1-De­oxy-d-arabinitol

Jenkinson, S.F.; Cruz, F.P.; Booth, K.V.; Fleet, G.W.J.; Izumori, K.; Yu, C.-Y.; Watkin, D.J.

doi:10.1107/S1600536808012555

organic compounds

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Volume 64| Part 6| June 2008| Pages o1010-o1011

doi:10.1107/S1600536808012555

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1-Deoxy-D-arabinitol

Sarah F. Jenkinson,^a ^* Filipa P. Cruz,^a Kathrine V. Booth,^a George W. J. Fleet,^a Ken Izumori,^b Chu-Yi Yu ^c and David J. Watkin ^d

^aDepartment of Organic Chemistry, Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, England, ^bRare Sugar Research Centre, Kagawa University, 2393 Miki-cho, Kita-gun, Kagawa 761-0795, Japan, ^cLaboratory of Molecular Recognition and Selective Synthesis, Institute of Chemistry, Chinese Academy of Sciences, Beijing 10080, People's Republic of China, and ^dDepartment of Chemical Crystallography, Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, England
^*Correspondence e-mail: sarah.jenkinson@chem.ox.ac.uk

(Received 24 April 2008; accepted 29 April 2008; online 7 May 2008)

Addition of methyl lithium to D-erythrono-1,4-lactone followed by acid deprotection was shown, by X-ray crystallography, to give 1-deoxy-D-arabinitol, C₅H₁₂O₄, rather than 1-deoxy-D-ribitol as the major product. The crystal structure exists as hydrogen-bonded chains of molecules running parallel to the c axis which are further linked together by hydrogen bonds. Each molecule is a donor and an acceptor for four hydrogen bonds.

Related literature

For related literature see: Izumori (2002 , 2006 ); Granstrom et al. (2004 ); Beadle et al. (1992 ); Skytte (2002 ); Levin (2002 ); Howling & Callagan (2000 ); Bertelsen et al. (1999 ); Takata et al. (2005 ); Menavuvu et al. (2006 ); Sui et al. (2005 ); Hossain et al. (2006 ); Zehner et al. (1994 ); Donner et al. (1999 ); Yoshihara et al. (2008 ); Takai & Heathcock (1985 ); Zissis & Richtmyer (1954 ).

Experimental

Crystal data

C₅H₁₂O₄
M_r = 136.15
Tetragonal, I 4₁
a = 12.9873 (5) Å
c = 8.3679 (3) Å
V = 1411.41 (9) Å³
Z = 8
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 150 K
0.25 × 0.25 × 0.25 mm

Data collection

Nonius KappaCCD area-detector diffractometer
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ) T_min = 0.93, T_max = 0.97
3189 measured reflections
855 independent reflections
750 reflections with I > 2σ(I)
R_int = 0.020

Refinement

R[F² > 2σ(F²)] = 0.043
wR(F²) = 0.123
S = 1.00
855 reflections
82 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.39 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O8—H8⋯O8ⁱ	0.96	1.76	2.698 (4)	164
O6—H6⋯O6ⁱⁱ	1.00	1.98	2.712 (4)	128
O4—H4⋯O1ⁱⁱⁱ	0.98	1.77	2.718 (4)	162
O1—H1⋯O4^iv	1.05	2.03	2.712 (3)	120
Symmetry codes: (i) $[y+{\script{1\over 2}}, -x+1, z-{\script{1\over 4}}]$ ; (ii) $[y, -x+{\script{3\over 2}}, z+{\script{1\over 4}}]$ ; (iii) $[-y+{\script{3\over 2}}, x, z-{\script{1\over 4}}]$ ; (iv) $[-y+1, x-{\script{1\over 2}}, z+{\script{1\over 4}}]$ .

