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ISSN: 2414-3146

(8-Hy­dr­oxy-6-meth­­oxy-1-oxo-1H-isochromen-3-yl)methyl formate: a supra­molecular framework

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aInstitute of Chemistry, University of Neuchâtel, Av. de Bellevax 51, CH-2000 Neuchâtel, Switzerland, and bInstitute of Physics, University of Neuchâtel, rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
*Correspondence e-mail: helen.stoeckli-evans@unine.ch

Edited by S. Bernès, Benemérita Universidad Autónoma de Puebla, México (Received 7 October 2020; accepted 19 October 2020; online 23 October 2020)

In the title compound, C12H10O6, an intra­molecular O—H⋯O hydrogen bond forms an S(6) ring motif. The mol­ecule is essentially planar with an r.m.s. deviation of 0.051 Å for all non-H atoms. In the crystal mol­ecules are linked by C—H⋯O hydrogen bonds and a C—H⋯π inter­action, forming a supra­molecular framework.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

The title compound, I, is an inter­mediate in the synthesis of cytogenin, a naturally occurring isocoumarin that was first isolated from a cultured broth of Streptoverticillium eurocidicum (Kumagai et al., 1990[Kumagai, H., Masuda, T., Ohsono, M., Hattori, S., Naganawa, H., Sawa, T., Hamada, M., Ishizuka, M. & Takeuchi, T. (1990). J. Antibiot. 43, 1505-1507.], 1995[Kumagai, H., Masuda, T., Ishizuka, M. & Takeuchi, T. (1995). J. Antibiot. 48, 175-178.]). It was shown by these authors to have both anti­biotic properties and anti­tumor activity. The first synthesis of cytogenin was reported in 2004 (Saeed, 2004[Saeed, A. (2004). J. Heterocycl. Chem. 41, 975-978.]). More recently, a new synthetic route to cytogenin and similar isocoumarins has been reported (Gadakh & Sudalai, 2014[Gadakh, S. K. & Sudalai, A. (2014). RSC Adv. 4, 57658-57661.]).

As shown in Fig. 1[link], compound I was prepared via two pathways (see Synthesis and crystallization). The details of the syntheses of the precursors A and B and cytogenin have been described elsewhere (Tiouabi, 2005[Tiouabi, M. (2005). PhD Thesis, University of Neuchâtel, Switzerland.]).

[Figure 1]
Figure 1
The reaction pathways for the synthesis of compound I and cytogenin (Tiouabi, 2005[Tiouabi, M. (2005). PhD Thesis, University of Neuchâtel, Switzerland.]).

The mol­ecule of I (Fig. 2[link]), is essentially planar with an r.m.s. deviation of 0.051 Å for all non-H atoms (O1–O6/C1/C3–C13); the maximum deviations from this mean plane are 0.080 (6) Å for atom C12 and −0.091 (8) Å for atom C13. There is an intra­molecular O—H⋯O hydrogen bond present, forming an S(6) ring motif (Fig. 2[link] and Table 1[link]).

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C5–C10 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
O4—H40⋯O1 0.84 1.88 2.616 (5) 146
C4—H4⋯O1i 0.95 2.38 3.326 (6) 173
C5—H5⋯O2i 0.95 2.59 3.541 (6) 176
C7—H7⋯O6ii 0.95 2.55 3.499 (5) 175
C11—H11C⋯O6i 0.98 2.57 3.388 (8) 141
C12—H12BCgiii 0.99 2.88 3.788 (6) 153
Symmetry codes: (i) [-x+{\script{3\over 2}}, y-1, z+{\script{1\over 2}}]; (ii) [x-{\script{1\over 2}}, -y+1, z]; (iii) [-x+{\script{3\over 2}}, y, z-{\script{1\over 2}}].
[Figure 2]
Figure 2
A view of the mol­ecular structure of compound I, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. The intra­molecular O—H⋯O hydrogen bond (see Table 1[link]) is shown as a dashed line.

In the crystal, mol­ecules are linked by a series of C—H⋯O hydrogen bonds (Table 1[link]), forming inter­connected ribbons running normal to each other in planes (012) and (01[\overline{2}]): see Fig. 3[link]. These inter­actions lead to the formation of a supra­molecular framework, which is reinforced by a C—H⋯π inter­action (Fig. 4[link] and Table 1[link]).

