organic compounds
1,2-O-Isopropylidene-β-D-lyxo-furanose
aDepartamento de Química, Universidade Federal Rural de Pernambuco, 52171-900 Recife, PE, Brazil, and bChemistry Department, State University of New York, College at Buffalo, 1300 Elmwood Ave, Buffalo, NY 14222-1095, USA
*Correspondence e-mail: nazareay@buffalostate.edu
In the title compound C8H14O5, the pentofuranose five-membered ring has a twisted conformation on two carbon atoms while the five-membered ring of the isopropylidene group has an on an oxygen atom. Hydroxy groups are involved an infinite network of O—H⋯O hydrogen bonds that leads to the formation of a layer parallel to the (001) plane. Only weak C—H⋯O contacts exist between neighboring layers.
Keywords: crystal structure; carbohydrate; furanose.
CCDC reference: 2050681
Structure description
The title compound, C8H14O5, (1) together with its enantiomeric L form, are relatively rare derivatives and a limited volume of information is available for either of them. Our interest in 1 stems from the possibility of conducting deoxygenation at its C3 position to obtain 3-deoxy-1,2-O-isopropylidene-β-D-threo-pentofuranose as a chiral synthon for further synthetic work (Soares et al., 2013). Compound 1 was obtained from the known 1,2-O-isopropylidene-5-O-t-butyldiphenylsilyl-β-D-arabino-furanose 2 (Dahlman et al., 1986) via oxidation at the C3 position followed by reduction of the intermediate ulose. The reduction proceeded with a total stereoselection from the more accessible Re (α) side to furnish 1,2-O-isopropylidene-5-O–t-butyldiphenylsilyl-β-D-lyxo-furanose, whose desilylation gave the target 1. It should be pointed out that under these isopropylidenation conditions, D-lyxose furnished only its α,β-2,3-O-isopropylidenefuranose (Barbat et al., 1991). Compound 1 was previously obtained starting from D-glucose via D-gulose (Kuzuhara et al., 1971). The scarcity of any experimental data on 1 prompted us to examine its structure.
In the title compound (Fig. 1), the pentofuranose five-membered ring has twisted conformation on atoms C6 and C9 [Q = 0.3175 (12) Å, φ = 117.6 (2)°]. The five-membered ring of the isopropylidene group has an on atom O1 [Q(2) = 0.3192 (11) Å, φ = 187.1 (2)°]. Puckering parameters (Cremer & Pople, 1975) were calculated using PLATON (Spek, 2020). We have observed the same conformation of the isopropyledene fragment in other (Doboszewski & Nazarenko, 2003; Doboszewski et al., 2010).
In the crystal, the two hydroxy groups form an infinite network of O—H⋯O hydrogen bonds that leads to the formation of a layer parallel to the (001) plane (Table 1, Fig. 2). Only weak C—H⋯O (Fig. 3) contacts exist between neighboring layers; the C5⋯O4(− + x, − y, −z) distance is 3.389 (2) Å. Similar hydrogen bonds have been observed in various (Desiraju & Steiner, 1999). A short intramolecular contact between oxygen O1 and the H12B atom of a neighboring methylene group (Table 1) may additionally stabilize the conformation of the molecule. Therefore, all oxygen atoms of the title molecule participate in O—H⋯O or C—H⋯O interactions.
Synthesis and crystallization
The synthesis of the title compound is described in Kuzuhara et al. (1971) and Soares et al. (2013).
Refinement
Crystal data, data collection and structure . An additional dataset was collected using Cu Kα radiation, resulting in a of 0.09 (13) and a probability of the being correct of 1.000.
