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The stereochemistry of crystalline 1-deoxy-4-C-hydroxymethyl-3,4-O-isopropylidene-β-L-ribulofuranose, C9H16O5, was unequivocally established by X-ray crystallographic analysis to be the β-anomer; the absolute configuration was determined by the use of D-ribose as a starting material.
Supporting information
CCDC reference: 647273
Key indicators
- Single-crystal X-ray study
- T = 150 K
- Mean (C-C) = 0.003 Å
- R factor = 0.041
- wR factor = 0.106
- Data-to-parameter ratio = 10.4
checkCIF/PLATON results
No syntax errors found
Alert level B
ABSTM02_ALERT_3_B The ratio of expected to reported Tmax/Tmin(RR') is < 0.75
Tmin and Tmax reported: 0.690 0.990
Tmin(prime) and Tmax expected: 0.946 0.989
RR(prime) = 0.729
Please check that your absorption correction is appropriate.
PLAT061_ALERT_3_B Tmax/Tmin Range Test RR' too Large ............. 0.73
Alert level G
REFLT03_ALERT_4_G 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.
From the CIF: _diffrn_reflns_theta_max 27.46
From the CIF: _reflns_number_total 1315
Count of symmetry unique reflns 1351
Completeness (_total/calc) 97.34%
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
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1 = . S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2 = . S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3 = . S
0 ALERT level A = In general: serious problem
2 ALERT level B = Potentially serious problem
0 ALERT level C = Check and explain
4 ALERT level G = General alerts; check
3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
0 ALERT type 2 Indicator that the structure model may be wrong or deficient
2 ALERT type 3 Indicator that the structure quality may be low
1 ALERT type 4 Improvement, methodology, query or suggestion
0 ALERT type 5 Informative message, check
Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.
(2
R,3S,4
S)-4-(hydroxymethyl)-3,4-
O-isopropylidene-2-
methyltetrahydrofuran-2,3,4-triol
top
Crystal data top
C9H16O5 | F(000) = 440 |
Mr = 204.22 | Dx = 1.346 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 1245 reflections |
a = 6.2405 (2) Å | θ = 5–27° |
b = 10.8088 (3) Å | µ = 0.11 mm−1 |
c = 14.9369 (6) Å | T = 150 K |
V = 1007.53 (6) Å3 | Plate, colourless |
Z = 4 | 0.50 × 0.20 × 0.10 mm |
Data collection top
Nonius KappaCCD diffractometer | 1210 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.066 |
ω scans | θmax = 27.5°, θmin = 5.2° |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | h = −8→8 |
Tmin = 0.69, Tmax = 0.99 | k = −13→13 |
7730 measured reflections | l = −18→18 |
1315 independent reflections | |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.041 | H-atom parameters constrained |
