2-De­oxy-2,3-O-isopropyl­idene-2,4-di-C-methyl-β-l-arabinose

Booth, K.V.; Jenkinson, S.F.; Fleet, G.W.J.; Watkin, D.J.

doi:10.1107/S1600536809005777

organic compounds

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ISSN: 2056-9890

Volume 65| Part 3| March 2009| Page o570

doi:10.1107/S1600536809005777

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2-Deoxy-2,3-O-isopropylidene-2,4-di-C-methyl-β-L-arabinose

K. Victoria Booth,^a ^* Sarah F. Jenkinson,^a George W. J. Fleet ^a and David J. Watkin ^b

^aDepartment of Organic Chemistry, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, England, and ^bDepartment of Chemical Crystallography, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, England
^*Correspondence e-mail: victoria.booth@chem.ox.ac.uk

(Received 9 February 2009; accepted 18 February 2009; online 21 February 2009)

X-ray crystallography unequivocally confirmed the stereochemistry of the C atom at position 2 in the carbon scaffold of the title molecule, C₁₀H₁₈O₄. The pyranose ring exists in a chair conformation with the methyl group on the C atom in the 2 position in an equatorial configuration. The absolute stereochemistry was determined from the starting material. The crystal structure consists of O—H⋯O hydrogen-bonded chains of molecules running parallel to the b axis.

Related literature

For deoxy sugars see: Becker & Lowe (2003 ); Yoshihara et al. (2008 ); Gullapalli et al. (2007 ). For a related structure see: Booth et al. (2007 ).

Experimental

Crystal data

C₁₀H₁₈O₄
M_r = 202.25
Monoclinic, P 2₁
a = 6.0641 (3) Å
b = 13.4016 (7) Å
c = 6.8287 (3) Å
β = 102.596 (2)°
V = 541.60 (5) Å³
Z = 2
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 150 K
0.50 × 0.20 × 0.20 mm

Data collection

Nonius KappaCCD diffractometer
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ) T_min = 0.89, T_max = 0.98
5025 measured reflections
1266 independent reflections
1183 reflections with I > 2σ(I)
R_int = 0.036

Refinement

R[F² > 2σ(F²)] = 0.030
wR(F²) = 0.073
S = 0.98
1266 reflections
127 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.16 e Å⁻³
Δρ_min = −0.16 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O12—H121⋯O1ⁱ	0.86	1.93	2.786 (3)	179
Symmetry code: (i) $[-x+1, y-{\script{1\over 2}}, -z]$ .

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/S1600536809005777/lh2774sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809005777/lh2774Isup2.hkl

checkCIF report

Comment top

Deoxy sugars play an important role in the natural world; 2-deoxy ribose forms the sugar backbone of DNA whilst L-fucose, 6-deoxy-L-galactose, is involved in a wide range of mammalian glycan mediated responses (Becker and Lowe, 2003). Whilst the synthesis and biological evaluation of deoxy sugars is relatively common (Yoshihara et al., 2008; Gullapalli et al., 2007), examples of doubly branched analogues are to our knowledge, unknown.

Herein we report the structure of the novel deoxy aldose 3, generated by a short synthetic sequence from di-branched lactone 1 (Booth et al. 2007) (Fig. 1). Hydrogenation of the alkene functionality in 2 could give either epimer at position C-2 of lactone 3 or a mixture of both products. The reaction proved to be extremely stereospecific, generating only one product. Direct crystallization of lactone 3 generated poor quality crystals, however, after reduction to the lactol, crystallization was facile and X-ray crystallography showed the product to be the arabino compound 4 rather than the ribo compound 5. The absolute stereochemistry was determined from the use of 2-C-methyl-D-ribono-1,4-lactone as starting material.

The pyranose ring adopts a chair conformation with methyl group at position 2 (atom C10 in the crystallogrphic labelling scheme) in the equatorial position (Fig. 2). The crystal structure exists O—H···O hydrogen-bonded chains of molecules lying parallel to the b-axis (Fig. 3). Only classical hydrogen bonding has been considered. There are no unusual crystal packing features.

