organic compounds
(8-Hydroxy-6-methoxy-1-oxo-1H-isochromen-3-yl)methyl formate: a supramolecular framework
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
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.
Keywords: crystal structure; isocoumarin; cytogenin; hydrogen bonding; C—H⋯π interaction; supramolecular framework.
CCDC reference: 2039333
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, 1995). 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). More recently, a new synthetic route to cytogenin and similar has been reported (Gadakh & Sudalai, 2014).
As shown in Fig. 1, 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).
The molecule of I (Fig. 2), 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 and Table 1).
In the crystal, molecules are linked by a series of C—H⋯O hydrogen bonds (Table 1), forming interconnected ribbons running normal to each other in planes (012) and (01): see Fig. 3. These interactions lead to the formation of a supramolecular framework, which is reinforced by a C—H⋯π interaction (Fig. 4 and Table 1).
Synthesis and crystallization
The syntheses of the title compound, I, and cytogenin, are illustrated in Fig. 1. 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), 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 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 using dimethylchloride as On completion of the reaction, the mixture was diluted with ethyl acetate and then washed with an aqueous 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 using dimethylchloride as On completion of the reaction, the mixture was diluted with ethyl acetate and then washed with an aqueous of NaCl. The organic phase was dried using anhydrous Na2SO4, then purified by (silica, 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 . 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%.
details are summarized in Table 2
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Structural data
CCDC reference: 2039333
https://doi.org/10.1107/S2414314620013917/bh4057sup1.cif
contains datablocks I, Global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314620013917/bh4057Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314620013917/bh4057Isup3.cml
Data collection: EXPOSE in IPDS-I (Stoe & Cie, 2004); cell
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).C12H10O6 | Dx = 1.542 Mg m−3 |
Mr = 250.20 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, Pca21 | Cell parameters from 3909 reflections |
a = 25.006 (2) Å | θ = 2.2–25.8° |
b = 5.0337 (6) Å | µ = 0.13 mm−1 |
c = 8.5646 (6) Å | T = 173 K |
V = 1078.05 (17) Å3 | Block, colorless |
Z = 4 | 0.50 × 0.50 × 0.50 mm |
F(000) = 520 |
STOE IPDS 1 diffractometer | 2012 independent reflections |
Radiation source: fine-focus sealed tube | 1249 reflections with I > 2σ(I) |
Plane graphite monochromator | Rint = 0.070 |
φ rotation scans | θmax = 26.1°, θmin = 2.9° |
Absorption correction: multi-scan (MULABS; Spek, 2020) | h = −30→30 |
Tmin = 0.763, Tmax = 1.000 | k = −6→6 |
7630 measured reflections | l = −9→9 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.050 | H-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 reflections | Δρmax = 0.32 e Å−3 |