details are summarized in Table 2Structural data
CCDC reference: 2050681
https://doi.org/10.1107/S2414314620016302/zq4044sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314620016302/zq4044Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314620016302/zq4044Isup3.cdx
CuK(alpha) https://doi.org/10.1107/S2414314620016302/zq4044sup4.txt
file for confirmation. DOI:Data collection: APEX2 (Bruker, 2013); cell
SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009), Mercury (Macrae et al., 2020); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).C8H14O5 | Dx = 1.374 Mg m−3 |
Mr = 190.19 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 9980 reflections |
a = 5.9196 (3) Å | θ = 2.9–37.3° |
b = 7.3562 (4) Å | µ = 0.12 mm−1 |
c = 21.1126 (12) Å | T = 173 K |
V = 919.36 (9) Å3 | Block, colourless |
Z = 4 | 0.45 × 0.43 × 0.37 mm |
F(000) = 408 |
Bruker PHOTON-100 CMOS diffractometer | 4938 independent reflections |
Radiation source: sealed tube | 4094 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.029 |
Detector resolution: 10.4 pixels mm-1 | θmax = 37.8°, θmin = 2.9° |
φ and ω scans | h = −9→10 |
Absorption correction: multi-scan (SADABS; Krause et al., 2015) | k = −12→12 |
Tmin = 0.944, Tmax = 1.000 | l = −27→36 |
20693 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.043 | All H-atom parameters refined |
wR(F2) = 0.109 | w = 1/[σ2(Fo2) + (0.0654P)2 + 0.0319P] where P = (Fo2 + 2Fc2)/3 |
S = 1.03 | (Δ/σ)max < 0.001 |
4938 reflections | Δρmax = 0.41 e Å−3 |
174 parameters | Δρmin = −0.30 e Å−3 |
0 restraints | Absolute structure: Flack x determined using 1496 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
Primary atom site location: dual | Absolute structure parameter: 0.3 (2) |
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. All hydrogen atoms are refined in isotropic approximation. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.94830 (15) | 0.59218 (11) | 0.12758 (4) | 0.02153 (15) | |
O2 | 0.66312 (15) | 0.80371 (13) | 0.20056 (4) | 0.02597 (18) | |
H2 | 0.556 (4) | 0.878 (3) | 0.2138 (10) | 0.044 (6)* | |
O3 | 1.1047 (2) | 0.99300 (12) | 0.10435 (5) | 0.0312 (2) | |
O4 | 1.21881 (17) | 0.71302 (12) | 0.06429 (5) | 0.02782 (19) | |
O8 | 1.31943 (18) | 1.00933 (18) | 0.22671 (6) | 0.0398 (3) | |
H8 | 1.294 (4) | 1.090 (3) | 0.2540 (11) | 0.044 (6)* | |
C5 | 1.0438 (2) | 0.84268 (15) | 0.06643 (5) | 0.02228 (19) | |
H5 | 1.021 (4) | 0.887 (3) | 0.0247 (9) | 0.034 (5)* | |
C6 | 0.7654 (2) | 0.88480 (15) | 0.14745 (5) | 0.02169 (19) | |
H6 | 0.661 (3) | 0.966 (3) | 0.1270 (9) | 0.029 (5)* | |
C7 | 1.1331 (2) | 0.54276 (15) | 0.08756 (5) | 0.02213 (19) | |