Related literature top

For deoxy sugars see: Becker & Lowe (2003); Yoshihara et al. (2008); Gullapalli et al. (2007). For a related structure see: Booth et al. (2007).

Experimental top

The title compound was recrystallized from dichloromethane by slow evaporation: m.p. 349–352 K; [α]_D²⁵ -49.6 (c,0.15 in CHCl₃).

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 molecular structure showing the crystallographic labelling scheme. Displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
	Fig. 3. Packing diagram for the title compound projected along the a-axis. Hydrogen bonds are indicated by dotted lines.

2-Deoxy-2,3-O-isopropylidene-2,4-di-C-methyl-β-L-arabinose top

Crystal data top

C₁₀H₁₈O₄	F(000) = 220
M_r = 202.25	D_x = 1.240 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 1185 reflections
a = 6.0641 (3) Å	θ = 5–27°
b = 13.4016 (7) Å	µ = 0.10 mm⁻¹
c = 6.8287 (3) Å	T = 150 K
β = 102.596 (2)°	Plate, colourless
V = 541.60 (5) Å³	0.50 × 0.20 × 0.20 mm
Z = 2

Data collection top

Nonius KappaCCD diffractometer	1183 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.036
ω scans	θ_max = 27.5°, θ_min = 5.5°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −7→7
T_min = 0.89, T_max = 0.98	k = −13→17
5025 measured reflections	l = −8→8
1266 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)] = 0.030	H-atom parameters constrained
wR(F²) = 0.073	Method = Modified Sheldrick w = 1/[σ²(F²) + (0.03P)² + 0.12P], where P = [max(F_o²,0) + 2F_c²]/3
S = 0.98	(Δ/σ)_max = 0.000076
1266 reflections	Δρ_max = 0.16 e Å⁻³
127 parameters	Δρ_min = −0.16 e Å⁻³
1 restraint

Crystal data top

C₁₀H₁₈O₄	V = 541.60 (5) Å³
M_r = 202.25	Z = 2
Monoclinic, P2₁	Mo Kα radiation
a = 6.0641 (3) Å	µ = 0.10 mm⁻¹
b = 13.4016 (7) Å	T = 150 K
c = 6.8287 (3) Å	0.50 × 0.20 × 0.20 mm
β = 102.596 (2)°

Data collection top

Nonius KappaCCD diffractometer	1266 independent reflections
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	1183 reflections with I > 2σ(I)
T_min = 0.89, T_max = 0.98	R_int = 0.036
5025 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.030	1 restraint
wR(F²) = 0.073	H-atom parameters constrained
S = 0.98	Δρ_max = 0.16 e Å⁻³
1266 reflections	Δρ_min = −0.16 e Å⁻³
127 parameters

