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The structure of cubebin [systematic name: 3,4-bis­(1,3-benzodioxol-5-ylmeth­yl)tetra­hydro­furan-2-ol], C20H20O6, is stabilized by O—H...O and C—H...O hydrogen bonds.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807013487/bt2304sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807013487/bt2304Isup2.hkl
Contains datablock I

CCDC reference: 646747

Key indicators

  • Single-crystal X-ray study
  • T = 291 K
  • Mean [sigma](C-C) = 0.006 Å
  • R factor = 0.053
  • wR factor = 0.121
  • Data-to-parameter ratio = 9.4

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT026_ALERT_3_C Ratio Observed / Unique Reflections too Low .... 43 Perc. PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 6
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 28.44 From the CIF: _reflns_number_total 2212 Count of symmetry unique reflns 2427 Completeness (_total/calc) 91.14% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 0 Fraction of Friedel pairs measured 0.000 Are heavy atom types Z>Si present no PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1 = . R PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3 = . S
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 2 ALERT level C = Check and explain 4 ALERT level G = General alerts; check 3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SMART; data reduction: SAINT (Bruker, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: DIAMOND (Brandenburg, 2001); software used to prepare material for publication: PLATON (Spek, 2003), enCIFer (Allen et al., 2004) and publCIF (Westrip, 2007).

3,4-bis(1,3-benzodioxol-5-ylmethyl)tetrahydrofuran-2-ol top
Crystal data top
C20H20O6F(000) = 376
Mr = 356.36Dx = 1.358 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 741 reflections
a = 11.631 (2) Åθ = 1.5–28.4°
b = 5.5969 (10) ŵ = 0.10 mm1
c = 13.577 (2) ÅT = 291 K
β = 99.548 (3)°Elongated plate, colourless
V = 871.6 (3) Å30.3 × 0.2 × 0.1 mm
Z = 2
Data collection top
Bruker SMART CCD area-detector
diffractometer
2212 independent reflections
Radiation source: fine-focus sealed tube962 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.070
Detector resolution: 0.70 pixels mm-1θmax = 28.4°, θmin = 1.5°
φ and ω scansh = 1513
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
k = 77
Tmin = 0.944, Tmax = 0.989l = 1716
5459 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: full with fixed elements per cycleSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.053Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.121H-atom parameters constrained
