organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

α-D,L-Sorbose

aDepartment of Advanced Materials Science, Faculty of Engineering, Kagawa University, 2217-20 Hayashi-cho, Takamatsu, Kagawa 761-0396, Japan, bRare Sugar Research Center, Kagawa University, 2393 Ikenobe, Kagawa 761-0795, Japan, and cDepartment of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Kagawa 761-0795, Japan
*Correspondence e-mail: tishii@eng.kagawa-u.ac.jp

Edited by H. Ishida, Okayama University, Japan (Received 8 January 2018; accepted 18 January 2018; online 31 January 2018)

The racemic title compound, C6H12O6, consisting of C-4 epimers of psicose, was crystallized from an aqueous solution of an equimolar mixture of D- and L-sorboses. It was confirmed that D-sorbose (or L-sorbose) formed α-pyran­ose with a 4C1 (or 1C4) conformation where the anomer position was designated as carbon-1. The asymmetric unit comprises two crystallographically independent mol­ecules. In the crystal, mol­ecules are linked by O—H⋯O hydrogen bonds, forming a three-dimensional framework. The unit-cell volume of the title racemic α-D,L-sorbose is 1450.86 (6) Å3 (Z = 8), which is about 41 Å3 smaller than that of twice the amount of chiral α-L-sorbose [V = 745.942 Å3 (Z = 4)].

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

D- and L-sorboses are classified as rare sugars. L-Sorbose is the first L-form hexose found in nature (Nordenson et al., 1979[Nordenson, S., Takagi, S. & Jeffrey, G. A. (1979). Acta Cryst. B35, 1005-1007.]). In this study, we aimed to create a racemic single crystal including both D- and L-sorbose in a 1:1 ratio. There are two independent sorbose mol­ecules, A and B, in the asymmetric unit (Fig. 1[link]). Therefore, there are a total of eight sorbose mol­ecules (four L- and four D-forms) in the unit cell.

[Figure 1]
Figure 1
An ORTEP view of the title compound, mol­ecule A (left) and mol­ecule B (right), with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radii.

In the crystal, the D- and L-sorbose mol­ecules are linked weakly, as well as the strong homo-chiral DD (and LL) links, via O—H⋯O hydrogen bonds (Table 1[link]), forming a three-dimensional network (Fig. 2[link]). The crystal structure of the title compound with two independent mol­ecules in the asymmetric unit in space group P21/a (Z = 8) is significantly different from the structures previously reported by us, viz. racemic β-D,L-allose (P21/c, Z = 4; Ishii, Senoo et al., 2015a[Ishii, T., Senoo, T., Kozakai, T., Fukada, K. & Sakane, G. (2015a). Acta Cryst. E71, o139.]), β-D,L-psicose (Pna21, Z = 4; Ishii, Sakane et al., 2015[Ishii, T., Sakane, G., Yoshihara, A., Fukada, K. & Senoo, T. (2015). Acta Cryst. E71, o289-o290.]) and β-D,L-fructose (P[\overline{1}], Z = 2; Ishii, Senoo et al., 2015b[Ishii, T., Senoo, T., Yoshihara, A., Fukada, K. & Sakane, G. (2015b). Acta Cryst. E71, o719-o720.]), where each asymmetric unit consists of one mol­ecule.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1A⋯O4i 0.82 2.37 3.174 (3) 167
O2—H2A⋯O5ii 0.82 1.96 2.757 (2) 164
O3—H3A⋯O10 0.82 1.99 2.807 (2) 172
O4—H4A⋯O6iii 0.82 2.11 2.917 (2) 170
O5—H5A⋯O2iv 0.82 2.30 2.875 (2) 128
O5—H5A⋯O3iv 0.82 2.10 2.8683 (18) 156
O7—H7A⋯O9i 0.82 2.14 2.915 (2) 159
O7—H7A⋯O10i 0.82 2.52 3.047 (3) 123
O8—H8A⋯O11v 0.82 2.00 2.814 (2) 169
O9—H9A⋯O4vi 0.82 1.93 2.747 (2) 172
O10—H10A⋯O12iii 0.82 2.25 3.051 (2) 165
O11—H11A⋯O8iv 0.82 2.41 2.976 (2) 127
O11—H11A⋯O9iv 0.82 2.28 3.060 (2) 158
Symmetry codes: (i) x, y+1, z; (ii) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z]; (iii) x, y-1, z; (iv) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z]; (v) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+1]; (vi) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z].
[Figure 2]
Figure 2
A packing diagram of the title compound viewed down the b axis, showing the hydrogen-bonding network (dotted lines). In this figure, D and L denote the D- and L-forms, respectively.