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

	x	y	z	U_iso*/U_eq
O1	0.3944 (2)	0.39582 (13)	0.04435 (17)	0.0245
C2	0.4077 (3)	0.39975 (17)	0.2596 (2)	0.0228
O3	0.3257 (2)	0.30533 (13)	0.30874 (17)	0.0224
C4	0.1684 (3)	0.27174 (16)	0.1342 (2)	0.0195
C5	0.2816 (3)	0.30472 (16)	−0.0350 (2)	0.0213
C6	0.1137 (3)	0.32628 (18)	−0.2291 (3)	0.0299
C7	0.4647 (3)	0.23026 (16)	−0.0612 (3)	0.0275
O8	0.3798 (2)	0.13095 (14)	−0.0775 (2)	0.0287
C9	0.3274 (3)	0.10066 (16)	0.1088 (3)	0.0255
C10	0.1251 (3)	0.15996 (16)	0.1439 (3)	0.0220
C11	0.0585 (3)	0.13084 (17)	0.3391 (3)	0.0294
O12	0.2706 (2)	0.00005 (14)	0.0917 (2)	0.0322
C13	0.2595 (3)	0.48536 (17)	0.3003 (3)	0.0298
C14	0.6502 (3)	0.41048 (18)	0.3718 (3)	0.0312
H41	0.0240	0.3081	0.1185	0.0230*
H63	0.0358	0.2638	−0.2803	0.0479*
H62	0.1938	0.3530	−0.3250	0.0474*
H61	0.0028	0.3745	−0.2037	0.0467*
H71	0.5148	0.2448	−0.1837	0.0319*
H72	0.5917	0.2377	0.0580	0.0331*
H91	0.4639	0.1091	0.2207	0.0329*
H101	0.0017	0.1448	0.0295	0.0264*
H111	0.0082	0.0613	0.3332	0.0474*
H112	0.1891	0.1410	0.4520	0.0465*
H113	−0.0662	0.1730	0.3609	0.0474*
H132	0.2647	0.4876	0.4458	0.0489*
H131	0.3214	0.5481	0.2611	0.0489*
H133	0.1041	0.4759	0.2247	0.0491*
H142	0.6552	0.4165	0.5154	0.0457*
H143	0.7110	0.4711	0.3212	0.0458*
H141	0.7362	0.3515	0.3460	0.0456*
H121	0.3746	−0.0319	0.0515	0.0539*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0310 (7)	0.0222 (6)	0.0214 (6)	−0.0072 (5)	0.0082 (5)	−0.0002 (5)
C2	0.0259 (8)	0.0224 (9)	0.0208 (7)	−0.0045 (7)	0.0066 (6)	−0.0005 (7)
O3	0.0270 (6)	0.0202 (7)	0.0199 (6)	−0.0045 (5)	0.0047 (5)	−0.0001 (5)
C4	0.0190 (8)	0.0193 (9)	0.0205 (8)	−0.0003 (6)	0.0050 (6)	−0.0018 (6)
C5	0.0233 (8)	0.0199 (9)	0.0215 (8)	−0.0012 (7)	0.0069 (6)	−0.0017 (7)
C6	0.0358 (10)	0.0297 (11)	0.0223 (9)	0.0016 (8)	0.0025 (7)	0.0005 (8)
C7	0.0276 (9)	0.0248 (10)	0.0340 (10)	0.0003 (8)	0.0153 (8)	0.0019 (8)
O8	0.0363 (7)	0.0218 (7)	0.0333 (7)	0.0021 (6)	0.0190 (6)	0.0004 (6)
C9	0.0284 (9)	0.0196 (9)	0.0312 (9)	0.0013 (7)	0.0124 (7)	0.0023 (7)
C10	0.0212 (8)	0.0201 (9)	0.0257 (9)	−0.0015 (6)	0.0074 (6)	−0.0011 (7)
C11	0.0344 (10)	0.0236 (9)	0.0349 (10)	0.0002 (8)	0.0176 (8)	0.0011 (8)
O12	0.0366 (7)	0.0200 (7)	0.0450 (8)	0.0021 (6)	0.0198 (6)	−0.0011 (6)
C13	0.0327 (10)	0.0243 (10)	0.0354 (10)	−0.0004 (8)	0.0141 (8)	−0.0007 (8)
C14	0.0276 (9)	0.0324 (11)	0.0313 (9)	−0.0037 (8)	0.0013 (7)	−0.0021 (9)

Geometric parameters (Å, º) top

O1—C2	1.4553 (19)	O8—C9	1.436 (2)
O1—C5	1.446 (2)	C9—C10	1.524 (2)
C2—O3	1.426 (2)	C9—O12	1.390 (2)
C2—C13	1.520 (3)	C9—H91	1.003
C2—C14	1.510 (2)	C10—C11	1.525 (2)
O3—C4	1.427 (2)	C10—H101	0.978
C4—C5	1.533 (2)	C11—H111	0.979
C4—C10	1.525 (2)	C11—H112	0.987
C4—H41	0.987	C11—H113	0.981
C5—C6	1.513 (2)	O12—H121	0.855
C5—C7	1.532 (2)	C13—H132	0.988
C6—H63	0.986	C13—H131	0.982
C6—H62	0.965	C13—H133	0.979
C6—H61	0.975	C14—H142	0.978
C7—O8	1.423 (2)	C14—H143	0.986
C7—H71	0.970	C14—H141	0.984
C7—H72	0.996

