organic compounds
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
The racemic title compound, C6H12O6, consisting of C-4 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 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)].
Keywords: crystal structure; hydrogen bonding; racemic compound; rare sugar.
CCDC reference: 1812905
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). 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 (Fig. 1). Therefore, there are a total of eight sorbose molecules (four L- and four D-forms) in the unit cell.
In the crystal, the D- and L-sorbose molecules are linked weakly, as well as the strong homo-chiral D–D (and L–L) links, via O—H⋯O hydrogen bonds (Table 1), forming a three-dimensional network (Fig. 2). The of the title compound with two independent molecules in the in 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), β-D,L-psicose (Pna21, Z = 4; Ishii, Sakane et al., 2015) and β-D,L-fructose (P, Z = 2; Ishii, Senoo et al., 2015b), where each consists of one molecule.
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 using D-tagatose 3-epimerase (Khan et al., 1992; Itoh et al., 1995). 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 .
details are summarized in Table 2
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Structural data
CCDC reference: 1812905
https://doi.org/10.1107/S2414314618001141/is4024sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314618001141/is4024Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314618001141/is4024Isup3.cml
Data collection: RAPID-AUTO (Rigaku, 2009); cell
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).C6H12O6 | F(000) = 768.00 |
Mr = 180.16 | Dx = 1.649 Mg m−3 |
Monoclinic, P21/a | Cu Kα radiation, λ = 1.54187 Å |
a = 12.8152 (3) Å | Cell parameters from 15393 reflections |
b = 6.29489 (13) Å | θ = 3.6–68.3° |
c = 18.9482 (4) Å | µ = 1.31 mm−1 |
β = 108.3472 (12)° | T = 296 K |
V = 1450.86 (6) Å3 | Block, colorless |
Z = 8 | 0.10 × 0.10 × 0.10 mm |
Rigaku R-AXIS RAPID diffractometer | 2161 reflections with F2 > 2.0σ(F2) |
Detector resolution: 10.000 pixels mm-1 | Rint = 0.051 |
ω scans | θmax = 68.3°, θmin = 4.9° |
Absorption correction: multi-scan (ABSCOR; Rigaku, 1995) | h = −15→15 |
Tmin = 0.728, Tmax = 0.877 | k = −7→7 |
24139 measured reflections | l = −22→22 |
