organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

1,2-O-Iso­propyl­­idene-β-D-lyxo-furan­ose

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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

Edited by O. Blacque, University of Zürich, Switzerland (Received 9 December 2020; accepted 16 December 2020; online 22 December 2020)

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 envelope conformation 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.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

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[Soares, F. da Paixão, Silva, M. J. & Doboszewski, B. (2013). Carbohydr. Res. 380, 143-148.]). Compound 1 was obtained from the known 1,2-O-iso­propyl­idene-5-O-t-butyl­diphenyl­silyl-β-D-arabino-furan­ose 2 (Dahlman et al., 1986[Dahlman, O., Garegg, P. J., Mayer, H. & Schramek, S. (1986). Acta Chim. Scand. B 40, 15-20.]) 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-Ot-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[Barbat, J., Gelas, J. & Horton, D. (1991). Carbohydr. Res. 219, 115-121.]). Compound 1 was previously obtained starting from D-glucose via D-gulose (Kuzuhara et al., 1971[Kuzuhara, H., Terayama, H., Ohrui, H. & Emoto, S. (1971). Carbohydr. Res. 20, 165-169.]). The scarcity of any experimental data on 1 prompted us to examine its structure.

In the title compound (Fig. 1[link]), 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 envelope conformation on atom O1 [Q(2) = 0.3192 (11) Å, φ = 187.1 (2)°]. Puckering parameters (Cremer & Pople, 1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]) were calculated using PLATON (Spek, 2020[Spek, A. L. (2020). Acta Cryst. E76, 1-11.]). We have observed the same conformation of the iso­propyl­edene fragment in other carbohydrates (Doboszewski & Naza­renko, 2003[Doboszewski, B. & Naza­renko, A. Y. (2003). Acta Cryst. E59, 158-160.]; Doboszewski et al., 2010[Doboszewski, B., Silva, P. R. da, Nazarenko, A. Y. & Nemykin, V. N. (2010). Acta Cryst. E66, o3217-o3218.]).

[Figure 1]
Figure 1
The title compound with the atom-numbering scheme and 50% probability displacement ellipsoids

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[link], Fig. 2[link]). Only weak C—H⋯O (Fig. 3[link]) contacts exist between neighboring layers; the C5⋯O4(−[{1\over 2}] + x, [{3\over 2}] − y, −z) distance is 3.389 (2) Å. Similar hydrogen bonds have been observed in various carbohydrates (Desiraju & Steiner, 1999[Desiraju, G. R. & Steiner, T. (1999). The Weak Hydrogen Bond in Structural Chemistry and Biology. New York: Oxford University Press Inc.]). A short intra­molecular contact between oxygen O1 and the H12B atom of a neighboring methyl­ene group (Table 1[link]) 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.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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+{\script{1\over 2}}, -z+{\script{1\over 2}}].
[Figure 2]
Figure 2
Packing diagram of the title compound; view along [100] vector. Highlighted are the layers of mol­ecules connected via O—H⋯O hydrogen bonds.
[Figure 3]
Figure 3
Detail view of the inter­molecular C—H⋯O inter­actions.

Synthesis and crystallization

The synthesis of the title compound is described in Kuzuhara et al. (1971[Kuzuhara, H., Terayama, H., Ohrui, H. & Emoto, S. (1971). Carbohydr. Res. 20, 165-169.]) and Soares et al. (2013[Soares, F. da Paixão, Silva, M. J. & Doboszewski, B. (2013). Carbohydr. Res. 380, 143-148.]).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. An additional dataset was collected using Cu Kα radiation, resulting in a Flack parameter of 0.09 (13) and a probability of the absolute configuration being correct of 1.000.

Table 2
Experimental details

Crystal data
Chemical formula C8H14O5
Mr 190.19
Crystal system, space group Orthorhombic, P212121
Temperature (K) 173
a, b, c (Å) 5.9196 (3), 7.3562 (4), 21.1126 (12)
V3) 919.36 (9)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.12
Crystal size (mm) 0.45 × 0.43 × 0.37
 
Data collection
Diffractometer Bruker PHOTON-100 CMOS
Absorption correction Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.944, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 20693, 4938, 4094
Rint 0.029
(sin θ/λ)max−1) 0.862
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.109, 1.03
No. of reflections 4938
No. of parameters 174
H-atom treatment All H-atom parameters refined
Δρmax, Δρmin (e Å−3) 0.41, −0.30
Absolute structure Flack x determined using 1496 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter 0.3 (2) su large for Mo Kα?
Computer programs: APEX2 and SAINT (Bruker, 2013[Bruker (2013). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]) and Mercury (Macrae et al., 2020[Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M. & Wood, P. A. (2020). J. Appl. Cryst. 53, 226-235.]).

Structural data


Computing details top

Data collection: APEX2 (Bruker, 2013); cell refinement: 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).

