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

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2-De­­oxy-α-D-arabino-hexo­pyran­ose

aLudwig-Maximilians-Universität, Department Chemie und Biochemie, Butenandtstrasse 5–13, 81377 München, Germany
*Correspondence e-mail: kluef@cup.uni-muenchen.de

(Received 5 August 2011; accepted 29 August 2011; online 14 September 2011)

The title compound, C6H12O5, is the α-pyran­ose form of the reducing aldose 2-de­oxy-D-arabino-hexose. The six-membered pyran­ose ring adopts a 4C1 conformation, with the anomeric hy­droxy group in axial and the other substituents in equatorial positions. In the crystal, each of the four hy­droxy groups acts as an inter­molecular hydrogen-bond donor function, resulting in a three-dimensional hydrogen-bonded network.

Related literature

For the crystal structure of 2-de­oxy-β-D-arabino-hexopyran­ose, see: Maluszynska et al. (1981[Maluszynska, H., Ruble, J. R. & Jeffrey, G. A. (1981). Carbohydr. Res. 97, 199-204.]) and for the crystal structures of α-D-glucose and α-D-mannose, see Brown et al. (1965[Brown, G. M. & Levy, H. A. (1965). Science, 147, 1038-1039.]) and Longchambon et al. (1976[Longchambon, F., Avenel, D. & Neuman, A. (1976). Acta Cryst. B32, 1822-1826.]), respectively. For puckering parameters, see: Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]). Crystals of the title compound were obtained during the course of attemps to grow crystals of a phenyl­boronic acid ester of 2-de­oxy-D-arabino-hexose, see: Hess & Klüfers (2011[Hess, D. & Klüfers, P. (2011). Carbohydr. Res. doi:10.1016/j.carres.2011.05.031.]).

[Scheme 1]

Experimental

Crystal data
  • C6H12O5

  • Mr = 164.16

  • Orthorhombic, P 21 21 21

  • a = 4.8538 (2) Å

  • b = 9.5323 (4) Å

  • c = 15.6718 (6) Å

  • V = 725.12 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.13 mm−1

  • T = 200 K

  • 0.21 × 0.06 × 0.05 mm

Data collection
  • Nonius KappaCCD diffractometer

  • 5622 measured reflections

  • 1001 independent reflections

  • 937 reflections with I > 2σ(I)

  • Rint = 0.030

Refinement
  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 0.097

  • S = 1.14

  • 1001 reflections

  • 104 parameters

  • H-atom parameters constrained

  • Δρmax = 0.43 e Å−3

  • Δρmin = −0.19 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H81⋯O5i 0.84 1.95 2.780 (2) 171
O3—H83⋯O1ii 0.84 2.00 2.784 (2) 155
O4—H84⋯O6iii 0.84 1.94 2.776 (3) 174
O6—H86⋯O3iv 0.84 1.84 2.670 (2) 170
Symmetry codes: (i) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+2]; (ii) [-x, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iii) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+2]; (iv) [-x+{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}].

Data collection: COLLECT (Nonius, 2004[Nonius (2004). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and SCHAKAL99 (Keller, 1999[Keller, E. (1999). SCHAKAL99. University of Freiburg, Germany.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

2-Deoxy-D-arabino-hexose is the 2-deoxy derivate of both D-glucose and D-mannose. The crystals of the title compound were obtained in the course of attemps to grow crystals of a phenylboronic acid ester of 2-deoxy-D-arabino-hexose (Hess & Klüfers, 2011).

The bond lenghts and angles between the non-hydrogen atoms are normal. The pyranose ring adopts a slightly distorted 4C1 conformation, the puckering parameters (Cremer & Pople, 1975) being Q = 0.551 (2) Å and θ = 6.0 (2)° (Fig. 1). The exocyclic C6—O6 bond is orientated gauche-trans relative to the C5—O5 and C4—C5 bonds of the ring. In the crystal structure the compound forms a three-dimensional hydrogen-bonded network, where each hydroxy group acts as a donor in an intermolecular hydrogen bond to a different neighboring molecule. Acceptor functions are either the ring oxygen atom (O5) or the hydroxy oxygen atoms (O1, O3, O6). The hydrogen bond pattern is shown in Figure 2.

Related literature top

For the crystal structure of 2-deoxy-β-D-arabino-hexopyranose, see: Maluszynska et al. (1981) and for the crystal structures of α-D-glucose and α-D-mannose, see Brown et al. (1965) and Longchambon et al. (1976), respectively. For puckering parameters, see: Cremer & Pople (1975). Crystals of the title compound were obtained during the course of attemps to grow crystals of a phenylboronic acid ester of 2-deoxy-D-arabino-hexose, see: Hess & Klüfers (2011).

