6-De­oxy-3,4-O-isopropyl­idene-2-C-methyl-l-galactono-1,5-lactone

Jenkinson, S.F.; Parry, L.L.; Wilson, F.X.; Fleet, G.W.J.; Watkin, D.J.

doi:10.1107/S1600536811034957

organic compounds

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ISSN: 2056-9890

Volume 67| Part 9| September 2011| Pages o2531-o2532

doi:10.1107/S1600536811034957

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6-Deoxy-3,4-O-isopropylidene-2-C-methyl-L-galactono-1,5-lactone

Sarah F. Jenkinson,^a ^* Loren L. Parry,^a Francis X. Wilson,^b George W. J. Fleet ^a and David J. Watkin ^c

^aDepartment of Organic Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England, ^bSummit PLC, 91 Milton Park, Abingdon, Oxfordshire OX14 4RY, England, and ^cDepartment of Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England
^*Correspondence e-mail: sarah.jenkinson@chem.ox.ac.uk

(Received 18 August 2011; accepted 25 August 2011; online 31 August 2011)

X-ray crystallography unequivocally confirmed the stereochemistry of the 2-C-methyl group in the title molecule, C₁₀H₁₆O₅, in which the 1,5-lactone ring exists in a boat conformation. The absolute stereochemistry was determined by the use of D-ribose in the synthesis. The crystal exists as O—H⋯O hydrogen bonded chains of molecules running parallel to the a axis with each molecule acting as a donor and acceptor for one hydrogen bond.

Related literature

For branched iminosugars, see: Håkansson et al. (2007 , 2008 ); Asano et al. (2000 ); da Cruz et al. (2011 ); Best et al. (2010 ) and for branched sugars, see: Booth et al. (2008 , 2009 ); da Cruz et al. (2008 ); Hotchkiss et al. (2006 , 2007 ); Jenkinson et al. (2007 ); Jones et al. (2007 , 2008 ); Rao et al. (2008 ). For conformations of related 1,5-lactones, see: Baird et al. (1987 ); Booth et al. (2007a ,b ); Bruce et al. (1990 ); Punzo et al. (2005 , 2006 ); Dai et al. (2010 ).

Experimental

Crystal data

C₁₀H₁₆O₅
M_r = 216.23
Orthorhombic, P 2₁ 2₁ 2₁
a = 6.1132 (2) Å
b = 12.2963 (4) Å
c = 14.6367 (5) Å
V = 1100.24 (6) Å³
Z = 4
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 150 K
0.20 × 0.20 × 0.04 mm

Data collection

Nonius KappaCCD diffractometer
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ) T_min = 0.95, T_max = 1.00
8628 measured reflections
1454 independent reflections
1131 reflections with I > 2σ(I)
R_int = 0.067

Refinement

R[F² > 2σ(F²)] = 0.038
wR(F²) = 0.090
S = 0.89
1454 reflections
136 parameters
H-atom parameters constrained
Δρ_max = 0.40 e Å⁻³
Δρ_min = −0.29 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O11—H111⋯O1ⁱ	0.86	1.93	2.793 (3)	172
Symmetry code: (i) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+2]$ .

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/S1600536811034957/lh5321sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811034957/lh5321Isup2.hkl

checkCIF report

Comment top

2-C-Methyl branched sugars, as well as being chirons for the enantiospecific synthesis of complex targets (Hotchkiss et al., 2006; Hotchkiss et al., 2007; da Cruz et al., 2008; Booth et al., 2009) including 2'-C-methyl nucleosides (Jenkinson et al., 2007), are a class of rare sugars with chemotherapeutic potential (Rao et al., 2008; Jones et al., 2008; Booth et al., 2008). Branched iminosugars have also been shown to exhibit interesting biological activity. For example: 6-C-methyl-swainsonine is a more potent inhibitor of L-rhamnosidase than L-swainsonine (Håkansson et al., 2007; Håkansson et al., 2008; Asano et al., 2000); 4-C-methylDAB and 4-C-methylLAB are both potent and specific α-glucosidase inhibitors (da Cruz et al. 2011) and isoLAB has been shown to partially rescue the defective F508del-CFTR function and therefore may have a role in the study of cyctic fibrosis (Best et al., 2010).

