Crystal structure of β-d,l-allose

Ishii, T.; Senoo, T.; Kozakai, T.; Fukada, K.; Sakane, G.

doi:10.1107/S2056989015000353

organic compounds

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doi:10.1107/S2056989015000353

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Crystal structure of β-D,L-allose

Tomohiko Ishii,^a ^* Tatsuya Senoo,^a Taro Kozakai,^b Kazuhiro Fukada ^b and Genta Sakane ^c

^aDepartment of Advanced Materials Science, Faculty of Engineering, Kagawa University, 2217-20 Hayashi-cho, Takamatsu, Kagawa 761-0396, Japan, ^bDepartment of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Kagawa 761-0795, Japan, and ^cDepartment of Chemistry, Faculty of Science, Okayama University of Science, 1-1 Ridaicho, Kita-ku, Okayama 700-0005, Japan
^*Correspondence e-mail: tishii@eng.kagawa-u.ac.jp

Edited by H. Ishida, Okayama University, Japan (Received 4 December 2014; accepted 8 January 2015; online 31 January 2015)

The title compound, C₆H₁₂O₆, a C-3 position epimer of glucose, was crystallized from an equimolar mixture of D- and L-allose. It was confirmed that D-allose (L-allose) formed β-pyranose with a ⁴C₁ (¹C₄) conformation in the crystal. In the crystal, molecules are linked by O—H⋯O hydrogen bond, forming a three-dimensional framework. The cell volume of the racemic β-D,L-allose is 739.36 (3) Å³, which is about 10 Å³ smaller than that of chiral β-D-allose [V = 751.0 (2) Å³].

Keywords: crystal structure; racemic compound; rare sugar; O—H⋯O hydrogen bonding.

CCDC reference: 1037204

1. Related literature

For the crystal structure of the chiral β-D-allose, see: Kroon-Batenburg et al. (1984 ). For the crystal structure of racemic D,L-arabinose, see: Longchambon et al. (1985 ) and of chiral L-arabinose, see: Takagi & Jeffrey (1977 ). For the synthesis of chiral D- or L-allose, see: Menavuvu et al. (2006 ); Morimoto et al. (2006 , 2013 ); Shimonishi & Izumori (1996 ).

2. Experimental

2.1. Crystal data

C₆H₁₂O₆
M_r = 180.16
Monoclinic, P 2₁ /c
a = 4.98211 (10) Å
b = 12.5624 (3) Å
c = 11.8156 (3) Å
β = 91.1262 (14)°
V = 739.36 (3) Å³
Z = 4
Cu Kα radiation
μ = 1.29 mm⁻¹
T = 295 K
0.10 × 0.10 × 0.10 mm

2.2. Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.687, T_max = 0.879
12963 measured reflections
1350 independent reflections
1232 reflections with F² > 2σ(F²)
R_int = 0.075

2.3. Refinement

R[F² > 2σ(F²)] = 0.037
wR(F²) = 0.102
S = 1.07
1350 reflections
115 parameters
H-atom parameters constrained
Δρ_max = 0.37 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1A⋯O4ⁱ	0.82	1.88	2.6884 (16)	171
O2—H2A⋯O6ⁱ	0.82	1.99	2.8044 (16)	172
O3—H3A⋯O2ⁱⁱ	0.82	1.94	2.7494 (16)	169
O4—H4A⋯O1ⁱⁱⁱ	0.82	1.94	2.7384 (16)	163
O6—H6A⋯O5^iv	0.82	2.03	2.8439 (15)	171
Symmetry codes: (i) $[-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) -x, -y+2, -z+2; (iii) $[-x, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (iv) -x+1, -y+2, -z+1.

Data collection: RAPID-AUTO (Rigaku, 2009 ); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SIR2008 in Il Milione (Burla et al., 2007 ); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015 ); molecular graphics: CrystalStructure (Rigaku, 2010 ); software used to prepare material for publication: CrystalStructure.

Supporting information

CCDC reference: 1037204

Crystal structure: contains datablocks General, I. DOI: 10.1107/S2056989015000353/is5386sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015000353/is5386Isup2.hkl

