Synthesis, structure and Hirshfeld surface analysis of 2-oxo-2H-chromen-4-yl penta­noate

Bationo, V.; Kambo, K.R.; Sombié, C.B.; Semdé, R.; Francotte, P.; Djandé, A.

doi:10.1107/S205698902400584X

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ISSN: 2056-9890

Volume 80| Part 7| July 2024| Pages 767-770

https://doi.org/10.1107/S205698902400584X

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Synthesis, structure and Hirshfeld surface analysis of 2-oxo-2H-chromen-4-yl pentanoate

Valentin Bationo,^a Konan René Kambo,^b ^* Charles Bavouma Sombié,^c Rasmané Semdé,^c Pierre Francotte ^d and Abdoulaye Djandé ^a

^aDepartment of Chemistry, Doctoral School of Sciences and Technology, University Joseph KI-ZERBO, Laboratory of Molecular Chemistry and Materials, Research Team: Organic Chemistry and Phytochemistry, 03 BP 7021 Ouagadougou 03, Burkina Faso, ^bLaboratory of Environmental Science and Technology, University Jean Lorougnon GUEDE of Daloa, BP 150 Daloa, Côte d'Ivoire, ^cDoctoral School of Sciences and Health, University Joseph KI-ZERBO, Laboratory of Drug Development Center of Training, Research and Expertise in Pharmaceutical Sciences (CFOREM), 03 BP 7021 Ouagadougou 03, Burkina Faso, and ^dCenter for Interdisciplinary Research on Medicinal Chemistry, University of Liège, Avenue Hippocrate 15 (B36), B-4000, Liège, Belgium
^*Correspondence e-mail: kamborene@gmail.com

Edited by Y. Ozawa, University of Hyogo, Japan (Received 26 April 2024; accepted 16 June 2024; online 21 June 2024)

In the title compound, C₁₄H₁₄O₄, the dihedral angle between the coumarin ring system (r.m.s deviation = 0.016 Å) and the pentanoate ring is 36.26 (8)°. A short intramolecular C—H⋯O contact of 2.40 Å is observed. Hirshfeld surface analysis reveals that 46.1% of the intermolecular interactions are from H⋯H contacts, 28.6% are from H⋯O/O⋯H contacts and 14.7% are from H⋯C/C⋯H.

Keywords: crystal structure; coumarin structure; Hirshfeld surface analysis; interactions; hydrogen bonds.

CCDC reference: 2363131

1. Chemical context

Coumarins are naturally occurring molecules with a versatile range of activities. Their structural and physicochemical characteristics make them a privileged scaffold in medicinal chemistry and chemical biology (Carneiro et al., 2021 ). Historically, coumarins have been applied for the treatment of a variety of diseases due to their anticoagulant, anti-inflammatory, antiviral, antimicrobial, anticancer, antioxidant (Todorov et al., 2023 ) and anti-glaucoma (Ziki et al., 2023 ) activities. Their wide range of biological activities and the use of coumarin-containing drugs clinically have contributed to the growing interest in this class of heterocycles (Khandy et al., 2024 ). Given their importance, coumarin derivatives continue to be our field of research (Kambo et al., 2017 ; Hollauer et al., 2023 ). We report herein the synthesis, crystal structure, and Hirshfeld surface analysis of the title coumarin derivative.

2. Structural commentary

The molecular structure of the title coumarin derivative is illustrated in Fig. 1. An S(6) ring motif arises from an intramolecular C2—H2⋯O4 hydrogen bond (Table 1). As expected, the coumarin ring system is almost planar, with a maximum deviation from the plane of 0.016 (3) Å for atom C7. An inspection of the bond lengths shows that there is a slight asymmetry of the electronic distribution around the pyrone ring: the C1—C2 [1.336 (3) Å] and C2—C3 [1.437 (3) Å] bond lengths are shorter and longer, respectively, than those excepted for a C_ar—C_ar bond. This suggests that the electron density is preferentially located in the C1—C2 bond of the pyrone ring, as seen in other coumarin derivatives (Gomes et al., 2016 ; Ouédraogo et al., 2018 ).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C2—H2⋯O4	0.93	2.40	2.855 (3)	110
C5—H5⋯O1ⁱ	0.93	2.53	3.387 (3)	153
C11—H11B⋯O1ⁱⁱ	0.97	2.65	3.446 (3)	139
Symmetry codes: (i) $[-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

Figure 1
Molecular structure of the compound showing the atomic numbering system. Displacement ellipsoids are drawn at the 50% probability level.

