supplementary materials


is5352 scheme

Acta Cryst. (2014). E70, o569    [ doi:10.1107/S1600536814008046 ]

[beta]-D-Gulose

T. Ishii, S. Ohga, K. Fukada, K. Morimoto and G. Sakane

CCDC reference: 903430

Abstract top

The title compound, C6H12O6, a C-3 position epimer of D-galactose, crystallized from an aqueous solution, was confirmed as [beta]-D-pyran­ose with a 4C1 (C1) conformation. In the crystal, O-H...O hydrogen bonds between the hy­droxy groups at the C-1 and C-6 positions connect mol­ecules into a tape structure with an R33(11) ring motif running along the a-axis direction. The tapes are connected by further O-H...O hydrogen bonds, forming a three-dimensional network.

Comment top

The crystal system (orthorhombic), space group (P212121), and number of molecules in the unit cell (Z = 4) of the title compound are the same as for the typical hexose (C6H12O6) monosaccharides (Fukada et al., 2010). There is a difference in the hydrogen bonding patterns, having a circular chain network returning to the same molecule, and the intermolecular interactions between two adjacent β-D-gulose molecules in the crystal.

In an equatorial OH group at C-2 position, the hydrogen bond can be confirmed as a donor, which connects to the OH group at C-3 position of the neighboring molecule. However, for the axial OH groups at C-3 and C-4 positions, each has hydrogen bonds both as a donor and an acceptor to the OH groups at either the C-2 and C-4, or the C-3 and C-6 positions, respectively. In the OH group at the C-6 position, there is an intermolecular hydrogen bond between the OH group at C-4 position of the neighboring molecule, and there are two additional hydrogen bonds with the OH groups at different C-1 positions in these two different D-gulose molecules. There is an infinite hydrogen bonding chain along to the a-axis (···O1—H1A···O6—H6A···O1—H1A···), which is connecting to a finite chain (O2—H2A···O3—H3A···O4—H4A···O6—H6A). Therefore, the hydrogen bonding network can be categorized as Jeffrey's class (iv) (Jeffrey & Saenger, 1994; Jeffrey & Mitra, 1983). There is a step for returning to the same gulose molecule in an infinite chain (···gulose O1—H1A···O6—H6A···O1—H1A···gulose O6—H6A···). Such a significant circular hydrogen bonding ring should be treated differently from the typical infinite chain.

Related literature top

For related structures. see: Fukada et al. (2010). For the chemical synthesis of the title compound, see: Morimoto et al. (2013). For hydrogen-bonding networks, see: Jeffrey & Saenger (1994); Jeffrey & Mitra (1983).

Experimental top

D-Gulose was prepared from disaccharide lactitol by a combination of microbial and chemical reactions. 3-Ketolactitol, oxidized from lactitol by Agrobacterium tumefaciens, was reduced by chemical hydrogenation. The resulting product, D-gulosyl-(β-1, 4)-D-sorbitol containing D-gulose, was hydrolyzed by acid hydrolysis, and its subsequent hydrolysates were separated by chromatography. Lastly, a crude crystal from the concentrated D-gulose syrup was recovered by ethanol precipitation, and then its aqueous solution was recrystallized, resulting in pure D-gulose. The D-gulose was concentrated to a brix value in a range of approximately 85–90%. Ethanol (twice the volume of the resulting syrup) was added and the resulting solution was mixed vigorously. The resulting crystals were dissolved in ultrapure water and then concentrated and crystallized at room temperature. The specific optical rotation of D-gulose was analyzed using a polarimeter (JASCO P-1030 Tokyo). An optical rotation was also performed, providing [α]20D = -24.10 (authentic sample = -24.74). The 13C-NMR spectra of the isolated D-gulose was measured at 600 MHz in D2O using an ALPHA 600 system (Jeol Datum, Tokyo). All spectra were collected at 30 °C using trimethylsilyl propanoic acid as internal reference. All of the chemical shifts [δ = 94.6 (C1), 74.5 (C5), 71.9 (C3), 70.2 (C4), 69.8 (C2), 61.7 (C6)] corresponded well with an authentic D-gulose sample. These results indicate that the isolated material was D-gulose and that the current study was successful in preparing D-gulose. The gulose is a specialized member of the rare sugar family, therefore, the details regarding the synthesis, purification, and crystallization of gulose should be reported in a specialized journal (Morimoto et al., 2013).

