organic compounds
3,3′:5,6-Di-O-isopropylidene-3-C-hydroxymethyl-D-allono-1,4-lactone: an organic structure containing large unoccupied voids
aDepartment of Organic Chemistry, Chemical Research Laboratory, Oxford University, Mansfield Road, Oxford OX1 3TA, England, and bDepartment of Chemical Crystallography, Chemical Research Laboratory, Oxford University, Mansfield Road, Oxford OX1 3TA, England
*Correspondence e-mail: michela_simone@yahoo.co.uk
The Kiliani reaction of D-hamamelose with sodium cyanide, followed by acetonation, affords crystalline 3,3′:5,6-di-O-isopropylidene-3-C-hydroxymethyl-D-allono-1,4-lactone, C13H20O7, a carbon-branched sugar with potential as an enantiomerically pure carbohydrate scaffold. The lactone has one single free hydroxyl group unprotected, with six other functional groups protected in a single step as or The resulting is unusual in that it contains large voids (544 Å3) within which there is no evidence of included solvent.
Comment
At present, there are very few accessible branched carbohydrate scaffolds (Lichtenthaler & Peters, 2004; Bols, 1996) for use in the synthesis of complex enantiomerically pure targets (Simone et al., 2005). The reactions of calcium oxide on Amadori 1-deoxyamino-ketoses (Hotchkiss et al., 2006) and the Kiliani reaction of cyanide with (Hotchkiss et al., 2004; Soengas et al., 2005) allow the preparation of 2-C-methyl and 2-C-hydroxymethyl in relatively short sequences. However, syntheses of bearing a carbon branch at C-3 are very rare (Bream et al., 2006). One approach to such chirons is the Kiliani cyanide reaction on 2-C-hydroxymethyl sugars [such as hamamelose (1)] to produce 3-C-hydroxymethyl [such as (2) and (4)]. The experimental details for the Kiliani reaction of D-hamamelose (1) with cyanide to give a mixture of the two branched sugar (2) and (4), followed by treatment with dimethoxypropane to afford a separable mixture of the two diacetonides (3) and (5), have been reported in a previous paper (Parker et al., 2006).
A significant number of ambiguities arise from the formation of possible et al., 2006). This paper firmly assigns the structure of the second crystalline product as the branched allono-lactone (3) formed from lactone formation from the C-4 hydroxyl group; the of (3) is determined by the use of D-ribose as the starting material for the synthesis. It is noteworthy that both (3) and (5) have only the C-2 hydroxyl group unprotected; the sequence provides access to two sugars with seven functional groups but with six of the them protected in one simple step.
the sites for the formation of cyclic and the sizes of both the lactone and ketal rings. This is an area in which X-ray crystallography is needed to have any confidence at all in the structures of diacetonides obtained by this short procedure. The of the altrono-diacetonide (5), formed from the lactone (4) derived by of the branched C-3′ hydroxymethyl group on to the carboxylic acid, has been established by X-ray crystallography (ParkerThe component molecules have no unusual torsion angles, and show no evidence of internal strain. The relatively large anisotropic displacement parameters for the methyl groups and O atoms in the acetonide protecting group may indicate some ring fluxion (Fig. 1).
The 3) within which there is no evidence for included solvent (Fig. 2). The voids are big enough to have contained dichloromethane, but the maximum residual electron density is only 0.2 e Å−3. We do not know if the voids in the dry crystals ever contained solvent, though generally solvent loss from organic crystals is associated with either a total loss of crystallinity, or at least a degradation of the crystal quality. In this case the crystals remained glass-clear.
is unusual in that it contains substantial voids (544 ÅThe structure consists of a tight helix (Fig. 3), involving O—H⋯Oi hydrogen bonds (Table 1), which runs parallel to the c axis at (½, ½, z). The main parts of the molecule hang off this backbone like leaves from a tree. The tips of the `leaves' of four separate helices meet to form a second helix at (0, 0, z). The `leaves' of each pair of adjacent hydrogen-bonded helices (separated by because of the 41 axis) interleave along (0, 0, z), but there is no evidence for particularly strong interactions at these points.