Experimental top

2-Deoxy-D-arabino-hexose (0.164 g, 1 mmol) was dissolved in 1 ml of water and a solution of phenylboronic acid (0.122 g, 1 mmol) in 1 ml of methanol was added. The obtained solution was stirred at ambient temperature for 2 h. The solvent was then removed under reduced pressure. The remaining solid was dissolved in aceton and slowly evaporated to give colourless crystals suitable for X-ray analysis.

Refinement top

Since the compound is a weak anomalous scatterer, 662 Friedel pairs were merged. The absolute structure was assigned according to the known stereochemistry of the starting material. Carbon-bound as well as oxygen-bound H atoms were placed in calculated positions (C—H 0.99 Å for CH2-groups, C—H 1.00 Å for CH-groups and O—H 0.84 Å for hydoxy groups) and were included in the refinement in the riding model approximation, with Uiso(H) set to 1.2Ueq(C) for the CH2-groups and CH-groups and 1.5Ueq(O) for the hydroxy groups.

Structure description top

2-Deoxy-D-arabino-hexose is the 2-deoxy derivate of both D-glucose and D-mannose. The crystals of the title compound were obtained in the course of attemps to grow crystals of a phenylboronic acid ester of 2-deoxy-D-arabino-hexose (Hess & Klüfers, 2011).

The bond lenghts and angles between the non-hydrogen atoms are normal. The pyranose ring adopts a slightly distorted 4C1 conformation, the puckering parameters (Cremer & Pople, 1975) being Q = 0.551 (2) Å and θ = 6.0 (2)° (Fig. 1). The exocyclic C6—O6 bond is orientated gauche-trans relative to the C5—O5 and C4—C5 bonds of the ring. In the crystal structure the compound forms a three-dimensional hydrogen-bonded network, where each hydroxy group acts as a donor in an intermolecular hydrogen bond to a different neighboring molecule. Acceptor functions are either the ring oxygen atom (O5) or the hydroxy oxygen atoms (O1, O3, O6). The hydrogen bond pattern is shown in Figure 2.

For the crystal structure of 2-deoxy-β-D-arabino-hexopyranose, see: Maluszynska et al. (1981) and for the crystal structures of α-D-glucose and α-D-mannose, see Brown et al. (1965) and Longchambon et al. (1976), respectively. For puckering parameters, see: Cremer & Pople (1975). Crystals of the title compound were obtained during the course of attemps to grow crystals of a phenylboronic acid ester of 2-deoxy-D-arabino-hexose, see: Hess & Klüfers (2011).