2658 independent reflections |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.044 | H-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 reflections | Δρmax = 0.57 e Å−3 |
228 parameters | Δρmin = −0.29 e Å−3 |
0 restraints | Extinction correction: SHELXL2013 (Sheldrick, 2015) |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0027 (4) |
Secondary atom site location: difference Fourier map |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.22822 (19) | 0.7791 (3) | 0.22185 (11) | 0.0629 (6) | |
O2 | 0.14999 (12) | 0.4920 (2) | 0.04746 (8) | 0.0319 (4) | |
O3 | 0.18382 (11) | 0.2570 (3) | 0.17113 (8) | 0.0338 (4) | |
O4 | 0.39585 (13) | 0.0849 (3) | 0.17903 (8) | 0.0385 (4) | |
O5 | 0.47216 (12) | 0.2681 (3) | 0.05987 (8) | 0.0404 (4) | |
O6 | 0.30811 (11) | 0.6926 (2) | 0.10091 (8) | 0.0294 (4) | |
O7 | 0.02816 (17) | 0.8374 (3) | 0.28347 (10) | 0.0547 (5) | |
O8 | 0.09763 (13) | 0.5097 (3) | 0.44959 (8) | 0.0345 (4) | |
O9 | 0.02314 (12) | 0.2877 (3) | 0.31816 (9) | 0.0368 (4) | |
O10 | 0.23099 (15) | 0.1206 (3) | 0.31891 (9) | 0.0433 (4) | |
O11 | 0.41443 (12) | 0.2925 (3) | 0.43820 (8) | 0.0386 (4) | |
O12 | 0.21295 (11) | 0.7176 (2) | 0.40376 (8) | 0.0295 (4) | |
C1 | 0.16229 (19) | 0.7191 (4) | 0.15089 (13) | 0.0380 (5) | |
C2 | 0.22188 (16) | 0.5705 (3) | 0.11388 (10) | 0.0246 (4) | |
C3 | 0.27148 (15) | 0.3795 (3) | 0.16199 (11) | 0.0239 (4) | |
C4 | 0.34130 (16) | 0.2480 (3) | 0.12745 (11) | 0.0265 (5) | |
C5 | 0.42487 (16) | 0.3835 (4) | 0.10693 (11) | 0.0274 (5) | |
C6 | 0.37037 (17) | 0.5755 (4) | 0.06332 (12) | 0.0318 (5) | |
C7 | 0.02122 (18) | 0.7524 (4) | 0.35030 (13) | 0.0365 (5) | |
C8 | 0.11366 (16) | 0.5985 (3) | 0.38604 (11) | 0.0252 (4) | |
C9 | 0.12015 (16) | 0.4150 (3) | 0.33493 (11) | 0.0256 (4) | |
C10 | 0.21984 (16) | 0.2770 (3) | 0.37048 (11) | 0.0266 (4) | |
C11 | 0.32302 (16) | 0.4106 (3) | 0.39376 (11) | 0.0268 (5) | |
C12 | 0.30878 (16) | 0.5961 (4) | 0.44065 (12) | 0.0320 (5) | |
H3A | 0.20162 | 0.20895 | 0.21349 | 0.0405* | |
H9B | 0.12621 | 0.47356 | 0.28846 | 0.0307* | |
H11A | 0.44627 | 0.23745 | 0.4115 | 0.0463* | |
H10B | 0.21093 | 0.20623 | 0.4143 | 0.0319* | |
H8A | 0.0954 | 0.60463 | 0.47871 | 0.0414* | |
H5B | 0.48263 | 0.4284 | 0.15205 | 0.0329* | |
H2A | 0.11709 | 0.59116 | 0.02195 | 0.0383* | |
H6A | 0.42617 | 0.66733 | 0.05503 | 0.0381* | |
H6B | 0.32208 | 0.53027 | 0.01517 | 0.0381* | |
H9A | −0.02006 | 0.32465 | 0.27811 | 0.0442* | |
H11B | 0.33855 | 0.46362 | 0.34947 | 0.0321* | |
