β-d-Altrose

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

doi:10.1107/S1600536809000397

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 2| February 2009| Page o280

doi:10.1107/S1600536809000397

Open

access

β-D-Altrose

Yuji Watanabe,^a Hiromi Yoshida,^a Kosei Takeda,^a Tomohiko Ishi ^b and Shigehiro Kamitori ^a ^*

^aDivision of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan, and ^bFaculty of Engineering, Kagawa University, 2217-20 Hayashi-machi, Takamatsu, Kagawa 761-0396, Japan
^*Correspondence e-mail: kamitori@med.kagawa-u.ac.jp

(Received 11 December 2008; accepted 6 January 2009; online 10 January 2009)

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.

Related literature

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

Experimental

Crystal data

C₆H₁₂O₆
M_r = 180.16
Trigonal, P 3₂
a = 7.1749 (13) Å
c = 12.7415 (15) Å
V = 568.04 (16) Å³
Z = 3
Cu Kα radiation
μ = 1.25 mm⁻¹
T = 293 (2) K
0.30 × 0.30 × 0.30 mm

Data collection

Rigaku RAPID2 diffractometer
Absorption correction: none
6207 measured reflections
736 independent reflections
719 reflections with I > 2σ(I)
R_int = 0.113

Refinement

R[F² > 2σ(F²)] = 0.046
wR(F²) = 0.125
S = 1.15
736 reflections
109 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.24 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—HO1⋯O4ⁱ	0.82	1.97	2.743 (5)	156
O2—HO2⋯O3ⁱⁱ	0.82	1.96	2.768 (5)	169
O3—HO3⋯O6ⁱⁱⁱ	0.82	1.88	2.672 (5)	162
O4—HO4⋯O1^iv	0.82	1.94	2.748 (5)	167
O6—HO6⋯O2^v	0.82	1.96	2.776 (4)	174
Symmetry codes: (i) x-1, y, z; (ii) $[-x+y, -x+2, z+{\script{1\over 3}}]$ ; (iii) $[-x+y+1, -x+2, z+{\script{1\over 3}}]$ ; (iv) $[-x+y, -x+1, z+{\script{1\over 3}}]$ ; (v) $[-y+1, x-y+1, z-{\script{1\over 3}}]$ .

Data collection: PROCESS-AUTO (Rigaku, 1998 ); cell refinement: PROCESS-AUTO; data reduction: PROCESS-AUTO; 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.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809000397/gk2181sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809000397/gk2181Isup2.hkl

checkCIF report

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.

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

	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.
	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

C₆H₁₂O₆	D_x = 1.580 Mg m⁻³
M_r = 180.16	Cu Kα radiation, λ = 1.54178 Å
Trigonal, P3₂	Cell parameters from 2323 reflections
Hall symbol: P 32	θ = 7.2–68.0°
a = 7.1749 (13) Å	µ = 1.25 mm⁻¹
c = 12.7415 (15) Å	T = 293 K
V = 568.04 (16) Å³	Block, colorless
Z = 3	0.30 × 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 tube	R_int = 0.113
Graphite monochromator	θ_max = 71.8°, θ_min = 7.1°
ω scans	h = −8→8
6207 measured reflections	k = −8→8
736 independent reflections	l = −15→14

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)] = 0.046	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.125	H-atom parameters constrained
S = 1.15	w = 1/[σ²(F_o²) + (0.0525P)² + 0.4167P] where P = (F_o² + 2F_c²)/3
736 reflections	(Δ/σ)_max < 0.001
109 parameters	Δρ_max = 0.24 e Å⁻³
1 restraint	Δρ_min = −0.24 e Å⁻³

Crystal data top

C₆H₁₂O₆	Z = 3
M_r = 180.16	Cu Kα radiation
Trigonal, P3₂	µ = 1.25 mm⁻¹
a = 7.1749 (13) Å	T = 293 K
c = 12.7415 (15) Å	0.30 × 0.30 × 0.30 mm
V = 568.04 (16) Å³

Data collection top

Rigaku RAPID2 diffractometer	719 reflections with I > 2σ(I)
6207 measured reflections	R_int = 0.113
736 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.046	1 restraint
wR(F²) = 0.125	H-atom parameters constrained
S = 1.15	Δρ_max = 0.24 e Å⁻³
736 reflections	Δρ_min = −0.24 e Å⁻³
109 parameters