Computing details top

Data collection: COLLECT (Nonius, 2004); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO (Otwinowski & Minor, 1997) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and SCHAKAL99 (Keller, 1999); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. ORTEP-representation of the asymmetric unit of the title compound, with atom labels and anisotropic displacement ellipsoids (drawn at 50% probability level) for non-H atoms.
[Figure 2] Fig. 2. SCHAKAL-representation of hydrogen bonds in the crystal packing of the title compound viewed along the a axis.
2-Deoxy-α-D-arabino-hexopyranose top
Crystal data top
C6H12O5F(000) = 352
Mr = 164.16Dx = 1.504 (1) Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 2672 reflections
a = 4.8538 (2) Åθ = 3.1–27.5°
b = 9.5323 (4) ŵ = 0.13 mm1
c = 15.6718 (6) ÅT = 200 K
V = 725.12 (5) Å3Rod, colourless
Z = 40.21 × 0.06 × 0.05 mm
Data collection top
Nonius KappaCCD
diffractometer
937 reflections with I > 2σ(I)
Radiation source: rotating anodeRint = 0.030
MONTEL, graded multilayered X-ray optics monochromatorθmax = 27.5°, θmin = 3.4°
CCD; rotation images; thick slices scansh = 66
5622 measured reflectionsk = 1212
1001 independent reflectionsl = 2020
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.097H-atom parameters constrained
S = 1.14 w = 1/[σ2(Fo2) + (0.0454P)2 + 0.298P]
where P = (Fo2 + 2Fc2)/3
1001 reflections(Δ/σ)max < 0.001
104 parametersΔρmax = 0.43 e Å3
0 restraintsΔρmin = 0.19 e Å3
Crystal data top
C6H12O5V = 725.12 (5) Å3
Mr = 164.16Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 4.8538 (2) ŵ = 0.13 mm1
b = 9.5323 (4) ÅT = 200 K
c = 15.6718 (6) Å0.21 × 0.06 × 0.05 mm
Data collection top
Nonius KappaCCD
diffractometer
937 reflections with I > 2σ(I)
5622 measured reflectionsRint = 0.030
1001 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0350 restraints
wR(F2) = 0.097H-atom parameters constrained
S = 1.14Δρmax = 0.43 e Å3
1001 reflectionsΔρmin = 0.19 e Å3
104 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.0906 (4)0.75609 (18)0.88687 (10)0.0296 (4)
H810.14300.80300.92920.044*
O30.3063 (4)0.45829 (17)0.72256 (9)0.0308 (4)
H830.21790.38920.70360.046*
O40.0700 (4)0.28748 (16)0.85187 (10)0.0292 (4)
H840.16420.22020.87050.044*
O50.2069 (4)0.61635 (15)0.96649 (9)0.0251 (4)
O60.0846 (4)0.42652 (18)1.09339 (9)0.0305 (4)
H860.00490.45501.13770.046*
C10.1847 (6)0.7158 (2)0.89833 (14)0.0259 (5)
H10.29570.80080.91320.031*
C20.2911 (5)0.6559 (2)0.81511 (13)0.0248 (5)
H2A0.24630.72130.76810.030*
H2B0.49410.64730.81820.030*
C30.1683 (5)0.5136 (2)0.79562 (12)0.0229 (5)
H30.03250.52430.78280.027*
C40.2049 (5)0.4156 (2)0.87086 (12)0.0219 (4)
H40.40550.39800.88060.026*
C50.0780 (5)0.4826 (2)0.95053 (12)0.0219 (4)
H50.12350.49750.94060.026*
C60.1161 (5)0.3944 (2)1.02968 (13)0.0263 (5)
H6A0.10170.29391.01430.032*
H6B0.30260.41081.05320.032*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0353 (9)0.0299 (8)0.0238 (7)0.0080 (8)0.0022 (7)0.0000 (7)
O30.0436 (10)0.0274 (8)0.0214 (7)0.0055 (8)0.0082 (8)0.0041 (6)
O40.0396 (9)0.0213 (7)0.0269 (8)0.0068 (8)0.0051 (8)0.0013 (6)
O50.0372 (9)0.0192 (7)0.0189 (6)0.0015 (7)0.0060 (7)0.0002 (6)
O60.0379 (9)0.0340 (9)0.0195 (7)0.0042 (8)0.0005 (7)0.0010 (6)
C10.0346 (12)0.0215 (10)0.0216 (9)0.0010 (10)0.0013 (10)0.0013 (8)
C20.0297 (11)0.0221 (10)0.0226 (9)0.0003 (10)0.0013 (10)0.0023 (8)
C30.0261 (11)0.0256 (10)0.0170 (8)0.0004 (10)0.0017 (8)0.0003 (8)
C40.0261 (10)0.0186 (10)0.0211 (9)0.0016 (9)0.0034 (9)0.0015 (7)
C50.0265 (10)0.0206 (9)0.0186 (9)0.0012 (9)0.0049 (9)0.0003 (7)
C60.0357 (12)0.0239 (10)0.0192 (9)0.0020 (10)0.0017 (9)0.0010 (8)
Geometric parameters (Å, º) top
O1—C11.402 (3)C2—C31.512 (3)
O1—H810.8400C2—H2A0.9900
O3—C31.428 (2)C2—H2B0.9900
O3—H830.8400C3—C41.515 (3)
O4—C41.418 (3)C3—H31.0000
O4—H840.8400C4—C51.532 (3)
O5—C11.433 (3)C4—H41.0000
O5—C51.442 (3)C5—C61.510 (3)
O6—C61.428 (3)C5—H51.0000
O6—H860.8400C6—H6A0.9900
C1—C21.515 (3)C6—H6B0.9900
C1—H11.0000
C1—O1—H81109.5C2—C3—H3109.5
C3—O3—H83109.5C4—C3—H3109.5
C4—O4—H84109.5O4—C4—C3108.28 (16)
C1—O5—C5115.04 (15)O4—C4—C5110.16 (18)
C6—O6—H86109.5C3—C4—C5109.27 (17)
O1—C1—O5110.39 (19)O4—C4—H4109.7
O1—C1—C2108.54 (19)C3—C4—H4109.7
O5—C1—C2111.50 (18)C5—C4—H4109.7
O1—C1—H1108.8O5—C5—C6107.26 (16)
O5—C1—H1108.8O5—C5—C4109.60 (18)
C2—C1—H1108.8C6—C5—C4112.82 (17)
C3—C2—C1112.20 (18)O5—C5—H5109.0
C3—C2—H2A109.2C6—C5—H5109.0
C1—C2—H2A109.2C4—C5—H5109.0
C3—C2—H2B109.2O6—C6—C5111.79 (18)
C1—C2—H2B109.2O6—C6—H6A109.3
H2A—C2—H2B107.9C5—C6—H6A109.3
O3—C3—C2107.95 (17)O6—C6—H6B109.3
O3—C3—C4109.96 (17)C5—C6—H6B109.3
C2—C3—C4110.45 (16)H6A—C6—H6B107.9
O3—C3—H3109.5
C5—O5—C1—O166.3 (2)C2—C3—C4—C556.0 (2)
C5—O5—C1—C254.4 (3)C1—O5—C5—C6178.49 (18)
O1—C1—C2—C371.6 (2)C1—O5—C5—C458.7 (2)
O5—C1—C2—C350.2 (3)O4—C4—C5—O5176.95 (16)
C1—C2—C3—O3172.65 (19)C3—C4—C5—O558.1 (2)
C1—C2—C3—C452.4 (2)O4—C4—C5—C663.6 (2)
O3—C3—C4—O465.0 (2)C3—C4—C5—C6177.56 (19)
C2—C3—C4—O4175.95 (18)O5—C5—C6—O681.9 (2)
O3—C3—C4—C5174.99 (18)C4—C5—C6—O6157.32 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H81···O5i0.841.952.780 (2)171
O3—H83···O1ii0.842.002.784 (2)155
O4—H84···O6iii0.841.942.776 (3)174
O6—H86···O3iv0.841.842.670 (2)170
Symmetry codes: (i) x1/2, y+3/2, z+2; (ii) x, y1/2, z+3/2; (iii) x+1/2, y+1/2, z+2; (iv) x+1/2, y+1, z+1/2.

