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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 71| Part 5| May 2015| Pages o289-o290
https://doi.org/10.1107/S2056989015006623

Crystal structure of β-D,L-psicose

Tomohiko Ishii,a* Genta Sakane,b Akihide Yoshihara,c Kazuhiro Fukadad and Tatsuya Senooa

aDepartment of Advanced Materials Science, Faculty of Engineering, Kagawa University, 2217-20 Hayashi-cho, Takamatsu, Kagawa 761-0396, Japan, bDepartment of Chemistry, Faculty of Science, Okayama University of Science, 1-1 Ridaicho, Kita-ku, Okayama 700-0005, Japan, cRare Sugar Research Center, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Kagawa 761-0795, Japan, and dDepartment 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 19 March 2015; accepted 2 April 2015; online 9 April 2015)

The title compound, C6H12O6, a C-3 position epimer of fructose, was crystallized from an aqueous solution of equimolar mixture of D- and L-psicose (1,3,4,5,6-penta­hydroxy­hexan-2-one, ribo-2-hexulose, allulose), and it was confirmed that D-psicose (or L-psicose) formed β-pyran­ose with a 2C5 (or 5C2) conformation. In the crystal, an O—H⋯O hydrogen bond between the hy­droxy groups at the C-3 and C-2 positions connects homochiral mol­ecules into a column along the b axis. The columns are linked by other O—H⋯O hydrogen bonds between D- and L-psicose mol­ecules, forming a three-dimensional network. An intra­molecular O—H⋯O hydrogen bond is also observed. The cell volume of racemic β-D,L-psicose [763.21 (6) Å3] is almost the same as that of chiral β-D-psicose [753.06 Å3].

CCDC reference: 1057484

Similar articles

1. Related literature

For the crystal structure of the chiral β-D-psicose, see: Kwiecien et al. (2008[Kwiecien, A., Slepokura, K. & Lis, T. (2008). Carbohydr. Res. 343, 2336-2339.]); Fukada et al. (2010[Fukada, K., Ishii, T., Tanaka, K., Yamaji, M., Yamaoka, Y., Kobashi, K. & Izumori, K. (2010). Bull. Chem. Soc. Jpn, 83, 1193-1197.]). For the synthesis of the chiral D-psicose, see: Itoh et al. (1995[Itoh, H., Sato, T. & Izumori, K. (1995). J. Ferment. Bioeng. 80, 101-103.]); Takeshita et al. (2000[Takeshita, K., Suga, A., Takada, G. & Izumori, K. (2000). J. Biosci. Bioeng. 90, 453-455.]). For the synthesis of the chiral L-psicose, see: Takeshita et al. (1996[Takeshita, K., Shimonishi, T. & Izumori, K. (1996). J. Ferment. Bioeng. 81, 212-215.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C6H12O6

  • Mr = 180.16

  • Orthorhombic, P n a 21

  • a = 11.2629 (5) Å

  • b = 5.3552 (3) Å

  • c = 12.6538 (6) Å

  • V = 763.21 (6) Å3

  • Z = 4

  • Cu Kα radiation

  • μ = 1.25 mm−1

  • T = 296 K

  • 0.10 × 0.10 × 0.10 mm

2.2. Data collection

  • Rigaku R-AXIS RAPID diffractometer

  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.442, Tmax = 0.883

  • 12119 measured reflections

  • 1400 independent reflections

  • 1295 reflections with F2 > 2σ(F2)

  • Rint = 0.139

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.048

  • wR(F2) = 0.102

  • S = 1.04

  • 1400 reflections

  • 116 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.25 e Å−3

  • Δρmin = −0.23 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 666 Friedel pairs

  • Absolute structure parameter: 0.1 (4)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O1—H1A⋯O3i 0.82 1.91 2.715 (3) 168
O2—H2A⋯O4ii 0.82 1.92 2.724 (3) 166
O3—H3A⋯O2iii 0.82 2.20 2.874 (3) 140
O3—H3A⋯O5 0.82 2.36 2.822 (4) 117
O4—H4A⋯O6iv 0.82 2.14 2.829 (3) 141
O5—H5A⋯O1v 0.82 1.94 2.746 (4) 169
Symmetry codes: (i) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z]; (ii) [x-{\script{1\over 2}}, -y+{\script{5\over 2}}, z]; (iii) x, y-1, z; (iv) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z]; (v) [-x+{\script{3\over 2}}, y-{\script{1\over 2}}, z+{\script{1\over 2}}].