3. Supramolecular features and Hirshfeld surface analysis

In the crystal, C5—H5⋯O1 hydrogen bonds link molecules into infinite chains along the [001] direction (Table 1, Fig. 2) and the C11—H11B⋯O1 interactions contribute to the crystal cohesion. The intermolecular interactions were quantified using Hirshfeld surface analysis. This approach is a graphical tool for visualization and understanding of intermolecular interactions. The Hirshfeld surface analysis was performed, and the two-dimensional (2D) fingerprint plots were generated with CrystalExplorer 17 (Spackman et al., 2021 ). Fig. 3 shows the Hirshfeld surface plotted over d_norm (normalized contact distance) and Fig. 4 the 2D fingerprint plots..

Figure 2
Part of crystalline packing of the title compound showing a parallel chain in the [001] direction. Dashed lines indicate hydrogen bonds. H atoms not involved in hydrogen-bonding interactions have been omitted for clarity.

Figure 3
The Hirshfeld surface mapped over d_norm for visualizing the intermolecular contacts of the title compound.

Figure 4
Fingerprint plots for the title compound showing (a) C⋯C, (b) H⋯H, (c) O⋯H/H⋯O and (d) C⋯H/H⋯C interactions. The outline of the full fingerprint is shown in grey. d_i is the closest internal distance from a given point on the Hirshfeld surface and d_e is the closest external contact.

4. Database survey

A search of the Cambridge structural Database (CSD; Groom et al., 2016 ; updated to April 2024) found seven coumarins structures with substituents at the 4-positions (XUFGOW, Kavitha et al., 2015 ; NUZJOJ, Vinduvahini et al., 2016 ; UDOGIF01, Anitha et al., 2016 , HUYVEE, Anitha et al., 2015 ; NAGWAW, Ravi et al., 2016 ; DIWPAE, Hollauer et al., 2023). All seven have structural parameters very similar to this one, including essentially planar chromene portions.

5. Synthesis and crystallization

To a solution of valeroyl chloride (6.17 mmol, ∼0.8 ml) in dried diethyl ether (16 ml) was added dried pyridine (2.31 ml; 4.7 molar equivalents) and 4-hydroxycoumarin (6.17 mmol, 1 g) in small portions over 30 min, with vigorous stirring. The reaction mixture was left stirring at room temperature for 3 h.

The mixture was then poured in a separating funnel containing 40 ml of chloroform and washed with diluted hydrochloric acid solution until the pH was 2–3. The organic layer was extracted, washed with water to neutrality, dried over MgSO₄ and the solvent removed. The crude product was filtered off with suction, washed with n-hexane and recrystallized from acetone. Dirty white crystals of the title compound were obtained in a good yield (78%), m.p. 408–409 K.

6. Refinement details

Crystal data, data collection and structure refinement details are summarized in Table 2. Hydrogen atoms were located in a difference-Fourier map, but were positioned with idealized geometry and refined isotropically using a riding model (HFIX command), U_iso(H) = 1.5U_eq(C-methyl) and 1.2U_eq(C) for all other H atoms.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₄H₁₄O₄
M_r	246.25
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	295
a, b, c (Å)	9.57455 (13), 9.29660 (17), 14.5761 (2)
β (°)	100.9517 (14)
V (Å³)	1273.80 (3)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	0.78
Crystal size (mm)	0.26 × 0.22 × 0.18

Data collection
Diffractometer	Rigaku Oxford Diffraction SuperNova, Dual, Atlas 2
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2023 $[Rigaku OD (2023). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.869, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	13663, 2492, 2107
R_int	0.024
(sin θ/λ)_max (Å⁻¹)	0.618