Synthesis and crystallization

L-Sorbose was purchased from Wako Pure Chemical Industries. D-Sorbose was prepared by microbial oxidation of galactitol to D-tagatose followed by enzymatic epimerization using D-tagatose 3-epimerase (Khan et al., 1992[Khan, A. R., Takahata, S., Okaya, H., Tsumura, T. & Izumori, K. (1992). J. Ferment. Bioeng. 74, 149-152.]; Itoh et al., 1995[Itoh, H., Sato, T., Takeuchi, T., Khan, A. R. & Izumori, K. (1995). J. Ferment. Bioeng. 79, 184-185.]). L-Sorbose and D-sorbose were each dissolved in hot water to give a 30 wt% solution and the solutions were mixed in equal volume. Single crystals were obtained from the mixed solution by keeping it at 20°C.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C6H12O6
Mr 180.16
Crystal system, space group Monoclinic, P21/a
Temperature (K) 296
a, b, c (Å) 12.8152 (3), 6.29489 (13), 18.9482 (4)
β (°) 108.3472 (12)
V3) 1450.86 (6)
Z 8
Radiation type Cu Kα
μ (mm−1) 1.31
Crystal size (mm) 0.10 × 0.10 × 0.10
 
Data collection
Diffractometer Rigaku R-AXIS RAPID
Absorption correction Multi-scan (ABSCOR; Rigaku, 1995[Rigaku (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.])
Tmin, Tmax 0.728, 0.877
No. of measured, independent and observed [F2 > 2.0σ(F2)] reflections 24139, 2658, 2161
Rint 0.051
(sin θ/λ)max−1) 0.602
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.044, 0.120, 1.08
No. of reflections 2658
No. of parameters 228
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.57, −0.29
Computer programs: RAPID-AUTO (Rigaku, 2009[Rigaku (2009). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]), SIR2011 (Burla et al., 2012[Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Mallamo, M., Mazzone, A., Polidori, G. & Spagna, R. (2012). J. Appl. Cryst. 45, 357-361.]), SHELXL2013 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and CrystalStructure (Rigaku, 2014[Rigaku (2014). CrystalStructure. Rigaku Corporation, Tokyo, Japan.]).

Structural data


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: SIR2011 (Burla et al., 2012); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015); molecular graphics: CrystalStructure (Rigaku, 2014); software used to prepare material for publication: CrystalStructure (Rigaku, 2014).

α-D,L-Sorbose top
Crystal data top
C6H12O6F(000) = 768.00
Mr = 180.16Dx = 1.649 Mg m3
Monoclinic, P21/aCu Kα radiation, λ = 1.54187 Å
a = 12.8152 (3) ÅCell parameters from 15393 reflections
b = 6.29489 (13) Åθ = 3.6–68.3°
c = 18.9482 (4) ŵ = 1.31 mm1
β = 108.3472 (12)°T = 296 K
V = 1450.86 (6) Å3Block, colorless
Z = 80.10 × 0.10 × 0.10 mm
Data collection top
Rigaku R-AXIS RAPID
diffractometer
2161 reflections with F2 > 2.0σ(F2)
Detector resolution: 10.000 pixels mm-1Rint = 0.051
ω scansθmax = 68.3°, θmin = 4.9°
Absorption correction: multi-scan
(ABSCOR; Rigaku, 1995)
h = 1515
Tmin = 0.728, Tmax = 0.877k = 77
24139 measured reflectionsl = 2222
2658 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.044H-atom parameters constrained
wR(F2) = 0.120 w = 1/[σ2(Fo2) + (0.055P)2 + 0.7784P]
where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max < 0.001
2658 reflectionsΔρmax = 0.57 e Å3
228 parametersΔρmin = 0.29 e Å3
0 restraintsExtinction correction: SHELXL2013 (Sheldrick, 2015)
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0027 (4)
Secondary atom site location: difference Fourier map
Special details top

Geometry. ENTER SPECIAL DETAILS OF THE MOLECULAR GEOMETRY

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 sigma(F2) is used only for calculating R-factor (gt).