Data collection: RAPID-AUTO (Rigaku, 2009[Rigaku (2009). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: 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.]); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]); molecular graphics: CrystalStructure (Rigaku, 2014[Rigaku (2014). CrystalStructure. Rigaku Corporation, Tokyo, Japan.]); software used to prepare material for publication: CrystalStructure.

Supporting information

CCDC reference: 1057484

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989015006623/is5394sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989015006623/is5394Isup2.hkl

checkCIF report


Comment top

In the crystal of the title compound, the D- and L-molecules are located alternatively in a-c plane, so that the main hydrogen bonding networks can be created between D- and L-molecules. An additional hydrogen bonding between two D-molecules (and two L-molecules) are observed along to the b-axis (O3—H3A···O2iii; Table 1). The molecular structure of D-psicose (or L-psicose) is β-pyranose form with a 2C5 (or 5C2) conformation. Orientations of two OH groups at C-3 and C-5 positions are axial, therefore an intramolecular hydrogen bonding can be observed (O3—H3A···O5; 2.36 Å) [hereafter, (O3···O5)]. The intramolecular hydrogen bonding unit (O3···O5) shown in the racemic D,L-crystal has also observed in a chiral D-crystal (Fukada et al., 2010). In the chiral one, one-dimensional hydrogen bonding chain, that is (O3···O5) -> (O3···O5) -> (O3···O5) ->···, can be observed by connecting through an another hydrogen bonding between two D-molecule units (O5—H5···O3). On the other hand in the case of the racemic one, the L-molecule (or D-molecule) plays as a role of a bridging between two adjacent intramolecular hydrogen bonding in D-molecule (or L-molecule) (O3···O5) units, that is (D O3···O5) -> (L O1) -> (D O3···O5) -> (L O1) -> ··· (or, (L O3···O5) -> (D O1) -> (L O3···O5) -> (D O1) -> ···). Concerning the intermolecular hydrogen bonding, there are four kinds of bondings are also observed between D- and L- psicose molecules (O1—H1A···O3 (a-axis), O2—H2A···O4, O4—H4A···O6 (a-axis), and O5—H5A···O1 (c-axis),). The cell volume of racemic β-D,L-psicose [763.21 (6) Å3 at r.t.] is almost the same as that of chiral β-D-psicose [753.06 Å3 at r.t.].

Related literature top

For the crystal structure of the chiral β-D-psicose, see: Kwiecien et al. (2008); Fukada et al. (2010). For the synthesis of the chiral D-psicose, see: Itoh et al. (1995); Takeshita et al. (2000). For the synthesis of the chiral L-psicose, see: Takeshita et al. (1996).

Experimental top

D-Psicose was prepared from D-fructose by enzymatic epimerization using D-tagatose 3-epimerase (Itoh et al., 1995; Takeshita et al., 2000). L-Psicose was prepared from allitol by microbial oxidation using Gluconobacter frateurii IFO 3254 (Takeshita et al., 1996). D-Psicose and L-psicose were mixed in equal amount and dissolved in hot water to give 60, 65, 70, 75, and 80 wt% solution. And these samples were kept at 10, 20, and 30 °C. After one day, small crystals were obtained in 65, 70, 75, and 80 wt% solution at 10, 20, and 30 °C.

Refinement top

H atoms bounded to methine-type C (H3B, H4B, H5B) 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 (H1B, H1C, H6A, H6B) 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, H5A) 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.