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

	x	y	z	U_iso*/U_eq
C1	0.3898 (7)	1.0634 (7)	0.3892 (3)	0.0257 (9)
H1	0.4984	1.1575	0.3381	0.031*
C2	0.4763 (7)	1.1433 (7)	0.4977 (4)	0.0299 (10)
H2	0.5069	1.2918	0.5054	0.036*
C3	0.6856 (7)	1.1365 (7)	0.5119 (4)	0.0309 (10)
H3	0.7366	1.1760	0.5843	0.037*
C4	0.6474 (7)	0.9113 (8)	0.4889 (4)	0.0288 (9)
H4	0.5474	0.8118	0.5415	0.035*
C5	0.5476 (6)	0.8366 (7)	0.3805 (3)	0.0253 (8)
H5	0.6491	0.9295	0.3267	0.030*
C6	0.4840 (8)	0.6073 (7)	0.3594 (4)	0.0306 (9)
H6A	0.6000	0.5832	0.3807	0.037*
H6B	0.3583	0.5139	0.4011	0.037*
O1	0.1989 (5)	1.0605 (6)	0.3667 (2)	0.0349 (8)
HO1	0.1136	1.0032	0.4151	0.042*
O2	0.3161 (5)	1.0090 (5)	0.5728 (3)	0.0309 (7)
HO2	0.3499	1.0649	0.6309	0.037*
O3	0.8420 (6)	1.2911 (6)	0.4415 (3)	0.0435 (9)
HO3	0.9453	1.3817	0.4750	0.052*
O4	0.8438 (6)	0.9049 (7)	0.4941 (3)	0.0441 (9)
HO4	0.8688	0.8905	0.5555	0.053*
O5	0.3537 (5)	0.8494 (5)	0.3754 (3)	0.0267 (7)
O6	0.4365 (5)	0.5522 (5)	0.2508 (3)	0.0362 (8)
HO6	0.3057	0.4819	0.2428	0.043*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.034 (2)	0.028 (2)	0.021 (2)	0.0197 (17)	−0.0044 (17)	−0.0027 (16)
C2	0.037 (2)	0.027 (2)	0.020 (2)	0.0118 (19)	0.0030 (18)	0.0018 (16)
C3	0.027 (2)	0.035 (2)	0.018 (2)	0.0056 (18)	0.0015 (17)	0.0001 (16)
C4	0.025 (2)	0.044 (2)	0.018 (2)	0.0172 (19)	0.0026 (16)	0.0059 (18)
C5	0.026 (2)	0.030 (2)	0.024 (2)	0.0169 (17)	0.0009 (15)	0.0031 (16)
C6	0.038 (2)	0.036 (2)	0.022 (2)	0.021 (2)	0.0038 (18)	0.0017 (18)
O1	0.0384 (17)	0.0461 (18)	0.0308 (18)	0.0291 (15)	0.0000 (13)	−0.0011 (14)
O2	0.0343 (17)	0.0324 (16)	0.0248 (15)	0.0157 (14)	0.0036 (13)	−0.0009 (13)
O3	0.0348 (18)	0.0380 (19)	0.0288 (18)	−0.0034 (14)	0.0043 (15)	0.0018 (15)
O4	0.0302 (17)	0.077 (3)	0.0334 (19)	0.0334 (19)	−0.0011 (14)	0.0063 (18)
O5	0.0262 (15)	0.0278 (15)	0.0283 (15)	0.0152 (13)	−0.0072 (12)	−0.0043 (12)
O6	0.0282 (15)	0.0430 (18)	0.0367 (19)	0.0172 (15)	0.0019 (13)	−0.0121 (15)

Geometric parameters (Å, º) top

C1—O1	1.389 (5)	C4—H4	0.9800
C1—O5	1.435 (5)	C5—O5	1.441 (5)
C1—C2	1.506 (6)	C5—C6	1.495 (6)
C1—H1	0.9800	C5—H5	0.9800
C2—O2	1.435 (5)	C6—O6	1.432 (6)
C2—C3	1.537 (6)	C6—H6A	0.9700
C2—H2	0.9800	C6—H6B	0.9700
C3—O3	1.431 (5)	O1—HO1	0.8199
C3—C4	1.526 (6)	O2—HO2	0.8188
C3—H3	0.9800	O3—HO3	0.8199
C4—O4	1.434 (5)	O4—HO4	0.8206
C4—C5	1.524 (6)	O6—HO6	0.8199