166 parameters | Δρmin = −0.27 e Å−3 |
1 restraint | Extinction correction: (SHELXL-2018/3; Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.061 (11) |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.68528 (13) | 0.9547 (7) | −0.0918 (5) | 0.0500 (9) | |
O2 | 0.75876 (11) | 0.7819 (6) | 0.0089 (4) | 0.0461 (9) | |
O3 | 0.58898 (11) | 0.0468 (7) | 0.3437 (5) | 0.0511 (10) | |
O4 | 0.59095 (13) | 0.7730 (7) | −0.0142 (5) | 0.0531 (10) | |
H40 | 0.613134 | 0.862673 | −0.065697 | 0.080* | |
O5 | 0.86682 (12) | 0.4224 (8) | 0.1774 (5) | 0.0657 (12) | |
O6 | 0.94909 (14) | 0.5664 (9) | 0.1136 (6) | 0.0732 (13) | |
C1 | 0.70366 (17) | 0.7848 (9) | −0.0037 (6) | 0.0433 (11) | |
C3 | 0.78373 (18) | 0.5948 (9) | 0.1006 (7) | 0.0428 (12) | |
C4 | 0.75774 (17) | 0.4136 (9) | 0.1838 (6) | 0.0443 (12) | |
H4 | 0.776871 | 0.288244 | 0.245052 | 0.053* | |
C5 | 0.67032 (17) | 0.2286 (9) | 0.2657 (6) | 0.0438 (11) | |
H5 | 0.687823 | 0.104223 | 0.331620 | 0.053* | |
C6 | 0.61467 (17) | 0.2302 (9) | 0.2549 (7) | 0.0434 (12) | |
C7 | 0.58804 (17) | 0.4147 (10) | 0.1602 (7) | 0.0455 (12) | |
H7 | 0.550100 | 0.414965 | 0.154550 | 0.055* | |
C8 | 0.61731 (18) | 0.5950 (9) | 0.0759 (6) | 0.0437 (13) | |
C9 | 0.67425 (17) | 0.5970 (9) | 0.0848 (7) | 0.0399 (11) | |
C10 | 0.69987 (16) | 0.4093 (9) | 0.1799 (7) | 0.0411 (11) | |
C11 | 0.53177 (17) | 0.0277 (11) | 0.3310 (8) | 0.0614 (15) | |
H11C | 0.518847 | −0.116607 | 0.397911 | 0.092* | |
H11B | 0.521957 | −0.008880 | 0.222346 | 0.092* | |
H11A | 0.515514 | 0.195648 | 0.364158 | 0.092* | |
C12 | 0.84306 (18) | 0.6344 (10) | 0.0911 (7) | 0.0493 (13) | |
H12B | 0.855082 | 0.629778 | −0.019002 | 0.059* | |
H12A | 0.853189 | 0.807981 | 0.136752 | 0.059* | |
C13 | 0.92037 (19) | 0.4136 (14) | 0.1770 (10) | 0.0726 (19) | |
H13 | 0.936777 | 0.272176 | 0.232693 | 0.087* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0486 (18) | 0.0487 (18) | 0.053 (2) | 0.0019 (15) | −0.0012 (16) | 0.0089 (19) |
O2 | 0.0381 (16) | 0.0448 (17) | 0.055 (2) | −0.0039 (13) | −0.0010 (15) | 0.0043 (17) |
O3 | 0.0330 (15) | 0.0564 (19) | 0.064 (3) | −0.0051 (14) | 0.0021 (16) | 0.0138 (19) |
O4 | 0.0425 (17) | 0.055 (2) | 0.062 (3) | 0.0046 (16) | −0.0054 (17) | 0.0109 (19) |
O5 | 0.0318 (16) | 0.076 (2) | 0.089 (3) | −0.0021 (17) | −0.002 (2) | 0.026 (2) |
O6 | 0.040 (2) | 0.099 (3) | 0.080 (3) | −0.012 (2) | 0.0013 (19) | 0.016 (3) |
C1 | 0.036 (2) | 0.046 (3) | 0.048 (3) | 0.0014 (19) | 0.001 (2) | −0.001 (2) |
C3 | 0.035 (2) | 0.045 (2) | 0.048 (3) | 0.003 (2) | −0.002 (2) | −0.002 (2) |
C4 | 0.038 (2) | 0.044 (2) | 0.051 (3) | 0.0004 (19) | −0.004 (2) | −0.002 (2) |
C5 | 0.034 (2) | 0.044 (2) | 0.053 (3) | −0.001 (2) | −0.004 (2) | 0.002 (2) |
C6 | 0.038 (2) | 0.039 (2) | 0.053 (3) | −0.0005 (19) | 0.002 (2) | 0.001 (2) |
C7 | 0.035 (2) | 0.048 (2) | 0.053 (4) | −0.003 (2) | −0.003 (2) | −0.002 (2) |
C8 | 0.036 (2) | 0.044 (3) | 0.052 (4) | 0.003 (2) | −0.002 (2) | 0.001 (2) |
C9 | 0.033 (2) | 0.038 (2) | 0.049 (3) | 0.0002 (19) | −0.001 (2) | 0.001 (2) |
C10 | 0.035 (2) | 0.041 (2) | 0.048 (3) | 0.0008 (18) | 0.000 (2) | −0.001 (2) |