Data collection: COLLECT (Nonius, 2001 ); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994 ); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 ); molecular graphics: CAMERON (Watkin et al., 1996 ); software used to prepare material for publication: CRYSTALS.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808012555/lh2622sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808012555/lh2622Isup2.hkl

checkCIF report

Comment top

The demand for the large scale production of rare sugars by biotechnological (Izumori, 2006; Izumori, 2002; Granstrom et al., 2004) and chemical (Beadle et al., 1992) methods is driven by the demand for alternative foodstuffs (Skytte, 2002) and D-tagatose itself is used as a low calorie sweetener (Levin, 2002; Howling & Callagan, 2000; Bertelsen et al. 1999) Rare monosaccharides have been found to demonstrate interesting pharmaceutical properties, for example, D-psicose (Takata et al., 2005; Menavuvu et al., 2006) and D-allose (Sui et al., 2005; Hossain et al., 2006) have significant chemotherapeutic properties and D-tagatose has been found to be an anti-hyperglycemic agent (Zehner et al., 1994; Donner et al., 1999) and therefore potentially useful in the treatment of diabetes.

The methodology developed by Izumori et al. (2002, 2006) for the interconversion of tetroses, pentoses and hexoses by enzymatic oxidation, inversion at C3 with a single epimerase, and reduction to the aldose has been seen to be generally applicable for the 1-deoxy ketohexoses (Yoshihara et al., 2008). In order to investigate the viability of this process to the corresponding pentoses and thus to evaluate their therapeutic potential 1-deoxy-D-arabinitol was synthesized, in 3 steps, from 2,3-O-isopropylidene-D-erythronolactone 1 (Fig.1). It has previously been seen that the four diastereomeric tetraols are very difficult to distinguish between by NMR spectroscopy (Takai & Heathcock, 1985). X-ray crystallography confirmed that the major product was the arabinitol 4 rather than the ribitol 3 which differs only in the stereochemistry at the C2 position (Fig. 2).

The molecules are linked by three hydrogen bonding systems and the structure consists of alternating spiral chains of O6—H6···O6 or O8—H8···O8 hydrogen-bonded molecules running parallel to the c-axis (Fig. 3) interconnected by O1—H1···O4—H4···O1 hydrogen bonds (Fig.4). Each molecule is a donor and acceptor for 4 hydrogen bonds (Fig. 5).

In summary, the stereochemistry at C2 of the title compound 1-deoxy-D-arabinitol 4 was firmly established by X-ray crystallography, the absolute configuration is determined by the use of D-erythronolactone as the starting material. As well as the potential biological properties of 1-deoxy ketoses, they are likely to provide a new set of building blocks for the synthesis of a wide variety of complex biomolecules.

Related literature top

For related literature see: Izumori (2002, 2006); Granstrom et al. (2004); Beadle et al. (1992); Skytte (2002); Levin (2002); Howling & Callagan (2000); Bertelsen et al. (1999); Takata et al. (2005); Menavuvu et al. (2006); Sui et al. (2005); Hossain et al. (2006); Zehner et al. (1994); Donner et al. (1999); Yoshihara et al. (2008); Takai & Heathcock (1985); Zissis & Richtmyer (1954).

Experimental top

The title compound was recrystallized from hot methanol: m.p. 398–400 K; [α]_D²¹ +0.8 (c, 8 in H₂O) {Lit. (Zissis & Richtmyer, 1954) m.p. 129–131°C; [α]_D²⁰ +0.7 (c, 10 in H₂O; l, 4)}.

Computing details top

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).

Figures top

	Fig. 1. Synthetic scheme.
	Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
	Fig. 3. Packing diagram showing the O6—H6···O6 and O8—H8···O8 hydrogen bonds.
	Fig. 4. Packing diagram showing the O1—H1···O4—H4···O1 hydrogen bonds.
	Fig. 5. Packing diagram for the compound projected along the c-axis. Each molecule is a donor and an acceptor for 4 hydrogen-bonds.

