Synthesis, characterization, crystal structure and

Chemical Data Collections 9–10 (2017) 1–10

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Synthesis, characterization, crystal structure and Hirshfeld surface analysis of ethyl 2-(2-oxo-2H-chromen-4-yloxy) acetate Mahima Jyothi a,1, Naveen Shivalingegowda b,1, Zabiulla a, Yasser Hussein Issa Mohammed a, Neratur Krishnappagowda Lokanath c, Shaukath Ara Khanum a,∗ a

Department of Chemistry, Yuvaraja’s College, University of Mysore, Mysuru -570 005, India Institution of Excellence, Vijnana Bhavana, Manasagangotri, University of Mysore, Mysuru- 570 006, India c Department of Studies in Physics, Manasagangotri, University of Mysore, Mysuru- 570 006, India b

a r t i c l e

i n f o

Article history: Received 30 January 2017 Revised 20 February 2017 Accepted 23 February 2017 Available online 24 February 2017 Keywords: 4-hydroxycoumarin Eaton’s reagent X-ray diffraction Hirshfeld surface analysis Fingerprint plots

∗

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a b s t r a c t The title compound ethyl 2-(2-oxo-2H-chromen-4-yloxy) acetate has been synthesized and characterized by NMR, IR and mass spectral studies, and finally the structure was confirmed by single crystal X-ray diffraction studies. The title compound C13 H12 O5 crystallizes in the orthorhombic space group P21 21 21 with a single molecule in the asymmetric unit and the unit cell parame˚ b = 7.9867(10) A, ˚ c = 28.300(4) A, ˚ and Z = 4. ters, a = 5.1037(7) A, The crystal structure of the title compound exhibit several C–H •••O intermolecular interactions resulting in a three dimensional architecture. Further, the Hirshfeld surface analysis reveals the nature of intermolecular contacts. The fingerprint plot provides the information about the percentage contribution which clearly states that H…H (37.4%) bonding appears to be a major contributor in the crystal packing, whereas the O…H (33.2%), C…H (20.2%) from the intermolecular contacts to the surface. © 2017 Published by Elsevier B.V.

Corresponding author. E-mail address: [email protected] (S.A. Khanum). These authors have made equal contributions in the manuscript.

http://dx.doi.org/10.1016/j.cdc.2017.02.004 2405-8300/© 2017 Published by Elsevier B.V.

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M. Jyothi et al. / Chemical Data Collections 9–10 (2017) 1–10

Specification table

Subject area

Organic Chemistry, Crystallography

Compounds Data category Data acquisition format Data type Procedure

Ethyl 2-(2-oxo-2H-chromen-4-yloxy) acetate 1 H NMR, 13 C NMR, Mass Spectra, Crystallographic data CIF for crystallography Analyzed The compound C13 H12 O5 , ethyl 2-(2-oxo-2H-chromen-4-yloxy) acetate was synthesized and a white colored rectangular shaped crystals of the compound were obtained by slow evaporation technique. A single crystal of dimension 0.28 × 0.26 × 0.24 mm3 of the title compound was selected and X-ray intensity data was collected at a temperature of 296 K on a Bruker Proteum2 CCD diffractometer equipped with an X-ray generator operating at 45 kV and 10 mA, using CuKα radiation of wavelength 1.54178 A˚ Data was collected from 24 frames per set with different settings of ϕ (0° and 90°), keeping the scan width of 0.5° and exposure time of 2 s. CCDC 1511979, URL: https://summary.ccdc.cam.ac.uk/structure-summary-form