Experimental
The title compound, (3), was crystallized by dissolving it in dichloromethane, adding a few drops of cyclohexane and allowing the slow competitive evaporation of the two solvents until needle-like colourless crystals formed [m.p. 353 K (dichloromethane/cyclohexane)]. MS–ES− (m/z): 287.2 ([M − H]−, 15%); HRMS (MS ES+): found 311.1101 [M + Na]+ C13H20NaO7 requires 311.1101; [α]D23: +5.5 (c 1.25 in chloroform); νmax (thin film): 3445 (br, OH), 2989 (CH2, CH3), 1800 (C=O) cm−1; δH (C6D6, 400 MHz): 1.20, 1.31, 1.36, 1.38 [12H, 4 × s, 2 × C(CH3)2], 3.30–3.40 (1H, br s, OH-2), 3.51 (1H, ddd, JH-5,H-4 = 8.5 Hz, JH-5,H-6 = 6.7 Hz, JH-5,H-6′ = 5.3 Hz, H-5), 3.75 (1H, dd, JH-6,H-6′ = 9.5 Hz, JH-6,H-5 = 6.6 Hz, H-6), 3.82 (1H, dd, JH-6′,H-6 = 9.5 Hz, JH-6′,H-5 = 5.3 Hz, H-6′), 3.97 (1H, d, JH-3,H-3′ = 10.0 Hz H-3), 4.20 (1H, s, H-2), 4.26 (1H, d, JH-4,H-5 = 8.6 Hz, H-4), 4.55 (1H, d, JH-3′,H-3 = 10.0 Hz, H-3′); δC (C6D6, 100 MHz): 24.8, 25.5, 26.5, 26.9 [2 × C(CH3)2], 65.3 (C-3′), 65.8 (C-6), 67.0 (C-2), 73.7 (C-5), 84.9 (C-3), 85.0 (C-4), 110.7, 111.2 [2 × C(CH3)2], 173.2 (C=O).
Crystal data
|
Refinement
In the absence of significant Uiso(H) = 1.2 or 1.5 times Ueq(parent atom)], after which the positions were refined with riding constraints.
Friedel pairs were merged and the assigned from the starting materials The H atoms were all located in a difference map, but those attached to C atoms were repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry [C—H = 0.93–0.98, O—H = 0.82 Å andData collection: COLLECT (Nonius, 2001).; cell DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.
Supporting information
https://doi.org/10.1107/S1600536807002061/sj2196sup1.cif
contains datablocks 3, global. DOI:Structure factors: contains datablock 3. DOI: https://doi.org/10.1107/S1600536807002061/sj21963sup2.hkl
Data collection: COLLECT (Nonius, 2001).; cell
DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.C13H20O7 | Dx = 1.037 Mg m−3 |
Mr = 288.30 | Mo Kα radiation, λ = 0.71073 Å |
Tetragonal, P41 | Cell parameters from 21907 reflections |
Hall symbol: P 4w | θ = 5–28° |
a = 14.1641 (4) Å | µ = 0.08 mm−1 |
c = 9.2045 (3) Å | T = 150 K |
V = 1846.62 (10) Å3 | Needle, colourless |
Z = 4 | 0.44 × 0.12 × 0.10 mm |
F(000) = 616 |
Nonius KappaCCD diffractometer | 1802 reflections with I > 3σ(I) |
Graphite monochromator | Rint = 0.068 |
ω scans | θmax = 27.6°, θmin = 5.2° |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | h = −12→13 |