Experimental details

Crystal data
Chemical formulaC6H12O5
Mr164.16
Crystal system, space groupOrthorhombic, P212121
Temperature (K)200
a, b, c (Å)4.8538 (2), 9.5323 (4), 15.6718 (6)
V3)725.12 (5)
Z4
Radiation typeMo Kα
µ (mm1)0.13
Crystal size (mm)0.21 × 0.06 × 0.05
Data collection
DiffractometerNonius KappaCCD
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
5622, 1001, 937
Rint0.030
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.097, 1.14
No. of reflections1001
No. of parameters104
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.43, 0.19

Computer programs: COLLECT (Nonius, 2004), SCALEPACK (Otwinowski & Minor, 1997), DENZO (Otwinowski & Minor, 1997) and SCALEPACK, SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and SCHAKAL99 (Keller, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H81···O5i0.841.952.780 (2)170.7
O3—H83···O1ii0.842.002.784 (2)154.9
O4—H84···O6iii0.841.942.776 (3)173.7
O6—H86···O3iv0.841.842.670 (2)169.9
Symmetry codes: (i) x1/2, y+3/2, z+2; (ii) x, y1/2, z+3/2; (iii) x+1/2, y+1/2, z+2; (iv) x+1/2, y+1, z+1/2.
 

Acknowledgements

The authors thank Moritz Reichvilser for experimental support.

References

First citationBrown, G. M. & Levy, H. A. (1965). Science, 147, 1038–1039.  CSD CrossRef PubMed CAS Web of Science Google Scholar
First citationCremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358.  CrossRef CAS Web of Science Google Scholar
First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals Google Scholar
First citationHess, D. & Klüfers, P. (2011). Carbohydr. Res. doi:10.1016/j.carres.2011.05.031.  Google Scholar
First citationKeller, E. (1999). SCHAKAL99. University of Freiburg, Germany.  Google Scholar
First citationLongchambon, F., Avenel, D. & Neuman, A. (1976). Acta Cryst. B32, 1822–1826.  CSD CrossRef CAS IUCr Journals Web of Science Google Scholar
First citationMaluszynska, H., Ruble, J. R. & Jeffrey, G. A. (1981). Carbohydr. Res. 97, 199–204.  CSD CrossRef CAS Web of Science Google Scholar
First citationNonius (2004). COLLECT. Nonius BV, Delft, The Netherlands.  Google Scholar
First citationOtwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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