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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2024 Jun 21;80(Pt 7):767–770. doi: 10.1107/S205698902400584X

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, Abdoulaye Djandé a
Editor: Y Ozawae
PMCID: PMC11223708  PMID: 38974164

In the title compound, the dihedral angle between the coumarin ring system and the penta­noate ring is 36.26 (8)°. A short intra­molecular C—H⋯O contact is observed.

Keywords: crystal structure, coumarin structure, Hirshfeld surface analysis, inter­actions, hydrogen bonds

Abstract

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.

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.1.

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 Car—Car 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 ▸).

Figure 1.

Figure 1

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

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
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Symmetry codes: (i) Inline graphic; (ii) Inline graphic.

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 dnorm (normalized contact distance) and Fig. 4 ▸ the 2D fingerprint plots..

Figure 2.

Figure 2

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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.

Figure 3

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The Hirshfeld surface mapped over dnorm for visualizing the inter­molecular contacts of the title compound.

Figure 4.

Figure 4

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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. di is the closest inter­nal distance from a given point on the Hirshfeld surface and de 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), Uiso(H) = 1.5Ueq(C-meth­yl) and 1.2Ueq(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 ▸)
Tmin, Tmax 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
Δρmax, Δρmin (e Å−3) 0.30, −0.27
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Computer programs: CrysAlis PRO (Rigaku OD, 2023 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL2013 (Sheldrick, 2015b ▸), PLATON (Spek, 2020 ▸), ORTEP-III Burnett & Johnson, 1996 ▸), WinGX (Farrugia, 2012 ▸) and publCIF (Westrip, 2010 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S205698902400584X/ox2005sup1.cif

e-80-00767-sup1.cif (425.6KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S205698902400584X/ox2005Isup3.hkl

e-80-00767-Isup3.hkl (199.7KB, hkl)
e-80-00767-Isup3.cml (4.9KB, cml)

Supporting information file. DOI: 10.1107/S205698902400584X/ox2005Isup3.cml

CCDC reference: 2363131

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

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

supplementary crystallographic information

2-Oxo-2H-chromen-4-yl pentanoate . Crystal data

C14H14O4 F(000) = 520
Mr = 246.25 Dx = 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
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2-Oxo-2H-chromen-4-yl pentanoate . Data collection

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 Rint = 0.024
Detector resolution: 5.3045 pixels mm-1 θmax = 72.4°, θmin = 4.7°
ω scan h = −11→11
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2023) k = −11→9
Tmin = 0.869, Tmax = 1.000 l = −18→17
13663 measured reflections
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2-Oxo-2H-chromen-4-yl pentanoate . Refinement

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(Fo2) + (0.0899P)2 + 0.3573P] where P = (Fo2 + 2Fc2)/3
S = 1.08 (Δ/σ)max < 0.001
2492 reflections Δρmax = 0.30 e Å−3
164 parameters Δρmin = −0.27 e Å−3
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2-Oxo-2H-chromen-4-yl pentanoate . Special details

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.
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2-Oxo-2H-chromen-4-yl pentanoate . Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
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*
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2-Oxo-2H-chromen-4-yl pentanoate . Atomic displacement parameters (Å2)

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)
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2-Oxo-2H-chromen-4-yl pentanoate . Geometric parameters (Å, º)

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)
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2-Oxo-2H-chromen-4-yl pentanoate . Hydrogen-bond geometry (Å, º)

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

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S205698902400584X/ox2005sup1.cif

e-80-00767-sup1.cif (425.6KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S205698902400584X/ox2005Isup3.hkl

e-80-00767-Isup3.hkl (199.7KB, hkl)
e-80-00767-Isup3.cml (4.9KB, cml)

Supporting information file. DOI: 10.1107/S205698902400584X/ox2005Isup3.cml

CCDC reference: 2363131

Additional supporting information: crystallographic information; 3D view; checkCIF report

Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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