1,2-O-Isopropylidene-β-D-lyxo-furanose top
Crystal data top
C8H14O5Dx = 1.374 Mg m3
Mr = 190.19Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121Cell parameters from 9980 reflections
a = 5.9196 (3) Åθ = 2.9–37.3°
b = 7.3562 (4) ŵ = 0.12 mm1
c = 21.1126 (12) ÅT = 173 K
V = 919.36 (9) Å3Block, colourless
Z = 40.45 × 0.43 × 0.37 mm
F(000) = 408
Data collection top
Bruker PHOTON-100 CMOS
diffractometer
4938 independent reflections
Radiation source: sealed tube4094 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.029
Detector resolution: 10.4 pixels mm-1θmax = 37.8°, θmin = 2.9°
φ and ω scansh = 910
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)
k = 1212
Tmin = 0.944, Tmax = 1.000l = 2736
20693 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.043All 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 reflectionsΔρmax = 0.41 e Å3
174 parametersΔρmin = 0.30 e Å3
0 restraintsAbsolute structure: Flack x determined using 1496 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Primary atom site location: dualAbsolute structure parameter: 0.3 (2)
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.94830 (15)0.59218 (11)0.12758 (4)0.02153 (15)
O20.66312 (15)0.80371 (13)0.20056 (4)0.02597 (18)
H20.556 (4)0.878 (3)0.2138 (10)0.044 (6)*
O31.1047 (2)0.99300 (12)0.10435 (5)0.0312 (2)
O41.21881 (17)0.71302 (12)0.06429 (5)0.02782 (19)
O81.31943 (18)1.00933 (18)0.22671 (6)0.0398 (3)
H81.294 (4)1.090 (3)0.2540 (11)0.044 (6)*
C51.0438 (2)0.84268 (15)0.06643 (5)0.02228 (19)
H51.021 (4)0.887 (3)0.0247 (9)0.034 (5)*
C60.7654 (2)0.88480 (15)0.14745 (5)0.02169 (19)
H60.661 (3)0.966 (3)0.1270 (9)0.029 (5)*
C71.1331 (2)0.54276 (15)0.08756 (5)0.02213 (19)
C90.9802 (2)0.99245 (15)0.16300 (5)0.0234 (2)
H90.946 (3)1.122 (2)0.1724 (8)0.021 (4)*
C100.8456 (2)0.74699 (15)0.09853 (5)0.02134 (18)
H100.728 (4)0.710 (3)0.0702 (8)0.029 (5)*
C111.3131 (2)0.45089 (18)0.12639 (7)0.0291 (2)
H11A1.446 (5)0.431 (4)0.0981 (11)0.057 (7)*
H11B1.367 (4)0.524 (3)0.1593 (11)0.039 (5)*
H11C1.264 (4)0.337 (3)0.1401 (9)0.040 (5)*
C121.1131 (2)0.91394 (18)0.21779 (6)0.0272 (2)
H12A1.027 (4)0.919 (3)0.2536 (9)0.027 (4)*
H12B1.143 (3)0.789 (3)0.2097 (9)0.030 (5)*
C131.0527 (3)0.4265 (2)0.03239 (7)0.0335 (3)
H13A0.942 (4)0.487 (3)0.0070 (10)0.038 (5)*
H13B1.178 (4)0.399 (3)0.0052 (11)0.039 (5)*
H13C0.997 (4)0.314 (3)0.0495 (11)0.048 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0226 (4)0.0202 (3)0.0218 (3)0.0006 (3)0.0036 (3)0.0012 (3)
O20.0209 (4)0.0287 (4)0.0283 (4)0.0024 (3)0.0084 (3)0.0056 (3)
O30.0406 (5)0.0230 (4)0.0302 (4)0.0094 (4)0.0161 (4)0.0036 (3)
O40.0254 (4)0.0216 (3)0.0364 (4)0.0009 (3)0.0104 (3)0.0034 (3)
O80.0203 (4)0.0466 (6)0.0527 (6)0.0001 (4)0.0012 (4)0.0295 (5)
C50.0271 (5)0.0219 (4)0.0178 (4)0.0010 (4)0.0032 (4)0.0018 (3)
C60.0197 (4)0.0237 (4)0.0216 (4)0.0030 (4)0.0022 (3)0.0031 (4)
C70.0245 (5)0.0190 (4)0.0229 (4)0.0015 (3)0.0036 (4)0.0009 (3)