O1—C1—O5	108.1 (3)	O4—C4—H4	108.6
O1—C1—C2	114.3 (4)	C5—C4—H4	108.6
O5—C1—C2	109.8 (3)	C3—C4—H4	108.6
O1—C1—H1	108.2	O5—C5—C6	106.8 (3)
O5—C1—H1	108.2	O5—C5—C4	108.5 (3)
C2—C1—H1	108.2	C6—C5—C4	112.5 (3)
O2—C2—C1	108.5 (4)	O5—C5—H5	109.7
O2—C2—C3	111.5 (4)	C6—C5—H5	109.7
C1—C2—C3	108.7 (4)	C4—C5—H5	109.7
O2—C2—H2	109.4	O6—C6—C5	112.2 (4)
C1—C2—H2	109.4	O6—C6—H6A	109.2
C3—C2—H2	109.4	C5—C6—H6A	109.2
O3—C3—C4	110.9 (4)	O6—C6—H6B	109.2
O3—C3—C2	107.5 (4)	C5—C6—H6B	109.2
C4—C3—C2	110.5 (3)	H6A—C6—H6B	107.9
O3—C3—H3	109.3	C1—O1—HO1	109.6
C4—C3—H3	109.3	C2—O2—HO2	109.4
C2—C3—H3	109.3	C3—O3—HO3	109.6
O4—C4—C5	109.0 (4)	C4—O4—HO4	109.1
O4—C4—C3	111.5 (4)	C1—O5—C5	113.6 (3)
C5—C4—C3	110.5 (4)	C6—O6—HO6	109.3

O1—C1—C2—O2	58.2 (5)	C2—C3—C4—C5	54.3 (5)
O5—C1—C2—O2	−63.4 (4)	O4—C4—C5—O5	−178.4 (3)
O1—C1—C2—C3	179.6 (3)	C3—C4—C5—O5	−55.6 (4)
O5—C1—C2—C3	58.1 (4)	O4—C4—C5—C6	63.7 (5)
O2—C2—C3—O3	−174.0 (3)	C3—C4—C5—C6	−173.4 (4)
C1—C2—C3—O3	66.4 (4)	O5—C5—C6—O6	74.4 (4)
O2—C2—C3—C4	64.8 (5)	C4—C5—C6—O6	−166.8 (3)
C1—C2—C3—C4	−54.8 (5)	O1—C1—O5—C5	170.9 (3)
O3—C3—C4—O4	56.6 (5)	C2—C1—O5—C5	−63.9 (4)
C2—C3—C4—O4	175.7 (4)	C6—C5—O5—C1	−177.1 (3)
O3—C3—C4—C5	−64.8 (5)	C4—C5—O5—C1	61.5 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—HO1···O4ⁱ	0.82	1.97	2.743 (5)	156
O2—HO2···O3ⁱⁱ	0.82	1.96	2.768 (5)	169
O3—HO3···O6ⁱⁱⁱ	0.82	1.88	2.672 (5)	162
O4—HO4···O1^iv	0.82	1.94	2.748 (5)	167
O6—HO6···O2^v	0.82	1.96	2.776 (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.

Experimental details

Crystal data
Chemical formula	C₆H₁₂O₆
M_r	180.16
Crystal system, space group	Trigonal, P3₂
Temperature (K)	293
a, c (Å)	7.1749 (13), 12.7415 (15)
V (Å³)	568.04 (16)
Z	3
Radiation type	Cu Kα
µ (mm⁻¹)	1.25
Crystal size (mm)	0.30 × 0.30 × 0.30

Data collection
Diffractometer	Rigaku RAPID2 diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	6207, 736, 719
R_int	0.113
(sin θ/λ)_max (Å⁻¹)	0.616

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.046, 0.125, 1.15
No. of reflections	736
No. of parameters	109
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.24, −0.24

Computer programs: PROCESS-AUTO (Rigaku, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 (Farrugia, 1997).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—HO1···O4ⁱ	0.82	1.97	2.743 (5)	156
O2—HO2···O3ⁱⁱ	0.82	1.96	2.768 (5)	169
O3—HO3···O6ⁱⁱⁱ	0.82	1.88	2.672 (5)	162
O4—HO4···O1^iv	0.82	1.94	2.748 (5)	167
O6—HO6···O2^v	0.82	1.96	2.776 (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

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

Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA. Google Scholar
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Gatehouse, B. M. & Poppleton, B. J. (1971). Acta Cryst. B27, 871–876. CSD CrossRef CAS IUCr Journals Web of Science Google Scholar
Rigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar