1′-Deoxy-1′-hydroxy­methyl-1,2′-O-iso­propyl­idene-β-D-arabino­furan­ose

The six-membered ring of the title compound, C₉H₁₆O₅, adopts a chair conformation, while the furan­ose five-membered ring has an envelope conformation. The packing is stabilized by a two-dimensional network of intermolecular hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.036
• wR factor = 0.081
• Data-to-parameter ratio = 9.2

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

General Notes



REFLT_03
         From the CIF: _diffrn_reflns_theta_max           27.55
         From the CIF: _reflns_number_total               1211
         Count of symmetry unique reflns         1213
         Completeness (_total/calc)             99.84%
         TEST3: Check Friedels for noncentro structure
         Estimate of Friedel pairs measured         0
         Fraction of Friedel pairs measured     0.000
         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.

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S1. Comment

C-Glycosides have received much attention recently as the building blocks for synthetic purposes or as mimics of the naturally occurring compounds (Jimenez-Barbero et al., 2001; Du & Linhardt, 1998; Postema, 1995; Levy & Tang, 1995). Nucleosides with a methylene or an ethylene linker between the carbohydrate and the nucleobase were prepared for antiviral screening or for incorporation into antisense sequences (Boal et al., 1996; Doboszewski, 1997; Efimtseva et al., 1995; Hossain et al., 1996). A novel approach (Doboszewski, 1997) to obtain a carbohydrate substrate suitable for conversion into nucleosides is shown in the Scheme below. Easy separation of anomers was possible after the final isopropylidenation step because the product (II) does not react with acetone. The target product, (I), was also obtained via acid-catalyzed dehydration of D-mannitol or 1,6-di-O-benzoyl-D-mannitol followed by isopropylidenation (Koerner et al., 1977). Acetonide (I) spontaneously crystallized upon standing in a refrigerator to form well resolved crystals which were subjected to X-ray study. Some further results dealing with the synthesis of C-glycosyl substrates with the lyxo configuration suitable for conversion into C-analogs of the nucleoside have been recently published (Doboszewski, 2002).

The bond distances in (I) are in good agreement with values observed in related compounds (Allen et al., 1987). The six-membered ring adopts a chair conformation, while the five-membered ring has an envelope conformation with the C3 atom located out of mean plane. The packing is stabilized by two-dimensional network of hydrogen bonds employing both hydroxy groups of the compound (I). The shortest C—H···O contact is longer than 3.45 Å and hardly can play a significant role in intermolecular interactions.

S2. Experimental

Compound (I) spontaneously crystallized from the reaction mixture upon standing in the refrigerator to yield well formed prismatic crystals. The absolute structure was known from the synthetic route; m.p. 388–390 K, α_D 27° (c 1.5, EtOH). All H atoms were fixed geometrically and allowed to ride on their parent C and O atoms.

Computing details

Data collection: P4 Software (Siemens, 1995); cell refinement: P4 Software; data reduction: P4 Software; program(s) used to solve structure: SHELXS86 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: PLATON (Spek, 1990).

Figures

	Fig. 1. View of the molecule of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. The molecular packing of (I).

1'-deoxy-1'-hydroxymethyl-1,2'-O-isopropylidene-β-D-arabinofuranose

Crystal data

C9H16O5	F(000) = 220
Mr = 204.22	Dx = 1.371 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 24 reflections
a = 6.227 (5) Å	θ = 12–13°
b = 9.817 (8) Å	µ = 0.11 mm^−1
c = 8.292 (5) Å	T = 293 K
β = 102.56 (5)°	Prism, colourless
V = 494.8 (6) Å^3	0.32 × 0.28 × 0.27 mm
Z = 2

Data collection

Siemens P4 diffractometer	Rint = 0.019
Radiation source: fine-focus sealed tube	θmax = 27.6°, θmin = 2.5°
Graphite monochromator	h = 0→8
ω scans	k = 0→12
1315 measured reflections	l = −10→10
1211 independent reflections	3 standard reflections every 100 reflections
1007 reflections with I > 2σ(I)	intensity decay: <1%

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.081	H-atom parameters constrained
S = 1.06	w = 1/[σ^2(Fo^2) + (0.039P)^2 + 0.0294P] where P = (Fo^2 + 2Fc^2)/3
1211 reflections	(Δ/σ)max < 0.001
131 parameters	Δρmax = 0.13 e Å^−3
1 restraint	Δρmin = −0.15 e Å^−3