[Figure 3]
Figure 3
A partial view of the crystal packing of compound I, viewed normal to plane (011). Hydrogen bonds (see Table 1[link]) are shown as dashed lines.
[Figure 4]
Figure 4
A view along the a axis of the crystal packing of compound I. Hydrogen bonds and C—H⋯π inter­actions (see Table 1[link]) are shown as dashed lines.

Synthesis and crystallization

The syntheses of the title compound, I, and cytogenin, are illustrated in Fig. 1[link]. The syntheses of the precursors, 3-(bromo­meth­yl)-8-hy­droxy-6-meth­oxy-1H-isochromen-1-one (A), 3-(bromo­meth­yl)-6-meth­oxy-1-oxo-1H-isochromen-8-yl acetate (B), and cytogenin, are described in the PhD thesis of Tiouabi (2005[Tiouabi, M. (2005). PhD Thesis, University of Neuchâtel, Switzerland.]), which can be downloaded from the website https://doc.rero.ch/record, a digital library where many theses of Swiss universities are deposited. The numbering scheme of I in Fig. 1[link] is with reference to the NMR spectra.

Method 1: The hy­droxy­bromo­isocoumarin A (0.14 g, 0.49 mmol) was dissolved with stirring in 5 ml of anhydrous DMF in a 50 ml flask equipped with a magnetic stirrer and under an atmosphere of argon. HCO2Na (0.167 g, 2.46 mmol) was added and the mixture was stirred overnight at room temperature. The evolution of the reaction was monitored by thin-layer chromatography, using di­methyl­chloride as eluent. On completion of the reaction, the mixture was diluted with ethyl acetate and then washed with an aqueous saturated solution of NaCl. The organic phase was dried using anhydrous Na2SO4, then filtered and concentrated using a rotary evaporator, yielding compound I in the form of a white solid (yield 0.118 g, 96%).

Method 2: The acet­oxy­bromo­isocoumarin B (34.2 mg, 0.104 mmol) was dissolved with stirring in 3 ml of anhydrous DMF in a 50 ml flask equipped with a magnetic stirrer and under an atmosphere of argon. HCO2Na (47 mg, 0.69 mmol) was added, the temperature was raised to 80°C and the mixture stirred for 4 h. The evolution of the reaction was monitored by thin-layer chromatography, using di­methyl­chloride as eluent. On completion of the reaction, the mixture was diluted with ethyl acetate and then washed with an aqueous saturated solution of NaCl. The organic phase was dried using anhydrous Na2SO4, then purified by column chromatography (silica, eluent CH2Cl2/hexane 10/1). Compound I was obtained in the form of a white solid (yield 18.7 mg, 72%).

Analytical data for I: Rf (CH2Cl2, UV) 0.44. 1H NMR (400 MHz, CDCl3, 298 K): 3.90 (s, 3H, OCH3), 4.99 (s, 2H, CH2–3a), 6.42 (d, Jm = 2.3 Hz, 1H, ArH-7), 6.53 (s, 1H, H-4), 6.55 (d, Jm = 2.3 Hz, 1H, ArH-5), 8.17 (s, 1H, CHO-3 b), 11.0 (s, 1H, OH-8). 13C NMR (100 Hz, CDCl3, 298 K, HETCOR-SR/LR): 56.19 C(OCH3), 61.61 C(3a), 100.67 C(9), 101.80 C(5), 103.13 C(7), 107.82 C(4), 138.21 C(10), 150.27 C(3), 160.37 C(3 b), 164.23 C(1), 165.75 C(8), 167.35 C(6). HR–MS [ESI(+)]: ms 273.03634 [M + Na]+. IR (KBr disk, cm−1): 3129 br, 1728 s, 1690 vs, 1622 m, 1400 vs, 1164 vs, 1064 w.

