2-De­oxy-α-d-arabino-hexopyran­ose

Hess, D.; Klüfers, P.

doi:10.1107/S1600536811035264

organic compounds

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Volume 67| Part 10| October 2011| Page o2615

https://doi.org/10.1107/S1600536811035264

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2-Deoxy-α-D-arabino-hexopyranose

David Hess ^a and Peter Klüfers ^a ^*

^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 ) 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

Crystal data

C₆H₁₂O₅
M_r = 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)
R_int = 0.030

Refinement

R[F² > 2σ(F²)] = 0.035
wR(F²) = 0.097
S = 1.14
1001 reflections
104 parameters
H-atom parameters constrained
Δρ_max = 0.43 e Å⁻³
Δρ_min = −0.19 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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⋯O3^iv	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 ); 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.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536811035264/kj2184sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536811035264/kj2184Isup2.hkl

checkCIF report

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.

Structure description 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).

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

	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.
	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

C₆H₁₂O₅	F(000) = 352
M_r = 164.16	D_x = 1.504 (1) Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 2672 reflections
a = 4.8538 (2) Å	θ = 3.1–27.5°
b = 9.5323 (4) Å	µ = 0.13 mm⁻¹
c = 15.6718 (6) Å	T = 200 K
V = 725.12 (5) Å³	Rod, colourless
Z = 4	0.21 × 0.06 × 0.05 mm

Data collection top

Nonius KappaCCD diffractometer	937 reflections with I > 2σ(I)
Radiation source: rotating anode	R_int = 0.030
MONTEL, graded multilayered X-ray optics monochromator	θ_max = 27.5°, θ_min = 3.4°
CCD; rotation images; thick slices scans	h = −6→6
5622 measured reflections	k = −12→12
1001 independent reflections	l = −20→20

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.035	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.097	H-atom parameters constrained
S = 1.14	w = 1/[σ²(F_o²) + (0.0454P)² + 0.298P] where P = (F_o² + 2F_c²)/3
1001 reflections	(Δ/σ)_max < 0.001
104 parameters	Δρ_max = 0.43 e Å⁻³
0 restraints	Δρ_min = −0.19 e Å⁻³

Crystal data top

C₆H₁₂O₅	V = 725.12 (5) Å³
M_r = 164.16	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 4.8538 (2) Å	µ = 0.13 mm⁻¹
b = 9.5323 (4) Å	T = 200 K
c = 15.6718 (6) Å	0.21 × 0.06 × 0.05 mm

Data collection top

Nonius KappaCCD diffractometer	937 reflections with I > 2σ(I)
5622 measured reflections	R_int = 0.030
1001 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.035	0 restraints
wR(F²) = 0.097	H-atom parameters constrained
S = 1.14	Δρ_max = 0.43 e Å⁻³
1001 reflections	Δρ_min = −0.19 e Å⁻³
104 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	−0.0906 (4)	0.75609 (18)	0.88687 (10)	0.0296 (4)
H81	−0.1430	0.8030	0.9292	0.044*
O3	0.3063 (4)	0.45829 (17)	0.72256 (9)	0.0308 (4)
H83	0.2179	0.3892	0.7036	0.046*
O4	0.0700 (4)	0.28748 (16)	0.85187 (10)	0.0292 (4)
H84	0.1642	0.2202	0.8705	0.044*
O5	0.2069 (4)	0.61635 (15)	0.96649 (9)	0.0251 (4)
O6	−0.0846 (4)	0.42652 (18)	1.09339 (9)	0.0305 (4)
H86	−0.0049	0.4550	1.1377	0.046*
C1	0.1847 (6)	0.7158 (2)	0.89833 (14)	0.0259 (5)
H1	0.2957	0.8008	0.9132	0.031*
C2	0.2911 (5)	0.6559 (2)	0.81511 (13)	0.0248 (5)
H2A	0.2463	0.7213	0.7681	0.030*
H2B	0.4941	0.6473	0.8182	0.030*
C3	0.1683 (5)	0.5136 (2)	0.79562 (12)	0.0229 (5)
H3	−0.0325	0.5243	0.7828	0.027*
C4	0.2049 (5)	0.4156 (2)	0.87086 (12)	0.0219 (4)
H4	0.4055	0.3980	0.8806	0.026*
C5	0.0780 (5)	0.4826 (2)	0.95053 (12)	0.0219 (4)
H5	−0.1235	0.4975	0.9406	0.026*
C6	0.1161 (5)	0.3944 (2)	1.02968 (13)	0.0263 (5)
H6A	0.1017	0.2939	1.0143	0.032*
H6B	0.3026	0.4108	1.0532	0.032*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0353 (9)	0.0299 (8)	0.0238 (7)	0.0080 (8)	0.0022 (7)	0.0000 (7)
O3	0.0436 (10)	0.0274 (8)	0.0214 (7)	−0.0055 (8)	0.0082 (8)	−0.0041 (6)
O4	0.0396 (9)	0.0213 (7)	0.0269 (8)	−0.0068 (8)	−0.0051 (8)	−0.0013 (6)
O5	0.0372 (9)	0.0192 (7)	0.0189 (6)	−0.0015 (7)	−0.0060 (7)	−0.0002 (6)
O6	0.0379 (9)	0.0340 (9)	0.0195 (7)	−0.0042 (8)	0.0005 (7)	−0.0010 (6)
C1	0.0346 (12)	0.0215 (10)	0.0216 (9)	0.0010 (10)	−0.0013 (10)	0.0013 (8)
C2	0.0297 (11)	0.0221 (10)	0.0226 (9)	−0.0003 (10)	0.0013 (10)	0.0023 (8)
C3	0.0261 (11)	0.0256 (10)	0.0170 (8)	0.0004 (10)	0.0017 (8)	−0.0003 (8)
C4	0.0261 (10)	0.0186 (10)	0.0211 (9)	−0.0016 (9)	−0.0034 (9)	−0.0015 (7)
C5	0.0265 (10)	0.0206 (9)	0.0186 (9)	−0.0012 (9)	−0.0049 (9)	0.0003 (7)
C6	0.0357 (12)	0.0239 (10)	0.0192 (9)	0.0020 (10)	−0.0017 (9)	0.0010 (8)

