Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536801004196/ya6004sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536801004196/ya6004Isup2.hkl |
CCDC reference: 162830
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (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.
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).
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.
C13H14O4 | Dx = 1.373 Mg m−3 |
Mr = 234.24 | Cu Kα radiation, λ = 1.54180 Å |
Orthorhombic, P212121 | Cell parameters from 25 reflections |
a = 5.729 (1) Å | θ = 5.2–15.2° |
b = 10.079 (2) Å | µ = 0.85 mm−1 |
c = 19.622 (4) Å | T = 293 K |
V = 1133.0 (4) Å3 | Rectangular plate, colourless |
Z = 4 | 0.45 × 0.35 × 0.20 mm |
F(000) = 496 |
Syntex P21 diffractometer | 1969 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.056 |
Graphite monochromator | θmax = 80.1°, θmin = 4.5° |
θ/2θ scans | h = 0→7 |
Absorption correction: ψ scan (North et al., 1968) | k = 0→12 |
Tmin = 0.656, Tmax = 0.845 | l = −25→25 |
2583 measured reflections | 2 standard reflections every 100 reflections |
2259 independent reflections | intensity decay: 15% |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | All 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 = 1.09 | Δρmax = 0.19 e Å−3 |
2259 reflections | Δρmin = −0.26 e Å−3 |
211 parameters | Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
0 restraints | Extinction coefficient: 0.0083 (9) |
Primary atom site location: structure-invariant direct methods | Absolute structure: (Flack, 1983). No Fridel pairs. |
Secondary atom site location: difference Fourier map | Absolute structure parameter: −0.03 (19) |
C13H14O4 | V = 1133.0 (4) Å3 |
Mr = 234.24 | Z = 4 |
Orthorhombic, P212121 | Cu Kα radiation |
a = 5.729 (1) Å | µ = 0.85 mm−1 |
b = 10.079 (2) Å | T = 293 K |
c = 19.622 (4) Å | 0.45 × 0.35 × 0.20 mm |
Syntex P21 diffractometer | 1969 reflections with I > 2σ(I) |
Absorption correction: ψ scan (North et al., 1968) | Rint = 0.056 |
Tmin = 0.656, Tmax = 0.845 | 2 standard reflections every 100 reflections |
2583 measured reflections | intensity decay: 15% |
2259 independent reflections |
R[F2 > 2σ(F2)] = 0.033 | All H-atom parameters refined |
wR(F2) = 0.088 | Δρmax = 0.19 e Å−3 |
S = 1.09 | Δρmin = −0.26 e Å−3 |
2259 reflections | Absolute structure: (Flack, 1983). No Fridel pairs. |
211 parameters | Absolute structure parameter: −0.03 (19) |
0 restraints |
x | y | z | Uiso*/Ueq | ||
C1 | −0.4214 (2) | 0.24478 (18) | 0.29568 (8) | 0.0445 (4) | |