Refinement top

H atoms bounded to methine-type C (H1B, H2B, H3B, H4B, H5A) were positioned geometrically and refined using a riding model with C—H = 0.98 Å and Uiso(H) = 1.2Ueq(C). H atoms bounded to methylene-type C (H6B, H6C) were positioned geometrically and refined using a riding model with C—H = 0.97 Å and Uiso(H) = 1.2Ueq(C). H atoms bounded to O (H1A, H2A, H3A, H4A, H6A) were positioned geometrically and refined using a riding model with O—H = 0.82 Å and Uiso(H) = 1.2Ueq(O), allowing for free rotation of the OH groups.

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, 2008); molecular graphics: CrystalStructure (Rigaku, 2010); software used to prepare material for publication: CrystalStructure (Rigaku, 2010).

Figures top
[Figure 1] 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.
[Figure 2] Fig. 2. Part of the crystal structure of the title compound with hydrogen-bonding network represented as light blue dashed lines, viewed down the c axis. The hydrogen atoms are omitted for clarity.
β-D-Gulose top
Crystal data top
C6H12O6F(000) = 384.00
Mr = 180.16Dx = 1.614 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.54187 Å
Hall symbol: P 2ac 2abCell parameters from 7124 reflections
a = 7.0800 (3) Åθ = 4.2–68.2°
b = 9.8644 (3) ŵ = 1.28 mm1
c = 10.6156 (4) ÅT = 294 K
V = 741.39 (4) Å3Block, colorless
Z = 40.10 × 0.10 × 0.10 mm
Data collection top
Rigaku R-AXIS RAPID II
diffractometer
1199 reflections with F2 > 2σ(F2)
Detector resolution: 10.000 pixels mm-1Rint = 0.070
ω scansθmax = 68.2°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
h = 88
Tmin = 0.645, Tmax = 0.879k = 1111
7803 measured reflectionsl = 1212
1358 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.073 w = 1/[σ2(Fo2) + (0.0261P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
1358 reflectionsΔρmax = 0.14 e Å3
116 parametersΔρmin = 0.14 e Å3
0 restraintsExtinction correction: SHELXL2013 (Sheldrick, 2008)
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0063 (12)
Secondary atom site location: difference Fourier map
Crystal data top
C6H12O6V = 741.39 (4) Å3
Mr = 180.16Z = 4
Orthorhombic, P212121Cu Kα radiation
a = 7.0800 (3) ŵ = 1.28 mm1
b = 9.8644 (3) ÅT = 294 K
c = 10.6156 (4) Å0.10 × 0.10 × 0.10 mm
Data collection top
Rigaku R-AXIS RAPID II
diffractometer
1358 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
1199 reflections with F2 > 2σ(F2)
Tmin = 0.645, Tmax = 0.879Rint = 0.070
7803 measured reflectionsθmax = 68.2°
