Crystal structure of 6-de­oxy-α-l-psico­furan­ose

Akihide Yoshihara; Tomohiko Ishii; Tatsuya Kamakura; Hiroaki Taguchi; Kazuhiro Fukada

doi:10.1107/S2056989015022215

. 2015 Nov 28;71(Pt 12):o993–o994. doi: 10.1107/S2056989015022215

Crystal structure of 6-deoxy-α-l-psicofuranose

Akihide Yoshihara ^a, Tomohiko Ishii ^b,^*, Tatsuya Kamakura ^b, Hiroaki Taguchi ^b, Kazuhiro Fukada ^c

PMCID: PMC4719940 PMID: 26870568

Abstract

The title compound, C₆H₁₂O₅, was crystallized from an aqueous solution of 6-deoxy-l-psicose (6-deoxy-l-allulose, (3S,4S,5S)-1,3,4,5-tetrahydroxyhexan-2-one), and the molecule was confirmed as α-furanose with a ³ T ₄ (or E ₄) conformation, which is a predominant tautomer in solution. This five-membered furanose ring structure is the second example in the field of the 6-deoxy-ketohexose family. The cell volume of the title compound [742.67 (7) Å³, Z = 4 at room temperature] is only 1.4% smaller than that of β-d-psicopyranose, C₆H₁₂O₆ (753.056 Å³, Z = 4 at room temperature).

Keywords: crystal structure, hydrogen bonding, deoxy compound, rare sugar

Related literature

For the predominant tautomer, α-furanose, of 6-deoxy-l-psicose in aqueous solution, see: Yoshihara et al. (2015 ▸). For the crystal structure of chiral β-d-psicose, see: Kwiecień et al. (2008 ▸); Fukada et al. (2010 ▸). For the crystal structure of racemic β-D,l-psicose, see: Ishii et al. (2015 ▸). For the synthesis of 6-deoxy-l-psicose, see: Shompoosang et al. (2014 ▸). For the crystal structures of 6-deoxy-α-l-sorbofuranose and 6-deoxy-α-d-sorbofuranose, see: Swaminathan et al. (1979 ▸); Rao et al. (1981 ▸); Jones et al. (2006 ▸). graphic file with name e-71-0o993-scheme1.jpg

Experimental

Crystal data

C₆H₁₂O₅
M _r = 164.16
Orthorhombic,
a = 5.7853 (3) Å
b = 8.9442 (5) Å
c = 14.3528 (8) Å
V = 742.69 (7) Å³
Z = 4
Cu Kα radiation
μ = 1.12 mm⁻¹
T = 296 K
0.10 × 0.10 × 0.10 mm

Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ▸) T _min = 0.732, T _max = 0.894
13299 measured reflections
1358 independent reflections
1330 reflections with F ² > 2σ(F ²)
R _int = 0.072

Refinement

R[F ² > 2σ(F ²)] = 0.027
wR(F ²) = 0.065
S = 1.08
1358 reflections
105 parameters
H-atom parameters constrained
Δρ_max = 0.15 e Å⁻³
Δρ_min = −0.14 e Å⁻³
Absolute structure: Flack x determined using 521 quotients [(I ⁺)−(I ⁻)]/[(I ⁺)+(I ⁻)] (Parsons & Flack, 2004 ▸)
Absolute structure parameter: 0.03 (8)

Data collection: RAPID-AUTO (Rigaku, 2009 ▸); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: Il Milione (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.

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015022215/is5433sup1.cif

e-71-0o993-sup1.cif^{(399.3KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015022215/is5433Isup2.hkl

e-71-0o993-Isup2.hkl^{(110KB, hkl)}

Click here for additional data file.^{(427KB, png)}

Supporting information file. DOI: 10.1107/S2056989015022215/is5433Isup3.png

Click here for additional data file.^{(1.2MB, tif)}

ORTEP . DOI: 10.1107/S2056989015022215/is5433fig1.tif

An 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.

Click here for additional data file.^{(2.8MB, tif)}

a . DOI: 10.1107/S2056989015022215/is5433fig2.tif

A packing diagram of the title compound viewed down the a-axis, showing the hydrogen-bonding network (green dashed lines).

