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The absolute configuration of the asymmetric centre (8S) formed during PdII-catalyzed oxy­carbonyl­ation was established by X-ray analysis of the title compound (alternatively 3,6-an­hydro-2-deoxy-D-lyxo-1,5-hexonolactone), C13H14O4.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536801004196/ya6004sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536801004196/ya6004Isup2.hkl
Contains datablock I

CCDC reference: 162830

Key indicators

  • Single-crystal X-ray study
  • T = 293 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.033
  • wR factor = 0.088
  • Data-to-parameter ratio = 10.7

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

General Notes

REFLT_03 From the CIF: _diffrn_reflns_theta_max 80.10 From the CIF: _reflns_number_total 2259 Count of symmetry unique reflns 1466 Completeness (_total/calc) 154.09% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 793 Fraction of Friedel pairs measured 0.541 Are heavy atom types Z>Si present no 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.

Comment top

The title compound (alternative name: 3,6-anhydro-2-deoxy-D-lyxo-1,5-hexonolactone), (I), was prepared by palladium(II)-catalyzed oxycarbonylation (Gracza et al., 1991) of (2R,3S)-3-O-benzylpent-4-ene-1,2,3-triol (Fürfsner et al., 1991; Babjak, 1999). The molecular structure of the title compound with the atom-numbering scheme is shown in Fig. 1, and bond distances and angles are listed in Table 1. The S configuration of the newly formed asymmetric centre at the C8 atom determined by the refinement of Flack parameter [x = -0.03 (19); Flack, 1983] was confirmed by a comparison of the configuration of the chiral centres at the C1 and C5 atoms (1R and 5R) with the known configurations of the corresponding atoms in the starting compounds, commercially available D-mannose, as determined in Fürfsner et al. (1991) and Babjak (1999).

Experimental top

The title compound was prepared from 3-O-benzylated triol by PdII-bicyclization. A 50-ml fask, purged with CO and connected to a balloon with CO, was charged with PdCl2 (18 mg, 0.1 mmol, 0.1 equivalent), CuCl2 (anhydrous, 402 mg, 3 mmol, 3 equivalent), NaOAc (anhydrous, 246 mg, 3 mmol, 3 equivalents), a (2R, 3S)-3-O-benzyl-pent-4-ene-1,2,3-triol (208 mg, 1 mmol), and AcOH (10 ml). The mixture was stirred at room temperature for 16 h. The crude product was purified by column chromatography on silica gel and recrystallized from ethyl acetate/hexane (m.p. 365–366 K, [α]D20 = -49, c = 0.15, CHCl3).

Computing details top

Data collection: P21 Software (Syntex, 1973); cell refinement: P21 Software; data reduction: XP21 (Pavelčík, 1993); program(s) used to solve structure: SHELXS86 (Sheldrick, 1985); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP (Johnson, 1965); software used to prepare material for publication: SHELXL97.