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.9599 (3)	0.37827 (19)	0.6661 (2)	0.0444 (5)
O2	0.6509 (3)	0.2918 (2)	0.33347 (19)	0.0443 (5)
H2B	0.5661	0.2373	0.2777	0.053*
O3	1.0429 (2)	0.14562 (18)	0.91387 (18)	0.0374 (4)
O4	0.7019 (2)	0.13557 (16)	0.73154 (18)	0.0340 (4)
O5	0.6728 (3)	0.59401 (19)	0.7728 (2)	0.0485 (5)
H5B	0.7633	0.5951	0.8610	0.058*
C1	1.1580 (4)	0.1771 (3)	0.7875 (3)	0.0393 (6)
H1A	1.2242	0.0946	0.7560	0.047*
H1B	1.2755	0.2408	0.8307	0.047*
C2	1.0080 (4)	0.2385 (3)	0.6358 (3)	0.0340 (5)
H2	1.0806	0.2339	0.5423	0.041*
C3	0.7855 (4)	0.1680 (2)	0.5896 (3)	0.0313 (5)
H3	0.7884	0.0886	0.5185	0.038*
C4	0.6365 (4)	0.2807 (3)	0.5015 (3)	0.0328 (5)
H4	0.4839	0.2670	0.5112	0.039*
C5	0.7341 (4)	0.4094 (2)	0.5932 (3)	0.0330 (5)
H5A	0.7300	0.4831	0.5128	0.040*
C6	0.6184 (4)	0.4567 (3)	0.7258 (3)	0.0407 (6)
H6A	0.4605	0.4492	0.6852	0.049*
H6B	0.6598	0.3982	0.8218	0.049*
C7	0.8488 (4)	0.0640 (3)	0.8591 (3)	0.0358 (6)
C8	0.7361 (5)	0.0589 (4)	1.0017 (3)	0.0583 (9)
H8A	0.7070	0.1499	1.0335	0.070*
H8B	0.8293	0.0134	1.0933	0.070*
H8C	0.5999	0.0101	0.9695	0.070*
C9	0.9057 (5)	−0.0757 (3)	0.8030 (4)	0.0533 (7)
H9A	0.7729	−0.1262	0.7625	0.064*
H9B	0.9952	−0.1234	0.8945	0.064*
H9C	0.9851	−0.0662	0.7165	0.064*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0319 (8)	0.0336 (10)	0.0627 (12)	−0.0064 (8)	−0.0009 (8)	−0.0048 (9)
O2	0.0509 (11)	0.0500 (12)	0.0287 (8)	−0.0077 (10)	0.0013 (7)	0.0009 (9)
O3	0.0349 (8)	0.0417 (10)	0.0321 (8)	−0.0021 (8)	−0.0004 (7)	−0.0005 (8)
O4	0.0268 (8)	0.0382 (10)	0.0350 (8)	0.0000 (7)	0.0025 (7)	0.0090 (7)
O5	0.0583 (12)	0.0365 (10)	0.0418 (10)	0.0120 (9)	−0.0088 (8)	−0.0059 (8)
C1	0.0266 (10)	0.0422 (14)	0.0471 (13)	−0.0023 (11)	0.0038 (10)	0.0013 (12)
C2	0.0305 (11)	0.0354 (13)	0.0379 (12)	−0.0026 (10)	0.0111 (9)	−0.0013 (11)
C3	0.0345 (12)	0.0295 (12)	0.0295 (11)	−0.0015 (10)	0.0061 (9)	−0.0021 (9)
C4	0.0311 (11)	0.0377 (13)	0.0283 (10)	−0.0034 (11)	0.0035 (9)	0.0012 (10)
C5	0.0330 (11)	0.0320 (12)	0.0320 (12)	−0.0013 (10)	0.0028 (9)	0.0061 (10)
C6	0.0436 (14)	0.0358 (14)	0.0397 (13)	0.0043 (12)	0.0025 (11)	−0.0009 (11)
C7	0.0297 (12)	0.0371 (16)	0.0370 (12)	−0.0008 (11)	−0.0008 (10)	0.0068 (11)
C8	0.0465 (15)	0.082 (2)	0.0477 (16)	0.0091 (16)	0.0126 (13)	0.0303 (17)
C9	0.0519 (16)	0.0299 (14)	0.0708 (19)	−0.0006 (12)	−0.0026 (14)	0.0073 (13)

Geometric parameters (Å, º)