H5A | 0.53459 | 0.2308 | 0.08379 | 0.0485* | |
H4B | 0.29326 | 0.18044 | 0.08229 | 0.0318* | |
H4A | 0.3784 | −0.032 | 0.15987 | 0.0462* | |
H3B | 0.31745 | 0.42981 | 0.21083 | 0.0287* | |
H10A | 0.22195 | 0.00214 | 0.334 | 0.0519* | |
H12A | 0.30313 | 0.54341 | 0.48742 | 0.0384* | |
H12B | 0.37304 | 0.68699 | 0.45164 | 0.0384* | |
H7A | 0.04068 | 0.96523 | 0.28858 | 0.0657* | |
H7C | −0.04858 | 0.67955 | 0.34064 | 0.0438* | |
H7B | 0.02309 | 0.8675 | 0.38472 | 0.0438* | |
H1C | 0.13966 | 0.84507 | 0.1204 | 0.0456* | |
H1B | 0.09662 | 0.64956 | 0.1545 | 0.0456* | |
H1A | 0.27758 | 0.85718 | 0.2184 | 0.0755* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0933 (16) | 0.0493 (13) | 0.0544 (11) | −0.0043 (11) | 0.0348 (11) | −0.0184 (10) |
O2 | 0.0312 (8) | 0.0310 (9) | 0.0263 (7) | 0.0003 (6) | −0.0014 (6) | 0.0014 (6) |
O3 | 0.0312 (8) | 0.0350 (9) | 0.0338 (8) | −0.0052 (7) | 0.0082 (6) | 0.0102 (7) |
O4 | 0.0426 (9) | 0.0250 (9) | 0.0381 (9) | 0.0065 (7) | −0.0013 (7) | 0.0029 (7) |
O5 | 0.0260 (8) | 0.0569 (11) | 0.0355 (9) | 0.0092 (8) | 0.0055 (6) | −0.0126 (8) |
O6 | 0.0308 (8) | 0.0237 (8) | 0.0363 (8) | −0.0023 (6) | 0.0143 (6) | 0.0013 (6) |
O7 | 0.0706 (12) | 0.0396 (11) | 0.0503 (11) | 0.0128 (10) | 0.0138 (9) | 0.0158 (9) |
O8 | 0.0441 (9) | 0.0336 (9) | 0.0306 (8) | 0.0027 (7) | 0.0186 (7) | 0.0023 (7) |
O9 | 0.0317 (8) | 0.0305 (9) | 0.0390 (9) | −0.0099 (7) | −0.0021 (6) | 0.0024 (7) |
O10 | 0.0629 (11) | 0.0260 (9) | 0.0445 (10) | 0.0004 (8) | 0.0221 (8) | −0.0111 (7) |
O11 | 0.0311 (8) | 0.0520 (11) | 0.0333 (8) | 0.0158 (7) | 0.0112 (6) | 0.0034 (7) |
O12 | 0.0252 (7) | 0.0241 (8) | 0.0370 (8) | −0.0021 (6) | 0.0066 (6) | −0.0042 (6) |
C1 | 0.0465 (13) | 0.0292 (13) | 0.0444 (13) | 0.0053 (10) | 0.0231 (11) | 0.0009 (10) |
C2 | 0.0252 (10) | 0.0223 (11) | 0.0259 (10) | −0.0023 (8) | 0.0076 (8) | −0.0008 (8) |
C3 | 0.0252 (10) | 0.0221 (11) | 0.0220 (9) | −0.0038 (8) | 0.0039 (8) | −0.0002 (8) |
C4 | 0.0254 (10) | 0.0252 (11) | 0.0230 (10) | 0.0015 (8) | −0.0007 (8) | −0.0019 (8) |
C5 | 0.0224 (9) | 0.0339 (13) | 0.0231 (10) | 0.0020 (9) | 0.0030 (8) | −0.0054 (9) |
C6 | 0.0283 (11) | 0.0375 (13) | 0.0315 (11) | 0.0032 (9) | 0.0123 (9) | 0.0040 (10) |
C7 | 0.0319 (11) | 0.0285 (13) | 0.0475 (14) | 0.0044 (9) | 0.0103 (10) | 0.0052 (10) |
C8 | 0.0247 (10) | 0.0230 (11) | 0.0283 (10) | −0.0012 (8) | 0.0087 (8) | 0.0019 (8) |
