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Crystal structure of 2-hy­dr­oxy-3-(prop-2-yn-1-yl)naphthalene-1,4-dione

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aDepartamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte Minas Gerais, CEP 31.270-901, Brazil, and bDepartamento de Física, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, CEP 31.270-901, Brazil
*Correspondence e-mail: raquelgeisi@hotmail.com

Edited by H. Ishida, Okayama University, Japan (Received 10 July 2018; accepted 16 August 2018; online 24 August 2018)

The naphtho­quinone unit of the title compound, C13H8O3, is essentially planar, with an r.m.s. deviation of 0.013 Å for the non-H atoms. The essentially linear propargyl group is tilted by ca 113° relative to the naphtho­quinone plane. In the crystal, mol­ecules are linked via a pair of O—H⋯O hydrogen bonds, forming an inversion dimer. The dimers are further linked via pairs of C—H⋯O hydrogen bonds into a tape structure along [20[\overline{1}]]. No ππ stacking is observed in the present case as it could be expected for naphtho­quinone derivatives.

1. Chemical context

Lawsone (2-hy­droxy­naphtalene-1,4-dione), 1, shows prom­ising in the synthesis of analogues of atovaquone, 2, an anti­malarial drug (Nixon et al., 2013[Nixon, G. L., Moss, D. M., Shone, A. E., Lalloo, D. G., Fisher, N., O'Neill, P. M., Ward, S. A. & Biagini, G. A. (2013). J. Antimicrob. Chemother. 68, 977-985.]) also used in immunosuppressed patients affected by pneumonia caused by Pneumocystis carinii (Cirioni et al., 1995[Cirioni, O., Giacometti, A., Balducci, M., Burzacchini, F. & Scalise, G. (1995). J. Antimicrob. Chemother. 36, 740-741.]; Comley et al., 1995[Comley, J. C. W., Yeates, C. L. & Frend, T. J. (1995). J. Antimicrob. Chemother. 39, 806-809.]). Recent studies have shown that it can be also useful in the fight against cancer (Fiorillo et al., 2016[Fiorillo, M., Lamb, R., Tanowitz, H. B., Mutti, L., Krstic-Demonacos, M., Cappello, A. R., Martinez-Outschoorn, U. E., Sotgia, F. & Lisanti, M. F. (2016). Oncotarget, 7, 34084-34099.]; Ashton et al., 2016[Ashton, T. M., Fokas, E., Kunz-Schughart, L. A., Folkes, L. K., Anbalagan, S., Huether, M., Kelly, C. J., Pirovano, G., Buffa, F. M., Hammond, E. M., Stratford, M., Muschel, R. J., Higgins, G. S. & Mckenna, W. G. (2016). Nat. Commun. 7, 12308.]). Thus far unknown, 2-hy­droxy-3-(prop-2-yn-1-yl)naphthalene-1,4-dione (3) was obtained in a two steps one-pot procedure by reacting 1 with propargyl iodide, prepared in situ from propargyl bromide and potassium iodide. It opens the possibility for the synthesis of triazoles at the C3 position of 1 by [2 + 3] alkyne–azide 1,3-dipolar cyclo­addition enabling the preparation of 3-substituted lawsone derivatives with potential pharmacological activity, including atovaquone (2) analogues.

[Scheme 1]

Treatment of 1 with a base leads to the formation of the corresponding enolate that can be O- or C-alkyl­ated depending on the nature of the counter-ion, reaction conditions and nature of the alkyl electrophile (Jordão et al., 2015[Jordão, A. K., Vargas, M. D., Pinto, A. C., da Silva, F. de C. & Ferreira, V. F. (2015). RSC Adv. 5, 67909-67943.]). When 1 was reacted with propargyl bromide and sodium carbonate in DMF the 2-O-propargyl derivative was obtained in 20% yield (Valença et al., 2017[Valença, W. O., Baiju, T. V., Brito, F. G., Araujo, M. H., Pessoa, C., Cavalcanti, B. C., Simore, C. A., Jacob, C., Namboothiri, I. N. N. & da Silva Júnior, E. N. (2017). ChemistrySelect, 2, 4301-4308.]). The 3-C-propargyl deriv­ative had not been described thus far. In view of the importance of acetyl­enic compounds for [2 + 3] alkyne–azide 1,3-dipolar cyclo­addition reactions, known as the click reaction, we decided to investigate the 2-O- versus 3-C-propargylation of 1. The 3-C-propargyl derivative is considered to be an inter­esting inter­mediate for the synthesis of 3-triazolo analogues of atovaquone, 2, and other bioactive 1,4-naphtho­quinones. After evaluating the influence of organic and inorganic bases, protic and aprotic solvents, alkyl­ating agents, temperature and reaction time, we obtained 3 in 28% yield. No product of O-alkyl­ation was observed in the reaction mixture.