Refinement top
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.073Δρmax = 0.14 e Å3
S = 1.05Δρmin = 0.14 e Å3
1358 reflectionsAbsolute structure: ?
116 parametersAbsolute structure parameter: ?
0 restraintsRogers parameter: ?
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
xyzUiso*/Ueq
O10.6475 (3)0.4070 (3)1.02633 (16)0.0367 (6)
O20.7927 (3)0.6435 (3)0.89378 (15)0.0385 (6)
O30.4219 (3)0.7683 (2)0.87238 (18)0.0369 (6)
O40.3674 (3)0.49846 (18)0.64349 (14)0.0295 (5)
O50.3828 (2)0.41908 (19)0.90855 (15)0.0259 (5)
O60.0053 (3)0.35032 (19)0.92624 (16)0.0304 (5)
C10.5316 (4)0.4977 (3)0.9615 (2)0.0270 (7)
C20.6282 (4)0.5724 (3)0.8553 (2)0.0257 (6)
C30.4871 (4)0.6654 (3)0.7890 (2)0.0266 (7)
C40.3165 (4)0.5860 (3)0.7452 (2)0.0255 (7)
C50.2385 (4)0.5021 (3)0.8521 (2)0.0234 (6)
C60.0815 (4)0.4071 (3)0.8155 (3)0.0277 (7)
H1A0.74680.39710.98760.0441*
H1B0.47860.56351.02100.0324*
H2A0.77260.68110.96140.0462*
H2B0.66820.50420.79370.0308*
H3A0.48270.83790.86080.0443*
H3B0.54830.70770.71610.0319*
H4A0.39710.54410.58210.0354*
H4B0.21910.64950.71640.0306*
H5A0.19020.56410.91670.0281*
H6A0.03670.27400.93860.0364*
H6B0.01250.45590.76690.0333*
H6C0.13150.33480.76340.0333*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0251 (10)0.0477 (13)0.0374 (11)0.0010 (11)0.0001 (9)0.0157 (11)
O20.0320 (11)0.0493 (15)0.0341 (11)0.0151 (10)0.0014 (9)0.0041 (11)
O30.0461 (13)0.0227 (12)0.0420 (11)0.0050 (10)0.0113 (10)0.0076 (10)
O40.0416 (12)0.0273 (12)0.0196 (9)0.0012 (10)0.0020 (9)0.0013 (8)
O50.0241 (9)0.0231 (10)0.0305 (10)0.0011 (9)0.0031 (8)0.0033 (9)
O60.0276 (10)0.0251 (11)0.0384 (10)0.0001 (9)0.0042 (9)0.0057 (9)
C10.0263 (14)0.0289 (17)0.0258 (13)0.0003 (13)0.0030 (13)0.0012 (12)
C20.0230 (13)0.0283 (16)0.0257 (13)0.0054 (13)0.0010 (12)0.0013 (13)
C30.0302 (15)0.0242 (17)0.0253 (13)0.0006 (13)0.0060 (13)0.0002 (12)
C40.0284 (14)0.0251 (15)0.0231 (13)0.0058 (14)0.0004 (12)0.0016 (13)
C50.0225 (13)0.0247 (15)0.0231 (12)0.0041 (11)0.0019 (12)0.0011 (12)
C60.0265 (14)0.0320 (17)0.0248 (13)0.0019 (14)0.0006 (11)0.0001 (13)
Geometric parameters (Å, º) top
O1—C11.396 (4)O1—H1A0.820
O2—C21.420 (3)O2—H2A0.820
O3—C31.424 (4)O3—H3A0.820
O4—C41.429 (3)O4—H4A0.820
O5—C11.424 (3)O6—H6A0.820
O5—C51.440 (3)C1—H1B0.980
O6—C61.439 (3)C2—H2B0.980
C1—C21.510 (4)C3—H3B0.980
C2—C31.527 (4)C4—H4B0.980
C3—C41.513 (4)C5—H5A0.980
C4—C51.510 (4)C6—H6B0.970
C5—C61.505 (4)C6—H6C0.970
O3···H2A2.7927O6···H4Aviii2.0992
