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Acta Cryst. (2009). E65, o280    [ doi:10.1107/S1600536809000397 ]

[beta]-D-Altrose

Y. Watanabe, H. Yoshida, K. Takeda, T. Ishi and S. Kamitori

Abstract top

The molecule of the title compound, C6H12O6, [systematic name: (2R,3S,4R,5R,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol] adopts a 4C1 chair conformation with the anomeric hydroxyl group in the equatorial position. All hydroxyl groups act as donors and acceptors in hydrogen bonding and the molecule is involved in ten intermolecular O-H...O interactions [O...O = 2.672 (5)-2.776 (4) Å] with eight neighbouring molecules. Two independent O-H...O-H... helices extending along the z axis are found in this structure.

Comment top

The molecular structure of β-D-altrose is shown in Fig. 1. The aldopyranose ring adopts a 4C1 chair conformation and the anomer hydroxyl group is in equatorial position pointing to a β-anomer structure. All bond distances and angles between non-hydrogen atoms of β-D-altrose are in the normal range, and torsion angles along C—C and C—O bonds show staggered conformations.

The crystal of β-D-altrose belongs to a trigonal crystal system, space group <it>P</it>32, which is for the first time found in the crystal structure of aldohexoses.

Related literature top

For the crystal structure of methyl α-D-altrose, see: Gatehouse et al. (1971).

Experimental top

D-Altrose was purchased from Sigma-Aldrich Ltd., Japan. Crystals were prepared by dissolving 20 mg of D-altrose in distilled water (4 ml). Suitable crystals for X-ray data collection were obtained by slow evaporation of this solution at 293 K.

Refinement top

In the absence of significant anomalous scattering effects, Friedel pairs were averaged. The absolute structure was assigned from the known hand of the starting material. Hydrogen atoms were treated as riding, with C—H distances of 0.97-0.98 Å and O—H distances of 0.82 Å and Uiso(H) = 1.2Ueq(C,O).