Tmin = 0.96, Tmax = 0.99 | k = 0→18 |
21907 measured reflections | l = 0→11 |
2229 independent reflections |
Refinement on F | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.046 | H-atom parameters constrained |
wR(F2) = 0.044 | Modified Chebychev polynomial (Watkin, 1994; Prince, 1982) with coefficients 1.09 0.255 0.726 and Robust Weighting (Prince, 1982); W = [weight][1-(δF/6σF)2]2 |
S = 1.04 | (Δ/σ)max = 0.010 |
1802 reflections | Δρmax = 0.22 e Å−3 |
181 parameters | Δρmin = −0.21 e Å−3 |
1 restraint |
x | y | z | Uiso*/Ueq | ||
C1 | 0.40908 (17) | 0.29983 (17) | 0.2555 (3) | 0.0322 | |
C2 | 0.50778 (16) | 0.34055 (15) | 0.2595 (2) | 0.0292 | |
C3 | 0.56325 (17) | 0.26748 (16) | 0.1741 (2) | 0.0306 | |
C4 | 0.51393 (17) | 0.17588 (17) | 0.2218 (3) | 0.0340 | |
C5 | 0.54440 (19) | 0.13445 (17) | 0.3650 (3) | 0.0384 | |
C6 | 0.4755 (2) | 0.06101 (19) | 0.4243 (4) | 0.0493 | |
O1 | 0.33445 (12) | 0.34056 (13) | 0.2657 (2) | 0.0401 | |
O2 | 0.51303 (12) | 0.43275 (11) | 0.20539 (19) | 0.0336 | |
O3 | 0.54536 (12) | 0.28276 (12) | 0.02234 (18) | 0.0340 | |
O4 | 0.41413 (12) | 0.20543 (12) | 0.2386 (2) | 0.0367 | |
O5 | 0.62892 (15) | 0.08096 (13) | 0.3439 (3) | 0.0522 | |
O6 | 0.53620 (16) | 0.00210 (14) | 0.5075 (3) | 0.0579 | |
C7 | 0.67037 (18) | 0.27177 (18) | 0.1852 (3) | 0.0356 | |
O8 | 0.69994 (13) | 0.24162 (13) | 0.0446 (2) | 0.0409 | |
C8 | 0.63374 (18) | 0.27831 (18) | −0.0555 (3) | 0.0356 | |
C9 | 0.6603 (2) | 0.3780 (2) | −0.1031 (3) | 0.0434 | |
C10 | 0.6248 (2) | 0.2097 (2) | −0.1803 (3) | 0.0477 | |
C11 | 0.6237 (2) | −0.0037 (2) | 0.4304 (3) | 0.0510 | |
C12 | 0.6225 (4) | −0.0873 (2) | 0.3307 (5) | 0.0805 | |
C13 | 0.7021 (3) | −0.0043 (3) | 0.5393 (4) | 0.0793 | |
H1 | 0.5317 | 0.4678 | 0.2677 | 0.0507* | |
H21 | 0.5308 | 0.3403 | 0.3595 | 0.0347* | |
H41 | 0.5201 | 0.1275 | 0.1480 | 0.0411* | |
H51 | 0.5523 | 0.1854 | 0.4369 | 0.0454* | |
H61 | 0.4264 | 0.0889 | 0.4849 | 0.0586* | |
H62 | 0.4459 | 0.0254 | 0.3444 | 0.0580* | |
H71 | 0.6906 | 0.3361 | 0.2042 | 0.0413* | |
H72 | 0.6947 | 0.2293 | 0.2595 | 0.0417* | |
H91 | 0.7203 | 0.3782 | −0.1548 | 0.0642* | |
H92 | 0.6673 | 0.4189 | −0.0191 | 0.0647* | |
H93 | 0.6102 | 0.4041 | −0.1660 | 0.0643* | |
H101 | 0.6850 | 0.2058 | −0.2287 | 0.0703* | |
H102 | 0.5776 | 0.2310 | −0.2491 | 0.0705* | |
H103 | 0.6073 | 0.1473 | −0.1420 | 0.0706* | |
H121 | 0.6216 | −0.1447 | 0.3883 | 0.1191* | |
H122 | 0.6795 | −0.0864 | 0.2731 | 0.1185* | |
H123 | 0.5676 | −0.0845 | 0.2679 | 0.1184* | |