H atoms were positioned geometrically (C—H = 0.98 or 0.97 Å, and O—H = 0.82 Å) and refined using as riding with Uiso(H) = 1.2Ueq(C or O), allowing for free rotation of the OH groups.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.22822 (19)0.7791 (3)0.22185 (11)0.0629 (6)
O20.14999 (12)0.4920 (2)0.04746 (8)0.0319 (4)
O30.18382 (11)0.2570 (3)0.17113 (8)0.0338 (4)
O40.39585 (13)0.0849 (3)0.17903 (8)0.0385 (4)
O50.47216 (12)0.2681 (3)0.05987 (8)0.0404 (4)
O60.30811 (11)0.6926 (2)0.10091 (8)0.0294 (4)
O70.02816 (17)0.8374 (3)0.28347 (10)0.0547 (5)
O80.09763 (13)0.5097 (3)0.44959 (8)0.0345 (4)
O90.02314 (12)0.2877 (3)0.31816 (9)0.0368 (4)
O100.23099 (15)0.1206 (3)0.31891 (9)0.0433 (4)
O110.41443 (12)0.2925 (3)0.43820 (8)0.0386 (4)
O120.21295 (11)0.7176 (2)0.40376 (8)0.0295 (4)
C10.16229 (19)0.7191 (4)0.15089 (13)0.0380 (5)
C20.22188 (16)0.5705 (3)0.11388 (10)0.0246 (4)
C30.27148 (15)0.3795 (3)0.16199 (11)0.0239 (4)
C40.34130 (16)0.2480 (3)0.12745 (11)0.0265 (5)
C50.42487 (16)0.3835 (4)0.10693 (11)0.0274 (5)
C60.37037 (17)0.5755 (4)0.06332 (12)0.0318 (5)
C70.02122 (18)0.7524 (4)0.35030 (13)0.0365 (5)
C80.11366 (16)0.5985 (3)0.38604 (11)0.0252 (4)
C90.12015 (16)0.4150 (3)0.33493 (11)0.0256 (4)
C100.21984 (16)0.2770 (3)0.37048 (11)0.0266 (4)
C110.32302 (16)0.4106 (3)0.39376 (11)0.0268 (5)
C120.30878 (16)0.5961 (4)0.44065 (12)0.0320 (5)
H3A0.201620.208950.213490.0405*
H9B0.126210.473560.288460.0307*
H11A0.446270.237450.41150.0463*
H10B0.210930.206230.41430.0319*
H8A0.09540.604630.478710.0414*
H5B0.482630.42840.152050.0329*
H2A0.117090.591160.021950.0383*
H6A0.426170.667330.055030.0381*
H6B0.322080.530270.015170.0381*
H9A0.020060.324650.278110.0442*
H11B0.338550.463620.349470.0321*
H5A0.534590.23080.083790.0485*
H4B0.293260.180440.082290.0318*
H4A0.37840.0320.159870.0462*
H3B0.317450.429810.210830.0287*
H10A0.221950.002140.3340.0519*
H12A0.303130.543410.487420.0384*
H12B0.373040.686990.451640.0384*
H7A0.040680.965230.288580.0657*
H7C0.048580.679550.340640.0438*
H7B0.023090.86750.384720.0438*
H1C0.139660.845070.12040.0456*
H1B0.096620.649560.15450.0456*
H1A0.277580.857180.21840.0755*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0933 (16)0.0493 (13)0.0544 (11)0.0043 (11)0.0348 (11)0.0184 (10)
O20.0312 (8)0.0310 (9)0.0263 (7)0.0003 (6)0.0014 (6)0.0014 (6)
O30.0312 (8)0.0350 (9)0.0338 (8)0.0052 (7)0.0082 (6)0.0102 (7)
O40.0426 (9)0.0250 (9)0.0381 (9)0.0065 (7)0.0013 (7)0.0029 (7)
O50.0260 (8)0.0569 (11)0.0355 (9)0.0092 (8)0.0055 (6)0.0126 (8)
O60.0308 (8)0.0237 (8)0.0363 (8)0.0023 (6)0.0143 (6)0.0013 (6)
O70.0706 (12)0.0396 (11)0.0503 (11)0.0128 (10)0.0138 (9)0.0158 (9)
O80.0441 (9)0.0336 (9)0.0306 (8)0.0027 (7)0.0186 (7)0.0023 (7)