Geometric parameters (Å, º) top

O1—C1	1.402 (3)	C2—C3	1.512 (3)
O1—H81	0.8400	C2—H2A	0.9900
O3—C3	1.428 (2)	C2—H2B	0.9900
O3—H83	0.8400	C3—C4	1.515 (3)
O4—C4	1.418 (3)	C3—H3	1.0000
O4—H84	0.8400	C4—C5	1.532 (3)
O5—C1	1.433 (3)	C4—H4	1.0000
O5—C5	1.442 (3)	C5—C6	1.510 (3)
O6—C6	1.428 (3)	C5—H5	1.0000
O6—H86	0.8400	C6—H6A	0.9900
C1—C2	1.515 (3)	C6—H6B	0.9900
C1—H1	1.0000

C1—O1—H81	109.5	C2—C3—H3	109.5
C3—O3—H83	109.5	C4—C3—H3	109.5
C4—O4—H84	109.5	O4—C4—C3	108.28 (16)
C1—O5—C5	115.04 (15)	O4—C4—C5	110.16 (18)
C6—O6—H86	109.5	C3—C4—C5	109.27 (17)
O1—C1—O5	110.39 (19)	O4—C4—H4	109.7
O1—C1—C2	108.54 (19)	C3—C4—H4	109.7
O5—C1—C2	111.50 (18)	C5—C4—H4	109.7
O1—C1—H1	108.8	O5—C5—C6	107.26 (16)
O5—C1—H1	108.8	O5—C5—C4	109.60 (18)
C2—C1—H1	108.8	C6—C5—C4	112.82 (17)
C3—C2—C1	112.20 (18)	O5—C5—H5	109.0
C3—C2—H2A	109.2	C6—C5—H5	109.0
C1—C2—H2A	109.2	C4—C5—H5	109.0
C3—C2—H2B	109.2	O6—C6—C5	111.79 (18)
C1—C2—H2B	109.2	O6—C6—H6A	109.3
H2A—C2—H2B	107.9	C5—C6—H6A	109.3
O3—C3—C2	107.95 (17)	O6—C6—H6B	109.3
O3—C3—C4	109.96 (17)	C5—C6—H6B	109.3
C2—C3—C4	110.45 (16)	H6A—C6—H6B	107.9
O3—C3—H3	109.5

C5—O5—C1—O1	66.3 (2)	C2—C3—C4—C5	56.0 (2)
C5—O5—C1—C2	−54.4 (3)	C1—O5—C5—C6	−178.49 (18)
O1—C1—C2—C3	−71.6 (2)	C1—O5—C5—C4	58.7 (2)
O5—C1—C2—C3	50.2 (3)	O4—C4—C5—O5	−176.95 (16)
C1—C2—C3—O3	−172.65 (19)	C3—C4—C5—O5	−58.1 (2)
C1—C2—C3—C4	−52.4 (2)	O4—C4—C5—C6	63.6 (2)
O3—C3—C4—O4	−65.0 (2)	C3—C4—C5—C6	−177.56 (19)
C2—C3—C4—O4	175.95 (18)	O5—C5—C6—O6	81.9 (2)
O3—C3—C4—C5	174.99 (18)	C4—C5—C6—O6	−157.32 (19)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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···O3^iv	0.84	1.84	2.670 (2)	170

Symmetry codes: (i) x−1/2, −y+3/2, −z+2; (ii) −x, y−1/2, −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 formula	C₆H₁₂O₅
M_r	164.16
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	200
a, b, c (Å)	4.8538 (2), 9.5323 (4), 15.6718 (6)
V (Å³)	725.12 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.13
Crystal size (mm)	0.21 × 0.06 × 0.05

Data collection
Diffractometer	Nonius KappaCCD
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	5622, 1001, 937
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.035, 0.097, 1.14
No. of reflections	1001
No. of parameters	104
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	D—H···A
O1—H81···O5ⁱ	0.84	1.95	2.780 (2)	170.7
O3—H83···O1ⁱⁱ	0.84	2.00	2.784 (2)	154.9
O4—H84···O6ⁱⁱⁱ	0.84	1.94	2.776 (3)	173.7
O6—H86···O3^iv	0.84	1.84	2.670 (2)	169.9

Symmetry codes: (i) x−1/2, −y+3/2, −z+2; (ii) −x, y−1/2, −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

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