C9 | 0.0288 (10) | 0.0229 (11) | 0.0230 (10) | −0.0054 (8) | 0.0051 (8) | 0.0016 (8) |
C10 | 0.0352 (11) | 0.0238 (11) | 0.0224 (10) | 0.0009 (9) | 0.0115 (8) | −0.0006 (8) |
C11 | 0.0266 (10) | 0.0313 (12) | 0.0231 (10) | 0.0042 (9) | 0.0089 (8) | 0.0007 (8) |
C12 | 0.0244 (10) | 0.0361 (13) | 0.0319 (11) | 0.0000 (9) | 0.0037 (8) | −0.0093 (9) |
O1—C1 | 1.396 (3) | O1—H1A | 0.820 |
O2—C2 | 1.395 (2) | O2—H2A | 0.820 |
O3—C3 | 1.418 (3) | O3—H3A | 0.820 |
O4—C4 | 1.438 (2) | O4—H4A | 0.820 |
O5—C5 | 1.425 (3) | O5—H5A | 0.820 |
O6—C2 | 1.429 (3) | O7—H7A | 0.820 |
O6—C6 | 1.430 (3) | O8—H8A | 0.820 |
O7—C7 | 1.403 (3) | O9—H9A | 0.820 |
O8—C8 | 1.400 (3) | O10—H10A | 0.820 |
O9—C9 | 1.428 (3) | O11—H11A | 0.820 |
O10—C10 | 1.426 (3) | C1—H1C | 0.970 |
O11—C11 | 1.419 (2) | C1—H1B | 0.970 |
O12—C8 | 1.423 (2) | C3—H3B | 0.980 |
O12—C12 | 1.429 (2) | C4—H4B | 0.980 |
C1—C2 | 1.512 (3) | C5—H5B | 0.980 |
C2—C3 | 1.522 (3) | C6—H6A | 0.970 |
C3—C4 | 1.511 (3) | C6—H6B | 0.970 |
C4—C5 | 1.513 (3) | C7—H7C | 0.970 |
C5—C6 | 1.506 (3) | C7—H7B | 0.970 |
C7—C8 | 1.515 (3) | C9—H9B | 0.980 |
C8—C9 | 1.526 (3) | C10—H10B | 0.980 |
C9—C10 | 1.516 (3) | C11—H11B | 0.980 |
C10—C11 | 1.511 (3) | C12—H12A | 0.970 |
C11—C12 | 1.513 (3) | C12—H12B | 0.970 |
C2—O6—C6 | 113.05 (16) | C8—O8—H8A | 109.471 |
C8—O12—C12 | 113.61 (15) | C9—O9—H9A | 109.472 |
O1—C1—C2 | 111.89 (19) | C10—O10—H10A | 109.479 |
O2—C2—O6 | 111.22 (16) | C11—O11—H11A | 109.476 |
O2—C2—C1 | 110.54 (16) | O1—C1—H1C | 109.244 |
O2—C2—C3 | 107.06 (16) | O1—C1—H1B | 109.242 |
O6—C2—C1 | 106.13 (17) | C2—C1—H1C | 109.230 |
O6—C2—C3 | 109.14 (15) | C2—C1—H1B | 109.231 |
C1—C2—C3 | 112.80 (18) | H1C—C1—H1B | 107.914 |
O3—C3—C2 | 107.78 (15) | O3—C3—H3B | 108.924 |
O3—C3—C4 | 110.78 (16) | C2—C3—H3B | 108.914 |
C2—C3—C4 | 111.47 (18) | C4—C3—H3B | 108.910 |
O4—C4—C3 | 108.92 (17) | O4—C4—H4B | 108.731 |
O4—C4—C5 | 110.20 (16) | C3—C4—H4B | 108.728 |
C3—C4—C5 | 111.47 (17) | C5—C4—H4B | 108.740 |
O5—C5—C4 | 110.39 (18) | O5—C5—H5B | 109.860 |
O5—C5—C6 | 106.31 (18) | C4—C5—H5B | 109.868 |
C4—C5—C6 | 110.49 (17) | C6—C5—H5B | 109.864 |
O6—C6—C5 | 112.05 (19) | O6—C6—H6A | 109.207 |
O7—C7—C8 | 112.6 (2) | O6—C6—H6B | 109.204 |
O8—C8—O12 | 111.70 (15) | C5—C6—H6A | 109.202 |
O8—C8—C7 | 109.51 (19) | C5—C6—H6B | 109.203 |
O8—C8—C9 | 107.19 (16) | H6A—C6—H6B | 107.889 |
O12—C8—C7 | 106.49 (16) | O7—C7—H7C | 109.070 |
O12—C8—C9 | 108.98 (18) | O7—C7—H7B | 109.069 |