Figures top
[Figure 1] Fig. 1. The molecular structure of (1R,5R,8S)-8-benzyloxy-2,6-dioxabicyclo[3.2.1]octane-3-one with the atom numbering and 30% probability displacement ellipsoids. H atoms are shown as spheres of arbitary radii.
(1R,5R,8S)-8-benzyloxy-2,6-dioxabicyclo[3.2.1]octane-3-one top
Crystal data top
C13H14O4Dx = 1.373 Mg m3
Mr = 234.24Cu Kα radiation, λ = 1.54180 Å
Orthorhombic, P212121Cell parameters from 25 reflections
a = 5.729 (1) Åθ = 5.2–15.2°
b = 10.079 (2) ŵ = 0.85 mm1
c = 19.622 (4) ÅT = 293 K
V = 1133.0 (4) Å3Rectangular plate, colourless
Z = 40.45 × 0.35 × 0.20 mm
F(000) = 496
Data collection top
Syntex P21
diffractometer
1969 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.056
Graphite monochromatorθmax = 80.1°, θmin = 4.5°
θ/2θ scansh = 07
Absorption correction: ψ scan
(North et al., 1968)
k = 012
Tmin = 0.656, Tmax = 0.845l = 2525
2583 measured reflections2 standard reflections every 100 reflections
2259 independent reflections intensity decay: 15%
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullAll H-atom parameters refined
R[F2 > 2σ(F2)] = 0.033 w = 1/[σ2(Fo2) + (0.0559P)2 + 0.055P]
wR(F2) = 0.088(Δ/σ)max < 0.001
S = 1.09Δρmax = 0.19 e Å3
2259 reflectionsΔρmin = 0.26 e Å3
211 parametersExtinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.0083 (9)
Primary atom site location: structure-invariant direct methodsAbsolute structure: (Flack, 1983). No Fridel pairs.
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.03 (19)
Crystal data top
C13H14O4V = 1133.0 (4) Å3
Mr = 234.24Z = 4
Orthorhombic, P212121Cu Kα radiation
a = 5.729 (1) ŵ = 0.85 mm1
b = 10.079 (2) ÅT = 293 K
c = 19.622 (4) Å0.45 × 0.35 × 0.20 mm
Data collection top
Syntex P21
diffractometer
1969 reflections with I > 2σ(I)
Absorption correction: ψ scan
(North et al., 1968)
Rint = 0.056
Tmin = 0.656, Tmax = 0.8452 standard reflections every 100 reflections
2583 measured reflections intensity decay: 15%
2259 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.033All H-atom parameters refined
wR(F2) = 0.088Δρmax = 0.19 e Å3
S = 1.09Δρmin = 0.26 e Å3
2259 reflectionsAbsolute structure: (Flack, 1983). No Fridel pairs.
211 parametersAbsolute structure parameter: 0.03 (19)
0 restraints
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.4214 (2)0.24478 (18)0.29568 (8)0.0445 (4)
O20.4622 (2)0.37260 (14)0.32678 (6)0.0538 (3)
C30.2930 (4)0.46570 (19)0.32421 (9)0.0529 (4)
C40.0674 (3)0.43483 (18)0.28864 (9)0.0473 (4)
C50.0524 (2)0.29627 (16)0.26008 (7)0.0376 (3)
O60.02398 (17)0.20177 (11)0.31404 (5)0.0428 (3)
C70.2526 (3)0.1624 (2)0.33694 (9)0.0475 (4)
C80.2892 (3)0.25985 (17)0.22971 (7)0.0391 (3)
O90.3347 (4)0.57093 (18)0.35005 (9)0.0915 (6)
O100.38899 (18)0.35580 (12)0.18662 (5)0.0432 (3)
C110.2684 (4)0.3619 (3)0.12267 (9)0.0634 (6)
C120.4202 (3)0.42940 (19)0.07084 (7)0.0439 (4)
C130.3498 (3)0.5472 (2)0.04215 (10)0.0553 (4)
C140.4850 (4)0.6068 (3)0.00776 (11)0.0713 (7)
C150.6913 (4)0.5506 (3)0.02770 (9)0.0698 (6)
C160.7632 (3)0.4337 (3)0.00136 (10)0.0634 (6)
C170.6279 (3)0.3725 (2)0.05074 (9)0.0521 (4)
H10.056 (4)0.490 (2)0.2511 (11)0.057*
H20.280 (3)0.175 (2)0.2055 (10)0.045*
H30.263 (3)0.180 (2)0.3841 (11)0.046*
H40.692 (5)0.285 (3)0.0733 (13)0.079*
H50.222 (5)0.268 (3)0.1109 (15)0.087*