1-Deoxy-D-arabinitol top

Crystal data top

C₅H₁₂O₄	D_x = 1.281 Mg m⁻³
M_r = 136.15	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, I4₁	Cell parameters from 815 reflections
Hall symbol: I 4bw	θ = 5–27°
a = 12.9873 (5) Å	µ = 0.11 mm⁻¹
c = 8.3679 (3) Å	T = 150 K
V = 1411.41 (9) Å³	Block, colourless
Z = 8	0.25 × 0.25 × 0.25 mm
F(000) = 592

Data collection top

Nonius KappaCCD area-detector diffractometer	750 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.020
ω scans	θ_max = 27.5°, θ_min = 5.3°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −16→16
T_min = 0.93, T_max = 0.97	k = −11→11
3189 measured reflections	l = −10→10
855 independent reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.043	H-atom parameters constrained
wR(F²) = 0.123	w = 1/[σ²(F²) + ( 0.07P)² + 1.26P], where P = (max(F_o²,0) + 2F_c²)/3
S = 1.00	(Δ/σ)_max = 0.002
855 reflections	Δρ_max = 0.34 e Å⁻³
82 parameters	Δρ_min = −0.39 e Å⁻³
1 restraint

Crystal data top

C₅H₁₂O₄	Z = 8
M_r = 136.15	Mo Kα radiation
Tetragonal, I4₁	µ = 0.11 mm⁻¹
a = 12.9873 (5) Å	T = 150 K
c = 8.3679 (3) Å	0.25 × 0.25 × 0.25 mm
V = 1411.41 (9) Å³

Data collection top

Nonius KappaCCD area-detector diffractometer	855 independent reflections
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	750 reflections with I > 2σ(I)
T_min = 0.93, T_max = 0.97	R_int = 0.020
3189 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.043	1 restraint
wR(F²) = 0.123	H-atom parameters constrained
S = 1.00	Δρ_max = 0.34 e Å⁻³
855 reflections	Δρ_min = −0.39 e Å⁻³
82 parameters

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

	x	y	z	U_iso*/U_eq
O1	0.64776 (13)	0.51955 (15)	0.6622 (3)	0.0211
C2	0.75127 (18)	0.5139 (2)	0.6068 (4)	0.0186
C3	0.7537 (2)	0.4842 (2)	0.4296 (4)	0.0187
O4	0.85700 (13)	0.48073 (16)	0.3723 (3)	0.0237
C5	0.6897 (2)	0.5564 (2)	0.3268 (4)	0.0235
O6	0.73116 (15)	0.65798 (14)	0.3242 (3)	0.0250
C7	0.8135 (2)	0.4417 (2)	0.7135 (4)	0.0208
O8	0.76689 (14)	0.34124 (13)	0.7126 (3)	0.0216
C9	0.8162 (3)	0.4788 (2)	0.8844 (4)	0.0371
H21	0.7853	0.5822	0.6286	0.0184*
H31	0.7208	0.4168	0.4126	0.0196*
H51	0.6985	0.5315	0.2238	0.0277*
H52	0.6191	0.5542	0.3475	0.0271*
H71	0.8827	0.4379	0.6604	0.0259*
H91	0.8413	0.4265	0.9544	0.0541*
H92	0.8595	0.5396	0.8958	0.0548*
H93	0.7474	0.4971	0.9202	0.0552*
H1	0.6194	0.4722	0.5703	0.0308*
H8	0.7975	0.2944	0.6379	0.0334*
H6	0.7418	0.6761	0.4388	0.0359*
H4	0.9070	0.5369	0.3651	0.0365*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0197 (10)	0.0197 (9)	0.0240 (12)	0.0010 (7)	0.0042 (9)	−0.0023 (9)
C2	0.0139 (13)	0.0193 (12)	0.0225 (16)	−0.0037 (9)	0.0006 (12)	−0.0001 (13)
C3	0.0176 (14)	0.0167 (12)	0.0218 (17)	−0.0006 (9)	−0.0011 (12)	0.0010 (13)
O4	0.0169 (9)	0.0213 (9)	0.0329 (14)	0.0015 (7)	0.0061 (10)	0.0035 (10)
C5	0.0223 (14)	0.0269 (15)	0.0214 (16)	0.0014 (11)	0.0013 (13)	0.0032 (15)
O6	0.0308 (11)	0.0215 (10)	0.0227 (12)	0.0025 (8)	0.0056 (11)	0.0046 (10)
C7	0.0201 (13)	0.0204 (13)	0.0218 (16)	−0.0035 (10)	−0.0045 (13)	−0.0004 (13)
O8	0.0254 (10)	0.0189 (10)	0.0204 (12)	0.0010 (7)	0.0049 (10)	0.0000 (9)
C9	0.053 (2)	0.0332 (16)	0.0253 (15)	−0.0023 (15)	−0.0149 (15)	−0.0036 (13)