Data accessibility

1. Rationale C-4 substituted coumarin derivatives showed tremendous cytotoxic activity against cancer cells with different pathways such as aromatase inhibition, sulphatase inhibition, selective estrogen receptor modulator and down-regulator, 17bHSD3 inhibition, Cdc25 inhibition, protein kinase inhibition, microtubulin inhibition, DNA intercalation, apoptosis inhibition, HSP90 inhibition, NF-kB and quinone reductase induction [1–6]. In the light of this knowledge, 4-hydroxycoumarin derivatives have been synthesized. They are a wide class of natural and synthetic compounds that showed versatile pharmacological activities including anti-viral [7], analgesic [8], anti-arthritis [9], anti-inflammatory [10], anti-pyretic [11], anti-bacterial [12], anti-microbial [13], antioxidant [14], anti-HIV [15,16], and anticoagulants activity for thrombophlebitis [17], pulmonary embolism [18], and certain cardiac conditions [19], and with these observations in mind and as part of our ongoing research on such molecules, the title compound ethyl 2-(2-oxo-2H-chromen-4-yloxy) acetate from 4-hydroxycoumarin has been synthesized, characterized and studied for its solid state conformation by X-ray studies. 2. Procedure 2.1. Materials and methods The chemicals were purchased from Aldrich Chemical Co. Analytical TLC was performed on 0.25 mm silica gel plates (Merck 60 F254 ) using solvent system ethylacetate: hexane (4:6). Melting points were determined on a Chemi Line micro controller based melting point apparatus with a digital thermometer. The IR spectrum was recorded by the potassium bromide pellet method on FT-IR Agilent spectrophotometer, NMR spectra were recorded on a Bruker 400 MHz NMR spectrophotometer in DMSO and chemical shifts were recorded in parts per million relative to tetramethylsilane (TMS), used as an internal standard. Mass spectra was obtained with a VG70-70H spectrophotometer and important fragments are given with their relative intensities in the brackets. Elemental analysis results were within 0.4% of the calculated value. 2.1.1. Procedure for the synthesis of 4-hydroxycoumarin A mixture of phenol (1, 1.88 g, 20 mmol) and Meldrum’s acid (2, 2.88 g, 20 mmol) was stirred at 90 °C for 4 hrs under solvent free condition. After cooling to room temperature, the reaction mixture was partitioned with ethyl acetate and saturated sodium bicarbonate solution .The aqueous layer was acidified to pH = 1–2 with conc. hydrochloric acid and extracted with methylene chloride several times. The combined extracts were dried over magnesium sulphate and concentrated to give malonic acid monophenyl ester 3 of 3.31 g (92%). A mixture of 3 (180 mg, 1 mmol) and Eaton’s reagent (3 mL) was stirred at 70 °C for 1 hr and then water was added to this mixture while stirring vigorously. The precipitate was filtered by suction, washed with water, and dried in the air to give a solid compound


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Fig. 1. Schematic representation of synthesis of the title compound.

