (2) | 0.053 (2) | −0.0029 (18) | 0.015 (2) | −0.0033 (19) |
C13 | 0.0361 (18) | 0.042 (2) | 0.041 (2) | −0.0002 (15) | 0.0096 (16) | 0.0013 (16) |
C14 | 0.057 (2) | 0.035 (2) | 0.068 (3) | −0.0008 (18) | 0.016 (2) | −0.004 (2) |
C15 | 0.143 (6) | 0.051 (3) | 0.096 (5) | −0.019 (3) | 0.061 (5) | 0.000 (3) |
C16 | 0.087 (4) | 0.057 (3) | 0.082 (4) | −0.007 (3) | 0.013 (3) | −0.024 (3) |
C17 | 0.067 (3) | 0.063 (3) | 0.117 (5) | 0.021 (3) | 0.002 (3) | −0.008 (3) |
I1—C6 | 2.096 (4) | C9—H9A | 0.97 |
O1—C7 | 1.193 (5) | C9—H9B | 0.97 |
C1—C2 | 1.382 (6) | C10—C11 | 1.312 (8) |
C1—C6 | 1.395 (6) | C10—H10 | 0.93 |
C1—C7 | 1.514 (5) | C11—C12 | 1.497 (6) |
O2—C13 | 1.331 (5) | C11—H11 | 0.93 |
O2—C14 | 1.476 (5) | C12—H12A | 0.97 |
C2—C3 | 1.382 (6) | C12—H12B | 0.97 |
C2—H2 | 0.93 | C14—C16 | 1.508 (8) |
O3—C13 | 1.197 (5) | C14—C15 | 1.511 (8) |
C3—C4 | 1.373 (7) | C14—C17 | 1.512 (7) |
C3—H3 | 0.93 | C15—H15A | 0.96 |
C4—C5 | 1.371 (7) | C15—H15B | 0.96 |
C4—H4 | 0.93 | C15—H15C | 0.96 |
C7—C8 | 1.540 (6) | C16—H16A | 0.96 |
C6—C5 | 1.389 (7) | C16—H16B | 0.96 |
C5—H5 | 0.93 | C16—H16C | 0.96 |
C8—C13 | 1.516 (5) | C17—H17A | 0.96 |
C8—C12 | 1.561 (6) | C17—H17B | 0.96 |
C8—C9 | 1.568 (5) | C17—H17C | 0.96 |
C9—C10 | 1.489 (7) | ||
C2—C1—C6 | 118.2 (4) | C10—C11—C12 | 113.1 (4) |
C2—C1—C7 | 118.9 (4) | C10—C11—H11 | 123.4 |
C6—C1—C7 | 122.9 (4) | C12—C11—H11 | 123.4 |
C13—O2—C14 | 122.5 (3) | C11—C12—C8 | 103.4 (4) |
C1—C2—C3 | 121.7 (4) | C11—C12—H12A | 111.1 |
C1—C2—H2 | 119.2 | C8—C12—H12A | 111.1 |
C3—C2—H2 | 119.2 | C11—C12—H12B | 111.1 |
C4—C3—C2 | 119.4 (4) | C8—C12—H12B | 111.1 |
C4—C3—H3 | 120.3 | H12A—C12—H12B | 109.1 |
C2—C3—H3 | 120.3 | O3—C13—O2 | 125.3 (4) |
C5—C4—C3 | 120.2 (4) | O3—C13—C8 | 124.9 (4) |
C5—C4—H4 | 119.9 | O2—C13—C8 | 109.7 (3) |
C3—C4—H4 | 119.9 | O2—C14—C16 | 102.5 (4) |
O1—C7—C1 | 121.2 (4) | O2—C14—C15 | 109.0 (4) |
O1—C7—C8 | 121.5 (4) | C16—C14—C15 | 110.4 (5) |
C1—C7—C8 | 117.1 (3) | O2—C14—C17 | 109.1 (4) |
C5—C6—C1 | 119.9 (4) | C16—C14—C17 | 111.1 (5) |
C5—C6—I1 | 116.5 (3) | C15—C14—C17 | 114.1 (6) |
C1—C6—I1 | 123.4 (3) | C14—C15—H15A | 109.5 |
C4—C5—C6 | 120.5 (4) | C14—C15—H15B | 109.5 |
C4—C5—H5 | 119.8 | H15A—C15—H15B | 109.5 |
C6—C5—H5 | 119.8 | C14—C15—H15C | 109.5 |