C90.0254 (5)0.0200 (4)0.0248 (4)0.0010 (4)0.0074 (4)0.0021 (4)
C100.0204 (4)0.0242 (4)0.0194 (4)0.0005 (3)0.0017 (3)0.0006 (3)
C110.0261 (5)0.0259 (5)0.0351 (6)0.0023 (4)0.0018 (5)0.0018 (5)
C120.0228 (5)0.0307 (5)0.0280 (5)0.0011 (4)0.0006 (4)0.0080 (4)
C130.0401 (7)0.0305 (6)0.0298 (5)0.0008 (5)0.0020 (5)0.0109 (5)
Geometric parameters (Å, º) top
O1—C71.4291 (14)C6—C101.5230 (16)
O1—C101.4292 (14)C7—C111.5049 (18)
O2—H20.88 (3)C7—C131.5214 (17)
O2—C61.4071 (14)C9—H90.993 (17)
O3—C51.4120 (14)C9—C121.5135 (18)
O3—C91.4409 (14)C10—H100.95 (2)
O4—C51.4090 (15)C11—H11A1.00 (3)
O4—C71.4380 (14)C11—H11B0.94 (2)
O8—H80.84 (3)C11—H11C0.93 (3)
O8—C121.4210 (17)C12—H12A0.91 (2)
C5—H50.947 (19)C12—H12B0.95 (2)
C5—C101.5267 (16)C13—H13A0.96 (2)
C6—H60.96 (2)C13—H13B0.96 (2)
C6—C91.5334 (17)C13—H13C0.96 (3)
C10—O1—C7105.93 (8)C12—C9—C6113.43 (10)
C6—O2—H2107.3 (14)C12—C9—H9108.6 (10)
C5—O3—C9110.76 (9)O1—C10—C5103.36 (9)
C5—O4—C7108.61 (9)O1—C10—C6111.84 (8)
C12—O8—H8106.6 (17)O1—C10—H10110.7 (12)
O3—C5—H5107.2 (12)C5—C10—H10114.3 (11)
O3—C5—C10107.79 (9)C6—C10—C5103.51 (9)
O4—C5—O3111.14 (10)C6—C10—H10112.6 (12)
O4—C5—H5107.7 (13)C7—C11—H11A107.4 (15)
O4—C5—C10105.50 (9)C7—C11—H11B112.8 (14)
C10—C5—H5117.5 (14)C7—C11—H11C110.7 (13)
O2—C6—H6110.1 (12)H11A—C11—H11B105 (2)
O2—C6—C9113.91 (9)H11A—C11—H11C107 (2)
O2—C6—C10113.10 (9)H11B—C11—H11C113.2 (18)
C9—C6—H6107.9 (12)O8—C12—C9111.08 (11)
C10—C6—H6108.1 (12)O8—C12—H12A110.5 (13)
C10—C6—C9103.33 (9)O8—C12—H12B110.0 (12)
O1—C7—O4104.51 (8)C9—C12—H12A109.2 (12)
O1—C7—C11109.53 (10)C9—C12—H12B109.1 (12)
O1—C7—C13110.88 (10)H12A—C12—H12B106.9 (16)
O4—C7—C11109.11 (10)C7—C13—H13A112.5 (13)
O4—C7—C13109.77 (10)C7—C13—H13B109.5 (14)
C11—C7—C13112.71 (11)C7—C13—H13C107.8 (13)
O3—C9—C6103.98 (9)H13A—C13—H13B107.1 (18)
O3—C9—H9105.9 (10)H13A—C13—H13C112 (2)
O3—C9—C12113.08 (11)H13B—C13—H13C108 (2)
C6—C9—H9111.5 (11)
O2—C6—C9—O3155.65 (9)C6—C9—C12—O8175.05 (9)
O2—C6—C9—C1232.41 (13)C7—O1—C10—C531.62 (10)
O2—C6—C10—O141.18 (13)C7—O1—C10—C6142.34 (9)
O2—C6—C10—C5151.81 (9)C7—O4—C5—O3121.62 (10)
O3—C5—C10—O1102.57 (10)C7—O4—C5—C105.06 (12)
O3—C5—C10—C614.19 (12)C9—O3—C5—O4108.31 (11)
O3—C9—C12—O856.97 (13)C9—O3—C5—C106.84 (13)
O4—C5—C10—O116.25 (11)C9—C6—C10—O182.45 (11)
O4—C5—C10—C6133.01 (9)C9—C6—C10—C528.18 (11)
C5—O3—C9—C624.89 (13)C10—O1—C7—O435.34 (11)
C5—O3—C9—C1298.58 (12)C10—O1—C7—C11152.12 (9)
C5—O4—C7—O124.63 (12)C10—O1—C7—C1382.87 (11)
C5—O4—C7—C11141.71 (10)C10—C6—C9—O332.55 (11)
C5—O4—C7—C1394.33 (12)C10—C6—C9—C1290.68 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2···O8i0.88 (2)1.72 (2)2.5946 (15)169 (2)
O8—H8···O2ii0.84 (2)1.86 (2)2.6567 (16)158 (2)
C12—H12B···O10.95 (2)2.54 (2)3.1908 (15)126.1 (14)
Symmetry codes: (i) x1, 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.

References

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