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO (Rigaku, 1998); data reduction: PROCESS-AUTO (Rigaku, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A view of the molecule of β-D-altrose, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. Crystal packing of β-D-altrose, with two helices along the z axis shown as dashed lines.
(2R,3S,4R,5R,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol top
Crystal data top
C6H12O6Dx = 1.580 Mg m−3
Mr = 180.16Cu Kα radiation, λ = 1.54178 Å
Trigonal, P32Cell parameters from 2323 reflections
Hall symbol: P 32θ = 7.2–68.0°
a = 7.1749 (13) ŵ = 1.25 mm−1
c = 12.7415 (15) ÅT = 293 K
V = 568.04 (16) Å3Block, colorless
Z = 30.30 × 0.30 × 0.30 mm
F(000) = 288
Data collection top
Rigaku RAPID2
diffractometer		719 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.113
graphiteθmax = 71.8°, θmin = 7.1°
ω scansh = −8→8
6207 measured reflectionsk = −8→8
736 independent reflectionsl = −15→14
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.046Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.125H-atom parameters constrained
S = 1.15 w = 1/[σ2(Fo2) + (0.0525P)2 + 0.4167P]
where P = (Fo2 + 2Fc2)/3
736 reflections(Δ/σ)max < 0.001
109 parametersΔρmax = 0.24 e Å−3
1 restraintΔρmin = −0.24 e Å−3
Crystal data top
C6H12O6Z = 3
Mr = 180.16Cu Kα radiation
Trigonal, P32µ = 1.25 mm−1
a = 7.1749 (13) ÅT = 293 K
c = 12.7415 (15) Å0.30 × 0.30 × 0.30 mm
V = 568.04 (16) Å3
Data collection top
Rigaku RAPID2
diffractometer		719 reflections with I > 2σ(I)
6207 measured reflectionsRint = 0.113
736 independent reflectionsθmax = 71.8°
Refinement top
R[F2 > 2σ(F2)] = 0.046H-atom parameters constrained
wR(F2) = 0.125Δρmax = 0.24 e Å−3
S = 1.15Δρmin = −0.24 e Å−3
736 reflectionsAbsolute structure: ?
109 parametersFlack parameter: ?
1 restraintRogers parameter: ?
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. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.3898 (7)1.0634 (7)0.3892 (3)0.0257 (9)
H10.49841.15750.33810.031*
C20.4763 (7)1.1433 (7)0.4977 (4)0.0299 (10)
H20.50691.29180.50540.036*
C30.6856 (7)1.1365 (7)0.5119 (4)0.0309 (10)
H30.73661.17600.58430.037*
C40.6474 (7)0.9113 (8)0.4889 (4)0.0288 (9)
H40.54740.81180.54150.035*
C50.5476 (6)0.8366 (7)0.3805 (3)0.0253 (8)
H50.64910.92950.32670.030*
C60.4840 (8)0.6073 (7)0.3594 (4)0.0306 (9)
H6A0.60000.58320.38070.037*
H6B0.35830.51390.40110.037*
O10.1989 (5)1.0605 (6)0.3667 (2)0.0349 (8)
HO10.11361.00320.41510.042*
O20.3161 (5)1.0090 (5)0.5728 (3)0.0309 (7)
HO20.34991.06490.63090.037*
O30.8420 (6)1.2911 (6)0.4415 (3)0.0435 (9)
HO30.94531.38170.47500.052*
O40.8438 (6)0.9049 (7)0.4941 (3)0.0441 (9)
HO40.86880.89050.55550.053*
O50.3537 (5)0.8494 (5)0.3754 (3)0.0267 (7)
O60.4365 (5)0.5522 (5)0.2508 (3)0.0362 (8)
HO60.30570.48190.24280.043*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.034 (2)0.028 (2)0.021 (2)0.0197 (17)−0.0044 (17)−0.0027 (16)
C20.037 (2)0.027 (2)0.020 (2)0.0118 (19)0.0030 (18)0.0018 (16)
C30.027 (2)0.035 (2)0.018 (2)0.0056 (18)0.0015 (17)0.0001 (16)
C40.025 (2)0.044 (2)0.018 (2)0.0172 (19)0.0026 (16)0.0059 (18)
C50.026 (2)0.030 (2)0.024 (2)0.0169 (17)0.0009 (15)0.0031 (16)