C2—O1—C5	109.06 (12)	C7—O8—C9	109.94 (14)
O1—C2—O3	105.09 (13)	O8—C9—C10	109.46 (14)
O1—C2—C13	107.90 (14)	O8—C9—O12	107.37 (15)
O3—C2—C13	112.10 (14)	C10—C9—O12	109.02 (14)
O1—C2—C14	110.45 (13)	O8—C9—H91	109.8
O3—C2—C14	108.43 (15)	C10—C9—H91	112.3
C13—C2—C14	112.62 (16)	O12—C9—H91	108.7
C2—O3—C4	106.69 (12)	C4—C10—C9	110.70 (13)
O3—C4—C5	102.17 (13)	C4—C10—C11	111.73 (15)
O3—C4—C10	111.32 (14)	C9—C10—C11	112.32 (15)
C5—C4—C10	115.19 (14)	C4—C10—H101	106.2
O3—C4—H41	110.5	C9—C10—H101	105.6
C5—C4—H41	108.0	C11—C10—H101	110.0
C10—C4—H41	109.4	C10—C11—H111	110.3
C4—C5—O1	102.36 (13)	C10—C11—H112	109.1
C4—C5—C6	112.89 (15)	H111—C11—H112	110.6
O1—C5—C6	109.89 (15)	C10—C11—H113	110.2
C4—C5—C7	110.82 (15)	H111—C11—H113	108.2
O1—C5—C7	107.33 (13)	H112—C11—H113	108.4
C6—C5—C7	112.89 (15)	C9—O12—H121	109.0
C5—C6—H63	109.1	C2—C13—H132	108.4
C5—C6—H62	108.8	C2—C13—H131	108.7
H63—C6—H62	110.3	H132—C13—H131	108.6
C5—C6—H61	109.2	C2—C13—H133	110.2
H63—C6—H61	109.3	H132—C13—H133	110.5
H62—C6—H61	110.1	H131—C13—H133	110.4
C5—C7—O8	111.05 (14)	C2—C14—H142	109.3
C5—C7—H71	109.9	C2—C14—H143	107.3
O8—C7—H71	107.2	H142—C14—H143	110.6
C5—C7—H72	106.9	C2—C14—H141	109.1
O8—C7—H72	111.1	H142—C14—H141	110.1
H71—C7—H72	110.7	H143—C14—H141	110.3

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C6—H61···O12ⁱ	0.97	2.59	3.562 (3)	173
O12—H121···O1ⁱⁱ	0.86	1.93	2.786 (3)	179

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

Experimental details

Crystal data
Chemical formula	C₁₀H₁₈O₄
M_r	202.25
Crystal system, space group	Monoclinic, P2₁
Temperature (K)	150
a, b, c (Å)	6.0641 (3), 13.4016 (7), 6.8287 (3)
β (°)	102.596 (2)
V (Å³)	541.60 (5)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.10
Crystal size (mm)	0.50 × 0.20 × 0.20

Data collection
Diffractometer	Nonius KappaCCD diffractometer
Absorption correction	Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)
T_min, T_max	0.89, 0.98
No. of measured, independent and observed [I > 2σ(I)] reflections	5025, 1266, 1183
R_int	0.036
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.030, 0.073, 0.98
No. of reflections	1266
No. of parameters	127
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.16

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O12—H121···O1ⁱ	0.86	1.93	2.786 (3)	179

Symmetry code: (i) −x+1, y−1/2, −z.

Acknowledgements

We would like to thank the Chemical Crystallography Department and ALT at Oxford University for use of the difractometers.

References

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