2. Structural commentary

The molecular structure of the title compound, 3, is shown in Fig. 1[link]. The naphtho­quinone unit is essentially planar, with an r.m.s. deviation of 0.013 Å for the non-H atoms. The C—O bond lengths [C1—O1 = 1.2217 (18) Å, C2—O3 = 1.3412 (18) Å and C4—O2 = 1.2488 (19) Å] confirm the presence of 2-hy­droxy­naphthalene-1,4-dione in the crystalline state and are in agreement with the lengths found by Dekkers et al. (1996[Dekkers, J., Kooijman, H., Kroon, J. & Grech, E. (1996). Acta Cryst. C52, 2896-2899.]). The 1H and 13C NMR spectra and HMBC experiments confirm atoms C1 and C4 as carbonyls, as well as a hy­droxy group at C2. The propargyl group adopts a nearly perpendic­ular position [C3—C11—C12 = 112.70 (14)°] regarding the naphthalene ring system to avoid hindrance with the O2 and O3 atoms. The naphthoquinone ring system is characterized by the torsion angles C4—C3—C11—C12 = −100.96 (19)° and C2—C3—C11—C12 = 79.9 (2)°.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound 3. Displacement ellipsoids are drawn at the 50% probability level.

3. Supra­molecular features

In the crystal, O—H⋯O and C—H⋯O hydrogen bonds (O3—H3⋯O1i and C5—H5⋯O2ii; symmetry codes as in Table 1[link]) are responsible for an infinite tape structure running along [20[\overline{1}]]. All the naphtho­quinone units are arranged in a parallel manner with respect to each other, as shown in Fig. 2[link]. ππ stacking inter­actions are expected for naphtho­quinone derivatives (Meyer et al., 2003[Meyer, E. A., Castellano, R. K. & Diederich, F. (2003). Angew. Chem. 42, 1210-1250.]). However, this type of inter­action is not observed here, probably because of the C3 propargyl substituent.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O3—H3⋯O1i 0.89 (3) 2.06 (3) 2.8118 (19) 142 (3)
C5—H5⋯O2ii 0.93 2.49 3.231 (2) 137
Symmetry codes: (i) -x+2, -y+1, -z; (ii) -x, -y+1, -z+1.
[Figure 2]
Figure 2
A packing diagram of the title compound.

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.39, last update May 2018; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) for 2-hy­droxy-naphthalene-1,4-dione revealed 40 structures and approximately 787 structures which possess the naphthalene-1,4-dione moiety. 2-Hy­droxy-3-(3-oxobut­yl)naphthalene-1,4-dione (Nasiri et al., 2006[Nasiri, H. R., Madej, M. G., Lancaster, C. R. D., Schwalbe, H. & Bolte, M. (2006). Acta Cryst. C62, o671-o673.]) and 2-hy­droxy-3-(methyl-prop-1-en-1-yl)naphthalene-1,4-dione (Alcantara Emiliano et al., 2016[Alcantara Emiliano, S., Welma Duarte Silva, S., Alves Pereira, M., R. dos Santos Malta, V. & Luciano Balliano, T. (2016). Acta Cryst. E72, 188-190.]), compounds with structural similarity to the title compound, were also found. These compounds present a group linked to C3 with an angle nearly perpendicular to the naphtho­quinone ring.