Colourless block-like crystals of I were obtained by slow evaporation of a solution in chloro­form.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. Intensity data were measured using a Stoe IPDS I, a one-circle diffractometer. The alert diffrn_reflns_laue_measured_fraction_full value (0.947) below minimum (0.95) is given. This involves 29 random reflections out of the expected 1034 for the IUCr cut-off limit of (sin θ)/λ = 0.6 Å−1; viz. 2.8%.

Table 2
Experimental details

Crystal data
Chemical formula C12H10O6
Mr 250.20
Crystal system, space group Orthorhombic, Pca21
Temperature (K) 173
a, b, c (Å) 25.006 (2), 5.0337 (6), 8.5646 (6)
V3) 1078.05 (17)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.13
Crystal size (mm) 0.50 × 0.50 × 0.50
 
Data collection
Diffractometer STOE IPDS 1
Absorption correction Multi-scan (MULABS; Spek, 2020[Spek, A. L. (2020). Acta Cryst. E76, 1-11.])
Tmin, Tmax 0.763, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 7630, 2012, 1249
Rint 0.070
(sin θ/λ)max−1) 0.619
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.050, 0.135, 0.91
No. of reflections 2012
No. of parameters 166
No. of restraints 1
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.32, −0.27
Computer programs: EXPOSE, CELL and INTEGRATE in IPDS-I (Stoe & Cie, 2004[Stoe & Cie (2004). IPDS1 Bedienungshandbuch. Stoe & Cie GmbH, Darmstadt, Germany.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), Mercury (Macrae et al., 2020[Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M. & Wood, P. A. (2020). J. Appl. Cryst. 53, 226-235.]), SHELXL2018/3 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), PLATON (Spek, 2020[Spek, A. L. (2020). Acta Cryst. E76, 1-11.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Structural data


Computing details top

Data collection: EXPOSE in IPDS-I (Stoe & Cie, 2004); cell refinement: CELL in IPDS-I (Stoe & Cie, 2004); data reduction: INTEGRATE in IPDS-I (Stoe & Cie, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2020); software used to prepare material for publication: SHELXL2018/3 (Sheldrick, 2015), PLATON (Spek, 2020) and publCIF (Westrip, 2010).

(8-Hydroxy-6-methoxy-1-oxo-1H-isochromen-3-yl)methyl formate top
Crystal data top
C12H10O6Dx = 1.542 Mg m3
Mr = 250.20Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pca21Cell parameters from 3909 reflections
a = 25.006 (2) Åθ = 2.2–25.8°
b = 5.0337 (6) ŵ = 0.13 mm1
c = 8.5646 (6) ÅT = 173 K
V = 1078.05 (17) Å3Block, colorless
Z = 40.50 × 0.50 × 0.50 mm
F(000) = 520
Data collection top
STOE IPDS 1
diffractometer
2012 independent reflections
Radiation source: fine-focus sealed tube1249 reflections with I > 2σ(I)
Plane graphite monochromatorRint = 0.070
φ rotation scansθmax = 26.1°, θmin = 2.9°
Absorption correction: multi-scan
(MULABS; Spek, 2020)
h = 3030
Tmin = 0.763, Tmax = 1.000k = 66
7630 measured reflectionsl = 99
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.050H-atom parameters constrained
wR(F2) = 0.135 w = 1/[σ2(Fo2) + (0.0852P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.91(Δ/σ)max < 0.001
2012 reflectionsΔρmax = 0.32 e Å3
166 parametersΔρmin = 0.27 e Å3
1 restraintExtinction correction: (SHELXL-2018/3; Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.061 (11)
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.

Refinement. Flack x = 0.223 (999) by classical fit to all intensities 1.664 (999) from 481 selected quotients (Parsons' method)