S = 0.99 w = 1/[σ2(Fo2) + (0.0445P)2]
where P = (Fo2 + 2Fc2)/3
2212 reflections(Δ/σ)max = 0.002
235 parametersΔρmax = 0.15 e Å3
1 restraintΔρmin = 0.16 e Å3
Special details top

Experimental. Siemens SMART CCD diffractometer equipped with a normal focus, 2.4 kW sealed tube X-ray source (Mo Kα radiation, λ = 0.71073 Å) operating at 40 kV and 35 mA. The data collection covered about 1.3 hemisphere of reciprocal space by a combination of three sets of exposures; each set had a different φ angle (0, 90, 180 °) for the crystal and each exposure of 30 s covered 0.3° in ω to give a total of 1315 frames. The crystal-to-detector distance was 5.029 cm and the detector swing angle was -30°. Coverage of the unique set was over 99% complete. Crystal decay was monitored by repeating fifty frames from the initial set at the end of the data collection. The analysis of the duplicate reflections indicated that crystal decay was negligible. Unit-cell parameters were determined by a least-squares fit of 721 reflections in the range 1.52–28.44. Absorption and other corrections were made using a multi-scan technique (SADABS; Sheldrick, 1996)

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.5123 (2)0.6948 (6)0.92797 (19)0.0669 (13)
O20.4101 (3)1.0461 (6)0.8799 (2)0.0670 (14)
O30.7643 (2)0.6936 (6)0.47714 (19)0.0684 (14)
O40.8821 (2)0.3713 (7)0.5262 (2)0.0748 (14)
O50.0201 (3)1.1777 (7)0.9281 (2)0.0863 (16)
O60.1625 (2)0.8933 (8)0.8829 (2)0.0886 (18)
C10.4003 (3)0.7965 (8)0.8966 (3)0.0525 (19)
C20.3541 (3)0.6753 (9)0.7977 (2)0.0457 (14)
C30.4657 (3)0.6445 (8)0.7521 (3)0.0446 (14)
C40.5586 (3)0.6050 (9)0.8449 (3)0.0624 (19)
C50.4613 (3)0.4444 (9)0.6750 (3)0.0591 (19)
C60.5749 (3)0.4140 (8)0.6361 (3)0.0469 (17)
C70.6097 (3)0.5858 (8)0.5727 (3)0.0503 (17)
C80.7130 (3)0.5523 (8)0.5405 (3)0.0450 (17)
C90.8791 (4)0.6053 (10)0.4868 (3)0.072 (2)
C100.7832 (3)0.3608 (9)0.5701 (3)0.0526 (19)
C110.7536 (3)0.1887 (9)0.6323 (3)0.0650 (19)
C120.6474 (4)0.2211 (9)0.6660 (3)0.0618 (19)
C130.2558 (3)0.8025 (9)0.7291 (3)0.0562 (18)
C140.1426 (3)0.8190 (8)0.7698 (3)0.0488 (17)
C150.1216 (3)1.0075 (8)0.8323 (3)0.0568 (17)
C160.0171 (4)1.0093 (9)0.8653 (3)0.0588 (19)
C170.1322 (4)1.1016 (11)0.9413 (4)0.094 (3)
C180.0655 (3)0.8429 (10)0.8399 (3)0.0586 (19)
C190.0499 (3)0.6557 (10)0.7793 (3)0.0687 (19)
C200.0569 (3)0.6473 (9)0.7447 (3)0.0593 (19)
H10.349000.765500.945600.0630*
H20.326300.515900.812200.0550*
H2A0.427201.115900.933400.0810*
H30.482300.795400.720700.0540*
H4A0.576200.436100.853700.0750*
H4B0.629800.689000.838000.0750*
H5A0.442100.295500.705000.0710*
H5B0.399700.478700.619400.0710*