5. Synthesis and crystallization

The synthetic scheme is shown in Fig. 3[link]. A mixture of propargyl bromide (0.75 ml, 4.47 mmol) and sodium iodide (1.30 g, 5.33 mmol) in dry acetone (3.5 ml) was stirred for 30 min at room temperature in a closed system. Then, a solution of lawsone (0.1 g, 2.4 mmol) and diiso­propyl­ethyl­amine (0.51 ml, 2.93 mmol) in a 2:1 (v/v) mixture of water/tert-butanol (24 ml) was added and the reaction mixture was stirred for a further 24 h at 353 K. The reaction was quenched with di­chloro­methane (ca 40 ml) and the heterogeneous mixture was transferred to a separatory funnel. The aqueous phase was separated and the organic layer was extracted with 1 mol l−1 hydro­chloric acid (3 × 40 ml) and water (3 × 40 ml). The organic layer was dried over anhydrous sodium sulfate and concentrated to dryness. The crude red solid product (0.45 g) was purified by column chromatography (silica) using a 99.5:0.5 (v/v) mixture of hexa­ne/tert-butanol containing 0.1% of acetic acid as eluent. Pure title compound was obtained in 28% yield (0.143 g, m.p. 396.7–397.2 K). Single crystals suitable for X-ray analysis were obtained by slow evaporation of a hexa­ne/tert-butanol solution (ca 0.5 mg ml−1) at room temperature. The infrared and NMR spectral data and corresponding spectra of 3 are available in the supporting information.

[Figure 3]
Figure 3
The synthetic scheme of the title compound, 3; (i) propargyl bromide, sodium iodide and dry acetone, 0.5 h; (ii) diiso­propyl­ethyl­amine and t-BuOH/H2O, 353 K, 24 h.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. C-bound H atoms were placed geometrically (C—H = 0.93–0.97 Å) and were refined as riding with Uiso(H) = 1.2Ueq(C). The O-bound H atom was located in a difference Fourier map and freely refined [O—H = 0.89 (3) Å].

Table 2
Experimental details

Crystal data
Chemical formula C13H8O3
Mr 212.19
Crystal system, space group Triclinic, P[\overline{1}]
Temperature (K) 293
a, b, c (Å) 5.3695 (4), 9.5278 (8), 10.2972 (9)
α, β, γ (°) 96.814 (7), 93.432 (7), 102.977 (7)
V3) 507.68 (8)
Z 2
Radiation type Mo Kα
μ (mm−1) 0.10
Crystal size (mm) 0.4 × 0.2 × 0.05
 
Data collection
Diffractometer Rigaku Xcalibur Atlas Gemini ultra
Absorption correction Multi-scan (CrysAlis PRO; Rigaku OD, 2015[Rigaku OD (2015). CrysAlis PRO. Rigaku Oxford Diffaction, Yarnton, Oxfordshire, England.])
Tmin, Tmax 0.720, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 7946, 2508, 1563
Rint 0.033
(sin θ/λ)max−1) 0.695
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.147, 1.05
No. of reflections 2508
No. of parameters 149
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.21, −0.5
Computer programs: CrysAlis PRO (Rigaku OD, 2015[Rigaku OD (2015). CrysAlis PRO. Rigaku Oxford Diffaction, Yarnton, Oxfordshire, England.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.][Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]).

Supporting information


Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2015); cell refinement: CrysAlis PRO (Rigaku OD, 2015); data reduction: CrysAlis PRO (Rigaku OD, 2015); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