checkCIF report

Comment top

Orientations of three hydrogen atoms (H1A, H2A, H4A) located on three equatorial OH groups at C-1, C-2 and C-4 positions are perpendicular to the pyranose ring. A hydrogen atom (H3A) on the axial OH group at C-3 position is located along to the radial direction. Therefore, it is inconvenient to obtain the intramolecular hydrogen bonding. Only a weak intramolecular hydrogen bonding (O4—H4A···O3) is found in the racemic β-D,L-allose, with long interatomic distance (H4A···O3; 2.49 Å) and the small bond angle (O4—H4A···O3; 106°). In the case of the chiral β-D-allose, there are five hydrogen bonding (O1—H1A···O4, O2—H2A···O6, O3—H3A···O2, O4—H4A···O1, O6—H6A···O5) observed between two adjacent D-allose molecules (Kroon-Batenburg et al., 1984). These five hydrogen bondings are also observed in the racemic β-D,L-allose with a same corresponding sequential number. Three of them (O1—H1A···O4ⁱ, O2—H2A···O6ⁱ and O4—H4A···O1ⁱⁱⁱ; Table 1) are used for creating the hydrogen bonding network between two adjacent D-molecules or L-molecules, forming a homochiral layer parallel to the ab-plane. The remaining hydrogen bonds (O3—H3A···O2ⁱⁱ and O6—H6A···O5^iv; Table 1) are used for connecting between the D- and L-allose molecules. An example of the unit cell volume of racemic compound less than that of chiral one was also found in the case of racemic D,L-arabinose (V = 596.516 Å³ at 175 K; Longchambon et al., 1985) and chiral L-arabinose (V = 598.661 Å³ at 123 K; Takagi et al., 1977).

Related literature top

For the crystal structure of the chiral β-D-allose, see: Kroon-Batenburg et al. (1984). For the crystal structure of racemic D,L-arabinose, see: Longchambon et al. (1985) and of chiral L-arabinose, see: Takagi & Jeffrey (1977). For the synthesis of chiral D- or L-allose, see: Menavuvu et al. (2006); Morimoto et al. (2006, 2013); Shimonishi & Izumori (1996).

Experimental top

D-Allose and L-allose were biosynthesized from D-psicose and L-psicose using L-rhammose isomerase (Menavuvu et al., 2006; Morimoto et al., 2006) and L-ribose isomerase (Shimonishi et al., 1996; Morimoto et al., 2013), respectively. Equimolar mixture of D-allose and L-allose was dissolved in water to give 15 wt% solution, and then it was kept at 30 °C. After two days, small crystals appeared and they were grown at 25 °C for two weeks yielded prism-shaped crystals of sufficient size. Melting point of the obtained crystals was confirmed to be 181 °C, which was 30–35 °C higher than the melting point of β-D-allose.

Computing details top

Data collection: RAPID-AUTO (Rigaku, 2009); cell refinement: RAPID-AUTO (Rigaku, 2009); data reduction: RAPID-AUTO (Rigaku, 2009); program(s) used to solve structure: SIR2008 in Il Milione (Burla et al., 2007); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015); molecular graphics: CrystalStructure (Rigaku, 2010); software used to prepare material for publication: CrystalStructure (Rigaku, 2010).

Figures top

	Fig. 1. ORTEP view of the title compound with the atom-labeling scheme. The thermal ellipsoids of all non-hydrogen atoms are drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radius.
	Fig. 2. Part of the crystal structure of the title compound with hydrogen-bonding network represented as light green dashed lines, viewed down the tilted a axis. The hydrogen atoms are omitted for clarity.
	Fig. 3. Part of the crystal structure of the chiral β-D-allose (Kroon-Batenburg et al., 1984) with hydrogen-bonding network represented as light blue dashed lines, viewed down the a axis. The hydrogen atoms are omitted for clarity.

β-D,L-Allose top

Crystal data top

C₆H₁₂O₆	F(000) = 384.00
M_r = 180.16	D_x = 1.618 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54187 Å
Hall symbol: -P 2ybc	Cell parameters from 11709 reflections
a = 4.98211 (10) Å	θ = 3.5–68.2°
b = 12.5624 (3) Å	µ = 1.29 mm⁻¹
c = 11.8156 (3) Å	T = 295 K
β = 91.1262 (14)°	Block, colorless
V = 739.36 (3) Å³	0.10 × 0.10 × 0.10 mm
Z = 4

Data collection top

Rigaku R-AXIS RAPID diffractometer	1232 reflections with F² > 2σ(F²)
Detector resolution: 10.000 pixels mm^-1	R_int = 0.075
ω scans	θ_max = 68.2°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −6→6
T_min = 0.687, T_max = 0.879	k = −15→15
12963 measured reflections	l = −14→14
1350 independent reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.037	H-atom parameters constrained
wR(F²) = 0.102	w = 1/[σ²(F_o²) + (0.0463P)² + 0.3535P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max = 0.001
1350 reflections	Δρ_max = 0.37 e Å⁻³
115 parameters	Δρ_min = −0.22 e Å⁻³
0 restraints	Extinction correction: SHELXL2013 (Sheldrick, 2015)
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0159 (15)
Secondary atom site location: difference Fourier map