O2 | −0.4622 (2) | 0.37260 (14) | 0.32678 (6) | 0.0538 (3) | |
C3 | −0.2930 (4) | 0.46570 (19) | 0.32421 (9) | 0.0529 (4) | |
C4 | −0.0674 (3) | 0.43483 (18) | 0.28864 (9) | 0.0473 (4) | |
C5 | −0.0524 (2) | 0.29627 (16) | 0.26008 (7) | 0.0376 (3) | |
O6 | −0.02398 (17) | 0.20177 (11) | 0.31404 (5) | 0.0428 (3) | |
C7 | −0.2526 (3) | 0.1624 (2) | 0.33694 (9) | 0.0475 (4) | |
C8 | −0.2892 (3) | 0.25985 (17) | 0.22971 (7) | 0.0391 (3) | |
O9 | −0.3347 (4) | 0.57093 (18) | 0.35005 (9) | 0.0915 (6) | |
O10 | −0.38899 (18) | 0.35580 (12) | 0.18662 (5) | 0.0432 (3) | |
C11 | −0.2684 (4) | 0.3619 (3) | 0.12267 (9) | 0.0634 (6) | |
C12 | −0.4202 (3) | 0.42940 (19) | 0.07084 (7) | 0.0439 (4) | |
C13 | −0.3498 (3) | 0.5472 (2) | 0.04215 (10) | 0.0553 (4) | |
C14 | −0.4850 (4) | 0.6068 (3) | −0.00776 (11) | 0.0713 (7) | |
C15 | −0.6913 (4) | 0.5506 (3) | −0.02770 (9) | 0.0698 (6) | |
C16 | −0.7632 (3) | 0.4337 (3) | 0.00136 (10) | 0.0634 (6) | |
C17 | −0.6279 (3) | 0.3725 (2) | 0.05074 (9) | 0.0521 (4) | |
H1 | −0.056 (4) | 0.490 (2) | 0.2511 (11) | 0.057* | |
H2 | −0.280 (3) | 0.175 (2) | 0.2055 (10) | 0.045* | |
H3 | −0.263 (3) | 0.180 (2) | 0.3841 (11) | 0.046* | |
H4 | −0.692 (5) | 0.285 (3) | 0.0733 (13) | 0.079* | |
H5 | −0.222 (5) | 0.268 (3) | 0.1109 (15) | 0.087* | |
H6 | −0.793 (6) | 0.592 (3) | −0.0682 (17) | 0.120* | |
H7 | −0.275 (4) | 0.060 (3) | 0.3251 (11) | 0.061* | |
H8 | −0.427 (5) | 0.686 (3) | −0.0256 (15) | 0.088* | |
H9 | 0.080 (4) | 0.2857 (19) | 0.2291 (10) | 0.045* | |
H10 | 0.060 (4) | 0.451 (2) | 0.3212 (11) | 0.058* | |
H11 | −0.200 (5) | 0.583 (3) | 0.0566 (14) | 0.088* | |
H12 | −0.917 (6) | 0.396 (3) | −0.0149 (14) | 0.088* | |
H13 | −0.568 (4) | 0.210 (2) | 0.2920 (10) | 0.044* | |
H15 | −0.102 (8) | 0.412 (3) | 0.1285 (19) | 0.124* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0329 (6) | 0.0518 (10) | 0.0488 (8) | −0.0036 (7) | 0.0012 (6) | 0.0074 (7) |
O2 | 0.0477 (6) | 0.0656 (8) | 0.0482 (6) | 0.0152 (6) | 0.0113 (5) | 0.0008 (5) |
C3 | 0.0699 (10) | 0.0454 (11) | 0.0435 (8) | 0.0187 (9) | −0.0059 (7) | −0.0023 (7) |
C4 | 0.0488 (7) | 0.0423 (9) | 0.0508 (8) | −0.0055 (7) | −0.0073 (7) | 0.0074 (7) |
C5 | 0.0308 (6) | 0.0416 (9) | 0.0404 (7) | 0.0042 (6) | 0.0012 (5) | 0.0078 (6) |
O6 | 0.0374 (5) | 0.0433 (6) | 0.0476 (6) | 0.0040 (4) | −0.0043 (4) | 0.0130 (5) |
C7 | 0.0455 (8) | 0.0505 (11) | 0.0464 (8) | −0.0043 (7) | −0.0001 (6) | 0.0138 (7) |
C8 | 0.0389 (6) | 0.0403 (9) | 0.0379 (6) | 0.0057 (6) | −0.0043 (6) | 0.0010 (6) |
O9 | 0.1342 (16) | 0.0565 (10) | 0.0839 (10) | 0.0363 (11) | −0.0030 (12) | −0.0191 (8) |