H131 | 0.6983 | −0.0602 | 0.6003 | 0.1178* | |
H132 | 0.7623 | −0.0033 | 0.4884 | 0.1177* | |
H133 | 0.6982 | 0.0510 | 0.5999 | 0.1178* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0403 (13) | 0.0401 (12) | 0.0161 (8) | −0.0017 (10) | 0.0017 (9) | 0.0035 (9) |
C2 | 0.0405 (12) | 0.0301 (11) | 0.0169 (9) | 0.0024 (9) | −0.0033 (9) | 0.0022 (9) |
C3 | 0.0429 (13) | 0.0302 (11) | 0.0188 (10) | −0.0015 (9) | −0.0003 (9) | 0.0012 (8) |
C4 | 0.0432 (13) | 0.0297 (11) | 0.0292 (11) | −0.004 (1) | 0.0058 (9) | −0.0041 (9) |
C5 | 0.0508 (14) | 0.0277 (11) | 0.0368 (12) | 0.0027 (10) | 0.0091 (11) | 0.0047 (10) |
C6 | 0.0598 (17) | 0.0355 (13) | 0.0526 (17) | 0.0019 (12) | 0.0124 (14) | 0.0173 (13) |
O1 | 0.0380 (9) | 0.0546 (10) | 0.0278 (8) | 0.0050 (8) | 0.0042 (7) | 0.0055 (8) |
O2 | 0.0501 (10) | 0.0280 (8) | 0.0228 (7) | −0.0023 (7) | −0.0088 (7) | 0.0007 (6) |
O3 | 0.0403 (9) | 0.0442 (9) | 0.0174 (7) | −0.0029 (7) | 0.0011 (6) | 0.0016 (7) |
O4 | 0.0390 (9) | 0.0369 (9) | 0.0343 (9) | −0.0044 (7) | 0.0035 (7) | 0.0001 (7) |
O5 | 0.0550 (12) | 0.0410 (10) | 0.0606 (13) | 0.0091 (9) | 0.0166 (10) | 0.0154 (9) |
O6 | 0.0734 (13) | 0.0437 (10) | 0.0566 (13) | 0.0090 (10) | 0.0162 (12) | 0.0237 (10) |
C7 | 0.0403 (13) | 0.0397 (13) | 0.0269 (11) | 0.0011 (10) | 0.0059 (10) | 0.0042 (10) |
O8 | 0.0432 (10) | 0.0476 (10) | 0.0319 (9) | 0.0031 (8) | 0.0084 (7) | 0.0024 (8) |
C8 | 0.0410 (13) | 0.0407 (13) | 0.0250 (11) | −0.0021 (10) | 0.0054 (10) | 0.0018 (10) |
C9 | 0.0471 (15) | 0.0496 (15) | 0.0335 (12) | −0.0063 (12) | 0.0070 (11) | 0.0057 (12) |
C10 | 0.0611 (17) | 0.0499 (15) | 0.0320 (13) | 0.0003 (13) | 0.0107 (12) | −0.0074 (12) |
C11 | 0.0686 (19) | 0.0385 (14) | 0.0458 (15) | 0.0130 (13) | 0.0028 (14) | 0.0082 (12) |
C12 | 0.120 (3) | 0.0417 (17) | 0.080 (3) | 0.0111 (19) | 0.011 (2) | −0.0076 (18) |
C13 | 0.078 (2) | 0.103 (3) | 0.057 (2) | 0.011 (2) | −0.0075 (19) | 0.011 (2) |
C1—C2 | 1.513 (3) | O6—C11 | 1.430 (4) |
C1—O1 | 1.208 (3) | C7—O8 | 1.426 (3) |
C1—O4 | 1.348 (3) | C7—H71 | 0.972 |
C2—C3 | 1.519 (3) | C7—H72 | 0.974 |
C2—O2 | 1.400 (3) | O8—C8 | 1.413 (3) |
C2—H21 | 0.976 | C8—C9 | 1.526 (4) |
C3—C4 | 1.538 (3) | C8—C10 | 1.510 (4) |
C3—O3 | 1.436 (2) | C9—H91 | 0.974 |
C3—C7 | 1.522 (4) | C9—H92 | 0.971 |
C4—C5 | 1.506 (4) | C9—H93 | 0.987 |
C4—O4 | 1.482 (3) | C10—H101 | 0.963 |
C4—H41 | 0.968 | C10—H102 | 0.970 |
C5—C6 | 1.527 (4) | C10—H103 | 0.984 |
C5—O5 | 1.430 (3) | C11—C12 | 1.499 (5) |
