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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.
Supporting information
CCDC reference: 204689
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (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.
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, αD 27° (c 1.5, EtOH). All H atoms were fixed geometrically and allowed to ride on their parent C and O atoms.
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).
1'-deoxy-1'-hydroxymethyl-1,2'-
O-isopropylidene-
β-
D-arabinofuranose
top
Crystal data top
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) Å3 | 0.32 × 0.28 × 0.27 mm |
Z = 2 | |
Data collection top
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 top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.081 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.039P)2 + 0.0294P] where P = (Fo2 + 2Fc2)/3 |
1211 reflections | (Δ/σ)max < 0.001 |
131 parameters | Δρmax = 0.13 e Å−3 |
1 restraint | Δρmin = −0.15 e Å−3 |
Crystal data top
C9H16O5 | V = 494.8 (6) Å3 |
Mr = 204.22 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 6.227 (5) Å | µ = 0.11 mm−1 |
b = 9.817 (8) Å | T = 293 K |
c = 8.292 (5) Å | 0.32 × 0.28 × 0.27 mm |
β = 102.56 (5)° | |
Data collection top
Siemens P4 diffractometer | Rint = 0.019 |
1315 measured reflections | 3 standard reflections every 100 reflections |
1211 independent reflections | intensity decay: <1% |
1007 reflections with I > 2σ(I) | |
Refinement top
R[F2 > 2σ(F2)] = 0.036 | 1 restraint |
wR(F2) = 0.081 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.13 e Å−3 |
1211 reflections | Δρmin = −0.15 e Å−3 |
131 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | 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 (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
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) top
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) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2B···O5i | 0.82 | 2.02 | 2.800 (4) | 158 |
O5—H5B···O3ii | 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. |
Experimental details
Crystal data |
Chemical formula | C9H16O5 |
Mr | 204.22 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 293 |
a, b, c (Å) | 6.227 (5), 9.817 (8), 8.292 (5) |
β (°) | 102.56 (5) |
V (Å3) | 494.8 (6) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.32 × 0.28 × 0.27 |
|
Data collection |
Diffractometer | Siemens P4 diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1315, 1211, 1007 |
Rint | 0.019 |
(sin θ/λ)max (Å−1) | 0.651 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.081, 1.06 |
No. of reflections | 1211 |
No. of parameters | 131 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.13, −0.15 |
Selected geometric parameters (Å, º) topO1—C5 | 1.437 (3) | O4—C7 | 1.424 (3) |
O1—C2 | 1.439 (3) | C1—C2 | 1.519 (3) |
O3—C1 | 1.426 (3) | C2—C3 | 1.522 (3) |
O3—C7 | 1.438 (3) | C3—C4 | 1.524 (3) |
O4—C3 | 1.422 (3) | C4—C5 | 1.531 (3) |
| | | |
C5—O1—C2 | 110.59 (18) | O4—C3—C2 | 111.74 (18) |
C1—O3—C7 | 114.25 (17) | C2—C3—C4 | 102.5 (2) |
C3—O4—C7 | 115.70 (17) | C3—C4—C5 | 103.07 (17) |
O3—C1—C2 | 112.20 (19) | O1—C5—C4 | 106.25 (19) |
O1—C2—C3 | 105.33 (19) | O4—C7—O3 | 108.64 (19) |
C1—C2—C3 | 113.0 (2) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2B···O5i | 0.82 | 2.02 | 2.800 (4) | 158 |
O5—H5B···O3ii | 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. |
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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.