Crystal data top

C₆H₁₂O₆	V = 739.36 (3) Å³
M_r = 180.16	Z = 4
Monoclinic, P2₁/c	Cu Kα radiation
a = 4.98211 (10) Å	µ = 1.29 mm⁻¹
b = 12.5624 (3) Å	T = 295 K
c = 11.8156 (3) Å	0.10 × 0.10 × 0.10 mm
β = 91.1262 (14)°

Data collection top

Rigaku R-AXIS RAPID diffractometer	1350 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1232 reflections with F² > 2σ(F²)
T_min = 0.687, T_max = 0.879	R_int = 0.075
12963 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.037	0 restraints
wR(F²) = 0.102	H-atom parameters constrained
S = 1.07	Δρ_max = 0.37 e Å⁻³
1350 reflections	Δρ_min = −0.22 e Å⁻³
115 parameters

Special details top

Refinement. Refinement was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 σ(F²) is used only for calculating R-factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.1621 (3)	0.79703 (8)	0.67894 (10)	0.0283 (3)
O2	0.1676 (3)	0.85269 (9)	0.91826 (9)	0.0311 (4)
O3	−0.0213 (2)	1.05723 (8)	0.88005 (9)	0.0244 (3)
O4	0.3426 (3)	1.21319 (8)	0.80258 (10)	0.0270 (3)
O5	0.2673 (2)	0.96785 (8)	0.63757 (8)	0.0219 (3)
O6	0.6115 (3)	1.14807 (9)	0.56175 (9)	0.0282 (3)
C1	0.1454 (3)	0.90015 (11)	0.71937 (12)	0.0211 (4)
C2	0.2848 (3)	0.91736 (11)	0.83377 (12)	0.0207 (4)
C3	0.2552 (3)	1.03366 (11)	0.86734 (12)	0.0195 (4)
C4	0.3680 (3)	1.10357 (11)	0.77418 (12)	0.0189 (4)
C5	0.2263 (3)	1.07910 (11)	0.66196 (12)	0.0197 (4)
C6	0.3259 (4)	1.14427 (12)	0.56431 (13)	0.0259 (4)
H1A	0.3191	0.7774	0.6812	0.0340*
H1B	−0.0442	0.9196	0.7254	0.0254*
H2A	0.2377	0.7936	0.9180	0.0373*
H2B	0.4758	0.8998	0.8280	0.0248*
H3A	−0.0440	1.0847	0.9421	0.0293*
H3B	0.3529	1.0470	0.9387	0.0234*
H4B	0.5592	1.0872	0.7668	0.0226*
H4A	0.1849	1.2268	0.8151	0.0324*
H5A	0.0336	1.0920	0.6699	0.0237*
H6A	0.6640	1.1146	0.5069	0.0339*
H6C	0.2577	1.1140	0.4939	0.0311*
H6B	0.2565	1.2162	0.5702	0.0311*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0289 (7)	0.0177 (6)	0.0386 (7)	−0.0020 (5)	0.0058 (5)	−0.0067 (5)
O2	0.0465 (8)	0.0190 (6)	0.0283 (6)	0.0071 (5)	0.0162 (5)	0.0067 (5)
O3	0.0230 (6)	0.0284 (6)	0.0222 (6)	0.0063 (5)	0.0066 (4)	−0.0025 (5)
O4	0.0271 (6)	0.0147 (6)	0.0393 (7)	−0.0005 (4)	0.0044 (5)	−0.0042 (5)
O5	0.0292 (7)	0.0174 (6)	0.0193 (6)	−0.0019 (4)	0.0049 (5)	−0.0011 (4)
O6	0.0303 (7)	0.0300 (7)	0.0247 (6)	−0.0063 (5)	0.0089 (5)	−0.0044 (5)
C1	0.0232 (8)	0.0154 (8)	0.0250 (8)	−0.0019 (6)	0.0047 (6)	−0.0016 (6)
C2	0.0233 (8)	0.0182 (8)	0.0207 (8)	0.0035 (6)	0.0054 (6)	0.0030 (6)
C3	0.0202 (8)	0.0195 (8)	0.0187 (7)	0.0025 (6)	−0.0005 (6)	−0.0010 (6)
C4	0.0187 (8)	0.0139 (7)	0.0240 (8)	0.0013 (6)	0.0013 (6)	−0.0023 (6)
C5	0.0199 (8)	0.0165 (8)	0.0229 (8)	0.0017 (6)	0.0022 (6)	0.0002 (6)
C6	0.0282 (9)	0.0251 (8)	0.0245 (8)	0.0008 (6)	0.0025 (6)	0.0052 (7)