** Absolute structure cannot be determined reliably **

The hydroxyl H atom and the C-bound H atoms were included in calculated positions and treated as riding on their parent O or C atoms.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.68528 (13)0.9547 (7)0.0918 (5)0.0500 (9)
O20.75876 (11)0.7819 (6)0.0089 (4)0.0461 (9)
O30.58898 (11)0.0468 (7)0.3437 (5)0.0511 (10)
O40.59095 (13)0.7730 (7)0.0142 (5)0.0531 (10)
H400.6131340.8626730.0656970.080*
O50.86682 (12)0.4224 (8)0.1774 (5)0.0657 (12)
O60.94909 (14)0.5664 (9)0.1136 (6)0.0732 (13)
C10.70366 (17)0.7848 (9)0.0037 (6)0.0433 (11)
C30.78373 (18)0.5948 (9)0.1006 (7)0.0428 (12)
C40.75774 (17)0.4136 (9)0.1838 (6)0.0443 (12)
H40.7768710.2882440.2450520.053*
C50.67032 (17)0.2286 (9)0.2657 (6)0.0438 (11)
H50.6878230.1042230.3316200.053*
C60.61467 (17)0.2302 (9)0.2549 (7)0.0434 (12)
C70.58804 (17)0.4147 (10)0.1602 (7)0.0455 (12)
H70.5501000.4149650.1545500.055*
C80.61731 (18)0.5950 (9)0.0759 (6)0.0437 (13)
C90.67425 (17)0.5970 (9)0.0848 (7)0.0399 (11)
C100.69987 (16)0.4093 (9)0.1799 (7)0.0411 (11)
C110.53177 (17)0.0277 (11)0.3310 (8)0.0614 (15)
H11C0.5188470.1166070.3979110.092*
H11B0.5219570.0088800.2223460.092*
H11A0.5155140.1956480.3641580.092*
C120.84306 (18)0.6344 (10)0.0911 (7)0.0493 (13)
H12B0.8550820.6297780.0190020.059*
H12A0.8531890.8079810.1367520.059*
C130.92037 (19)0.4136 (14)0.1770 (10)0.0726 (19)
H130.9367770.2721760.2326930.087*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0486 (18)0.0487 (18)0.053 (2)0.0019 (15)0.0012 (16)0.0089 (19)
O20.0381 (16)0.0448 (17)0.055 (2)0.0039 (13)0.0010 (15)0.0043 (17)
O30.0330 (15)0.0564 (19)0.064 (3)0.0051 (14)0.0021 (16)0.0138 (19)
O40.0425 (17)0.055 (2)0.062 (3)0.0046 (16)0.0054 (17)0.0109 (19)
O50.0318 (16)0.076 (2)0.089 (3)0.0021 (17)0.002 (2)0.026 (2)
O60.040 (2)0.099 (3)0.080 (3)0.012 (2)0.0013 (19)0.016 (3)
C10.036 (2)0.046 (3)0.048 (3)0.0014 (19)0.001 (2)0.001 (2)
C30.035 (2)0.045 (2)0.048 (3)0.003 (2)0.002 (2)0.002 (2)
C40.038 (2)0.044 (2)0.051 (3)0.0004 (19)0.004 (2)0.002 (2)
C50.034 (2)0.044 (2)0.053 (3)0.001 (2)0.004 (2)0.002 (2)
C60.038 (2)0.039 (2)0.053 (3)0.0005 (19)0.002 (2)0.001 (2)
C70.035 (2)0.048 (2)0.053 (4)0.003 (2)0.003 (2)0.002 (2)
C80.036 (2)0.044 (3)0.052 (4)0.003 (2)0.002 (2)0.001 (2)
C90.033 (2)0.038 (2)0.049 (3)0.0002 (19)0.001 (2)0.001 (2)
C100.035 (2)0.041 (2)0.048 (3)0.0008 (18)0.000 (2)0.001 (2)
C110.031 (2)0.073 (3)0.080 (4)0.011 (2)0.001 (3)0.013 (3)
C120.036 (2)0.055 (3)0.057 (4)0.000 (2)0.002 (2)0.005 (3)
C130.031 (3)0.088 (4)0.098 (6)0.000 (3)0.003 (3)0.021 (4)