C60.038 (2)0.036 (2)0.022 (2)0.021 (2)0.0038 (18)0.0017 (18)
O10.0384 (17)0.0461 (18)0.0308 (18)0.0291 (15)0.0000 (13)−0.0011 (14)
O20.0343 (17)0.0324 (16)0.0248 (15)0.0157 (14)0.0036 (13)−0.0009 (13)
O30.0348 (18)0.0380 (19)0.0288 (18)−0.0034 (14)0.0043 (15)0.0018 (15)
O40.0302 (17)0.077 (3)0.0334 (19)0.0334 (19)−0.0011 (14)0.0063 (18)
O50.0262 (15)0.0278 (15)0.0283 (15)0.0152 (13)−0.0072 (12)−0.0043 (12)
O60.0282 (15)0.0430 (18)0.0367 (19)0.0172 (15)0.0019 (13)−0.0121 (15)
Geometric parameters (Å, °) top
C1—O11.389 (5)C4—H40.9800
C1—O51.435 (5)C5—O51.441 (5)
C1—C21.506 (6)C5—C61.495 (6)
C1—H10.9800C5—H50.9800
C2—O21.435 (5)C6—O61.432 (6)
C2—C31.537 (6)C6—H6A0.9700
C2—H20.9800C6—H6B0.9700
C3—O31.431 (5)O1—HO10.8199
C3—C41.526 (6)O2—HO20.8188
C3—H30.9800O3—HO30.8199
C4—O41.434 (5)O4—HO40.8206
C4—C51.524 (6)O6—HO60.8199
O1—C1—O5108.1 (3)O4—C4—H4108.6
O1—C1—C2114.3 (4)C5—C4—H4108.6
O5—C1—C2109.8 (3)C3—C4—H4108.6
O1—C1—H1108.2O5—C5—C6106.8 (3)
O5—C1—H1108.2O5—C5—C4108.5 (3)
C2—C1—H1108.2C6—C5—C4112.5 (3)
O2—C2—C1108.5 (4)O5—C5—H5109.7
O2—C2—C3111.5 (4)C6—C5—H5109.7
C1—C2—C3108.7 (4)C4—C5—H5109.7
O2—C2—H2109.4O6—C6—C5112.2 (4)
C1—C2—H2109.4O6—C6—H6A109.2
C3—C2—H2109.4C5—C6—H6A109.2
O3—C3—C4110.9 (4)O6—C6—H6B109.2
O3—C3—C2107.5 (4)C5—C6—H6B109.2
C4—C3—C2110.5 (3)H6A—C6—H6B107.9
O3—C3—H3109.3C1—O1—HO1109.6
C4—C3—H3109.3C2—O2—HO2109.4
C2—C3—H3109.3C3—O3—HO3109.6
O4—C4—C5109.0 (4)C4—O4—HO4109.1
O4—C4—C3111.5 (4)C1—O5—C5113.6 (3)
C5—C4—C3110.5 (4)C6—O6—HO6109.3
O1—C1—C2—O258.2 (5)C2—C3—C4—C554.3 (5)
O5—C1—C2—O2−63.4 (4)O4—C4—C5—O5−178.4 (3)
O1—C1—C2—C3179.6 (3)C3—C4—C5—O5−55.6 (4)
O5—C1—C2—C358.1 (4)O4—C4—C5—C663.7 (5)
O2—C2—C3—O3−174.0 (3)C3—C4—C5—C6−173.4 (4)
C1—C2—C3—O366.4 (4)O5—C5—C6—O674.4 (4)
O2—C2—C3—C464.8 (5)C4—C5—C6—O6−166.8 (3)
C1—C2—C3—C4−54.8 (5)O1—C1—O5—C5170.9 (3)
O3—C3—C4—O456.6 (5)C2—C1—O5—C5−63.9 (4)
C2—C3—C4—O4175.7 (4)C6—C5—O5—C1−177.1 (3)
O3—C3—C4—C5−64.8 (5)C4—C5—O5—C161.5 (4)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—HO1···O4i0.821.972.743 (5)156
O2—HO2···O3ii0.821.962.768 (5)169
O3—HO3···O6iii0.821.882.672 (5)162
O4—HO4···O1iv0.821.942.748 (5)167
O6—HO6···O2v0.821.962.776 (4)174
Symmetry codes: (i) x−1, y, z; (ii) −x+y, −x+2, z+1/3; (iii) −x+y+1, −x+2, z+1/3; (iv) −x+y, −x+1, z+1/3; (v) −y+1, x−y+1, z−1/3.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—HO1···O4i0.821.972.743 (5)156
O2—HO2···O3ii0.821.962.768 (5)169
O3—HO3···O6iii0.821.882.672 (5)162
O4—HO4···O1iv0.821.942.748 (5)167
O6—HO6···O2v0.821.962.776 (4)174
Symmetry codes: (i) x−1, y, z; (ii) −x+y, −x+2, z+1/3; (iii) −x+y+1, −x+2, z+1/3; (iv) −x+y, −x+1, z+1/3; (v) −y+1, x−y+1, z−1/3.
Acknowledgements top

This study was supported in part by a Grant-in-Aid for Young Scientists (B) (19770085) from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and by the Fund for Kagawa University Young Scientists 2007–8.

references
References top

Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.

Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.

Gatehouse, B. M. & Poppleton, B. J. (1971). Acta Cryst. B27, 871–876.

Rigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.