Geometric parameters (Å, º) top

O1—C1	1.3837 (18)	O1—H1A	0.820
O2—C2	1.4216 (19)	O2—H2A	0.820
O3—C3	1.4199 (18)	O3—H3A	0.820
O4—C4	1.4236 (18)	O4—H4A	0.820
O5—C1	1.4314 (18)	O6—H6A	0.820
O5—C5	1.4423 (18)	C1—H1B	0.980
O6—C6	1.425 (2)	C2—H2B	0.980
C1—C2	1.523 (2)	C3—H3B	0.980
C2—C3	1.522 (2)	C4—H4B	0.980
C3—C4	1.524 (2)	C5—H5A	0.980
C4—C5	1.521 (2)	C6—H6C	0.970
C5—C6	1.507 (2)	C6—H6B	0.970

C1—O5—C5	112.16 (11)	C6—O6—H6A	109.474
O1—C1—O5	107.10 (12)	O1—C1—H1B	108.857
O1—C1—C2	114.20 (12)	O5—C1—H1B	108.860
O5—C1—C2	108.84 (12)	C2—C1—H1B	108.859
O2—C2—C1	110.83 (12)	O2—C2—H2B	109.452
O2—C2—C3	108.80 (12)	C1—C2—H2B	109.449
C1—C2—C3	108.83 (12)	C3—C2—H2B	109.458
O3—C3—C2	109.09 (12)	O3—C3—H3B	109.847
O3—C3—C4	109.17 (12)	C2—C3—H3B	109.848
C2—C3—C4	109.02 (12)	C4—C3—H3B	109.842
O4—C4—C3	110.57 (12)	O4—C4—H4B	108.392
O4—C4—C5	111.04 (12)	C3—C4—H4B	108.388
C3—C4—C5	109.98 (12)	C5—C4—H4B	108.388
O5—C5—C4	107.75 (11)	O5—C5—H5A	108.775
O5—C5—C6	108.87 (12)	C4—C5—H5A	108.778
C4—C5—C6	113.79 (12)	C6—C5—H5A	108.780
O6—C6—C5	112.25 (13)	O6—C6—H6C	109.153
C1—O1—H1A	109.467	O6—C6—H6B	109.157
C2—O2—H2A	109.472	C5—C6—H6C	109.152
C3—O3—H3A	109.470	C5—C6—H6B	109.146
C4—O4—H4A	109.476	H6C—C6—H6B	107.880

C1—O5—C5—C4	63.92 (13)	C1—C2—C3—C4	−56.31 (14)
C1—O5—C5—C6	−172.24 (10)	O3—C3—C4—O4	60.68 (14)
C5—O5—C1—O1	171.24 (10)	O3—C3—C4—C5	−62.31 (13)
C5—O5—C1—C2	−64.83 (13)	C2—C3—C4—O4	179.76 (11)
O1—C1—C2—O2	−61.24 (16)	C2—C3—C4—C5	56.77 (14)
O1—C1—C2—C3	179.15 (11)	O4—C4—C5—O5	178.40 (10)
O5—C1—C2—O2	179.15 (10)	O4—C4—C5—C6	57.59 (15)
O5—C1—C2—C3	59.54 (14)	C3—C4—C5—O5	−58.88 (14)
O2—C2—C3—O3	−58.04 (14)	C3—C4—C5—C6	−179.69 (10)
O2—C2—C3—C4	−177.17 (10)	O5—C5—C6—O6	−74.12 (14)
C1—C2—C3—O3	62.82 (14)	C4—C5—C6—O6	46.06 (16)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···O4ⁱ	0.82	1.88	2.6884 (16)	171
O2—H2A···O6ⁱ	0.82	1.99	2.8044 (16)	172
O3—H3A···O2ⁱⁱ	0.82	1.94	2.7494 (16)	169
O4—H4A···O1ⁱⁱⁱ	0.82	1.94	2.7384 (16)	163
O4—H4A···O3	0.82	2.49	2.8333 (15)	106
O6—H6A···O5^iv	0.82	2.03	2.8439 (15)	171

Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x, −y+2, −z+2; (iii) −x, y+1/2, −z+3/2; (iv) −x+1, −y+2, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···O4ⁱ	0.82	1.88	2.6884 (16)	171
O2—H2A···O6ⁱ	0.82	1.99	2.8044 (16)	172
O3—H3A···O2ⁱⁱ	0.82	1.94	2.7494 (16)	169
O4—H4A···O1ⁱⁱⁱ	0.82	1.94	2.7384 (16)	163
O4—H4A···O3	0.82	2.49	2.8333 (15)	106
O6—H6A···O5^iv	0.82	2.03	2.8439 (15)	171

Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x, −y+2, −z+2; (iii) −x, y+1/2, −z+3/2; (iv) −x+1, −y+2, −z+1.

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