C13—C8—C7 | 111.9 (3) | H15A—C15—H15C | 109.5 |
C13—C8—C12 | 111.1 (3) | H15B—C15—H15C | 109.5 |
C7—C8—C12 | 110.5 (3) | C14—C16—H16A | 109.5 |
C13—C8—C9 | 107.8 (3) | C14—C16—H16B | 109.5 |
C7—C8—C9 | 110.7 (3) | H16A—C16—H16B | 109.5 |
C12—C8—C9 | 104.7 (3) | C14—C16—H16C | 109.5 |
C10—C9—C8 | 103.7 (4) | H16A—C16—H16C | 109.5 |
C10—C9—H9A | 111.0 | H16B—C16—H16C | 109.5 |
C8—C9—H9A | 111.0 | C14—C17—H17A | 109.5 |
C10—C9—H9B | 111.0 | C14—C17—H17B | 109.5 |
C8—C9—H9B | 111.0 | H17A—C17—H17B | 109.5 |
H9A—C9—H9B | 109.0 | C14—C17—H17C | 109.5 |
C11—C10—C9 | 112.8 (4) | H17A—C17—H17C | 109.5 |
C11—C10—H10 | 123.6 | H17B—C17—H17C | 109.5 |
C9—C10—H10 | 123.6 | ||
C6—C1—C2—C3 | −1.1 (7) | C13—C8—C9—C10 | 104.1 (4) |
C7—C1—C2—C3 | −179.9 (4) | C7—C8—C9—C10 | −133.3 (4) |
C1—C2—C3—C4 | −0.9 (7) | C12—C8—C9—C10 | −14.3 (5) |
C2—C3—C4—C5 | 0.6 (8) | C8—C9—C10—C11 | 9.5 (5) |
C2—C1—C7—O1 | 130.7 (5) | C9—C10—C11—C12 | −0.2 (6) |
C6—C1—C7—O1 | −48.0 (6) | C10—C11—C12—C8 | −9.2 (5) |
C2—C1—C7—C8 | −45.7 (5) | C13—C8—C12—C11 | −101.9 (4) |
C6—C1—C7—C8 | 135.7 (4) | C7—C8—C12—C11 | 133.3 (4) |
C2—C1—C6—C5 | 3.4 (6) | C9—C8—C12—C11 | 14.1 (4) |
C7—C1—C6—C5 | −177.9 (4) | C14—O2—C13—O3 | −0.9 (6) |
C2—C1—C6—I1 | 179.2 (3) | C14—O2—C13—C8 | −178.2 (3) |
C7—C1—C6—I1 | −2.2 (6) | C7—C8—C13—O3 | 133.6 (4) |
C3—C4—C5—C6 | 1.7 (8) | C12—C8—C13—O3 | 9.6 (5) |
C1—C6—C5—C4 | −3.7 (7) | C9—C8—C13—O3 | −104.5 (5) |
I1—C6—C5—C4 | −179.8 (4) | C7—C8—C13—O2 | −49.1 (4) |
O1—C7—C8—C13 | 150.6 (4) | C12—C8—C13—O2 | −173.1 (3) |
C1—C7—C8—C13 | −33.0 (5) | C9—C8—C13—O2 | 72.8 (4) |
O1—C7—C8—C12 | −85.0 (5) | C13—O2—C14—C16 | −180.0 (4) |
C1—C7—C8—C12 | 91.3 (4) | C13—O2—C14—C15 | 63.0 (6) |
O1—C7—C8—C9 | 30.4 (6) | C13—O2—C14—C17 | −62.2 (6) |
C1—C7—C8—C9 | −153.2 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···O3i | 0.93 | 2.48 | 3.219 (5) | 136 |
Symmetry code: (i) −x+1, −y+1, −z+1. |
Acknowledgements
Generous financial support from the National Natural Science Foundation of China (21602084) is greatly acknowledged.
Funding information
Funding for this research was provided by: National Natural Science Foundation of China (grant No. 21602084).
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