2-Hydroxy-3-(prop-2-yn-1-yl)naphthalene-1,4-dione top
Crystal data top
C13H8O3F(000) = 220
Mr = 212.19Dx = 1.388 Mg m3
Triclinic, P1Melting point = 396.8–397.5 K
a = 5.3695 (4) ÅMo Kα radiation, λ = 0.71073 Å
b = 9.5278 (8) ÅCell parameters from 1721 reflections
c = 10.2972 (9) Åθ = 3.2–28.7°
α = 96.814 (7)°µ = 0.10 mm1
β = 93.432 (7)°T = 293 K
γ = 102.977 (7)°Prism, colourless
V = 507.68 (8) Å30.4 × 0.2 × 0.05 mm
Z = 2
Data collection top
Rigaku Xcalibur Atlas Gemini ultra
diffractometer
2508 independent reflections
Radiation source: fine-focus sealed X-ray tube, Enhance (Mo) X-ray Source1563 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.033
Detector resolution: 10.4186 pixels mm-1θmax = 29.6°, θmin = 2.8°
ω scansh = 77
Absorption correction: multi-scan
(CrysAlis PRO; Rigaku OD, 2015)
k = 1212
Tmin = 0.720, Tmax = 1.000l = 1314
7946 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.051H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.147 w = 1/[σ2(Fo2) + (0.0639P)2 + 0.058P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
2508 reflectionsΔρmax = 0.21 e Å3
149 parametersΔρmin = 0.5 e Å3
0 restraints
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
xyzUiso*/Ueq
O30.6461 (3)0.33269 (14)0.01419 (12)0.0536 (4)
H30.796 (5)0.389 (3)0.002 (3)0.104 (10)*
O10.9195 (2)0.59305 (13)0.12532 (12)0.0518 (3)
O20.0447 (3)0.36386 (14)0.31887 (13)0.0647 (4)
C10.7232 (3)0.54469 (17)0.17533 (15)0.0388 (4)
C20.5615 (3)0.39989 (17)0.11881 (15)0.0403 (4)
C30.3415 (3)0.33844 (17)0.16560 (15)0.0419 (4)
C40.2483 (3)0.41556 (18)0.27733 (16)0.0431 (4)
C50.3230 (4)0.6358 (2)0.44404 (17)0.0511 (4)
H50.16930.59510.47670.061*
C60.4664 (4)0.7695 (2)0.50175 (19)0.0586 (5)
H60.41090.81820.57400.070*
C70.6917 (4)0.8311 (2)0.4525 (2)0.0642 (6)
H70.78710.92180.49150.077*
C80.7782 (3)0.7597 (2)0.34557 (18)0.0530 (5)
H80.93020.80210.31230.064*
C90.6345 (3)0.62361 (16)0.28851 (15)0.0389 (4)
C100.4061 (3)0.56178 (17)0.33796 (15)0.0397 (4)
C110.1798 (4)0.19019 (18)0.10516 (18)0.0536 (5)
H11A0.00540.18110.12900.064*
H11B0.17510.18330.01030.064*
C120.2779 (4)0.07067 (19)0.14761 (17)0.0552 (5)
C130.3566 (5)0.0258 (2)0.1781 (2)0.0829 (7)
H130.41960.10300.20260.099*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O30.0570 (8)0.0492 (7)0.0513 (7)0.0084 (6)0.0167 (6)0.0053 (5)
O10.0456 (7)0.0531 (7)0.0548 (7)0.0048 (6)0.0176 (6)0.0060 (5)
O20.0540 (8)0.0635 (9)0.0699 (9)0.0031 (6)0.0256 (7)0.0043 (7)
C10.0372 (9)0.0400 (8)0.0405 (8)0.0091 (7)0.0057 (7)0.0094 (6)
C20.0433 (9)0.0397 (9)0.0391 (9)0.0119 (7)0.0057 (7)0.0047 (6)
C30.0437 (9)0.0374 (8)0.0430 (9)0.0075 (7)0.0018 (7)0.0040 (7)
C40.0395 (9)0.0443 (9)0.0453 (9)0.0061 (7)0.0073 (7)0.0110 (7)
C50.0499 (10)0.0575 (11)0.0468 (10)0.0140 (8)0.0121 (8)0.0047 (8)
C60.0615 (12)0.0620 (12)0.0503 (10)0.0185 (10)0.0071 (9)0.0096 (8)