O10 | 0.0444 (5) | 0.0518 (7) | 0.0333 (5) | 0.0145 (5) | −0.0019 (4) | 0.0032 (5) |
C11 | 0.0558 (10) | 0.0961 (17) | 0.0383 (8) | 0.0321 (11) | 0.0035 (7) | 0.0131 (9) |
C12 | 0.0442 (7) | 0.0564 (10) | 0.0312 (6) | 0.0128 (7) | 0.0018 (5) | 0.0004 (6) |
C13 | 0.0473 (8) | 0.0631 (13) | 0.0557 (9) | −0.0015 (8) | 0.0052 (7) | 0.0044 (8) |
C14 | 0.0796 (14) | 0.0718 (16) | 0.0625 (11) | 0.0141 (11) | 0.0197 (11) | 0.0297 (11) |
C15 | 0.0736 (12) | 0.0996 (18) | 0.0362 (8) | 0.0353 (13) | −0.0060 (8) | 0.0049 (9) |
C16 | 0.0541 (10) | 0.0805 (16) | 0.0555 (10) | 0.0118 (10) | −0.0138 (8) | −0.0236 (10) |
C17 | 0.0527 (9) | 0.0479 (11) | 0.0557 (9) | 0.0046 (8) | 0.0042 (7) | −0.0069 (8) |
C1—O2 | 1.445 (2) | C8—H2 | 0.98 (2) |
C1—C7 | 1.510 (2) | O10—C11 | 1.4338 (19) |
C1—C8 | 1.507 (2) | C11—C12 | 1.501 (2) |
C1—H13 | 0.91 (2) | C11—H5 | 1.01 (3) |
O2—C3 | 1.350 (3) | C11—H15 | 1.08 (4) |
C3—C4 | 1.501 (3) | C12—C13 | 1.375 (3) |
C3—O9 | 1.200 (2) | C12—C17 | 1.378 (3) |
C4—C5 | 1.507 (3) | C13—C14 | 1.385 (3) |
C4—H1 | 0.93 (2) | C13—H11 | 0.98 (3) |
C4—H10 | 0.99 (2) | C14—C15 | 1.368 (4) |
C5—O6 | 1.4334 (17) | C14—H8 | 0.93 (3) |
C5—C8 | 1.527 (2) | C15—C16 | 1.372 (4) |
C5—H9 | 0.98 (2) | C15—H6 | 1.07 (4) |
O6—C7 | 1.4402 (19) | C16—C17 | 1.386 (3) |
C7—H3 | 0.94 (2) | C16—H12 | 1.01 (3) |
C7—H7 | 1.06 (3) | C17—H4 | 1.05 (3) |
C8—O10 | 1.4060 (17) | ||
O2—C1—C7 | 111.55 (14) | O10—C8—C5 | 115.50 (13) |
O2—C1—C8 | 110.74 (14) | C1—C8—C5 | 97.79 (11) |
C8—C1—C7 | 101.19 (12) | O10—C8—H2 | 109.2 (12) |
O2—C1—H13 | 103.1 (12) | C1—C8—H2 | 110.9 (12) |
C8—C1—H13 | 115.6 (12) | C5—C8—H2 | 110.6 (12) |
C7—C1—H13 | 114.9 (13) | C8—O10—C11 | 111.11 (12) |
C3—O2—C1 | 119.21 (12) | O10—C11—C12 | 109.48 (13) |
O9—C3—O2 | 117.1 (2) | O10—C11—H5 | 106.7 (17) |
O9—C3—C4 | 123.4 (2) | C12—C11—H5 | 114.9 (17) |
O2—C3—C4 | 119.43 (15) | O10—C11—H15 | 111 (2) |
C3—C4—C5 | 114.46 (15) | C12—C11—H15 | 112 (2) |
C3—C4—H1 | 107.7 (14) | H5—C11—H15 | 103 (3) |
C5—C4—H1 | 104.9 (13) | C13—C12—C17 | 119.68 (16) |
C3—C4—H10 | 107.7 (12) | C13—C12—C11 | 119.94 (18) |
C5—C4—H10 | 110.6 (13) | C17—C12—C11 | 120.37 (19) |
H1—C4—H10 | 111.4 (19) | C12—C13—C14 | 120.01 (19) |
O6—C5—C4 | 110.34 (12) | C12—C13—H11 | 117.5 (17) |
O6—C5—C8 | 103.25 (12) | C14—C13—H11 | 122.4 (17) |
C4—C5—C8 | 108.49 (13) | C15—C14—C13 | 120.4 (2) |
O6—C5—H9 | 107.4 (12) | C15—C14—H8 | 123.6 (18) |
C4—C5—H9 | 112.2 (11) | C13—C14—H8 | 116.1 (18) |
C8—C5—H9 | 114.8 (12) | C14—C15—C16 | 119.77 (18) |