C5—H51 | 0.986 | C11—C13 | 1.497 (5) |
C6—O6 | 1.422 (4) | C12—H121 | 0.972 |
C6—H61 | 0.975 | C12—H122 | 0.965 |
C6—H62 | 0.985 | C12—H123 | 0.970 |
O2—H1 | 0.803 | C13—H131 | 0.972 |
O3—C8 | 1.444 (3) | C13—H132 | 0.972 |
O5—C11 | 1.441 (3) | C13—H133 | 0.964 |
C2—C1—O1 | 128.7 (2) | C3—C7—H72 | 112.0 |
C2—C1—O4 | 109.39 (19) | O8—C7—H72 | 110.4 |
O1—C1—O4 | 121.9 (2) | H71—C7—H72 | 110.5 |
C1—C2—C3 | 101.88 (18) | C7—O8—C8 | 106.66 (18) |
C1—C2—O2 | 113.35 (18) | O3—C8—O8 | 105.54 (17) |
C3—C2—O2 | 115.11 (18) | O3—C8—C9 | 108.4 (2) |
C1—C2—H21 | 109.2 | O8—C8—C9 | 111.4 (2) |
C3—C2—H21 | 108.2 | O3—C8—C10 | 109.5 (2) |
O2—C2—H21 | 108.8 | O8—C8—C10 | 108.3 (2) |
C2—C3—C4 | 101.08 (18) | C9—C8—C10 | 113.4 (2) |
C2—C3—O3 | 108.02 (18) | C8—C9—H91 | 110.9 |
C4—C3—O3 | 108.96 (19) | C8—C9—H92 | 110.4 |
C2—C3—C7 | 117.0 (2) | H91—C9—H92 | 107.3 |
C4—C3—C7 | 117.86 (19) | C8—C9—H93 | 109.7 |
O3—C3—C7 | 103.63 (18) | H91—C9—H93 | 109.9 |
C3—C4—C5 | 116.7 (2) | H92—C9—H93 | 108.6 |
C3—C4—O4 | 103.00 (18) | C8—C10—H101 | 108.4 |
C5—C4—O4 | 106.95 (19) | C8—C10—H102 | 110.7 |
C3—C4—H41 | 110.8 | H101—C10—H102 | 109.1 |
C5—C4—H41 | 108.2 | C8—C10—H103 | 109.1 |
O4—C4—H41 | 111.1 | H101—C10—H103 | 109.7 |
C4—C5—C6 | 113.3 (2) | H102—C10—H103 | 109.8 |
C4—C5—O5 | 109.1 (2) | O5—C11—O6 | 105.7 (2) |
C6—C5—O5 | 102.86 (19) | O5—C11—C12 | 108.6 (3) |
C4—C5—H51 | 109.5 | O6—C11—C12 | 109.9 (3) |
C6—C5—H51 | 109.4 | O5—C11—C13 | 109.7 (3) |
O5—C5—H51 | 112.6 | O6—C11—C13 | 108.2 (3) |
C5—C6—O6 | 101.9 (2) | C12—C11—C13 | 114.4 (3) |
C5—C6—H61 | 112.6 | C11—C12—H121 | 109.1 |
O6—C6—H61 | 111.2 | C11—C12—H122 | 108.5 |
C5—C6—H62 | 110.7 | H121—C12—H122 | 108.8 |
O6—C6—H62 | 111.0 | C11—C12—H123 | 110.0 |
H61—C6—H62 | 109.3 | H121—C12—H123 | 110.4 |
C2—O2—H1 | 109.9 | H122—C12—H123 | 110.1 |
C3—O3—C8 | 108.84 (18) | C11—C13—H131 | 110.5 |
C4—O4—C1 | 110.04 (17) | C11—C13—H132 | 109.1 |
C5—O5—C11 | 108.8 (2) | H131—C13—H132 | 109.8 |
C6—O6—C11 | 106.9 (2) | C11—C13—H133 | 109.8 |
C3—C7—O8 | 102.68 (19) | H131—C13—H133 | 109.0 |
C3—C7—H71 | 110.1 | H132—C13—H133 | 108.5 |
O8—C7—H71 | 110.9 |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H1···O2i | 0.80 | 1.91 | 2.679 (2) | 160 |
Symmetry code: (i) −y+1, x, z+1/4. |
Acknowledgements
Financial support [to MS] provided through the European Community's Human Potential Programme under contract HPRN-CT-2002–00173 is gratefully acknowledged.
References
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