Structure description top

In the crystal of the title compound, the D- and L-molecules are located alternatively in a-c plane, so that the main hydrogen bonding networks can be created between D- and L-molecules. An additional hydrogen bonding between two D-molecules (and two L-molecules) are observed along to the b-axis (O3—H3A···O2iii; Table 1). The molecular structure of D-psicose (or L-psicose) is β-pyranose form with a 2C5 (or 5C2) conformation. Orientations of two OH groups at C-3 and C-5 positions are axial, therefore an intramolecular hydrogen bonding can be observed (O3—H3A···O5; 2.36 Å) [hereafter, (O3···O5)]. The intramolecular hydrogen bonding unit (O3···O5) shown in the racemic D,L-crystal has also observed in a chiral D-crystal (Fukada et al., 2010). In the chiral one, one-dimensional hydrogen bonding chain, that is (O3···O5) -> (O3···O5) -> (O3···O5) ->···, can be observed by connecting through an another hydrogen bonding between two D-molecule units (O5—H5···O3). On the other hand in the case of the racemic one, the L-molecule (or D-molecule) plays as a role of a bridging between two adjacent intramolecular hydrogen bonding in D-molecule (or L-molecule) (O3···O5) units, that is (D O3···O5) -> (L O1) -> (D O3···O5) -> (L O1) -> ··· (or, (L O3···O5) -> (D O1) -> (L O3···O5) -> (D O1) -> ···). Concerning the intermolecular hydrogen bonding, there are four kinds of bondings are also observed between D- and L- psicose molecules (O1—H1A···O3 (a-axis), O2—H2A···O4, O4—H4A···O6 (a-axis), and O5—H5A···O1 (c-axis),). The cell volume of racemic β-D,L-psicose [763.21 (6) Å3 at r.t.] is almost the same as that of chiral β-D-psicose [753.06 Å3 at r.t.].

For the crystal structure of the chiral β-D-psicose, see: Kwiecien et al. (2008); Fukada et al. (2010). For the synthesis of the chiral D-psicose, see: Itoh et al. (1995); Takeshita et al. (2000). For the synthesis of the chiral L-psicose, see: Takeshita et al. (1996).

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).