O90.0317 (8)0.0305 (9)0.0390 (9)0.0099 (7)0.0021 (6)0.0024 (7)
O100.0629 (11)0.0260 (9)0.0445 (10)0.0004 (8)0.0221 (8)0.0111 (7)
O110.0311 (8)0.0520 (11)0.0333 (8)0.0158 (7)0.0112 (6)0.0034 (7)
O120.0252 (7)0.0241 (8)0.0370 (8)0.0021 (6)0.0066 (6)0.0042 (6)
C10.0465 (13)0.0292 (13)0.0444 (13)0.0053 (10)0.0231 (11)0.0009 (10)
C20.0252 (10)0.0223 (11)0.0259 (10)0.0023 (8)0.0076 (8)0.0008 (8)
C30.0252 (10)0.0221 (11)0.0220 (9)0.0038 (8)0.0039 (8)0.0002 (8)
C40.0254 (10)0.0252 (11)0.0230 (10)0.0015 (8)0.0007 (8)0.0019 (8)
C50.0224 (9)0.0339 (13)0.0231 (10)0.0020 (9)0.0030 (8)0.0054 (9)
C60.0283 (11)0.0375 (13)0.0315 (11)0.0032 (9)0.0123 (9)0.0040 (10)
C70.0319 (11)0.0285 (13)0.0475 (14)0.0044 (9)0.0103 (10)0.0052 (10)
C80.0247 (10)0.0230 (11)0.0283 (10)0.0012 (8)0.0087 (8)0.0019 (8)
C90.0288 (10)0.0229 (11)0.0230 (10)0.0054 (8)0.0051 (8)0.0016 (8)
C100.0352 (11)0.0238 (11)0.0224 (10)0.0009 (9)0.0115 (8)0.0006 (8)
C110.0266 (10)0.0313 (12)0.0231 (10)0.0042 (9)0.0089 (8)0.0007 (8)
C120.0244 (10)0.0361 (13)0.0319 (11)0.0000 (9)0.0037 (8)0.0093 (9)
Geometric parameters (Å, º) top
O1—C11.396 (3)O1—H1A0.820
O2—C21.395 (2)O2—H2A0.820
O3—C31.418 (3)O3—H3A0.820
O4—C41.438 (2)O4—H4A0.820
O5—C51.425 (3)O5—H5A0.820
O6—C21.429 (3)O7—H7A0.820
O6—C61.430 (3)O8—H8A0.820
O7—C71.403 (3)O9—H9A0.820
O8—C81.400 (3)O10—H10A0.820
O9—C91.428 (3)O11—H11A0.820
O10—C101.426 (3)C1—H1C0.970
O11—C111.419 (2)C1—H1B0.970
O12—C81.423 (2)C3—H3B0.980
O12—C121.429 (2)C4—H4B0.980
C1—C21.512 (3)C5—H5B0.980
C2—C31.522 (3)C6—H6A0.970
C3—C41.511 (3)C6—H6B0.970
C4—C51.513 (3)C7—H7C0.970
C5—C61.506 (3)C7—H7B0.970
C7—C81.515 (3)C9—H9B0.980
C8—C91.526 (3)C10—H10B0.980
C9—C101.516 (3)C11—H11B0.980
C10—C111.511 (3)C12—H12A0.970
C11—C121.513 (3)C12—H12B0.970
C2—O6—C6113.05 (16)C8—O8—H8A109.471
C8—O12—C12113.61 (15)C9—O9—H9A109.472
O1—C1—C2111.89 (19)C10—O10—H10A109.479
O2—C2—O6111.22 (16)C11—O11—H11A109.476
O2—C2—C1110.54 (16)O1—C1—H1C109.244
O2—C2—C3107.06 (16)O1—C1—H1B109.242
O6—C2—C1106.13 (17)C2—C1—H1C109.230
O6—C2—C3109.14 (15)C2—C1—H1B109.231
C1—C2—C3112.80 (18)H1C—C1—H1B107.914
O3—C3—C2107.78 (15)O3—C3—H3B108.924
O3—C3—C4110.78 (16)C2—C3—H3B108.914
C2—C3—C4111.47 (18)C4—C3—H3B108.910
O4—C4—C3108.92 (17)O4—C4—H4B108.731
O4—C4—C5110.20 (16)C3—C4—H4B108.728
C3—C4—C5111.47 (17)C5—C4—H4B108.740
O5—C5—C4110.39 (18)O5—C5—H5B109.860
O5—C5—C6106.31 (18)C4—C5—H5B109.868
C4—C5—C6110.49 (17)C6—C5—H5B109.864
O6—C6—C5112.05 (19)O6—C6—H6A109.207
O7—C7—C8112.6 (2)O6—C6—H6B109.204
O8—C8—O12111.70 (15)C5—C6—H6A109.202
O8—C8—C7109.51 (19)C5—C6—H6B109.203
O8—C8—C9107.19 (16)H6A—C6—H6B107.889
O12—C8—C7106.49 (16)O7—C7—H7C109.070
O12—C8—C9108.98 (18)O7—C7—H7B109.069