H60.793 (6)0.592 (3)0.0682 (17)0.120*
H70.275 (4)0.060 (3)0.3251 (11)0.061*
H80.427 (5)0.686 (3)0.0256 (15)0.088*
H90.080 (4)0.2857 (19)0.2291 (10)0.045*
H100.060 (4)0.451 (2)0.3212 (11)0.058*
H110.200 (5)0.583 (3)0.0566 (14)0.088*
H120.917 (6)0.396 (3)0.0149 (14)0.088*
H130.568 (4)0.210 (2)0.2920 (10)0.044*
H150.102 (8)0.412 (3)0.1285 (19)0.124*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0329 (6)0.0518 (10)0.0488 (8)0.0036 (7)0.0012 (6)0.0074 (7)
O20.0477 (6)0.0656 (8)0.0482 (6)0.0152 (6)0.0113 (5)0.0008 (5)
C30.0699 (10)0.0454 (11)0.0435 (8)0.0187 (9)0.0059 (7)0.0023 (7)
C40.0488 (7)0.0423 (9)0.0508 (8)0.0055 (7)0.0073 (7)0.0074 (7)
C50.0308 (6)0.0416 (9)0.0404 (7)0.0042 (6)0.0012 (5)0.0078 (6)
O60.0374 (5)0.0433 (6)0.0476 (6)0.0040 (4)0.0043 (4)0.0130 (5)
C70.0455 (8)0.0505 (11)0.0464 (8)0.0043 (7)0.0001 (6)0.0138 (7)
C80.0389 (6)0.0403 (9)0.0379 (6)0.0057 (6)0.0043 (6)0.0010 (6)
O90.1342 (16)0.0565 (10)0.0839 (10)0.0363 (11)0.0030 (12)0.0191 (8)
O100.0444 (5)0.0518 (7)0.0333 (5)0.0145 (5)0.0019 (4)0.0032 (5)
C110.0558 (10)0.0961 (17)0.0383 (8)0.0321 (11)0.0035 (7)0.0131 (9)
C120.0442 (7)0.0564 (10)0.0312 (6)0.0128 (7)0.0018 (5)0.0004 (6)
C130.0473 (8)0.0631 (13)0.0557 (9)0.0015 (8)0.0052 (7)0.0044 (8)
C140.0796 (14)0.0718 (16)0.0625 (11)0.0141 (11)0.0197 (11)0.0297 (11)
C150.0736 (12)0.0996 (18)0.0362 (8)0.0353 (13)0.0060 (8)0.0049 (9)
C160.0541 (10)0.0805 (16)0.0555 (10)0.0118 (10)0.0138 (8)0.0236 (10)
C170.0527 (9)0.0479 (11)0.0557 (9)0.0046 (8)0.0042 (7)0.0069 (8)
Geometric parameters (Å, º) top
C1—O21.445 (2)C8—H20.98 (2)
C1—C71.510 (2)O10—C111.4338 (19)
C1—C81.507 (2)C11—C121.501 (2)
C1—H130.91 (2)C11—H51.01 (3)
O2—C31.350 (3)C11—H151.08 (4)
C3—C41.501 (3)C12—C131.375 (3)
C3—O91.200 (2)C12—C171.378 (3)
C4—C51.507 (3)C13—C141.385 (3)
C4—H10.93 (2)C13—H110.98 (3)
C4—H100.99 (2)C14—C151.368 (4)
C5—O61.4334 (17)C14—H80.93 (3)
C5—C81.527 (2)C15—C161.372 (4)
C5—H90.98 (2)C15—H61.07 (4)
O6—C71.4402 (19)C16—C171.386 (3)
C7—H30.94 (2)C16—H121.01 (3)
C7—H71.06 (3)C17—H41.05 (3)
C8—O101.4060 (17)
O2—C1—C7111.55 (14)O10—C8—C5115.50 (13)
O2—C1—C8110.74 (14)C1—C8—C597.79 (11)
C8—C1—C7101.19 (12)O10—C8—H2109.2 (12)
O2—C1—H13103.1 (12)C1—C8—H2110.9 (12)
C8—C1—H13115.6 (12)C5—C8—H2110.6 (12)
C7—C1—H13114.9 (13)C8—O10—C11111.11 (12)
C3—O2—C1119.21 (12)O10—C11—C12109.48 (13)
O9—C3—O2117.1 (2)O10—C11—H5106.7 (17)
O9—C3—C4123.4 (2)C12—C11—H5114.9 (17)
O2—C3—C4119.43 (15)O10—C11—H15111 (2)
C3—C4—C5114.46 (15)C12—C11—H15112 (2)
C3—C4—H1107.7 (14)H5—C11—H15103 (3)
C5—C4—H1104.9 (13)C13—C12—C17119.68 (16)
C3—C4—H10107.7 (12)C13—C12—C11119.94 (18)
C5—C4—H10110.6 (13)C17—C12—C11120.37 (19)
H1—C4—H10111.4 (19)C12—C13—C14120.01 (19)
O6—C5—C4110.34 (12)C12—C13—H11117.5 (17)
O6—C5—C8103.25 (12)C14—C13—H11122.4 (17)
C4—C5—C8108.49 (13)C15—C14—C13120.4 (2)
O6—C5—H9107.4 (12)C15—C14—H8123.6 (18)
C4—C5—H9112.2 (11)C13—C14—H8116.1 (18)
C8—C5—H9114.8 (12)C14—C15—C16119.77 (18)
C5—O6—C7108.07 (11)C14—C15—H6122 (2)
O6—C7—C1105.31 (12)C16—C15—H6118 (2)
O6—C7—H3108.0 (12)C15—C16—C17120.3 (2)
C1—C7—H3112.5 (12)C15—C16—H12117.0 (16)
O6—C7—H7107.9 (13)C17—C16—H12122.7 (16)
C1—C7—H7109.8 (12)C12—C17—C16119.9 (2)
H3—C7—H7113.0 (17)C12—C17—H4121.9 (15)
O10—C8—C1112.43 (13)C16—C17—H4118.1 (15)