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 green solid lines, viewed down the b-axis. The hydrogen atoms are omitted for clarity.
[Figure 3] Fig. 3. Part of the crystal structure of the chiral β-D-psicose (Fukada et al., 2010) with hydrogen-bonding network represented as green solid lines. The hydrogen atoms are omitted for clarity.
(I) top
Crystal data top
C6H12O6Dx = 1.568 Mg m−3
Mr = 180.16Cu Kα radiation, λ = 1.54187 Å
Orthorhombic, Pna21Cell parameters from 5584 reflections
a = 11.2629 (5) Åθ = 3.5–68.5°
b = 5.3552 (3) ŵ = 1.25 mm−1
c = 12.6538 (6) ÅT = 296 K
V = 763.21 (6) Å3Block, colorless
Z = 40.10 × 0.10 × 0.10 mm
F(000) = 384.00
Data collection top
Rigaku R-AXIS RAPID
diffractometer		1295 reflections with F2 > 2σ(F2)
Detector resolution: 10.000 pixels mm-1Rint = 0.139
ω scansθmax = 68.2°, θmin = 7.0°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)		h = −13→13
Tmin = 0.442, Tmax = 0.883k = −6→6
12119 measured reflectionsl = −15→15
1400 independent reflections
Refinement top
Refinement on F2H-atom parameters constrained
R[F2 > 2σ(F2)] = 0.048 w = 1/[σ2(Fo2) + (0.0359P)2]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.102(Δ/σ)max < 0.001
S = 1.04Δρmax = 0.25 e Å−3
1400 reflectionsΔρmin = −0.23 e Å−3
116 parametersExtinction correction: SHELXL
1 restraintExtinction coefficient: 0.039 (3)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 666 Friedel pairs
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.1 (4)
Hydrogen site location: inferred from neighbouring sites
Crystal data top
C6H12O6V = 763.21 (6) Å3
Mr = 180.16Z = 4
Orthorhombic, Pna21Cu Kα radiation
a = 11.2629 (5) ŵ = 1.25 mm−1
b = 5.3552 (3) ÅT = 296 K
c = 12.6538 (6) Å0.10 × 0.10 × 0.10 mm
Data collection top
Rigaku R-AXIS RAPID
diffractometer		1400 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)		1295 reflections with F2 > 2σ(F2)
Tmin = 0.442, Tmax = 0.883Rint = 0.139
12119 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.048H-atom parameters constrained
wR(F2) = 0.102Δρmax = 0.25 e Å−3
S = 1.04Δρmin = −0.23 e Å−3
1400 reflectionsAbsolute structure: Flack (1983), 666 Friedel pairs
116 parametersAbsolute structure parameter: 0.1 (4)
1 restraint
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 σ(F2) is used only for calculating R-factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.6428 (2)1.0475 (5)0.0101 (2)0.0321 (7)
O20.8138 (2)1.3225 (4)0.1244 (2)0.0283 (6)
O30.9712 (2)0.7407 (4)0.0986 (2)0.0278 (6)
O41.12635 (19)0.9941 (5)0.2360 (2)0.0306 (7)
O50.9520 (3)0.6941 (5)0.3201 (2)0.0368 (7)
O60.75926 (19)0.9487 (5)0.2068 (2)0.0243 (6)
C10.7610 (3)0.9600 (8)0.0218 (3)0.0275 (8)
C20.8199 (3)1.0614 (6)0.1199 (3)0.0211 (7)
C30.9525 (3)0.9956 (6)0.1238 (3)0.0223 (7)
C41.0049 (3)1.0665 (7)0.2306 (2)0.0233 (8)
C50.9337 (3)0.9564 (7)0.3210 (3)0.0266 (8)
C60.8044 (3)1.0258 (7)0.3083 (3)0.0289 (8)
H1B0.806951.00892−0.039680.0330*
H1C0.760420.779040.024970.0330*
H1A0.597720.957560.043840.0386*
H2A0.750431.364670.150740.0340*
H3A0.928320.653240.135610.0333*
H3B0.992731.09590.069850.0268*
H4B1.001471.248720.236910.0280*
H4A1.13130.841670.231980.0367*
H5A0.921920.632180.372940.0442*
H5B0.963221.02460.387920.0319*
H6A0.758280.947070.363780.0347*
H6B0.795661.205250.315440.0347*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0232 (14)0.0431 (18)0.0301 (13)−0.0019 (11)−0.0058 (11)0.0126 (12)