H70.563700.718900.553000.0600*
H9A0.931700.707700.531000.0870*
H9B0.904000.603300.422100.0870*
H110.801200.057400.651200.0780*
H120.624600.109900.709800.0740*
H13A0.281400.962900.716300.0680*
H13B0.241200.718900.665600.0680*
H150.176701.126700.850500.0680*
H17A0.188601.227100.920700.1130*
H17B0.132601.066701.011200.1130*
H190.107000.540100.761800.0820*
H200.070900.521800.703400.0710*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0573 (19)0.097 (3)0.0429 (16)0.018 (2)0.0023 (15)0.006 (2)
O20.084 (2)0.060 (3)0.054 (2)0.005 (2)0.0029 (17)0.0026 (18)
O30.060 (2)0.087 (3)0.0634 (19)0.004 (2)0.0254 (17)0.014 (2)
O40.055 (2)0.100 (3)0.072 (2)0.013 (2)0.0181 (18)0.007 (2)
O50.075 (2)0.081 (3)0.111 (3)0.005 (2)0.039 (2)0.029 (3)
O60.052 (2)0.123 (4)0.093 (3)0.008 (2)0.0186 (19)0.011 (3)
C10.047 (3)0.071 (4)0.039 (3)0.006 (3)0.006 (2)0.003 (3)
C20.040 (2)0.054 (3)0.043 (2)0.006 (2)0.0066 (19)0.010 (3)
C30.033 (2)0.057 (3)0.045 (2)0.007 (2)0.0096 (19)0.002 (3)
C40.048 (3)0.086 (4)0.054 (3)0.002 (3)0.011 (2)0.010 (3)
C50.056 (3)0.054 (4)0.069 (3)0.012 (3)0.015 (2)0.010 (3)
C60.041 (3)0.051 (3)0.049 (3)0.013 (3)0.008 (2)0.013 (3)
C70.051 (3)0.049 (3)0.051 (3)0.000 (2)0.009 (2)0.004 (3)
C80.047 (3)0.051 (3)0.039 (3)0.000 (3)0.013 (2)0.001 (2)
C90.055 (3)0.101 (5)0.064 (3)0.005 (3)0.021 (2)0.005 (4)
C100.044 (3)0.057 (4)0.056 (3)0.002 (3)0.006 (2)0.009 (3)
C110.063 (3)0.051 (4)0.078 (3)0.005 (3)0.003 (3)0.009 (3)
C120.073 (3)0.043 (4)0.070 (3)0.004 (3)0.014 (3)0.001 (3)
C130.048 (3)0.078 (4)0.041 (2)0.003 (3)0.003 (2)0.003 (3)
C140.046 (3)0.053 (3)0.046 (3)0.002 (3)0.004 (2)0.003 (3)
C150.053 (3)0.048 (3)0.070 (3)0.005 (3)0.012 (3)0.001 (3)
C160.057 (3)0.057 (4)0.063 (3)0.001 (3)0.012 (3)0.005 (3)
C170.072 (4)0.109 (6)0.107 (5)0.010 (4)0.029 (3)0.005 (5)
C180.037 (3)0.082 (4)0.055 (3)0.002 (3)0.002 (2)0.002 (3)
C190.052 (3)0.082 (4)0.068 (3)0.023 (3)0.002 (3)0.010 (4)
C200.058 (3)0.069 (4)0.048 (3)0.012 (3)0.000 (2)0.008 (3)
Geometric parameters (Å, º) top
O1—C11.421 (5)C14—C201.386 (6)
O1—C41.420 (5)C14—C151.401 (6)
O2—C11.423 (6)C15—C161.363 (6)
O3—C81.375 (5)C16—C181.341 (7)
O3—C91.409 (5)C18—C191.363 (7)
O4—C91.413 (7)C19—C201.400 (5)
O4—C101.382 (4)C1—H10.9800
O5—C161.387 (6)C2—H20.9800
O5—C171.411 (6)C3—H30.9800
O6—C171.421 (7)C4—H4A0.9700
O6—C181.383 (5)C4—H4B0.9700
O2—H2A0.8200C5—H5A0.9700
C1—C21.521 (5)C5—H5B0.9700
C2—C131.526 (5)C7—H70.9300
C2—C31.538 (5)C9—H9A0.9700
C3—C41.534 (6)C9—H9B0.9700
C3—C51.528 (6)C11—H110.9300
C5—C61.512 (5)C12—H120.9300
C6—C121.389 (6)C13—H13A0.9700
C6—C71.395 (6)C13—H13B0.9700
C7—C81.358 (5)C15—H150.9300
