Synthesis and crystal structure of tert-butyl 1-(2-iodo­benzo­yl)cyclo­pent-3-ene-1-carboxyl­ate

Yin, D.

doi:10.1107/S2056989019011514

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Volume 75| Part 9| September 2019| Pages 1383-1385

https://doi.org/10.1107/S2056989019011514

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Synthesis and crystal structure of tert-butyl 1-(2-iodobenzoyl)cyclopent-3-ene-1-carboxylate

Dejing Yin ^a ^*

^aSchool of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi in Jiangsu Province, People's Republic of China
^*Correspondence e-mail: ydjszlg@163.com

Edited by M. Weil, Vienna University of Technology, Austria (Received 8 July 2019; accepted 16 August 2019; online 30 August 2019)

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 reaction mechanism, 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 reaction mechanism if more detailed structural data are available. Herein, the synthesis and crystal structure 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 envelope conformation, 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)°.

Figure 1
The molecular structure of title compound, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 20% probability level.

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.

Table 1
Hydrogen-bond geometry (Å, °)

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.

Figure 2
A view along [010] of the crystal packing of the title compound. The intermolecular C—H⋯O hydrogen bonds are shown as orange dashed lines (Table 1

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 space group Pnma (CSD refcode CIQHAM; Yang et al., 2007 ), and 4-benzoyl-4-(methoxycarbonyl)cyclopentene in the space group P2₁/c, with four independent molecules in the asymmetric unit (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 refinement details are summarized in Table 2. 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 U_iso(H) = 1.5U_eq(C-methyl) and 1.2U_eq(C) for other H atoms.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₇H₁₉IO₃
M_r	398.22
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	299
a, b, c (Å)	9.4977 (2), 9.3635 (2), 19.8978 (4)
β (°)	102.752 (1)
V (Å³)	1725.90 (6)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	14.64
Crystal size (mm)	0.3 × 0.2 × 0.1

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2014 )
T_min, T_max	0.262, 0.753
No. of measured, independent and observed [I > 2σ(I)] reflections	16056, 3278, 2612
R_int	0.066
(sin θ/λ)_max (Å⁻¹)	0.610

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.051, 0.131, 1.06
No. of reflections	3278
No. of parameters	193
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.61, −1.22
Computer programs: APEX3 and SAINT (Bruker, 2014), SHELXT2014 (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ), DIAMOND (Brandenburg, 2006 ) and PLATON (Spek, 2009 ) and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 1899475

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989019011514/wm5513sup1.cif

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

checkCIF report

Computing details top

Data collection: APEX3 (Bruker, 2014); cell refinement: 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).

tert-Butyl 1-(2-iodobenzoyl)-cyclopent-3-ene-1-carboxylate top

Crystal data top

C₁₇H₁₉IO₃	F(000) = 792
M_r = 398.22	D_x = 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

Data collection top

Bruker APEXII CCD diffractometer	2612 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.066
Absorption correction: multi-scan (SADABS; Bruker, 2014)	θ_max = 70.1°, θ_min = 4.6°
T_min = 0.262, T_max = 0.753	h = −10→11
16056 measured reflections	k = −11→11
3278 independent reflections	l = −24→22

Refinement top

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(F_o²) + (0.0548P)² + 2.0895P] where P = (F_o² + 2F_c²)/3
3278 reflections	(Δ/σ)_max < 0.001
193 parameters	Δρ_max = 0.61 e Å⁻³
0 restraints	Δρ_min = −1.22 e Å⁻³

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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).

References

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