C70.0615 (13)0.0533 (11)0.0678 (13)0.0076 (10)0.0001 (10)0.0172 (9)
C80.0441 (10)0.0488 (10)0.0611 (11)0.0041 (8)0.0066 (8)0.0004 (8)
C90.0377 (9)0.0390 (8)0.0402 (8)0.0101 (7)0.0019 (7)0.0046 (6)
C100.0389 (9)0.0430 (9)0.0380 (8)0.0106 (7)0.0049 (7)0.0055 (7)
C110.0497 (10)0.0458 (10)0.0582 (11)0.0004 (8)0.0023 (9)0.0006 (8)
C120.0671 (12)0.0395 (10)0.0515 (10)0.0016 (9)0.0070 (9)0.0039 (8)
C130.113 (2)0.0483 (12)0.0862 (16)0.0257 (13)0.0048 (14)0.0002 (11)
Geometric parameters (Å, º) top
O3—H30.88 (3)C6—H60.9300
O3—C21.3426 (19)C6—C71.375 (3)
O1—C11.2217 (18)C7—H70.9300
O2—C41.2189 (19)C7—C81.384 (3)
C1—C21.485 (2)C8—H80.9300
C1—C91.473 (2)C8—C91.392 (2)
C2—C31.340 (2)C9—C101.390 (2)
C3—C41.465 (2)C11—H11A0.9700
C3—C111.521 (2)C11—H11B0.9700
C4—C101.499 (2)C11—C121.458 (3)
C5—H50.9300C12—C131.161 (3)
C5—C61.376 (3)C13—H130.9300
C5—C101.381 (2)
C2—O3—H3106.5 (17)C6—C7—C8120.80 (18)
O1—C1—C2118.90 (14)C8—C7—H7119.6
O1—C1—C9123.40 (15)C7—C8—H8120.5
C9—C1—C2117.69 (14)C7—C8—C9119.08 (17)
O3—C2—C1115.90 (14)C9—C8—H8120.5
C3—C2—O3120.71 (15)C8—C9—C1120.23 (15)
C3—C2—C1123.38 (14)C10—C9—C1119.71 (14)
C2—C3—C4119.88 (15)C10—C9—C8120.07 (15)
C2—C3—C11122.10 (15)C5—C10—C4119.53 (15)
C4—C3—C11118.01 (15)C5—C10—C9119.69 (15)
O2—C4—C3121.03 (16)C9—C10—C4120.78 (14)
O2—C4—C10120.40 (15)C3—C11—H11A109.1
C3—C4—C10118.56 (14)C3—C11—H11B109.1
C6—C5—H5119.8H11A—C11—H11B107.8
C6—C5—C10120.37 (17)C12—C11—C3112.70 (14)
C10—C5—H5119.8C12—C11—H11A109.1
C5—C6—H6120.0C12—C11—H11B109.1
C7—C6—C5119.98 (17)C13—C12—C11178.3 (2)
C7—C6—H6120.0C12—C13—H13180.0
C6—C7—H7119.6
O1—C1—C2—O30.4 (2)C4—C3—C11—C12100.96 (19)
O1—C1—C2—C3179.15 (16)O2—C4—C10—C52.0 (3)
C9—C1—C2—O3178.72 (14)O2—C4—C10—C9177.93 (16)
C9—C1—C2—C30.1 (2)C3—C4—C10—C5179.45 (16)
O1—C1—C9—C81.0 (2)C3—C4—C10—C90.7 (2)
O1—C1—C9—C10178.81 (15)C10—C5—C6—C71.0 (3)
C2—C1—C9—C8179.98 (14)C6—C5—C10—C4179.40 (17)
C2—C1—C9—C100.2 (2)C6—C5—C10—C90.7 (3)
O3—C2—C3—C4178.09 (15)C5—C6—C7—C80.5 (3)
O3—C2—C3—C111.0 (2)C6—C7—C8—C90.4 (3)
C1—C2—C3—C40.7 (2)C7—C8—C9—C1179.48 (16)
C1—C2—C3—C11179.77 (15)C7—C8—C9—C100.7 (3)
C2—C3—C4—O2177.64 (16)C1—C9—C10—C40.1 (2)
C2—C3—C4—C100.9 (2)C1—C9—C10—C5180.00 (16)
C11—C3—C4—O21.5 (2)C8—C9—C10—C4179.73 (15)
C11—C3—C4—C10179.92 (15)C8—C9—C10—C50.2 (2)
C2—C3—C11—C1279.9 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3···O1i0.89 (3)2.06 (3)2.8118 (19)142 (3)
C5—H5···O2ii0.932.493.231 (2)137
Symmetry codes: (i) x+2, y+1, z; (ii) x, y+1, z+1.
 

Funding information

Funding for this research was provided by: Conselho Nacional de Desenvolvimento Científico e Tecnológico (scholarship No. 303901/2017-9); Fundação de Amparo à Pesquisa do Estado de Minas Gerais (grant No. CDS-APQ-02541-15).

References

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