wR(F2) = 0.106 | w = 1/[σ2(F2) + (0.08P)2 + 0.46P], where P = [max(Fo2,0) + 2Fc2]/3 |
S = 0.84 | (Δ/σ)max = 0.000274 |
1315 reflections | Δρmax = 0.27 e Å−3 |
127 parameters | Δρmin = −0.27 e Å−3 |
0 restraints | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
C1 | 0.4665 (4) | 0.74459 (18) | 0.67571 (12) | 0.0180 | |
C2 | 0.5277 (4) | 0.60607 (18) | 0.68257 (13) | 0.0190 | |
C3 | 0.6693 (4) | 0.5833 (2) | 0.60104 (14) | 0.0212 | |
O4 | 0.7697 (2) | 0.69873 (13) | 0.58458 (9) | 0.0220 | |
C5 | 0.6151 (4) | 0.79423 (19) | 0.60212 (14) | 0.0213 | |
O6 | 0.5229 (3) | 0.55251 (15) | 0.53238 (9) | 0.0266 | |
C7 | 0.8450 (4) | 0.4880 (2) | 0.61209 (15) | 0.0294 | |
O8 | 0.6530 (3) | 0.59994 (14) | 0.76291 (9) | 0.0222 | |
C9 | 0.5781 (4) | 0.69651 (19) | 0.82087 (13) | 0.0226 | |
O10 | 0.5235 (3) | 0.79561 (12) | 0.76172 (9) | 0.0210 | |
C11 | 0.3864 (4) | 0.6512 (2) | 0.87373 (15) | 0.0286 | |
C12 | 0.7615 (4) | 0.7381 (2) | 0.87942 (15) | 0.0323 | |
C13 | 0.2320 (4) | 0.7688 (2) | 0.65531 (14) | 0.0223 | |
O14 | 0.1938 (3) | 0.89698 (14) | 0.63582 (10) | 0.0264 | |
H21 | 0.4078 | 0.5501 | 0.6842 | 0.0197* | |
H51 | 0.6816 | 0.8700 | 0.6206 | 0.0242* | |
H52 | 0.5301 | 0.8109 | 0.5501 | 0.0245* | |
H71 | 0.9168 | 0.4750 | 0.5561 | 0.0443* | |
H72 | 0.9529 | 0.5161 | 0.6535 | 0.0434* | |
H73 | 0.7893 | 0.4091 | 0.6316 | 0.0446* | |
H111 | 0.3425 | 0.7168 | 0.9127 | 0.0414* | |
H112 | 0.4397 | 0.5800 | 0.9060 | 0.0407* | |
H113 | 0.2763 | 0.6283 | 0.8313 | 0.0417* | |
H121 | 0.7204 | 0.8077 | 0.9152 | 0.0463* | |
H122 | 0.8003 | 0.6730 | 0.9227 | 0.0462* | |
H123 | 0.8950 | 0.7577 | 0.8453 | 0.0458* | |
H131 | 0.1463 | 0.7449 | 0.7073 | 0.0259* | |
H132 | 0.1832 | 0.7195 | 0.6031 | 0.0267* | |
H13 | 0.2537 | 0.9371 | 0.6774 | 0.0395* | |
H7 | 0.6052 | 0.5557 | 0.4890 | 0.0394* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C1 | 0.0228 (10) | 0.0161 (9) | 0.0152 (9) | −0.0002 (8) | −0.0028 (8) | −0.0014 (7) |
C2 | 0.0207 (10) | 0.0193 (9) | 0.0169 (9) | −0.0022 (8) | −0.0014 (8) | −0.0003 (7) |
C3 | 0.0248 (11) | 0.0209 (10) | 0.0179 (9) | −0.0023 (9) | 0.0016 (8) | −0.0011 (7) |
O4 | 0.0223 (7) | 0.0208 (7) | 0.0230 (7) | −0.0021 (6) | 0.0033 (6) | 0.0011 (5) |
C5 | 0.0254 (10) | 0.0188 (10) | 0.0196 (9) | 0.0001 (9) | 0.0012 (9) | 0.0011 (7) |
O6 | 0.0313 (8) | 0.0324 (8) | 0.0160 (6) | −0.0075 (7) | 0.0009 (7) | −0.0041 (6) |
C7 | 0.0337 (12) | 0.0245 (11) | 0.0299 (11) | 0.0059 (10) | 0.0077 (10) | 0.0000 (9) |
O8 | 0.0291 (8) | 0.0218 (7) | 0.0157 (6) | 0.0060 (7) | −0.0034 (6) | −0.0017 (5) |
C9 | 0.0314 (12) | 0.0208 (10) | 0.0156 (9) | 0.0050 (9) | −0.0028 (8) | −0.0010 (8) |