C7—C8—C9 | 113.04 (16) | C8—C7—H7C | 109.076 |
O9—C9—C8 | 110.39 (18) | C8—C7—H7B | 109.068 |
O9—C9—C10 | 109.27 (16) | H7C—C7—H7B | 107.828 |
C8—C9—C10 | 110.99 (15) | O9—C9—H9B | 108.714 |
O10—C10—C9 | 110.08 (15) | C8—C9—H9B | 108.713 |
O10—C10—C11 | 108.49 (19) | C10—C9—H9B | 108.709 |
C9—C10—C11 | 110.40 (17) | O10—C10—H10B | 109.288 |
O11—C11—C10 | 111.40 (17) | C9—C10—H10B | 109.283 |
O11—C11—C12 | 106.60 (15) | C11—C10—H10B | 109.285 |
C10—C11—C12 | 110.17 (18) | O11—C11—H11B | 109.539 |
O12—C12—C11 | 111.71 (15) | C10—C11—H11B | 109.544 |
C1—O1—H1A | 109.482 | C12—C11—H11B | 109.542 |
C2—O2—H2A | 109.473 | O12—C12—H12A | 109.276 |
C3—O3—H3A | 109.469 | O12—C12—H12B | 109.277 |
C4—O4—H4A | 109.472 | C11—C12—H12A | 109.279 |
C5—O5—H5A | 109.470 | C11—C12—H12B | 109.283 |
C7—O7—H7A | 109.468 | H12A—C12—H12B | 107.938 |
C2—O6—C6—C5 | −60.30 (17) | C3—C4—C5—O5 | −166.84 (13) |
C6—O6—C2—O2 | −57.58 (18) | C3—C4—C5—C6 | −49.53 (19) |
C6—O6—C2—C1 | −177.85 (12) | O5—C5—C6—O6 | 173.00 (14) |
C6—O6—C2—C3 | 60.32 (17) | C4—C5—C6—O6 | 53.2 (2) |
C8—O12—C12—C11 | 59.7 (2) | O7—C7—C8—O8 | −176.16 (15) |
C12—O12—C8—O8 | 58.4 (2) | O7—C7—C8—O12 | 62.9 (2) |
C12—O12—C8—C7 | 177.90 (15) | O7—C7—C8—C9 | −56.7 (2) |
C12—O12—C8—C9 | −59.9 (2) | O8—C8—C9—O9 | 56.92 (18) |
O1—C1—C2—O2 | 172.38 (18) | O8—C8—C9—C10 | −64.39 (19) |
O1—C1—C2—O6 | −66.9 (2) | O12—C8—C9—O9 | 177.97 (13) |
O1—C1—C2—C3 | 52.6 (2) | O12—C8—C9—C10 | 56.6 (2) |
O2—C2—C3—O3 | −57.0 (2) | C7—C8—C9—O9 | −63.8 (2) |
O2—C2—C3—C4 | 64.77 (19) | C7—C8—C9—C10 | 174.84 (17) |
O6—C2—C3—O3 | −177.49 (14) | O9—C9—C10—O10 | 64.2 (2) |
O6—C2—C3—C4 | −55.71 (18) | O9—C9—C10—C11 | −176.02 (15) |
C1—C2—C3—O3 | 64.81 (19) | C8—C9—C10—O10 | −173.79 (16) |
C1—C2—C3—C4 | −173.42 (14) | C8—C9—C10—C11 | −54.0 (2) |
O3—C3—C4—O4 | −66.54 (17) | O10—C10—C11—O11 | −69.2 (2) |
O3—C3—C4—C5 | 171.66 (12) | O10—C10—C11—C12 | 172.67 (13) |
C2—C3—C4—O4 | 173.44 (13) | C9—C10—C11—O11 | 170.05 (16) |
C2—C3—C4—C5 | 51.64 (18) | C9—C10—C11—C12 | 52.0 (2) |
O4—C4—C5—O5 | 72.10 (18) | O11—C11—C12—O12 | −175.14 (16) |
O4—C4—C5—C6 | −170.59 (14) | C10—C11—C12—O12 | −54.1 (2) |
D—H···A | D—H | H···A | D···A | 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+1/2, y+1/2, −z; (iii) x, y−1, z; (iv) x+1/2, −y+1/2, z; (v) −x+1/2, y+1/2, −z+1; (vi) x−1/2, −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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