5,6-O-Isopropyl­idene-3-C-methyl-D-mannono-1,4-lactone

The relative configuration of the title compound, C₁₀H₁₆O₆, was firmly established by X-ray crystallographic analysis. The absolute configuration was determined by the use of 2-C-methyl-D-arabinose as the starting material. The crystal structure exists as hydrogen-bonded sheets lying approximately perpendicular to c.

Key indicators

• Single-crystal X-ray study
• T = 150 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.040
• wR factor = 0.094
• Data-to-parameter ratio = 9.0

checkCIF/PLATON results

No syntax errors found



Alert level C
ABSTM02_ALERT_3_C  The ratio of expected to reported Tmax/Tmin(RR') is < 0.90
            Tmin and Tmax reported:      0.870     0.990
            Tmin(prime) and Tmax expected:      0.977     0.994
            RR(prime) =      0.895
            Please check that your absorption correction is appropriate.
PLAT061_ALERT_3_C Tmax/Tmin Range Test RR' too Large .............       0.89
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         O6

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           27.40
           From the CIF: _reflns_number_total               1310
           Count of symmetry unique reflns         1327
           Completeness (_total/calc)             98.72%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C12    = .          S
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   3 ALERT level C = Check and explain
   6 ALERT level G = General alerts; check

   4 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Carbohydrates are one of the most varied cheap chiral building blocks (Lichtenthaler & Peters, 2004) available. Currently, free sugars and their lactones with a carbon branch at C-3 have been relatively unstudied with only limited examples in the literarture. Examples of sugars with a carbon branch at C-3 include: a 3-C-methylpentonolactone of unknown stereochemistry, isolated from cigarette smoke (Schumacher et al., 1977); 3-C-methyl-D-mannose (Kwon et al., 2004), one of the components of the trisaccharide repeating unit of the polysaccharide from Helicobacter pylori (Kocharova et al., 2000); and a derivative of 3-C-methyl-L-mannose which is one of the sugars in a pentasaccharide hapten of the GPL of Mycobacterium avium serovar (Fekete et al., 2006).

The Kiliani ascension of 2-C-carbon-substituted carbohydrates has proved to be a valuable route towards 3-C-hydroxymethyl branched sugars (Parker et al., 2006; Simone et al., 2007) and 3-C-methyl branched sugars (Bream et al., 2006; Jones, Watkin et al. 2007). Recent biological studies on branched mannose derivatives have shown that this class of compound could have potential use as therapeutics (Mitchell et al. 2007).

The crystal structure exists as hydrogen bonded ribbons lying parallel to the ab-face (see Fig. 2).

Related literature

For related literature see: Mitchell et al. (2007); Hotchkiss et al. (2006); Soengas et al. (2005).

For related literature, see: Bream et al. (2006); Simone et al. (2007); Fekete et al. (2006); Görbitz (1999); Jenkinson et al. (2007); Jones et al. (2007); Kocharova et al. (2000); Kwon et al. (2004); Lichtenthaler & Peters (2004); Parker et al. (2006); Schumacher et al. (1977).

S2. Experimental

The reaction of cyanide in water with 2-C-methyl-D-arabinose (Jenkinson et al. 2007), derived from 2-C-methyl-D-arabinonolactone, (Hotchkiss et al., 2006), gave a mixture of isomeric lactones that could be separated by treatment with acetone and copper sulfate, in the presence of sulfuric acid, to afford three protected lactones. The title compound was crystallized from cyclohexane and ethyl acetate: m.p. 390–391 K; [α]_D²² +25.9 (c, 0.34 in acetone).

S3. Refinement

In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned on the basis of the starting material.

The relatively large ratio of minimum to maximum corrections applied in the multiscan process (1:1.15) reflect changes in the illuminated volume of the crystal. Changes in illuminated volume were kept to a minimum, and were taken into account (Görbitz, 1999) by the multi-scan inter-frame scaling (DENZO/SCALEPACK, Otwinowski & Minor, 1997).