of 4-hydroxycoumarin, 4 (82%). It was recrystallized using ethanol.m.p. 206 °C (lit.10b 211-213 °C); 1 H NMR (400 MHz, DMSO); δ 12.40 (s, 1H), 7.68 (d, 1H, J = 7.2 Hz), 7.53–7.48 (m, 1H), 7.24–7.18 (m, 2H), 5.95 (s, 1H, =CH); 13 C NMR (400 MHz, DMSO); δ 175.3, 167.2, 153.4, 130.2, 128.6, 125.2, 122.7, 119.3, 93.4; EI-MS: m/z (relintensity) 162 (M+, 38), 120 (74), 92 (83), 77 (17), 63 (100), 42 (48). Analysis: Calc. for C9 H6 O3 (162): C, 66.67; H, 3.73. Found: C, 66.59; H, 3.67%. 2.1.2. Procedure for synthesis of ethyl 2-(2-oxo-2H-chromen-4-yloxy) acetate (5) Ethyl chloroacetate (1.2 mol eq) was added to a solution of 4-hydroxycoumarin 4 (1.0 mol eq.) and potassium carbonate (1.5 mol Eq) in dry acetone (30 mL), and heated to 30–40 °C for 6 hrs. The progress of the reaction was monitored by TLC (mobile phase: ethyl acetate/hexane). After completion of the reaction, the mixture was cooled, and the solvent was removed by distillation. The residual mass was triturated with cold water to remove potassium carbonate and extracted with ether (3 × 30 ml). The ether layer was washed with a 10% sodium hydroxide solution (3 × 50 ml), followed by water (3 × 30 ml), and dried over anhydrous sodium sulphate and evaporated to dryness to obtain a crude solid, which, upon recrystallization with ethanol afforded the title compound 5. The schematic synthesis of the title compound 5 was accomplished by a synthetic procedure as shown in Fig. 1. Yield 86%, m.p. 100–102 °C and purity by HPLC 98%. IR (KBr, cm−1 ): 3079 (C–H, aromatic), 2986 (C– H, aliphatic), 1716 (C=O, lactone), 1704 (C=O, ester), 1622 (C=C, alkene); 1 H NMR (400 MHz, DMSO); δ 7.82–7.29 (m, 4H, Ar–H), 5.47 (s, 1H, –C=CH–), 4.57–4.54 (s, 2H, –OCH2 ), 4.34–4.32 (q, 2H,–O–CH2 – CH3 ), 2.13 (t, 3H, –CH3 ); 13 C NMR (400 MHz, DMSO); δ 168.57 (ethylene Ar -C–O) 164.35 (ester O– C=O), 161.5 (ring lactone –O–C=O), 150.7, 135.3, 133.2, 130.4, 128.3, 125.6, 101.4 (Ar-C), 91.3 (–OCH2 ), 65.52 (–CH2 –CH3 ), 54.7 (–CH3 ); EI-MS: m/z 249.0 [M + H]+ , 100%. Analysis: Calc. for C13 H12 O5 (248): C, 62.90; H, 4.87. Found: C, 62.81; H, 4.79%. Reagents and condition: (A) 90 °C, 4 h, 92% (B) Eaton’s reagent, 70 °C, 1 h, 82%. (C) Chloro ethyl acetate, K2 CO3 , dry acetone, 40 °C, 6 h, 86%. 2.1.3. Single crystal X-ray diffraction studies A white colored rectangle shaped single crystal of dimension 0.28 × 0.26 × 0.24 mm3 of the title compound was chosen for an X-ray diffraction study. The X-ray intensity data was collected at a temperature of 296 K on a Bruker Proteum2 CCD diffractometer equipped with an X-ray generator operating at 45 kV and 10 mA, using CuKα radiation of wavelength 1.54178 A˚ Data was collected from 24 frames per set with different settings of ϕ (0° and 90°), keeping the scan width of 0.5°, exposure time of 2 s, the sample to detector distance of 45.10 mm and 2θ value at 46.6° A complete data set was processed using SAINT PLUS [20]. The structure was solved by direct methods and refined by full-matrix least squares method on F2 using SHELXS and SHELXL programs [21]. All the non-hydrogen atoms were revealed in the first difference Fourier map itself. All the hydrogen atoms were positioned geometrically and refined using a riding model with Uiso (H) = 1.2 Ueq and 1.5 Ueq (O). After ten cycles of refinement, the final difference Fourier map showed peaks of no chemical significance and the residuals saturated to 0.0570. The geometrical calculations were carried out using the program PLATON [22]. The molecular and packing diagrams were generated using the software MERCURY [23]. The details of the crystal data and structure refinement are given in Table 1. Table 2 and Table 3 gives

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M. Jyothi et al. / Chemical Data Collections 9–10 (2017) 1–10 Table 1 Crystal data and structure refinement details. CCDC Number Empirical formula Formula weight Temperature Wavelength Reflns. for cell determination θ range for above Crystal system Space group Cell dimensions a = 5.1037(7) A˚ Volume Z Density(calculated) Absorption coefficient F0 0 0 Crystal size θ range for data collection Index ranges

Reflections collected Independent reflections Absorption correction Refinement method Data / restraints / parameters Goodness-of-fit on F2 Final [I > 2σ (I)] R indices (all data) Extinction coefficient Largest diff. peak and hole