D-ribose 1 was converted by a number of steps to the lactols 2 (Fig. 1). The reaction of 2 with sodium cyanide in water gave a chain extension to afford a single isolated crystalline product 3 (Fig. 2).

3,4-O-Isopropylidene-1,5-lactones, such as 3, invariably crystallize in boat conformations (Baird et al., 1987; Bruce et al., 1990; Punzo et al., 2005). The diastereoselectivity of the reaction may be rationalized by the formation of the lactone 3 with less steric congestion (Punzo et al., 2006; Booth et al., 2007a; Booth et al., 2007b; Dai et al. 2010) with the smaller hydroxy group rather than the methyl group in the flagpole position (Fig. 2). The structure of 3 was confirmed by the X-ray crystallographic analysis. The absolute configuration was assigned from the use of D-ribose as the starting material. The title compound exists as O—H···O hydrogen bonded chains of molecules running parallel to the a-axis (Fig. 3). Each molecule acts as a donor and acceptor for 1 hydrogen bond. Only classical hydrogen bonding has been considered.

Related literature top

For branched iminosugars, see: Håkansson et al. (2007, 2008); Asano et al. (2000); da Cruz et al. (2011); Best et al. (2010) and for branched sugars, see: Booth et al. (2008, 2009); da Cruz et al. (2008); Hotchkiss et al. (2006, 2007); Jenkinson et al. (2007); Jones et al. (2007, 2008); Rao et al. (2008). For conformations of related 1,5-lactones, see: Baird et al. (1987); Booth et al. (2007a,b); Bruce et al. (1990); Punzo et al. (2005, 2006); Dai et al. (2010).

Experimental top

The title compound was recrystallized by diffusion from a mixture of ethyl acetate and cyclohexane: m.p. 369–371 K; [α]_D²⁵ -84.6 (c, 1.03 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 title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
	Fig. 3. Packing diagram of the title compound projected along the b-axis. Hydrogen bonds are shown by dotted lines.

6-Deoxy-3,4-O-isopropylidene-2-C-methyl-L-galactono-1,5-lactone top

Crystal data top

C₁₀H₁₆O₅	F(000) = 464
M_r = 216.23	D_x = 1.305 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1433 reflections
a = 6.1132 (2) Å	θ = 5–27°
b = 12.2963 (4) Å	µ = 0.11 mm⁻¹
c = 14.6367 (5) Å	T = 150 K
V = 1100.24 (6) Å³	Plate, colourless
Z = 4	0.20 × 0.20 × 0.04 mm

Data collection top

Nonius KappaCCD diffractometer	1131 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.067
ω scans	θ_max = 27.5°, θ_min = 5.2°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −7→7
T_min = 0.95, T_max = 1.00	k = −15→15
8628 measured reflections	l = −18→19
1454 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)] = 0.038	H-atom parameters constrained
wR(F²) = 0.090	Method = Modified Sheldrick w = 1/[σ²(F²) + (0.06P)² + 0.14P], where P = [max(F_o²,0) + 2F_c²]/3
S = 0.89	(Δ/σ)_max = 0.000259
1454 reflections	Δρ_max = 0.40 e Å⁻³
136 parameters	Δρ_min = −0.29 e Å⁻³
0 restraints

Crystal data top

C₁₀H₁₆O₅	V = 1100.24 (6) Å³
M_r = 216.23	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 6.1132 (2) Å	µ = 0.11 mm⁻¹
b = 12.2963 (4) Å	T = 150 K
c = 14.6367 (5) Å	0.20 × 0.20 × 0.04 mm

Data collection top

Nonius KappaCCD diffractometer	1454 independent reflections
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	1131 reflections with I > 2σ(I)
T_min = 0.95, T_max = 1.00	R_int = 0.067
8628 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.038	0 restraints
wR(F²) = 0.090	H-atom parameters constrained
S = 0.89	Δρ_max = 0.40 e Å⁻³
1454 reflections	Δρ_min = −0.29 e Å⁻³
136 parameters