CCDC reference: 1437931

Additional supporting information: 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—H1A⋯O5ⁱ	0.82	2.02	2.839 (2)	177
O2—H2A⋯O1ⁱⁱ	0.82	2.13	2.819 (2)	142
O2—H2A⋯O3	0.82	2.08	2.592 (2)	121
O3—H3A⋯O2ⁱⁱⁱ	0.82	1.93	2.732 (2)	166
O4—H4A⋯O3^iv	0.82	2.24	2.902 (2)	138
O4—H4A⋯O4^iv	0.82	2.26	2.987 (2)	148

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) .

Acknowledgments

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

supplementary crystallographic information

S1. Comment

Psicose is classified into a rare sugar, and hardly exists in nature. In this study we prepare a single-crystal of 6-deoxy-L-psicose (Fig. 1), which is obtained by enzymatic isomerization of L-rhamnose, and investigate the structure by X-ray crystal analysis. The space group of this compound is orthorhombic P2₁2₁2₁, which is the same as that of β-D-psicopyranose (cf. D-psicose; Kwiecień et al., 2008; Fukada et al., 2010). The molecular weight of 6-deoxy-L-psicose (C₆H₁₂O₅; m.w. = 164.16) is about 10% smaller than that of D-psicose (180.16). On the other hand, the cell volume of 6-deoxy-α-L-psicofuranose is 742.67 (7) Å³ at r.t., which is a mere 1.4% smaller than that of β-D-psicopyranose (753.056 Å³ at r.t., cf. D-psicose; Kwiecień et al., 2008; Fukada et al., 2010). This imbalance of decreasing suggests that a weaker intermolecular interaction caused by a smaller molecular density can be expected. The melting point of 6-deoxy-α-L-psicofuranose has been observed to be 76 °C, which is about 30 °C lower than that of psicose (107.6 °C). This lower melting point is consistent with the suggested weaker intermolecular interaction.

We found that 6-deoxy-L-psicose molecules form a five-membered α-furanose ring structure in crystal. In the crystals of ketohexoses so far, six-membered pyranose ring structures have been mainly confirmed (cf. D-psicose; Kwiecień et al., 2008; Fukada et al., 2010, 1-deoxy-L-sorbose; Jones et al., 2006). Because of the deoxygenation in the 6-deoxy-L-psicose molecule, the carbonyl group at the C-2 position cannot form hemiacetal with the C-6 but with the C-5 hydroxyl group. It should be noted that the crystal structure of 6-deoxy-L-sorbose, C-4 epimer of 6-deoxy-L-psicose, was reported to be α-furanose; C3'-exo-C4'-endo, ₃T⁴ (Swaminathan et al., 1979). Therefore, the α-furanose structure observed in the crystal of 6-deoxy-L-psicose is the second example in 6-deoxy-ketohexose family, with ³T₄ (or E₄) conformation. An intramolecular hydrogen bond (O3—H3A···O5) has been observed both in a chiral D-psicose (Kwiecień et al., 2008; Fukada et al., 2010) and a racemic D,L-psicose (Ishii et al., 2015). This comes from two hydroxy groups located in a shorter distance from each other because of both axial conformations connecting to the C-3 and C-5 positions. On the other hand in the 6-deoxy-L-psicose, such an intramolecular hydrogen bond is not observed, because the hydroxy group at a C-5 position has been used for creating the ring structure. Intermolecular hydrogen bonds (O3—H3A···O2 and O1—H1A···O5) are also confirmed along the b-axis, and O4—H4A···O4 along the a-axis, as shown in Fig. 2.

S2. Experimental

6-Deoxy-L-psicose was prepared from L-rhamnose by immobilized L-rhamnose isomerase and immobilized D-tagatose 3-epimerase in the batch reaction (Shompoosang et al., 2014). After this reaction was reached equilibrium, the reaction mixture containing 6-deoxy-L-psicose was separated by column chromatography. The purified 6-deoxy-L-psicose solution was concentrated to 80% by evaporation. A seed crystal of 6-deoxy-L-psicose was added to the 80% 6-deoxy-L-psicose solution, which was kept at 30 °C. The tautomer ratio in aqueous solution at 30 °C is obtained as α-furanose: β-furanose: acyclic form = 72.9: 24.5: 2.69 (Yoshihara et al., 2015). After one day, single crystals were obtained.