C7—C8—C9113.04 (16)C8—C7—H7C109.076
O9—C9—C8110.39 (18)C8—C7—H7B109.068
O9—C9—C10109.27 (16)H7C—C7—H7B107.828
C8—C9—C10110.99 (15)O9—C9—H9B108.714
O10—C10—C9110.08 (15)C8—C9—H9B108.713
O10—C10—C11108.49 (19)C10—C9—H9B108.709
C9—C10—C11110.40 (17)O10—C10—H10B109.288
O11—C11—C10111.40 (17)C9—C10—H10B109.283
O11—C11—C12106.60 (15)C11—C10—H10B109.285
C10—C11—C12110.17 (18)O11—C11—H11B109.539
O12—C12—C11111.71 (15)C10—C11—H11B109.544
C1—O1—H1A109.482C12—C11—H11B109.542
C2—O2—H2A109.473O12—C12—H12A109.276
C3—O3—H3A109.469O12—C12—H12B109.277
C4—O4—H4A109.472C11—C12—H12A109.279
C5—O5—H5A109.470C11—C12—H12B109.283
C7—O7—H7A109.468H12A—C12—H12B107.938
C2—O6—C6—C560.30 (17)C3—C4—C5—O5166.84 (13)
C6—O6—C2—O257.58 (18)C3—C4—C5—C649.53 (19)
C6—O6—C2—C1177.85 (12)O5—C5—C6—O6173.00 (14)
C6—O6—C2—C360.32 (17)C4—C5—C6—O653.2 (2)
C8—O12—C12—C1159.7 (2)O7—C7—C8—O8176.16 (15)
C12—O12—C8—O858.4 (2)O7—C7—C8—O1262.9 (2)
C12—O12—C8—C7177.90 (15)O7—C7—C8—C956.7 (2)
C12—O12—C8—C959.9 (2)O8—C8—C9—O956.92 (18)
O1—C1—C2—O2172.38 (18)O8—C8—C9—C1064.39 (19)
O1—C1—C2—O666.9 (2)O12—C8—C9—O9177.97 (13)
O1—C1—C2—C352.6 (2)O12—C8—C9—C1056.6 (2)
O2—C2—C3—O357.0 (2)C7—C8—C9—O963.8 (2)
O2—C2—C3—C464.77 (19)C7—C8—C9—C10174.84 (17)
O6—C2—C3—O3177.49 (14)O9—C9—C10—O1064.2 (2)
O6—C2—C3—C455.71 (18)O9—C9—C10—C11176.02 (15)
C1—C2—C3—O364.81 (19)C8—C9—C10—O10173.79 (16)
C1—C2—C3—C4173.42 (14)C8—C9—C10—C1154.0 (2)
O3—C3—C4—O466.54 (17)O10—C10—C11—O1169.2 (2)
O3—C3—C4—C5171.66 (12)O10—C10—C11—C12172.67 (13)
C2—C3—C4—O4173.44 (13)C9—C10—C11—O11170.05 (16)
C2—C3—C4—C551.64 (18)C9—C10—C11—C1252.0 (2)
O4—C4—C5—O572.10 (18)O11—C11—C12—O12175.14 (16)
O4—C4—C5—C6170.59 (14)C10—C11—C12—O1254.1 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O4i0.822.373.174 (3)167
O2—H2A···O5ii0.821.962.757 (2)164
O3—H3A···O100.821.992.807 (2)172
O4—H4A···O6iii0.822.112.917 (2)170
O5—H5A···O2iv0.822.302.875 (2)128
O5—H5A···O3iv0.822.102.8683 (18)156
O7—H7A···O9i0.822.142.915 (2)159
O7—H7A···O10i0.822.523.047 (3)123
O8—H8A···O11v0.822.002.814 (2)169
O9—H9A···O4vi0.821.932.747 (2)172
O10—H10A···O12iii0.822.253.051 (2)165
O11—H11A···O8iv0.822.412.976 (2)127
O11—H11A···O9iv0.822.283.060 (2)158
Symmetry codes: (i) x, y+1, z; (ii) x+1/2, y+1/2, z; (iii) x, y1, z; (iv) x+1/2, y+1/2, z; (v) x+1/2, y+1/2, z+1; (vi) x1/2, y+1/2, z.
 

Acknowledgements

The authors are sincerely grateful to Professor Genta Sakane (Okayama University of Science) for excellent discussions and useful technical advice.

Funding information

The authors are grateful for Grants-in-Aid for Rare Sugar Research from Kagawa University.

References

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