C5—O6—C7 | 108.07 (11) | C14—C15—H6 | 122 (2) |
O6—C7—C1 | 105.31 (12) | C16—C15—H6 | 118 (2) |
O6—C7—H3 | 108.0 (12) | C15—C16—C17 | 120.3 (2) |
C1—C7—H3 | 112.5 (12) | C15—C16—H12 | 117.0 (16) |
O6—C7—H7 | 107.9 (13) | C17—C16—H12 | 122.7 (16) |
C1—C7—H7 | 109.8 (12) | C12—C17—C16 | 119.9 (2) |
H3—C7—H7 | 113.0 (17) | C12—C17—H4 | 121.9 (15) |
O10—C8—C1 | 112.43 (13) | C16—C17—H4 | 118.1 (15) |
Experimental details
Crystal data | |
Chemical formula | C13H14O4 |
Mr | 234.24 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 293 |
a, b, c (Å) | 5.729 (1), 10.079 (2), 19.622 (4) |
V (Å3) | 1133.0 (4) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 0.85 |
Crystal size (mm) | 0.45 × 0.35 × 0.20 |
Data collection | |
Diffractometer | Syntex P21 diffractometer |
Absorption correction | ψ scan (North et al., 1968) |
Tmin, Tmax | 0.656, 0.845 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2583, 2259, 1969 |
Rint | 0.056 |
(sin θ/λ)max (Å−1) | 0.639 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.033, 0.088, 1.09 |
No. of reflections | 2259 |
No. of parameters | 211 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.19, −0.26 |
Absolute structure | (Flack, 1983). No Fridel pairs. |
Absolute structure parameter | −0.03 (19) |
Computer programs: P21 Software (Syntex, 1973), P21 Software, XP21 (Pavelčík, 1993), SHELXS86 (Sheldrick, 1985), SHELXL97 (Sheldrick, 1997), ORTEP (Johnson, 1965), SHELXL97.
C1—O2 | 1.445 (2) | C8—O10 | 1.4060 (17) |
C1—C7 | 1.510 (2) | O10—C11 | 1.4338 (19) |
C1—C8 | 1.507 (2) | C11—C12 | 1.501 (2) |
O2—C3 | 1.350 (3) | C12—C13 | 1.375 (3) |
C3—C4 | 1.501 (3) | C12—C17 | 1.378 (3) |
C3—O9 | 1.200 (2) | C13—C14 | 1.385 (3) |
C4—C5 | 1.507 (3) | C14—C15 | 1.368 (4) |
C5—O6 | 1.4334 (17) | C15—C16 | 1.372 (4) |
C5—C8 | 1.527 (2) | C16—C17 | 1.386 (3) |
O6—C7 | 1.4402 (19) | ||
O2—C1—C7 | 111.55 (14) | O10—C8—C1 | 112.43 (13) |
O2—C1—C8 | 110.74 (14) | O10—C8—C5 | 115.50 (13) |
C8—C1—C7 | 101.19 (12) | C1—C8—C5 | 97.79 (11) |
C3—O2—C1 | 119.21 (12) | C8—O10—C11 | 111.11 (12) |
O9—C3—O2 | 117.1 (2) | O10—C11—C12 | 109.48 (13) |
O9—C3—C4 | 123.4 (2) | C13—C12—C17 | 119.68 (16) |
O2—C3—C4 | 119.43 (15) | C13—C12—C11 | 119.94 (18) |
C3—C4—C5 | 114.46 (15) | C17—C12—C11 | 120.37 (19) |
O6—C5—C4 | 110.34 (12) | C12—C13—C14 | 120.01 (19) |
O6—C5—C8 | 103.25 (12) | C15—C14—C13 | 120.4 (2) |
C4—C5—C8 | 108.49 (13) | C14—C15—C16 | 119.77 (18) |
C5—O6—C7 | 108.07 (11) | C15—C16—C17 | 120.3 (2) |
O6—C7—C1 | 105.31 (12) | C12—C17—C16 | 119.9 (2) |
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).