C8—C101.367 (6)C17—H17A0.9700
C10—C111.362 (6)C17—H17B0.9700
C11—C121.398 (6)C19—H190.9300
C13—C141.513 (5)C20—H200.9300
O1···O2i2.744 (4)C11···H19x2.9400
O1···C1i3.297 (5)C12···H4A3.0500
O2···O1ii2.744 (4)C13···H9Biii3.0400
O2···C153.317 (5)C13···H5B3.0200
O3···C5iii3.365 (5)C14···H9Biii3.0200
O3···O42.296 (5)C18···H11xiii3.0200
O4···C9iv3.182 (6)C20···H9Aviii3.0400
O5···C16v3.359 (5)H2···O2xii2.9000
O5···C17v3.297 (7)H2···H5A2.4700
O5···C19vi3.336 (6)H2A···O1ii1.9500
O5···O62.306 (5)H2A···C1ii2.9700
O5···C18v3.275 (5)H2A···C4ii2.9900
O1···H2Ai1.9500H3···O22.8200
O2···H32.8200H3···C72.9300
O2···H152.7200H3···H12vi2.4400
O2···H2vi2.9000H3···H13A2.5100
O2···H13A2.5100H4A···C62.9500
O2···H5Avi2.8300H4A···C123.0500
O3···H5Biii2.6600H4A···H5A2.4700
O3···H13Avii2.9000H4B···O6x2.6500
O4···H9Biv2.8900H5A···O2xii2.8300
O4···H13Bvii2.8900H5A···H22.4700
O4···H9Aiv2.5900H5A···H4A2.4700
O5···H17Bv2.8400H5A···H122.3500
O6···H4Bviii2.6500H5B···C133.0200
C1···C153.424 (5)H5B···H13B2.4500
C1···O1ii3.297 (5)H5B···O3vii2.6600
C4···C123.524 (6)H7···C6iii3.0000
C5···O3vii3.365 (5)H9A···C20x3.0400
C9···C13vii3.521 (6)H9A···O4ix2.5900
C9···O4ix3.182 (6)H9B···O4ix2.8900
C10···C19x3.568 (6)H9B···C13vii3.0400
C12···C43.524 (6)H9B···C14vii3.0200
C13···C9iii3.521 (6)H11···C18xiv3.0200
C15···C13.424 (5)H12···H3xii2.4400
C15···O23.317 (5)H12···H5A2.3500
C16···O5xi3.359 (5)H13A···O22.5100
C16···C17xi3.568 (7)H13A···H32.5100
C17···C16v3.568 (7)H13A···H152.5300
C17···O5xi3.297 (7)H13A···O3iii2.9000
C18···O5xi3.275 (5)H13B···C52.9700
C19···C10viii3.568 (6)H13B···H5B2.4500
C19···O5xii3.336 (6)H13B···H202.4000
C1···H2Ai2.9700H13B···O4iii2.8900
C4···H2Ai2.9900H15···O22.7200
C5···H13B2.9700H15···H13A2.5300
C6···H7vii3.0000H17B···O5xi2.8400
C6···H4A2.9500H19···C10viii2.8800
C7···H32.9300H19···C11viii2.9400
C10···H19x2.8800H20···H13B2.4000
C1—O1—C4110.7 (3)O2—C1—H1111.00
C8—O3—C9104.1 (3)C2—C1—H1111.00
C9—O4—C10103.5 (3)C1—C2—H2108.00
C16—O5—C17105.2 (4)C3—C2—H2108.00
C17—O6—C18105.0 (3)C13—C2—H2108.00
C1—O2—H2A110.00C2—C3—H3109.00
O1—C1—C2105.0 (3)C4—C3—H3109.00
O2—C1—C2108.9 (3)C5—C3—H3109.00
O1—C1—O2110.3 (3)O1—C4—H4A110.00
C1—C2—C3102.0 (3)O1—C4—H4B110.00
C3—C2—C13113.8 (3)C3—C4—H4A110.00
C1—C2—C13116.8 (4)C3—C4—H4B110.00
C2—C3—C4102.3 (3)H4A—C4—H4B109.00
C4—C3—C5113.3 (4)C3—C5—H5A109.00
C2—C3—C5115.1 (3)C3—C5—H5B109.00
O1—C4—C3107.1 (3)C6—C5—H5A109.00
C3—C5—C6113.0 (3)C6—C5—H5B109.00
C5—C6—C7119.9 (4)H5A—C5—H5B108.00
C5—C6—C12120.6 (4)C6—C7—H7121.00
C7—C6—C12119.5 (4)C8—C7—H7121.00
C6—C7—C8117.8 (4)O3—C9—H9A110.00
O3—C8—C7128.4 (4)O3—C9—H9B110.00
C7—C8—C10122.1 (4)O4—C9—H9A110.00
O3—C8—C10109.6 (3)O4—C9—H9B110.00