Geometric parameters (Å, º) top

O1—C2	1.424 (3)	C5—H51	0.927
O1—H1	1.051	C5—H52	0.934
C2—C3	1.532 (3)	O6—H6	0.997
C2—C7	1.527 (4)	C7—O8	1.438 (3)
C2—H21	1.008	C7—C9	1.510 (5)
C3—O4	1.425 (3)	C7—H71	1.004
C3—C5	1.520 (4)	O8—H8	0.959
C3—H31	0.985	C9—H91	0.954
O4—H4	0.978	C9—H92	0.974
C5—O6	1.425 (3)	C9—H93	0.972

C2—O1—H1	93.6	C3—C5—H52	114.4
O1—C2—C3	110.4 (2)	O6—C5—H52	113.8
O1—C2—C7	109.9 (3)	H51—C5—H52	106.4
C3—C2—C7	113.6 (2)	C5—O6—H6	104.9
O1—C2—H21	108.0	C2—C7—O8	109.4 (2)
C3—C2—H21	112.9	C2—C7—C9	111.7 (2)
C7—C2—H21	101.7	O8—C7—C9	107.7 (3)
C2—C3—O4	110.7 (2)	C2—C7—H71	104.2
C2—C3—C5	112.4 (2)	O8—C7—H71	109.3
O4—C3—C5	110.1 (2)	C9—C7—H71	114.4
C2—C3—H31	110.8	C7—O8—H8	113.9
O4—C3—H31	109.4	C7—C9—H91	111.2
C5—C3—H31	103.2	C7—C9—H92	111.4
C3—O4—H4	128.4	H91—C9—H92	108.7
C3—C5—O6	111.9 (2)	C7—C9—H93	110.4
C3—C5—H51	104.0	H91—C9—H93	107.4
O6—C5—H51	105.2	H92—C9—H93	107.6

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O8—H8···O8ⁱ	0.96	1.76	2.698 (4)	164
O6—H6···O6ⁱⁱ	1.00	1.98	2.712 (4)	128
O4—H4···O1ⁱⁱⁱ	0.98	1.77	2.718 (4)	162
O1—H1···O4^iv	1.05	2.03	2.712 (3)	120

Symmetry codes: (i) y+1/2, −x+1, z−1/4; (ii) y, −x+3/2, z+1/4; (iii) −y+3/2, x, z−1/4; (iv) −y+1, x−1/2, z+1/4.

Experimental details

Crystal data
Chemical formula	C₅H₁₂O₄
M_r	136.15
Crystal system, space group	Tetragonal, I4₁
Temperature (K)	150
a, c (Å)	12.9873 (5), 8.3679 (3)
V (Å³)	1411.41 (9)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.25 × 0.25 × 0.25

Data collection
Diffractometer	Nonius KappaCCD area-detector diffractometer
Absorption correction	Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)
T_min, T_max	0.93, 0.97
No. of measured, independent and observed [I > 2σ(I)] reflections	3189, 855, 750
R_int	0.020
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.123, 1.00
No. of reflections	855
No. of parameters	82
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.34, −0.39

Computer programs: COLLECT (Nonius, 2001), DENZO/SCALEPACK (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O8—H8···O8ⁱ	0.96	1.76	2.698 (4)	164
O6—H6···O6ⁱⁱ	1.00	1.98	2.712 (4)	128
O4—H4···O1ⁱⁱⁱ	0.98	1.77	2.718 (4)	162
O1—H1···O4^iv	1.05	2.03	2.712 (3)	120

Symmetry codes: (i) y+1/2, −x+1, z−1/4; (ii) y, −x+3/2, z+1/4; (iii) −y+3/2, x, z−1/4; (iv) −y+1, x−1/2, z+1/4.

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CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 64| Part 6| June 2008| Pages o1010-o1011

doi:10.1107/S1600536808012555

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