O1—C5	1.437 (3)	C3—H3	0.9800
O1—C2	1.439 (3)	C4—C5	1.531 (3)
O2—C4	1.420 (3)	C4—H4	0.9800
O2—H2B	0.8200	C5—C6	1.513 (4)
O3—C1	1.426 (3)	C5—H5A	0.9800
O3—C7	1.438 (3)	C6—H6A	0.9700
O4—C3	1.422 (3)	C6—H6B	0.9700
O4—C7	1.424 (3)	C7—C8	1.502 (4)
O5—C6	1.423 (3)	C7—C9	1.515 (4)
O5—H5B	0.8200	C8—H8A	0.9600
C1—C2	1.519 (3)	C8—H8B	0.9600
C1—H1A	0.9700	C8—H8C	0.9600
C1—H1B	0.9700	C9—H9A	0.9600
C2—C3	1.522 (3)	C9—H9B	0.9600
C2—H2	0.9800	C9—H9C	0.9600
C3—C4	1.524 (3)
C5—O1—C2	110.59 (18)	O1—C5—C4	106.25 (19)
C4—O2—H2B	109.5	C6—C5—C4	114.4 (2)
C1—O3—C7	114.25 (17)	O1—C5—H5A	108.8
C3—O4—C7	115.70 (17)	C6—C5—H5A	108.8
C6—O5—H5B	109.5	C4—C5—H5A	108.8
O3—C1—C2	112.20 (19)	O5—C6—C5	111.5 (2)
O3—C1—H1A	109.2	O5—C6—H6A	109.3
C2—C1—H1A	109.2	C5—C6—H6A	109.3
O3—C1—H1B	109.2	O5—C6—H6B	109.3
C2—C1—H1B	109.2	C5—C6—H6B	109.3
H1A—C1—H1B	107.9	H6A—C6—H6B	108.0
O1—C2—C1	110.4 (2)	O4—C7—O3	108.64 (19)
O1—C2—C3	105.33 (19)	O4—C7—C8	105.47 (19)
C1—C2—C3	113.0 (2)	O3—C7—C8	105.9 (2)
O1—C2—H2	109.4	O4—C7—C9	112.0 (2)
C1—C2—H2	109.4	O3—C7—C9	111.4 (2)
C3—C2—H2	109.4	C8—C7—C9	113.1 (2)
O4—C3—C2	111.74 (18)	C7—C8—H8A	109.5
O4—C3—C4	105.38 (17)	C7—C8—H8B	109.5
C2—C3—C4	102.5 (2)	H8A—C8—H8B	109.5
O4—C3—H3	112.2	C7—C8—H8C	109.5
C2—C3—H3	112.2	H8A—C8—H8C	109.5
C4—C3—H3	112.2	H8B—C8—H8C	109.5
O2—C4—C3	111.4 (2)	C7—C9—H9A	109.5
O2—C4—C5	108.7 (2)	C7—C9—H9B	109.5
C3—C4—C5	103.07 (17)	H9A—C9—H9B	109.5
O2—C4—H4	111.1	C7—C9—H9C	109.5
C3—C4—H4	111.1	H9A—C9—H9C	109.5
C5—C4—H4	111.1	H9B—C9—H9C	109.5
O1—C5—C6	109.7 (2)
C7—O3—C1—C2	52.1 (3)	C2—O1—C5—C6	120.8 (2)
C5—O1—C2—C1	−140.73 (19)	C2—O1—C5—C4	−3.4 (2)
C5—O1—C2—C3	−18.5 (3)	O2—C4—C5—O1	−94.7 (2)
O3—C1—C2—O1	76.0 (2)	C3—C4—C5—O1	23.6 (2)
O3—C1—C2—C3	−41.6 (3)	O2—C4—C5—C6	144.1 (2)
C7—O4—C3—C2	−51.0 (2)	C3—C4—C5—C6	−97.6 (2)
C7—O4—C3—C4	−161.65 (18)	O1—C5—C6—O5	77.5 (2)
O1—C2—C3—O4	−80.0 (2)	C4—C5—C6—O5	−163.27 (19)
C1—C2—C3—O4	40.6 (3)	C3—O4—C7—O3	59.3 (2)
O1—C2—C3—C4	32.5 (2)	C3—O4—C7—C8	172.5 (2)
C1—C2—C3—C4	153.0 (2)	C3—O4—C7—C9	−64.1 (2)
O4—C3—C4—O2	−160.24 (17)	C1—O3—C7—O4	−59.4 (2)
C2—C3—C4—O2	82.7 (2)	C1—O3—C7—C8	−172.3 (2)
O4—C3—C4—C5	83.3 (2)	C1—O3—C7—C9	64.4 (3)
C2—C3—C4—C5	−33.7 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2B···O5^i	0.82	2.02	2.800 (4)	158
O5—H5B···O3^ii	0.82	2.05	2.853 (4)	166

Symmetry codes: (i) −x+1, y−1/2, −z+1; (ii) −x+2, y+1/2, −z+2.