O4···H5A3.2256H1A···O6ii1.9284
O1···H6Ai1.9853H2A···O3ix2.1169
O2···H6Bii2.6723H3A···O4iii1.9072
O2···H6Ciii2.5757H3B···O5iii2.5179
O3···H2Aiv2.1169H4A···O6vi2.0992
O4···H3Av1.9072H5A···O4viii2.5185
O4···H5Avi2.5185H6A···O1x1.9853
O5···H3Bv2.5179H6B···O2vii2.6723
O6···H1Avii1.9284H6C···O2v2.5757
C1—O5—C5112.3 (2)C6—O6—H6A109.480
O1—C1—O5106.3 (2)O1—C1—H1B109.359
O1—C1—C2114.5 (2)O5—C1—H1B109.362
O5—C1—C2107.82 (18)C2—C1—H1B109.363
O2—C2—C1113.41 (19)O2—C2—H2B107.098
O2—C2—C3111.9 (3)C1—C2—H2B107.103
C1—C2—C3109.9 (2)C3—C2—H2B107.097
O3—C3—C2110.75 (19)O3—C3—H3B109.292
O3—C3—C4107.5 (2)C2—C3—H3B109.290
C2—C3—C4110.7 (3)C4—C3—H3B109.286
O4—C4—C3110.1 (2)O4—C4—H4B109.124
O4—C4—C5109.2 (3)C3—C4—H4B109.127
C3—C4—C5110.15 (19)C5—C4—H4B109.123
O5—C5—C4111.4 (2)O5—C5—H5A108.140
O5—C5—C6106.1 (3)C4—C5—H5A108.132
C4—C5—C6114.7 (2)C6—C5—H5A108.139
O6—C6—C5110.29 (19)O6—C6—H6B109.601
C1—O1—H1A109.471O6—C6—H6C109.595
C2—O2—H2A109.468C5—C6—H6B109.603
C3—O3—H3A109.466C5—C6—H6C109.595
C4—O4—H4A109.475H6B—C6—H6C108.127
C1—O5—C5—C461.5 (3)C1—C2—C3—C455.0 (3)
C1—O5—C5—C6173.06 (15)O3—C3—C4—O4168.99 (18)
C5—O5—C1—O1172.54 (16)O3—C3—C4—C570.5 (3)
C5—O5—C1—C264.2 (3)C2—C3—C4—O469.9 (3)
O1—C1—C2—O255.5 (3)C2—C3—C4—C550.5 (3)
O1—C1—C2—C3178.41 (18)O4—C4—C5—O568.1 (3)
O5—C1—C2—O2173.59 (19)O4—C4—C5—C652.5 (3)
O5—C1—C2—C360.4 (3)C3—C4—C5—O553.0 (3)
O2—C2—C3—O362.8 (3)C3—C4—C5—C6173.52 (19)
O2—C2—C3—C4178.08 (16)O5—C5—C6—O666.8 (3)
C1—C2—C3—O364.1 (3)C4—C5—C6—O6169.7 (2)
Symmetry codes: (i) x+1/2, y+1/2, z+2; (ii) x+1, y, z; (iii) x+1, y+1/2, z+3/2; (iv) x1/2, y+3/2, z+2; (v) x+1, y1/2, z+3/2; (vi) x+1/2, y+1, z1/2; (vii) x1, y, z; (viii) x+1/2, y+1, z+1/2; (ix) x+1/2, y+3/2, z+2; (x) x1/2, y+1/2, z+2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O6ii0.821.932.736 (3)168
O2—H2A···O3ix0.822.122.785 (3)139
O3—H3A···O4iii0.821.912.722 (3)173
O4—H4A···O6vi0.822.102.915 (3)173
O6—H6A···O1x0.821.992.805 (3)177
Symmetry codes: (ii) x+1, y, z; (iii) x+1, y+1/2, z+3/2; (vi) x+1/2, y+1, z1/2; (ix) x+1/2, y+3/2, z+2; (x) x1/2, y+1/2, z+2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O6i0.821.932.736 (3)168
O2—H2A···O3ii0.822.122.785 (3)139
O3—H3A···O4iii0.821.912.722 (3)173
O4—H4A···O6iv0.822.102.915 (3)173
O6—H6A···O1v0.821.992.805 (3)177
Symmetry codes: (i) x+1, y, z; (ii) x+1/2, y+3/2, z+2; (iii) x+1, y+1/2, z+3/2; (iv) x+1/2, y+1, z1/2; (v) x1/2, y+1/2, z+2.
references
References top

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