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

	x	y	z	U_iso*/U_eq
O1	−0.0165 (3)	0.80556 (12)	0.89995 (10)	0.0290
C2	0.1164 (4)	0.75275 (16)	0.85712 (12)	0.0226
O3	0.0426 (3)	0.68163 (11)	0.79561 (10)	0.0287
C4	0.1986 (4)	0.60986 (16)	0.74843 (14)	0.0289
C5	0.3861 (4)	0.67578 (16)	0.71001 (14)	0.0271
O6	0.3108 (3)	0.73556 (12)	0.63264 (9)	0.0355
C7	0.4068 (4)	0.84132 (17)	0.63637 (13)	0.0292
O8	0.4222 (3)	0.86365 (10)	0.73198 (9)	0.0261
C9	0.4744 (4)	0.76299 (15)	0.77626 (13)	0.0240
C10	0.3643 (4)	0.76166 (16)	0.86972 (13)	0.0221
O11	0.4337 (3)	0.66259 (11)	0.91228 (10)	0.0301
C12	0.4222 (4)	0.86099 (16)	0.92581 (13)	0.0277
C13	0.2506 (5)	0.92177 (19)	0.59465 (16)	0.0401
C14	0.6306 (5)	0.8415 (2)	0.59246 (16)	0.0422
C15	0.0664 (5)	0.55020 (19)	0.67809 (16)	0.0402
H41	0.2554	0.5572	0.7948	0.0338*
H51	0.5068	0.6260	0.6926	0.0337*
H91	0.6348	0.7543	0.7832	0.0290*
H121	0.5803	0.8627	0.9363	0.0432*
H122	0.3490	0.8570	0.9864	0.0426*
H123	0.3742	0.9272	0.8933	0.0431*
H131	0.3082	0.9961	0.6014	0.0583*
H132	0.2349	0.9048	0.5289	0.0582*
H133	0.1099	0.9171	0.6262	0.0586*
H141	0.6868	0.9161	0.5934	0.0627*
H142	0.7280	0.7929	0.6268	0.0622*
H143	0.6166	0.8179	0.5275	0.0623*
H153	0.1616	0.4999	0.6465	0.0610*
H152	−0.0508	0.5092	0.7077	0.0613*
H151	0.0062	0.6022	0.6340	0.0612*
H111	0.4361	0.6716	0.9708	0.0460*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0284 (9)	0.0329 (8)	0.0257 (7)	0.0061 (7)	0.0025 (7)	0.0035 (7)
C2	0.0264 (11)	0.0224 (10)	0.0191 (8)	0.0006 (10)	0.0006 (9)	0.0049 (9)
O3	0.0263 (8)	0.0302 (8)	0.0295 (8)	−0.0029 (7)	0.0011 (6)	−0.0051 (6)
C4	0.0344 (13)	0.0224 (10)	0.0299 (11)	0.0027 (9)	0.0008 (10)	−0.0023 (9)
C5	0.0315 (12)	0.0276 (10)	0.0222 (9)	0.0034 (10)	0.0012 (10)	−0.0035 (9)
O6	0.0500 (11)	0.0332 (8)	0.0234 (7)	−0.0145 (8)	−0.0068 (7)	0.0026 (7)
C7	0.0354 (13)	0.0305 (12)	0.0216 (10)	−0.0092 (11)	−0.0011 (10)	−0.0005 (9)
O8	0.0326 (8)	0.0250 (7)	0.0208 (7)	−0.0002 (7)	0.0006 (6)	0.0007 (6)
C9	0.0220 (11)	0.0253 (10)	0.0248 (9)	0.0032 (9)	0.0000 (9)	−0.0009 (9)
C10	0.0246 (11)	0.0198 (10)	0.0220 (9)	0.0042 (9)	−0.0017 (9)	0.0009 (8)
O11	0.0405 (9)	0.0267 (7)	0.0233 (7)	0.0089 (7)	−0.0047 (7)	0.0023 (6)
C12	0.0300 (12)	0.0288 (11)	0.0243 (10)	0.0005 (10)	−0.0028 (10)	−0.0022 (9)
C13	0.0453 (16)	0.0394 (13)	0.0355 (12)	−0.0026 (13)	−0.0080 (13)	0.0110 (12)
C14	0.0470 (16)	0.0480 (14)	0.0316 (11)	−0.0057 (14)	0.0137 (12)	−0.0004 (12)
C15	0.0509 (17)	0.0330 (12)	0.0368 (12)	−0.0104 (12)	−0.0011 (13)	−0.0088 (10)