Experimental details

Crystal data
Chemical formulaC13H14O4
Mr234.24
Crystal system, space groupOrthorhombic, P212121
Temperature (K)293
a, b, c (Å)5.729 (1), 10.079 (2), 19.622 (4)
V3)1133.0 (4)
Z4
Radiation typeCu Kα
µ (mm1)0.85
Crystal size (mm)0.45 × 0.35 × 0.20
Data collection
DiffractometerSyntex P21
diffractometer
Absorption correctionψ scan
(North et al., 1968)
Tmin, Tmax0.656, 0.845
No. of measured, independent and
observed [I > 2σ(I)] reflections
2583, 2259, 1969
Rint0.056
(sin θ/λ)max1)0.639
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.088, 1.09
No. of reflections2259
No. of parameters211
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.19, 0.26
Absolute structure(Flack, 1983). No Fridel pairs.
Absolute structure parameter0.03 (19)

Computer programs: P21 Software (Syntex, 1973), P21 Software, XP21 (Pavelčík, 1993), SHELXS86 (Sheldrick, 1985), SHELXL97 (Sheldrick, 1997), ORTEP (Johnson, 1965), SHELXL97.

Selected geometric parameters (Å, º) top
C1—O21.445 (2)C8—O101.4060 (17)
C1—C71.510 (2)O10—C111.4338 (19)
C1—C81.507 (2)C11—C121.501 (2)
O2—C31.350 (3)C12—C131.375 (3)
C3—C41.501 (3)C12—C171.378 (3)
C3—O91.200 (2)C13—C141.385 (3)
C4—C51.507 (3)C14—C151.368 (4)
C5—O61.4334 (17)C15—C161.372 (4)
C5—C81.527 (2)C16—C171.386 (3)
O6—C71.4402 (19)
O2—C1—C7111.55 (14)O10—C8—C1112.43 (13)
O2—C1—C8110.74 (14)O10—C8—C5115.50 (13)
C8—C1—C7101.19 (12)C1—C8—C597.79 (11)
C3—O2—C1119.21 (12)C8—O10—C11111.11 (12)
O9—C3—O2117.1 (2)O10—C11—C12109.48 (13)
O9—C3—C4123.4 (2)C13—C12—C17119.68 (16)
O2—C3—C4119.43 (15)C13—C12—C11119.94 (18)
C3—C4—C5114.46 (15)C17—C12—C11120.37 (19)
O6—C5—C4110.34 (12)C12—C13—C14120.01 (19)
O6—C5—C8103.25 (12)C15—C14—C13120.4 (2)
C4—C5—C8108.49 (13)C14—C15—C16119.77 (18)
C5—O6—C7108.07 (11)C15—C16—C17120.3 (2)
O6—C7—C1105.31 (12)C12—C17—C16119.9 (2)
 

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