O3—C9—O4108.9 (4)H9A—C9—H9B108.00
O4—C10—C8109.8 (4)C10—C11—H11122.00
C8—C10—C11122.5 (4)C12—C11—H11122.00
O4—C10—C11127.7 (4)C6—C12—H12119.00
C10—C11—C12116.0 (4)C11—C12—H12119.00
C6—C12—C11122.1 (4)C2—C13—H13A109.00
C2—C13—C14114.5 (3)C2—C13—H13B109.00
C13—C14—C20120.1 (4)C14—C13—H13A109.00
C15—C14—C20118.7 (3)C14—C13—H13B109.00
C13—C14—C15121.1 (4)H13A—C13—H13B107.00
C14—C15—C16117.3 (4)C14—C15—H15121.00
O5—C16—C15126.4 (4)C16—C15—H15121.00
O5—C16—C18110.3 (4)O5—C17—H17A110.00
C15—C16—C18123.4 (4)O5—C17—H17B110.00
O5—C17—O6109.0 (4)O6—C17—H17A110.00
O6—C18—C16110.5 (4)O6—C17—H17B110.00
O6—C18—C19127.7 (4)H17A—C17—H17B108.00
C16—C18—C19121.8 (4)C18—C19—H19122.00
C18—C19—C20116.3 (4)C20—C19—H19122.00
C14—C20—C19122.4 (4)C14—C20—H20119.00
O1—C1—H1111.00C19—C20—H20119.00
C4—O1—C1—O293.1 (4)C3—C5—C6—C12106.2 (5)
C4—O1—C1—C224.0 (4)C5—C6—C7—C8179.3 (4)
C1—O1—C4—C32.3 (5)C12—C6—C7—C81.8 (6)
C9—O3—C8—C7167.6 (4)C5—C6—C12—C11179.4 (4)
C9—O3—C8—C1012.0 (4)C7—C6—C12—C111.9 (6)
C8—O3—C9—O420.0 (4)C6—C7—C8—O3178.9 (4)
C10—O4—C9—O320.1 (4)C6—C7—C8—C101.5 (6)
C9—O4—C10—C812.5 (4)O3—C8—C10—O40.4 (5)
C9—O4—C10—C11168.8 (4)O3—C8—C10—C11179.2 (4)
C17—O5—C16—C15179.4 (5)C7—C8—C10—O4180.0 (4)
C17—O5—C16—C180.8 (5)C7—C8—C10—C111.2 (7)
C16—O5—C17—O62.3 (5)O4—C10—C11—C12179.7 (4)
C18—O6—C17—O52.8 (5)C8—C10—C11—C121.1 (6)
C17—O6—C18—C162.3 (5)C10—C11—C12—C61.5 (6)
C17—O6—C18—C19178.0 (5)C2—C13—C14—C1586.7 (5)
O1—C1—C2—C335.3 (4)C2—C13—C14—C2093.9 (5)
O1—C1—C2—C13160.0 (3)C13—C14—C15—C16179.7 (4)
O2—C1—C2—C382.8 (4)C20—C14—C15—C160.4 (6)
O2—C1—C2—C1341.9 (4)C13—C14—C20—C19179.2 (4)
C1—C2—C3—C432.9 (4)C15—C14—C20—C190.2 (6)
C1—C2—C3—C5156.2 (4)C14—C15—C16—O5179.4 (4)
C13—C2—C3—C4159.5 (4)C14—C15—C16—C180.9 (7)
C13—C2—C3—C577.2 (5)O5—C16—C18—O61.0 (5)
C1—C2—C13—C1465.7 (5)O5—C16—C18—C19179.4 (4)
C3—C2—C13—C14175.9 (4)C15—C16—C18—O6178.9 (4)
C2—C3—C4—O119.9 (5)C15—C16—C18—C190.8 (7)
C5—C3—C4—O1144.4 (3)O6—C18—C19—C20179.4 (4)
C2—C3—C5—C6177.3 (3)C16—C18—C19—C200.3 (7)
C4—C3—C5—C660.1 (5)C18—C19—C20—C140.2 (7)
C3—C5—C6—C771.2 (5)
Symmetry codes: (i) x+1, y1/2, z+2; (ii) x+1, y+1/2, z+2; (iii) x+1, y+1/2, z+1; (iv) x+2, y1/2, z+1; (v) x, y+1/2, z+2; (vi) x, y+1, z; (vii) x+1, y1/2, z+1; (viii) x1, y, z; (ix) x+2, y+1/2, z+1; (x) x+1, y, z; (xi) x, y1/2, z+2; (xii) x, y1, z; (xiii) x1, y+1, z; (xiv) x+1, y1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2A···O1ii0.821.952.744 (4)164
C9—H9A···O4ix0.972.593.182 (6)120
C13—H13A···O20.972.512.838 (5)100
Symmetry codes: (ii) x+1, y+1/2, z+2; (ix) x+2, y+1/2, z+1.
 

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