Geometric parameters (Å, º) top
O1—C11.230 (6)C5—C101.383 (7)
O2—C31.376 (6)C5—C61.395 (6)
O2—C11.382 (5)C5—H50.9500
O3—C61.358 (6)C6—C71.401 (7)
O3—C111.438 (5)C7—C81.371 (7)
O4—C81.354 (6)C7—H70.9500
O4—H400.8400C8—C91.426 (6)
O5—C131.340 (6)C9—C101.402 (7)
O5—C121.428 (6)C11—H11C0.9800
O6—C131.184 (7)C11—H11B0.9800
C1—C91.417 (7)C11—H11A0.9800
C3—C41.327 (7)C12—H12B0.9900
C3—C121.499 (6)C12—H12A0.9900
C4—C101.447 (6)C13—H130.9500
C4—H40.9500
C3—O2—C1120.3 (4)O4—C8—C9120.8 (4)
C6—O3—C11118.3 (4)C7—C8—C9120.6 (4)
C8—O4—H40109.5C10—C9—C1121.5 (4)
C13—O5—C12116.1 (4)C10—C9—C8118.8 (4)
O1—C1—O2115.3 (4)C1—C9—C8119.6 (4)
O1—C1—C9126.7 (4)C5—C10—C9120.5 (4)
O2—C1—C9117.9 (4)C5—C10—C4122.1 (4)
C4—C3—O2123.7 (4)C9—C10—C4117.4 (4)
C4—C3—C12127.2 (5)O3—C11—H11C109.5
O2—C3—C12109.1 (4)O3—C11—H11B109.5
C3—C4—C10119.2 (5)H11C—C11—H11B109.5
C3—C4—H4120.4O3—C11—H11A109.5
C10—C4—H4120.4H11C—C11—H11A109.5
C10—C5—C6119.6 (5)H11B—C11—H11A109.5
C10—C5—H5120.2O5—C12—C3106.5 (4)
C6—C5—H5120.2O5—C12—H12B110.4
O3—C6—C5115.5 (4)C3—C12—H12B110.4
O3—C6—C7123.4 (4)O5—C12—H12A110.4
C5—C6—C7121.1 (4)C3—C12—H12A110.4
C8—C7—C6119.3 (4)H12B—C12—H12A108.6
C8—C7—H7120.3O6—C13—O5125.8 (6)
C6—C7—H7120.3O6—C13—H13117.1
O4—C8—C7118.6 (4)O5—C13—H13117.1
C3—O2—C1—O1178.0 (4)O2—C1—C9—C8179.5 (4)
C3—O2—C1—C92.3 (6)O4—C8—C9—C10179.9 (5)
C1—O2—C3—C41.6 (7)C7—C8—C9—C100.8 (8)
C1—O2—C3—C12179.1 (4)O4—C8—C9—C11.0 (8)
O2—C3—C4—C100.2 (8)C7—C8—C9—C1179.9 (5)
C12—C3—C4—C10179.0 (5)C6—C5—C10—C91.3 (8)
C11—O3—C6—C5176.5 (5)C6—C5—C10—C4178.7 (5)
C11—O3—C6—C74.8 (8)C1—C9—C10—C5179.7 (5)
C10—C5—C6—O3179.7 (5)C8—C9—C10—C51.2 (8)
C10—C5—C6—C71.0 (8)C1—C9—C10—C40.3 (8)
O3—C6—C7—C8179.2 (5)C8—C9—C10—C4178.8 (5)
C5—C6—C7—C80.6 (8)C3—C4—C10—C5178.9 (5)
C6—C7—C8—O4179.6 (5)C3—C4—C10—C91.1 (8)
C6—C7—C8—C90.5 (8)C13—O5—C12—C3176.8 (5)
O1—C1—C9—C10179.0 (5)C4—C3—C12—O55.5 (8)
O2—C1—C9—C101.4 (7)O2—C3—C12—O5175.2 (4)
O1—C1—C9—C80.1 (8)C12—O5—C13—O60.9 (12)
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the C5–C10 ring.
D—H···AD—HH···AD···AD—H···A
O4—H40···O10.841.882.616 (5)146
C4—H4···O1i0.952.383.326 (6)173
C5—H5···O2i0.952.593.541 (6)176
C7—H7···O6ii0.952.553.499 (5)175
C11—H11C···O6i0.982.573.388 (8)141
C12—H12B···Cgiii0.992.883.788 (6)153
Symmetry codes: (i) x+3/2, y1, z+1/2; (ii) x1/2, y+1, z; (iii) x+3/2, y, z1/2.
 

Acknowledgements

RT and HSE are grateful to the Swiss National Science Foundation and the University of Neuchâtel for their support over the years.

References

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