Geometric parameters (Å, º) top

O1—C2	1.214 (2)	C9—H91	0.992
C2—O3	1.334 (2)	C10—O11	1.433 (2)
C2—C10	1.530 (3)	C10—C12	1.514 (3)
O3—C4	1.472 (3)	O11—H111	0.864
C4—C5	1.512 (3)	C12—H121	0.979
C4—C15	1.501 (3)	C12—H122	0.995
C4—H41	1.000	C12—H123	0.987
C5—O6	1.426 (2)	C13—H131	0.985
C5—C9	1.543 (3)	C13—H132	0.989
C5—H51	0.992	C13—H133	0.978
O6—C7	1.428 (3)	C14—H141	0.979
C7—O8	1.429 (2)	C14—H142	0.982
C7—C13	1.505 (3)	C14—H143	0.997
C7—C14	1.512 (3)	C15—H153	0.967
O8—C9	1.433 (2)	C15—H152	0.977
C9—C10	1.525 (3)	C15—H151	0.980

O1—C2—O3	118.2 (2)	C2—C10—O11	106.55 (17)
O1—C2—C10	124.18 (18)	C9—C10—O11	105.58 (16)
O3—C2—C10	117.60 (18)	C2—C10—C12	110.78 (18)
C2—O3—C4	119.38 (17)	C9—C10—C12	112.01 (17)
O3—C4—C5	110.13 (15)	O11—C10—C12	112.40 (15)
O3—C4—C15	105.41 (19)	C10—O11—H111	109.1
C5—C4—C15	114.54 (18)	C10—C12—H121	109.5
O3—C4—H41	107.1	C10—C12—H122	109.8
C5—C4—H41	109.7	H121—C12—H122	107.8
C15—C4—H41	109.6	C10—C12—H123	109.5
C4—C5—O6	109.09 (18)	H121—C12—H123	110.5
C4—C5—C9	113.83 (17)	H122—C12—H123	109.7
O6—C5—C9	104.69 (15)	C7—C13—H131	110.0
C4—C5—H51	109.2	C7—C13—H132	108.5
O6—C5—H51	110.7	H131—C13—H132	109.2
C9—C5—H51	109.3	C7—C13—H133	109.2
C5—O6—C7	107.85 (16)	H131—C13—H133	108.7
O6—C7—O8	103.85 (15)	H132—C13—H133	111.2
O6—C7—C13	108.81 (18)	C7—C14—H141	108.2
O8—C7—C13	108.23 (18)	C7—C14—H142	109.3
O6—C7—C14	110.92 (18)	H141—C14—H142	110.5
O8—C7—C14	110.89 (19)	C7—C14—H143	109.1
C13—C7—C14	113.65 (18)	H141—C14—H143	108.4
C7—O8—C9	106.95 (14)	H142—C14—H143	111.3
C5—C9—O8	103.77 (15)	C4—C15—H153	108.4
C5—C9—C10	113.70 (17)	C4—C15—H152	110.1
O8—C9—C10	108.47 (15)	H153—C15—H152	108.9
C5—C9—H91	109.6	C4—C15—H151	109.6
O8—C9—H91	111.1	H153—C15—H151	109.1
C10—C9—H91	110.1	H152—C15—H151	110.7
C2—C10—C9	109.25 (16)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C13—H131···O11ⁱ	0.99	2.59	3.536 (3)	161
O11—H111···O1ⁱⁱ	0.86	1.93	2.793 (3)	172

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

Experimental details

Crystal data
Chemical formula	C₁₀H₁₆O₅
M_r	216.23
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	150
a, b, c (Å)	6.1132 (2), 12.2963 (4), 14.6367 (5)
V (Å³)	1100.24 (6)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.20 × 0.20 × 0.04

Data collection
Diffractometer	Nonius KappaCCD diffractometer
Absorption correction	Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)
T_min, T_max	0.95, 1.00
No. of measured, independent and observed [I > 2σ(I)] reflections	8628, 1454, 1131
R_int	0.067
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.038, 0.090, 0.89
No. of reflections	1454
No. of parameters	136
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.40, −0.29

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
O11—H111···O1ⁱ	0.86	1.93	2.793 (3)	172

Symmetry code: (i) x+1/2, −y+3/2, −z+2.

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Volume 67| Part 9| September 2011| Pages o2531-o2532

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