C9 | 0.9802 (2) | 0.99245 (15) | 0.16300 (5) | 0.0234 (2) | |
H9 | 0.946 (3) | 1.122 (2) | 0.1724 (8) | 0.021 (4)* | |
C10 | 0.8456 (2) | 0.74699 (15) | 0.09853 (5) | 0.02134 (18) | |
H10 | 0.728 (4) | 0.710 (3) | 0.0702 (8) | 0.029 (5)* | |
C11 | 1.3131 (2) | 0.45089 (18) | 0.12639 (7) | 0.0291 (2) | |
H11A | 1.446 (5) | 0.431 (4) | 0.0981 (11) | 0.057 (7)* | |
H11B | 1.367 (4) | 0.524 (3) | 0.1593 (11) | 0.039 (5)* | |
H11C | 1.264 (4) | 0.337 (3) | 0.1401 (9) | 0.040 (5)* | |
C12 | 1.1131 (2) | 0.91394 (18) | 0.21779 (6) | 0.0272 (2) | |
H12A | 1.027 (4) | 0.919 (3) | 0.2536 (9) | 0.027 (4)* | |
H12B | 1.143 (3) | 0.789 (3) | 0.2097 (9) | 0.030 (5)* | |
C13 | 1.0527 (3) | 0.4265 (2) | 0.03239 (7) | 0.0335 (3) | |
H13A | 0.942 (4) | 0.487 (3) | 0.0070 (10) | 0.038 (5)* | |
H13B | 1.178 (4) | 0.399 (3) | 0.0052 (11) | 0.039 (5)* | |
H13C | 0.997 (4) | 0.314 (3) | 0.0495 (11) | 0.048 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0226 (4) | 0.0202 (3) | 0.0218 (3) | −0.0006 (3) | 0.0036 (3) | 0.0012 (3) |
O2 | 0.0209 (4) | 0.0287 (4) | 0.0283 (4) | 0.0024 (3) | 0.0084 (3) | 0.0056 (3) |
O3 | 0.0406 (5) | 0.0230 (4) | 0.0302 (4) | −0.0094 (4) | 0.0161 (4) | −0.0036 (3) |
O4 | 0.0254 (4) | 0.0216 (3) | 0.0364 (4) | 0.0009 (3) | 0.0104 (3) | 0.0034 (3) |
O8 | 0.0203 (4) | 0.0466 (6) | 0.0527 (6) | 0.0001 (4) | 0.0012 (4) | −0.0295 (5) |
C5 | 0.0271 (5) | 0.0219 (4) | 0.0178 (4) | 0.0010 (4) | 0.0032 (4) | 0.0018 (3) |
C6 | 0.0197 (4) | 0.0237 (4) | 0.0216 (4) | 0.0030 (4) | 0.0022 (3) | 0.0031 (4) |
C7 | 0.0245 (5) | 0.0190 (4) | 0.0229 (4) | −0.0015 (3) | 0.0036 (4) | −0.0009 (3) |
C9 | 0.0254 (5) | 0.0200 (4) | 0.0248 (4) | −0.0010 (4) | 0.0074 (4) | −0.0021 (4) |
C10 | 0.0204 (4) | 0.0242 (4) | 0.0194 (4) | −0.0005 (3) | −0.0017 (3) | 0.0006 (3) |
C11 | 0.0261 (5) | 0.0259 (5) | 0.0351 (6) | 0.0023 (4) | −0.0018 (5) | 0.0018 (5) |
C12 | 0.0228 (5) | 0.0307 (5) | 0.0280 (5) | −0.0011 (4) | −0.0006 (4) | −0.0080 (4) |
C13 | 0.0401 (7) | 0.0305 (6) | 0.0298 (5) | 0.0008 (5) | −0.0020 (5) | −0.0109 (5) |
O1—C7 | 1.4291 (14) | C6—C10 | 1.5230 (16) |
O1—C10 | 1.4292 (14) | C7—C11 | 1.5049 (18) |
O2—H2 | 0.88 (3) | C7—C13 | 1.5214 (17) |
O2—C6 | 1.4071 (14) | C9—H9 | 0.993 (17) |
O3—C5 | 1.4120 (14) | C9—C12 | 1.5135 (18) |
O3—C9 | 1.4409 (14) | C10—H10 | 0.95 (2) |
O4—C5 | 1.4090 (15) | C11—H11A | 1.00 (3) |
O4—C7 | 1.4380 (14) | C11—H11B | 0.94 (2) |
O8—H8 | 0.84 (3) | C11—H11C | 0.93 (3) |
O8—C12 | 1.4210 (17) | C12—H12A | 0.91 (2) |
C5—H5 | 0.947 (19) | C12—H12B | 0.95 (2) |
C5—C10 | 1.5267 (16) | C13—H13A | 0.96 (2) |
C6—H6 | 0.96 (2) | C13—H13B | 0.96 (2) |
C6—C9 | 1.5334 (17) | C13—H13C | 0.96 (3) |