CCDC 1,511,979 C13 H12 O5 248.23 296(2) K 1.54178 ˚ A 1501 5.76◦ to 59.86◦ Orthorhombic P 21 2,1 21 b = 7.9867(10) A˚ c = 28.300(4) A˚ 1153.6(3) A˚ 3 4 1.429 Mg/m3 0.935 mm−1 520 0.28 × 0.26 × 0.24 mm 5.76◦ to 59.86◦ −5 ≤ h ≤ 4 −8≤k≤8 −31 ≤ l ≤ 31 3953 1649 [Rint = 0.0530] multi-scan Full matrix least-squares on F 2 164/0 / 165 1.103 R1 = 0.0570, wR2 = 0.1595 R1 = 0.0630, wR2 = 0.1678 0.0088(18) 0.322 and − 0.322 eA˚ −3

Table 2 ˚ Bond lengths (A). Atoms

Length

Atoms

Length

O1-C7 O1-C8 O2-C8 O3-C1 O3-C10 O4-C11 O5-C11 O5-C12 C1-C9 C1-C2

1.371(5) 1.389(5) 1.205(5) 1.355(5) 1.425(5) 1.203(5) 1.344(5) 1.456(5) 1.352(6) 1.456(6)

C2-C3 C2-C7 C3-C4 C4-C5 C5-C6 C6-C7 C8-C9 C10-C11 C12-C13

1.393(6) 1.399(5) 1.374(6) 1.404(7) 1.397(7) 1.387(6) 1.448(6) 1.513(6) 1.505(7)

the list of bond lengths and bond angles which are in good agreement with the standard values. The ORTEP of the title compound is shown in Fig. 2.

2.1.4. Hirshfeld surface calculations The program Crystal Explorer 3.0 [24] was used to perform Hirshfeld surfaces computational analysis and to quantify the intermolecular interactions in terms of surface contribution and generating graphical representations, plotting 2D fingerprint plots [25,26], and generating electrostatic potential [27] with TONTO [28]. The electrostatic potential was mapped on Hirshfeld surfaces using HartreeFock (STO-3 G basis set) theory over the range of − 0.020 a.u. to + 0.020 a.u. The electrostatic potential


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Table 3 Bond angles (O ). Atoms

Angle

Atoms

Angle

C7-O1-C8 C1-O3-C10 C11-O5-C12 C9-C1-O3 C9-C1-C2 O3-C1-C2 C3-C2-C7 C3-C2-C1 C7-C2-C1 C4-C3-C2 C3-C4-C5 C6-C5-C4 C7-C6-C5

121.5(3) 118.4(3) 116.4(3) 125.5(4) 120.5(4) 114.1(3) 118.8(4) 124.4(4) 116.8(4) 121.0(4) 119.8(4) 120.2(4) 118.9(4)

O1-C7-C6 O1-C7-C2 C6-C7-C2 O2-C8-O1 O2-C8-C9 O1-C8-C9 C1-C9-C8 O3-C10-C11 O4-C11-O5 O4-C11-C10 O5-C11-C10 O5-C12-C13

116.2(3) 122.5(4) 121.3(4) 116.9(3) 125.8(4) 117.3(4) 121.5(4) 112.8(3) 125.8(4) 125.5(4) 108.7(3) 107.1(4)

Fig. 2. ORTEP of the molecule with thermal ellipsoids drawn at 50% probability.

surfaces are plotted with red region which is a negative electrostatic potential (hydrogen acceptors) and blue region which is a positive electrostatic potential (hydrogen donor). 3. Data, value and validation Single crystal X-ray diffraction studies revealed that the compound ethyl 2-(2-oxo-2H- chromen4-yloxy) acetate crystallized in the orthorhombic space group P21 21 21 with a single molecule in the asymmetric unit. The coumarin core has a planar conformation. The dihedral angle between the two

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M. Jyothi et al. / Chemical Data Collections 9–10 (2017) 1–10 Table 4 Intermolecular C—H…O Hydrogen bonding. D—H…A