O10 | 0.0315 (8) | 0.0180 (7) | 0.0134 (6) | 0.0005 (6) | −0.0038 (6) | −0.0017 (5) |
C11 | 0.0377 (13) | 0.0269 (11) | 0.0213 (10) | 0.0038 (10) | 0.0058 (10) | 0.0032 (8) |
C12 | 0.0392 (13) | 0.0329 (12) | 0.0248 (10) | 0.0015 (11) | −0.0131 (10) | −0.0036 (9) |
C13 | 0.0233 (10) | 0.0228 (10) | 0.0207 (9) | 0.0019 (9) | −0.0010 (8) | −0.0011 (8) |
O14 | 0.0336 (9) | 0.0233 (7) | 0.0223 (7) | 0.0065 (7) | −0.0091 (7) | −0.0031 (6) |
Geometric parameters (Å, º) top
C1—C2 | 1.549 (3) | C7—H73 | 0.966 |
C1—C5 | 1.535 (3) | O8—C9 | 1.434 (2) |
C1—O10 | 1.443 (2) | C9—O10 | 1.430 (2) |
C1—C13 | 1.518 (3) | C9—C11 | 1.515 (3) |
C2—C3 | 1.525 (3) | C9—C12 | 1.509 (3) |
C2—O8 | 1.434 (2) | C11—H111 | 0.957 |
C2—H21 | 0.963 | C11—H112 | 0.967 |
C3—O4 | 1.418 (3) | C11—H113 | 0.967 |
C3—O6 | 1.413 (3) | C12—H121 | 0.959 |
C3—C7 | 1.513 (3) | C12—H122 | 0.985 |
O4—C5 | 1.437 (3) | C12—H123 | 1.000 |
C5—H51 | 0.959 | C13—O14 | 1.436 (3) |
C5—H52 | 0.958 | C13—H131 | 0.978 |
O6—H7 | 0.827 | C13—H132 | 0.992 |
C7—H71 | 0.959 | O14—H13 | 0.845 |
C7—H72 | 0.964 | | |
| | | |
C2—C1—C5 | 103.68 (16) | H71—C7—H73 | 107.5 |
C2—C1—O10 | 104.47 (15) | H72—C7—H73 | 109.7 |
C5—C1—O10 | 110.81 (16) | C2—O8—C9 | 107.09 (15) |
C2—C1—C13 | 114.68 (17) | O8—C9—O10 | 104.47 (14) |
C5—C1—C13 | 112.24 (16) | O8—C9—C11 | 109.66 (18) |
O10—C1—C13 | 110.53 (18) | O10—C9—C11 | 112.11 (18) |
C1—C2—C3 | 104.25 (16) | O8—C9—C12 | 108.63 (19) |
C1—C2—O8 | 103.56 (15) | O10—C9—C12 | 108.42 (18) |
C3—C2—O8 | 110.17 (16) | C11—C9—C12 | 113.15 (18) |
C1—C2—H21 | 114.7 | C1—O10—C9 | 108.83 (14) |
C3—C2—H21 | 111.7 | C9—C11—H111 | 107.7 |
O8—C2—H21 | 111.9 | C9—C11—H112 | 104.2 |
C2—C3—O4 | 104.63 (16) | H111—C11—H112 | 112.6 |
C2—C3—O6 | 104.05 (16) | C9—C11—H113 | 107.6 |
O4—C3—O6 | 111.52 (17) | H111—C11—H113 | 112.6 |
C2—C3—C7 | 116.28 (18) | H112—C11—H113 | 111.6 |
O4—C3—C7 | 107.34 (18) | C9—C12—H121 | 110.8 |
O6—C3—C7 | 112.78 (18) | C9—C12—H122 | 110.7 |
C3—O4—C5 | 107.71 (15) | H121—C12—H122 | 105.1 |
C1—C5—O4 | 106.56 (16) | C9—C12—H123 | 113.5 |
C1—C5—H51 | 110.7 | H121—C12—H123 | 109.9 |
O4—C5—H51 | 112.1 | H122—C12—H123 | 106.4 |
C1—C5—H52 | 108.2 | C1—C13—O14 | 111.55 (18) |
O4—C5—H52 | 111.0 | C1—C13—H131 | 108.8 |
H51—C5—H52 | 108.2 | O14—C13—H131 | 109.0 |
C3—O6—H7 | 99.1 | C1—C13—H132 | 111.2 |
C3—C7—H71 | 110.1 | O14—C13—H132 | 107.9 |
C3—C7—H72 | 111.2 | H131—C13—H132 | 108.3 |
H71—C7—H72 | 106.2 | C13—O14—H13 | 105.8 |
C3—C7—H73 | 111.9 | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O14—H13···O8i | 0.85 | 2.06 | 2.831 (2) | 152 |
O6—H7···O14ii | 0.83 | 2.01 | 2.783 (2) | 155 |
Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) x+1/2, −y+3/2, −z+1. |
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