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

Doboszewski, B.; Nazarenko, A.Y.

doi:10.1107/S2414314620016302

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 5| Part 12| December 2020| x201630

https://doi.org/10.1107/S2414314620016302

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

Bogdan Doboszewski ^a and Alexander Y. Nazarenko ^b ^*

^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.

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 envelope conformation 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 carbohydrates (Doboszewski & Nazarenko, 2003 ; Doboszewski et al., 2010 ).

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, Fig. 2). Only weak C—H⋯O (Fig. 3) 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 ). 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.

Table 1
Hydrogen-bond geometry (Å, °)

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) ; (ii) $[-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

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
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) and Soares et al. (2013).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. 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
M_r	190.19
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	173
a, b, c (Å)	5.9196 (3), 7.3562 (4), 21.1126 (12)
V (Å³)	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 )
T_min, T_max	0.944, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	20693, 4938, 4094
R_int	0.029
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.41, −0.30
Absolute structure	Flack x determined using 1496 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.3 (2) su large for Mo Kα?
Computer programs: APEX2 and SAINT (Bruker, 2013 ), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ), OLEX2 (Dolomanov et al., 2009 ) and Mercury (Macrae et al., 2020 ).

Structural data

CCDC reference: 2050681

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314620016302/zq4044sup1.cif

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) CIF file for chirality confirmation. DOI: https://doi.org/10.1107/S2414314620016302/zq4044sup4.txt

checkCIF report

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

C₈H₁₄O₅	D_x = 1.374 Mg m⁻³
M_r = 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

Data collection top

Bruker PHOTON-100 CMOS diffractometer	4938 independent reflections
Radiation source: sealed tube	4094 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.029
Detector resolution: 10.4 pixels mm^-1	θ_max = 37.8°, θ_min = 2.9°
φ and ω scans	h = −9→10
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	k = −12→12
T_min = 0.944, T_max = 1.000	l = −27→36
20693 measured reflections

Refinement top

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(F_o²) + (0.0654P)² + 0.0319P] where P = (F_o² + 2F_c²)/3
S = 1.03	(Δ/σ)_max < 0.001
4938 reflections	Δρ_max = 0.41 e Å⁻³
174 parameters	Δρ_min = −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)

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

	x	y	z	U_iso*/U_eq
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)*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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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