β-d-Altrose

Abstract

The mol­ecule of the title compound, C₆H₁₂O₆, [systematic name: (2R,3S,4R,5R,6R)-6-(hydroxy­meth­yl)oxane-2,3,4,5-tetrol] adopts a ⁴ C ₁ 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,

• a = 7.1749 (13) Å

• c = 12.7415 (15) Å

• V = 568.04 (16) ų

• 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[F ² > 2σ(F ²)] = 0.046

• wR(F ²) = 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

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.

Supplementary Material

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

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⋯O1iv	0.82	1.94	2.748 (5)	167
O6—HO6⋯O2v	0.82	1.96	2.776 (4)	174

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

supplementary crystallographic information

Comment

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.

Experimental

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

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 U_iso(H) = 1.2Ueq(C,O).

Figures

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.

Crystal data

C6H12O6	Dx = 1.580 Mg m−3
Mr = 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

Rigaku RAPID2 diffractometer	719 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.113
graphite	θmax = 71.8°, θmin = 7.1°
ω scans	h = −8→8
6207 measured reflections	k = −8→8
736 independent reflections	l = −15→14

Refinement

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(Fo2) + (0.0525P)2 + 0.4167P] where P = (Fo2 + 2Fc2)/3
736 reflections	(Δ/σ)max < 0.001
109 parameters	Δρmax = 0.24 e Å−3
1 restraint	Δρmin = −0.24 e Å−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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, °)

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, °)

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···O1iv	0.82	1.94	2.748 (5)	167
O6—HO6···O2v	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.