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.056, 0.175, 1.08
No. of reflections	2492
No. of parameters	164
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.30, −0.27
Computer programs: CrysAlis PRO (Rigaku OD, 2023 $[Rigaku OD (2023). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ ), SHELXT (Sheldrick, 2015a ), SHELXL2013 (Sheldrick, 2015b ), PLATON (Spek, 2020 ), ORTEP-III Burnett & Johnson, 1996 ), WinGX (Farrugia, 2012 ) and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 2363131

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S205698902400584X/ox2005sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S205698902400584X/ox2005Isup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S205698902400584X/ox2005Isup3.cml

checkCIF report

Computing details top

2-Oxo-2H-chromen-4-yl pentanoate top

Crystal data top

C₁₄H₁₄O₄	F(000) = 520
M_r = 246.25	D_x = 1.284 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54184 Å
a = 9.57455 (13) Å	Cell parameters from 5988 reflections
b = 9.29660 (17) Å	θ = 6.2–72.3°
c = 14.5761 (2) Å	µ = 0.78 mm⁻¹
β = 100.9517 (14)°	T = 295 K
V = 1273.80 (3) Å³	Prism, colourless
Z = 4	0.26 × 0.22 × 0.18 mm

Data collection top

Rigaku Oxford Diffraction SuperNova, Dual, Atlas 2 diffractometer	2492 independent reflections
Radiation source: micro-focus sealed X-ray tube	2107 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.024
Detector resolution: 5.3045 pixels mm^-1	θ_max = 72.4°, θ_min = 4.7°
ω scan	h = −11→11
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2023)	k = −11→9
T_min = 0.869, T_max = 1.000	l = −18→17
13663 measured reflections

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.056	H-atom parameters constrained
wR(F²) = 0.175	w = 1/[σ²(F_o²) + (0.0899P)² + 0.3573P] where P = (F_o² + 2F_c²)/3
S = 1.08	(Δ/σ)_max < 0.001
2492 reflections	Δρ_max = 0.30 e Å⁻³
164 parameters	Δρ_min = −0.27 e Å⁻³

Special details top

Experimental. CrysAlisPro 1.171.42.102a (Rigaku Oxford Diffraction, 2023) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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
O1	0.8531 (2)	0.18982 (18)	0.34863 (13)	0.0878 (6)
O2	0.89842 (16)	0.42028 (16)	0.33853 (10)	0.0657 (4)
O3	0.73548 (14)	0.51487 (15)	0.57413 (9)	0.0611 (4)
O4	0.5562 (2)	0.3555 (2)	0.56376 (12)	0.0961 (7)
C1	0.78028 (18)	0.4741 (2)	0.49394 (12)	0.0521 (4)
C2	0.7829 (2)	0.3396 (2)	0.46205 (14)	0.0601 (5)
H2	0.7447	0.2654	0.4923	0.072*
C3	0.8442 (2)	0.3080 (2)	0.38166 (15)	0.0637 (5)
C4	0.89359 (19)	0.5596 (2)	0.36974 (13)	0.0552 (5)
C5	0.9492 (2)	0.6653 (3)	0.32029 (15)	0.0686 (6)
H5	0.9891	0.6417	0.2689	0.082*
C6	0.9443 (3)	0.8055 (3)	0.34855 (18)	0.0770 (7)
H6	0.9807	0.8776	0.3155	0.092*
C7	0.8862 (3)	0.8417 (2)	0.42546 (19)	0.0769 (6)
H7	0.8837	0.9373	0.4439	0.092*
C8	0.8321 (2)	0.7356 (2)	0.47459 (15)	0.0640 (5)
H8	0.7930	0.7600	0.5263	0.077*
C9	0.83527 (18)	0.5928 (2)	0.44771 (13)	0.0514 (4)
C10	0.6263 (2)	0.4471 (2)	0.60627 (13)	0.0588 (5)
C11	0.6104 (3)	0.5117 (3)	0.69639 (16)	0.0763 (7)
H11A	0.5905	0.6134	0.6862	0.092*
H11B	0.7010	0.5039	0.7392	0.092*
C12	0.4994 (3)	0.4499 (3)	0.74266 (16)	0.0776 (7)
H12A	0.4091	0.4569	0.6995	0.093*
H12B	0.5199	0.3484	0.7531	0.093*
C13	0.4818 (4)	0.5132 (4)	0.8311 (2)	0.1043 (11)
H13A	0.4636	0.6150	0.8203	0.125*
H13B	0.5723	0.5050	0.8739	0.125*
C14	0.3720 (4)	0.4574 (4)	0.8790 (2)	0.1154 (12)
H14A	0.2833	0.4508	0.8355	0.173*
H14B	0.3614	0.5211	0.9291	0.173*
H14C	0.3992	0.3637	0.9038	0.173*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.1124 (13)	0.0674 (10)	0.0945 (12)	−0.0079 (9)	0.0470 (10)	−0.0231 (9)
O2	0.0772 (9)	0.0669 (9)	0.0606 (8)	−0.0033 (7)	0.0327 (7)	−0.0066 (6)
O3	0.0666 (8)	0.0655 (9)	0.0593 (8)	−0.0121 (6)	0.0321 (6)	−0.0060 (6)
O4	0.0994 (12)	0.1166 (15)	0.0855 (11)	−0.0483 (11)	0.0512 (10)	−0.0319 (10)
C1	0.0498 (8)	0.0594 (11)	0.0511 (9)	−0.0023 (7)	0.0197 (7)	0.0002 (8)
C2	0.0676 (11)	0.0539 (11)	0.0645 (11)	−0.0058 (9)	0.0274 (9)	0.0005 (9)
C3	0.0685 (11)	0.0610 (12)	0.0661 (12)	−0.0034 (9)	0.0237 (9)	−0.0052 (9)
C4	0.0546 (9)	0.0614 (11)	0.0523 (9)	0.0002 (8)	0.0174 (7)	0.0041 (8)
C5	0.0726 (12)	0.0783 (14)	0.0605 (11)	−0.0048 (10)	0.0269 (10)	0.0116 (10)
C6	0.0829 (15)	0.0721 (15)	0.0812 (15)	−0.0046 (11)	0.0286 (12)	0.0243 (12)
C7	0.0876 (15)	0.0513 (12)	0.0967 (17)	−0.0010 (10)	0.0302 (13)	0.0088 (11)
C8	0.0666 (11)	0.0582 (12)	0.0728 (12)	0.0017 (9)	0.0276 (10)	0.0010 (10)
C9	0.0479 (8)	0.0549 (11)	0.0545 (9)	0.0003 (7)	0.0175 (7)	0.0036 (8)
C10	0.0585 (10)	0.0657 (12)	0.0568 (10)	−0.0064 (9)	0.0224 (8)	0.0035 (9)
C11	0.0903 (15)	0.0834 (16)	0.0652 (12)	−0.0196 (12)	0.0402 (11)	−0.0079 (11)
C12	0.0740 (13)	0.1044 (18)	0.0614 (12)	−0.0191 (13)	0.0304 (10)	−0.0062 (12)
C13	0.131 (2)	0.116 (2)	0.0846 (17)	−0.0419 (19)	0.0664 (17)	−0.0261 (16)
C14	0.117 (2)	0.167 (3)	0.0780 (17)	−0.043 (2)	0.0579 (17)	−0.0214 (19)

Geometric parameters (Å, º) top

O1—C3	1.209 (3)	C7—H7	0.9300
O2—C3	1.371 (2)	C8—C9	1.387 (3)
O2—C4	1.377 (2)	C8—H8	0.9300
O3—C1	1.373 (2)	C10—C11	1.478 (3)
O3—C10	1.377 (2)	C11—C12	1.479 (3)
O4—C10	1.184 (3)	C11—H11A	0.9700
C1—C2	1.336 (3)	C11—H11B	0.9700
C1—C9	1.443 (2)	C12—C13	1.455 (3)
C2—C3	1.437 (3)	C12—H12A	0.9700
C2—H2	0.9300	C12—H12B	0.9700
C4—C5	1.384 (3)	C13—C14	1.464 (3)
C4—C9	1.393 (3)	C13—H13A	0.9700
C5—C6	1.370 (3)	C13—H13B	0.9700
C5—H5	0.9300	C14—H14A	0.9600
C6—C7	1.384 (4)	C14—H14B	0.9600
C6—H6	0.9300	C14—H14C	0.9600
C7—C8	1.376 (3)

C3—O2—C4	121.71 (15)	C4—C9—C1	116.78 (17)
C1—O3—C10	122.95 (15)	O4—C10—O3	122.85 (18)
C2—C1—O3	125.75 (17)	O4—C10—C11	127.85 (18)
C2—C1—C9	121.34 (17)	O3—C10—C11	109.25 (17)
O3—C1—C9	112.80 (16)	C10—C11—C12	116.9 (2)
C1—C2—C3	120.85 (18)	C10—C11—H11A	108.1
C1—C2—H2	119.6	C12—C11—H11A	108.1
C3—C2—H2	119.6	C10—C11—H11B	108.1
O1—C3—O2	116.60 (19)	C12—C11—H11B	108.1
O1—C3—C2	125.5 (2)	H11A—C11—H11B	107.3
O2—C3—C2	117.86 (18)	C13—C12—C11	117.4 (2)
O2—C4—C5	117.11 (17)	C13—C12—H12A	107.9
O2—C4—C9	121.44 (17)	C11—C12—H12A	107.9
C5—C4—C9	121.45 (19)	C13—C12—H12B	107.9
C6—C5—C4	118.7 (2)	C11—C12—H12B	107.9
C6—C5—H5	120.6	H12A—C12—H12B	107.2
C4—C5—H5	120.6	C12—C13—C14	119.6 (3)
C5—C6—C7	121.1 (2)	C12—C13—H13A	107.4
C5—C6—H6	119.5	C14—C13—H13A	107.4
C7—C6—H6	119.5	C12—C13—H13B	107.4
C8—C7—C6	119.8 (2)	C14—C13—H13B	107.4
C8—C7—H7	120.1	H13A—C13—H13B	107.0
C6—C7—H7	120.1	C13—C14—H14A	109.5
C7—C8—C9	120.5 (2)	C13—C14—H14B	109.5
C7—C8—H8	119.7	H14A—C14—H14B	109.5
C9—C8—H8	119.7	C13—C14—H14C	109.5
C8—C9—C4	118.44 (17)	H14A—C14—H14C	109.5
C8—C9—C1	124.78 (17)	H14B—C14—H14C	109.5

C10—O3—C1—C2	−34.4 (3)	C7—C8—C9—C1	−179.4 (2)
C10—O3—C1—C9	149.38 (17)	O2—C4—C9—C8	−179.15 (17)
O3—C1—C2—C3	−174.29 (19)	C5—C4—C9—C8	0.9 (3)
C9—C1—C2—C3	1.6 (3)	O2—C4—C9—C1	0.0 (3)
C4—O2—C3—O1	179.69 (19)	C5—C4—C9—C1	179.97 (17)
C4—O2—C3—C2	−0.8 (3)	C2—C1—C9—C8	177.8 (2)
C1—C2—C3—O1	178.9 (2)	O3—C1—C9—C8	−5.9 (3)
C1—C2—C3—O2	−0.5 (3)	C2—C1—C9—C4	−1.3 (3)
C3—O2—C4—C5	−178.94 (18)	O3—C1—C9—C4	175.07 (16)
C3—O2—C4—C9	1.1 (3)	C1—O3—C10—O4	−5.5 (3)
O2—C4—C5—C6	179.07 (19)	C1—O3—C10—C11	176.86 (19)
C9—C4—C5—C6	−0.9 (3)	O4—C10—C11—C12	3.8 (4)
C4—C5—C6—C7	0.5 (4)	O3—C10—C11—C12	−178.7 (2)
C5—C6—C7—C8	−0.1 (4)	C10—C11—C12—C13	−179.5 (3)
C6—C7—C8—C9	0.0 (4)	C11—C12—C13—C14	179.1 (3)
C7—C8—C9—C4	−0.4 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O4	0.93	2.40	2.855 (3)	110
C5—H5···O1ⁱ	0.93	2.53	3.387 (3)	153
C11—H11B···O1ⁱⁱ	0.97	2.65	3.446 (3)	139

Symmetry codes: (i) −x+2, y+1/2, −z+1/2; (ii) x, −y+1/2, z+1/2.

Acknowledgements

The authors are grateful to the Spectropôle Service of the Faculty of Sciences and Techniques (Aix-Marseille, France) for the use of the diffractometer.

References

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