C10—O1—C7 | 105.93 (8) | C12—C9—C6 | 113.43 (10) |
C6—O2—H2 | 107.3 (14) | C12—C9—H9 | 108.6 (10) |
C5—O3—C9 | 110.76 (9) | O1—C10—C5 | 103.36 (9) |
C5—O4—C7 | 108.61 (9) | O1—C10—C6 | 111.84 (8) |
C12—O8—H8 | 106.6 (17) | O1—C10—H10 | 110.7 (12) |
O3—C5—H5 | 107.2 (12) | C5—C10—H10 | 114.3 (11) |
O3—C5—C10 | 107.79 (9) | C6—C10—C5 | 103.51 (9) |
O4—C5—O3 | 111.14 (10) | C6—C10—H10 | 112.6 (12) |
O4—C5—H5 | 107.7 (13) | C7—C11—H11A | 107.4 (15) |
O4—C5—C10 | 105.50 (9) | C7—C11—H11B | 112.8 (14) |
C10—C5—H5 | 117.5 (14) | C7—C11—H11C | 110.7 (13) |
O2—C6—H6 | 110.1 (12) | H11A—C11—H11B | 105 (2) |
O2—C6—C9 | 113.91 (9) | H11A—C11—H11C | 107 (2) |
O2—C6—C10 | 113.10 (9) | H11B—C11—H11C | 113.2 (18) |
C9—C6—H6 | 107.9 (12) | O8—C12—C9 | 111.08 (11) |
C10—C6—H6 | 108.1 (12) | O8—C12—H12A | 110.5 (13) |
C10—C6—C9 | 103.33 (9) | O8—C12—H12B | 110.0 (12) |
O1—C7—O4 | 104.51 (8) | C9—C12—H12A | 109.2 (12) |
O1—C7—C11 | 109.53 (10) | C9—C12—H12B | 109.1 (12) |
O1—C7—C13 | 110.88 (10) | H12A—C12—H12B | 106.9 (16) |
O4—C7—C11 | 109.11 (10) | C7—C13—H13A | 112.5 (13) |
O4—C7—C13 | 109.77 (10) | C7—C13—H13B | 109.5 (14) |
C11—C7—C13 | 112.71 (11) | C7—C13—H13C | 107.8 (13) |
O3—C9—C6 | 103.98 (9) | H13A—C13—H13B | 107.1 (18) |
O3—C9—H9 | 105.9 (10) | H13A—C13—H13C | 112 (2) |
O3—C9—C12 | 113.08 (11) | H13B—C13—H13C | 108 (2) |
C6—C9—H9 | 111.5 (11) | ||
O2—C6—C9—O3 | 155.65 (9) | C6—C9—C12—O8 | 175.05 (9) |
O2—C6—C9—C12 | 32.41 (13) | C7—O1—C10—C5 | −31.62 (10) |
O2—C6—C10—O1 | −41.18 (13) | C7—O1—C10—C6 | −142.34 (9) |
O2—C6—C10—C5 | −151.81 (9) | C7—O4—C5—O3 | 121.62 (10) |
O3—C5—C10—O1 | −102.57 (10) | C7—O4—C5—C10 | 5.06 (12) |
O3—C5—C10—C6 | 14.19 (12) | C9—O3—C5—O4 | −108.31 (11) |
O3—C9—C12—O8 | 56.97 (13) | C9—O3—C5—C10 | 6.84 (13) |
O4—C5—C10—O1 | 16.25 (11) | C9—C6—C10—O1 | 82.45 (11) |
O4—C5—C10—C6 | 133.01 (9) | C9—C6—C10—C5 | −28.18 (11) |
C5—O3—C9—C6 | −24.89 (13) | C10—O1—C7—O4 | 35.34 (11) |
C5—O3—C9—C12 | 98.58 (12) | C10—O1—C7—C11 | 152.12 (9) |
C5—O4—C7—O1 | −24.63 (12) | C10—O1—C7—C13 | −82.87 (11) |
C5—O4—C7—C11 | −141.71 (10) | C10—C6—C9—O3 | 32.55 (11) |
C5—O4—C7—C13 | 94.33 (12) | C10—C6—C9—C12 | −90.68 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2···O8i | 0.88 (2) | 1.72 (2) | 2.5946 (15) | 169 (2) |
O8—H8···O2ii | 0.84 (2) | 1.86 (2) | 2.6567 (16) | 158 (2) |
C12—H12B···O1 | 0.95 (2) | 2.54 (2) | 3.1908 (15) | 126.1 (14) |
Symmetry codes: (i) x−1, y, z; (ii) −x+2, y+1/2, −z+1/2. |
Funding information
Financial support from the State University of New York for the acquisition and maintenance of the X-ray diffractometer is gratefully acknowledged.
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