O20.0238 (12)0.0228 (13)0.0384 (14)0.0010 (9)0.0057 (11)0.0025 (13)
O30.0252 (12)0.0240 (13)0.0340 (14)0.0013 (10)0.0068 (10)−0.0020 (11)
O40.0193 (12)0.0265 (14)0.0459 (17)0.0004 (10)−0.0022 (10)0.0013 (12)
O50.0475 (17)0.0309 (15)0.0322 (15)0.0064 (12)0.0101 (11)0.0101 (12)
O60.0230 (12)0.0297 (14)0.0203 (11)−0.0057 (10)0.0027 (10)0.0002 (12)
C10.025 (2)0.032 (2)0.0254 (19)−0.0001 (15)−0.0001 (14)0.0024 (18)
C20.0211 (17)0.0228 (17)0.0195 (16)0.0012 (12)0.0034 (14)0.0043 (16)
C30.0197 (19)0.0233 (17)0.0239 (17)0.0009 (12)0.0038 (14)0.0042 (14)
C40.0189 (17)0.025 (2)0.0265 (19)0.0009 (13)0.0000 (13)0.0006 (15)
C50.030 (2)0.030 (2)0.0201 (17)0.0027 (14)−0.0011 (15)−0.0001 (15)
C60.0272 (18)0.039 (2)0.0209 (17)0.0006 (15)0.0055 (15)−0.0002 (15)
Geometric parameters (Å, º) top
O1—C11.419 (4)O1—H1A0.820
O2—C21.401 (4)O2—H2A0.820
O3—C31.418 (4)O3—H3A0.820
O4—C41.423 (4)O4—H4A0.820
O5—C51.419 (4)O5—H5A0.820
O6—C21.428 (4)C1—H1B0.970
O6—C61.442 (4)C1—H1C0.970
C1—C21.509 (5)C3—H3B0.980
C2—C31.535 (5)C4—H4B0.980
C3—C41.523 (5)C5—H5B0.980
C4—C51.516 (5)C6—H6A0.970
C5—C61.512 (5)C6—H6B0.970
C2—O6—C6113.3 (2)C4—O4—H4A109.469
O1—C1—C2112.3 (3)C5—O5—H5A109.469
O2—C2—O6111.6 (3)O1—C1—H1B109.152
O2—C2—C1111.8 (3)O1—C1—H1C109.152
O2—C2—C3106.0 (3)C2—C1—H1B109.145
O6—C2—C1105.7 (3)C2—C1—H1C109.145
O6—C2—C3110.1 (3)H1B—C1—H1C107.867
C1—C2—C3111.8 (3)O3—C3—H3B107.581
O3—C3—C2111.0 (3)C2—C3—H3B107.578
O3—C3—C4112.5 (3)C4—C3—H3B107.580
C2—C3—C4110.4 (3)O4—C4—H4B107.757
O4—C4—C3110.3 (3)C3—C4—H4B107.761
O4—C4—C5111.5 (3)C5—C4—H4B107.767
C3—C4—C5111.6 (3)O5—C5—H5B109.099
O5—C5—C4107.5 (3)C4—C5—H5B109.103
O5—C5—C6112.5 (3)C6—C5—H5B109.093
C4—C5—C6109.5 (3)O6—C6—H6A109.357
O6—C6—C5111.4 (3)O6—C6—H6B109.357
C1—O1—H1A109.471C5—C6—H6A109.358
C2—O2—H2A109.471C5—C6—H6B109.358
C3—O3—H3A109.470H6A—C6—H6B107.992
C2—O6—C6—C5−60.7 (3)C1—C2—C3—C4−171.7 (2)
C6—O6—C2—O2−58.2 (3)O3—C3—C4—O452.5 (3)
C6—O6—C2—C1−179.9 (2)O3—C3—C4—C5−72.0 (3)
C6—O6—C2—C359.2 (3)C2—C3—C4—O4177.1 (2)
O1—C1—C2—O2−53.5 (4)C2—C3—C4—C552.6 (3)
O1—C1—C2—O668.1 (3)O4—C4—C5—O5−54.2 (3)
O1—C1—C2—C3−172.1 (2)O4—C4—C5—C6−176.7 (2)
O2—C2—C3—O3−168.2 (2)C3—C4—C5—O569.6 (3)
O2—C2—C3—C466.4 (3)C3—C4—C5—C6−52.9 (3)
O6—C2—C3—O371.0 (3)O5—C5—C6—O6−63.8 (4)
O6—C2—C3—C4−54.4 (3)C4—C5—C6—O655.7 (4)
C1—C2—C3—O3−46.2 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O3i0.821.912.715 (3)168
O2—H2A···O4ii0.821.922.724 (3)166
O3—H3A···O2iii0.822.202.874 (3)140
O3—H3A···O50.822.362.822 (4)117
O4—H4A···O6iv0.822.142.829 (3)141
O5—H5A···O1v0.821.942.746 (4)169
Symmetry codes: (i) x−1/2, −y+3/2, z; (ii) x−1/2, −y+5/2, z; (iii) x, y−1, z; (iv) x+1/2, −y+3/2, z; (v) −x+3/2, y−1/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O3i0.821.912.715 (3)168
O2—H2A···O4ii0.821.922.724 (3)166
O3—H3A···O2iii0.822.202.874 (3)140
O3—H3A···O50.822.362.822 (4)117
O4—H4A···O6iv0.822.142.829 (3)141
O5—H5A···O1v0.821.942.746 (4)169
Symmetry codes: (i) x−1/2, −y+3/2, z; (ii) x−1/2, −y+5/2, z; (iii) x, y−1, z; (iv) x+1/2, −y+3/2, z; (v) −x+3/2, y−1/2, z+1/2.
 

Acknowledgements

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

References

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ISSN: 2056-9890
Volume 71| Part 5| May 2015| Pages o289-o290
https://doi.org/10.1107/S2056989015006623
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