C11 | 0.031 (2) | 0.073 (3) | 0.080 (4) | −0.011 (2) | −0.001 (3) | 0.013 (3) |
C12 | 0.036 (2) | 0.055 (3) | 0.057 (4) | 0.000 (2) | −0.002 (2) | 0.005 (3) |
C13 | 0.031 (3) | 0.088 (4) | 0.098 (6) | 0.000 (3) | −0.003 (3) | 0.021 (4) |
O1—C1 | 1.230 (6) | C5—C10 | 1.383 (7) |
O2—C3 | 1.376 (6) | C5—C6 | 1.395 (6) |
O2—C1 | 1.382 (5) | C5—H5 | 0.9500 |
O3—C6 | 1.358 (6) | C6—C7 | 1.401 (7) |
O3—C11 | 1.438 (5) | C7—C8 | 1.371 (7) |
O4—C8 | 1.354 (6) | C7—H7 | 0.9500 |
O4—H40 | 0.8400 | C8—C9 | 1.426 (6) |
O5—C13 | 1.340 (6) | C9—C10 | 1.402 (7) |
O5—C12 | 1.428 (6) | C11—H11C | 0.9800 |
O6—C13 | 1.184 (7) | C11—H11B | 0.9800 |
C1—C9 | 1.417 (7) | C11—H11A | 0.9800 |
C3—C4 | 1.327 (7) | C12—H12B | 0.9900 |
C3—C12 | 1.499 (6) | C12—H12A | 0.9900 |
C4—C10 | 1.447 (6) | C13—H13 | 0.9500 |
C4—H4 | 0.9500 | ||
C3—O2—C1 | 120.3 (4) | O4—C8—C9 | 120.8 (4) |
C6—O3—C11 | 118.3 (4) | C7—C8—C9 | 120.6 (4) |
C8—O4—H40 | 109.5 | C10—C9—C1 | 121.5 (4) |
C13—O5—C12 | 116.1 (4) | C10—C9—C8 | 118.8 (4) |
O1—C1—O2 | 115.3 (4) | C1—C9—C8 | 119.6 (4) |
O1—C1—C9 | 126.7 (4) | C5—C10—C9 | 120.5 (4) |
O2—C1—C9 | 117.9 (4) | C5—C10—C4 | 122.1 (4) |
C4—C3—O2 | 123.7 (4) | C9—C10—C4 | 117.4 (4) |
C4—C3—C12 | 127.2 (5) | O3—C11—H11C | 109.5 |
O2—C3—C12 | 109.1 (4) | O3—C11—H11B | 109.5 |
C3—C4—C10 | 119.2 (5) | H11C—C11—H11B | 109.5 |
C3—C4—H4 | 120.4 | O3—C11—H11A | 109.5 |
C10—C4—H4 | 120.4 | H11C—C11—H11A | 109.5 |
C10—C5—C6 | 119.6 (5) | H11B—C11—H11A | 109.5 |
C10—C5—H5 | 120.2 | O5—C12—C3 | 106.5 (4) |
C6—C5—H5 | 120.2 | O5—C12—H12B | 110.4 |
O3—C6—C5 | 115.5 (4) | C3—C12—H12B | 110.4 |
O3—C6—C7 | 123.4 (4) | O5—C12—H12A | 110.4 |
C5—C6—C7 | 121.1 (4) | C3—C12—H12A | 110.4 |
C8—C7—C6 | 119.3 (4) | H12B—C12—H12A | 108.6 |
C8—C7—H7 | 120.3 | O6—C13—O5 | 125.8 (6) |
C6—C7—H7 | 120.3 | O6—C13—H13 | 117.1 |
O4—C8—C7 | 118.6 (4) | O5—C13—H13 | 117.1 |
C3—O2—C1—O1 | −178.0 (4) | O2—C1—C9—C8 | 179.5 (4) |
C3—O2—C1—C9 | 2.3 (6) | O4—C8—C9—C10 | 179.9 (5) |
C1—O2—C3—C4 | −1.6 (7) | C7—C8—C9—C10 | 0.8 (8) |
C1—O2—C3—C12 | 179.1 (4) | O4—C8—C9—C1 | −1.0 (8) |
O2—C3—C4—C10 | −0.2 (8) | C7—C8—C9—C1 | 179.9 (5) |
C12—C3—C4—C10 | 179.0 (5) | C6—C5—C10—C9 | 1.3 (8) |
C11—O3—C6—C5 | −176.5 (5) | C6—C5—C10—C4 | −178.7 (5) |
C11—O3—C6—C7 | 4.8 (8) | C1—C9—C10—C5 | 179.7 (5) |
C10—C5—C6—O3 | −179.7 (5) | C8—C9—C10—C5 | −1.2 (8) |
C10—C5—C6—C7 | −1.0 (8) | C1—C9—C10—C4 | −0.3 (8) |
O3—C6—C7—C8 | 179.2 (5) | C8—C9—C10—C4 | 178.8 (5) |
C5—C6—C7—C8 | 0.6 (8) | C3—C4—C10—C5 | −178.9 (5) |
C6—C7—C8—O4 | −179.6 (5) | C3—C4—C10—C9 | 1.1 (8) |
C6—C7—C8—C9 | −0.5 (8) | C13—O5—C12—C3 | 176.8 (5) |
O1—C1—C9—C10 | 179.0 (5) | C4—C3—C12—O5 | 5.5 (8) |
O2—C1—C9—C10 | −1.4 (7) | O2—C3—C12—O5 | −175.2 (4) |
O1—C1—C9—C8 | −0.1 (8) | C12—O5—C13—O6 | 0.9 (12) |
Cg is the centroid of the C5–C10 ring. |
D—H···A | D—H | H···A | D···A | 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—H12B···Cgiii | 0.99 | 2.88 | 3.788 (6) | 153 |
Symmetry codes: (i) −x+3/2, y−1, z+1/2; (ii) x−1/2, −y+1, z; (iii) −x+3/2, y, z−1/2. |
Acknowledgements
RT and HSE are grateful to the Swiss National Science Foundation and the University of Neuchâtel for their support over the years.
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