D—H

H…A

D…A

D—H…A

C(4)–H(4)..O(2)i C(6)–H(6)..O(2)ii C(10)–H(10A)..O(4)iii C(10)–H(10B)..O(2)iii

0.93 0.93 0.97 0.97

2.57 2.54 2.52 2.58

3.458(5) 3.379(5) 3.489(5) 3.272(5)

161 150 176 129

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

Fig. 3. Packing of the molecules when viewed down along the b axis in a two dimensional structure.

six membered rings is 1.26(1)° indicating their mean planarity. The bond angles C1-C2-C3 and C6C7-O1 at the junction of the two rings are 114.1(3)° and 116.2(3)° respectively. Electron localization was found at the short C4-C15 bond with a length of 1.352(6)°. As in other coumarin compounds, an important asymmetry in the O–C-O bond angles has been detected at [O1-C8-O2 = 116.9(3)° and O2-C8-C9 = 125.8(4)°]. The structures exhibits intermolecular hydrogen bonds of the type C—H…O and are tabulated in Table 4. C10–H10A…O4 interactions link the molecules into C (4) chains running parallel to an axis. This chain is further strengthened by C10–H10B…O2 interactions that form C(7) chains. The adjacent chains are interlinked via C4–H4…O2 interactions that run down the b axis forming C(8) chains resulting in a two dimensional sheet in the ab plane (Fig. 3). The adjacent two dimensional sheets are interconnected by C(6) chains of C6–H6…O2 interactions along c axis, and thus, a three dimensional structure is displayed (Fig. 4).


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Fig. 4. Packing of the molecules viewed down along the c axis in a three dimensional structure.

3.1. Hirshfeld surface studies Hirshfeld surface analysis is an effective tool for exploring packing modes and intermolecular interactions in molecular crystals, as they provide a visual picture of intermolecular interactions and of molecular shapes in a crystalline environment. Surface features characteristic of different types of intermolecular interactions can be identified, and these features can be revealed by colour coding distances from the surface to the nearest atom exterior (de plots) or interior (di plots) to the surface. This gives a visual picture of different types of interactions present and also reflects their relative contributions from molecule to molecule. Further, 2D fingerprint plots (FP), in particular the breakdown of FP into specific atom…atom contacts in a crystal, provide a quantitative idea of the types of intermolecular contacts experienced by molecules in the bulk and presents this information in a convenient colour plot. Hirshfeld surfaces comprising dnorm surface and Fingerprint plots were generated

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Fig. 5. Fingerprint plots of the molecule.

Fig. 6. dnorm and electrostatic potential mapped on Hirshfeld surface for visualizing the intermolecular contacts.

and analysed for the title compound in order to explore the packing modes and intermolecular interactions. The two dimensional fingerprint plots from Hirshfeld surface analyses along with the electrostatic potential plots Fig. 5, illustrate the difference between the intermolecular interaction patterns and the relative contributions to the Hirshfeld surface (in percentage) for the major intermolecular contacts associated with the title compound. Importantly, H…H (37.4%) contacts appears to be a major contributor in the crystal packing, whereas the O…H (33.2%), C…H (20.2%), plots also reveal the


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information regarding the intermolecular hydrogen bonds thus supporting for C—H…O intermolecular interactions. This intermolecular contact is highlighted by conventional mapping of dnorm on molecular Hirshfeld surfaces and is shown in Fig. 6. The red spots over the surface indicate the inter contacts involved in hydrogen bond. The dark-red spots on the dnorm surface arise as a result of the short interatomic contacts, i.e., weak C—H…O hydrogen bonds, while the other intermolecular interactions appear as light-red spots. Acknowledgements The authors are thankful to the Institution of Excellence, Vijnana Bhavana, University of Mysore, Mysuru, for providing the X-ray intensity data. Zabiulla gratefully acknowledges the financial support provided by the Department of Science and Technology, New Delhi, Under INSPIRE-Fellowship scheme [IF140407]. Yasser Hussain Issa Mohammed thanks University of Hajah, Yemen for the financial support. 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