The H atoms were all located in a difference map, but those attached to carbon atoms were repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H in the range 0.93–0.98, O—H = 0.82 Å) and U_iso(H) (in the range 1.2–1.5 times U_eq of the parent atom), after which the positions were refined with riding constraints.

Computing details

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.

Figures

	Fig. 1. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
	Fig. 2. The packing of the title compound projected along the a-axis. Hydrogen bonds are shown as dotted lines.
	Fig. 3. The reaction scheme.

5,6-O-Isopropylidene-3-C-methyl-D-mannono-1,4-lactone

Crystal data

C10H16O6	F(000) = 248
Mr = 232.23	Dx = 1.387 Mg m^−3
Monoclinic, P21	Melting point: ?? K
Hall symbol: P 2yb	Mo Kα radiation, λ = 0.71073 Å
a = 5.9838 (3) Å	Cell parameters from 1263 reflections
b = 11.7424 (5) Å	θ = 5–27°
c = 7.9189 (5) Å	µ = 0.12 mm^−1
β = 91.8112 (18)°	T = 150 K
V = 556.14 (5) Å^3	Plate, colourless
Z = 2	0.20 × 0.20 × 0.05 mm

Data collection

Nonius KappaCCD diffractometer	1078 reflections with I > 2.0σ(I)
Graphite monochromator	Rint = 0.059
ω scans	θmax = 27.4°, θmin = 5.2°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −7→7
Tmin = 0.87, Tmax = 0.99	k = −15→15
5136 measured reflections	l = −10→10
1310 independent reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.040	H-atom parameters constrained
wR(F^2) = 0.094	w = 1/[σ^2(F^2) + (0.06P)^2 + 0.02P], where P = [max(Fo^2,0) + 2Fc^2]/3
S = 0.91	(Δ/σ)max = 0.000142
1310 reflections	Δρmax = 0.27 e Å^−3
145 parameters	Δρmin = −0.29 e Å^−3
1 restraint

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.3390 (4)	0.2320 (2)	0.9976 (3)	0.0194
C2	0.1635 (4)	0.3068 (2)	0.9080 (3)	0.0202
C3	0.2339 (4)	0.3664 (2)	0.7497 (3)	0.0209
O4	0.0474 (3)	0.43187 (18)	0.6849 (2)	0.0241
C5	0.0862 (4)	0.4539 (3)	0.5098 (3)	0.0262
O6	0.2150 (4)	0.3591 (2)	0.4546 (3)	0.0505
C7	0.2924 (4)	0.2945 (3)	0.5966 (4)	0.0269
C8	0.2197 (5)	0.5628 (3)	0.4909 (4)	0.0385
C9	−0.1355 (5)	0.4558 (3)	0.4145 (4)	0.0353
O10	−0.0229 (3)	0.22944 (17)	0.8686 (2)	0.0216
C11	−0.0132 (4)	0.1416 (2)	0.9765 (3)	0.0207
C12	0.1838 (4)	0.1572 (2)	1.1009 (3)	0.0215
O13	0.2833 (3)	0.05512 (19)	1.1556 (2)	0.0284
O14	−0.1473 (3)	0.06496 (18)	0.9717 (2)	0.0263
O15	0.4355 (3)	0.16416 (18)	0.8701 (2)	0.0222
C16	0.5120 (4)	0.2978 (3)	1.1032 (3)	0.0266
H21	0.1127	0.3647	0.9932	0.0251*
H31	0.3612	0.4177	0.7788	0.0250*
H71	0.4529	0.2827	0.5951	0.0338*
H72	0.2128	0.2210	0.6050	0.0333*
H81	0.2604	0.5685	0.3759	0.0592*
H82	0.3528	0.5599	0.5632	0.0594*
H83	0.1252	0.6273	0.5184	0.0589*
H91	−0.1026	0.4632	0.2952	0.0543*
H92	−0.2096	0.3842	0.4309	0.0545*
H93	−0.2261	0.5192	0.4510	0.0548*
H121	0.1288	0.2008	1.2001	0.0268*
H161	0.6123	0.2442	1.1622	0.0432*
H162	0.6000	0.3479	1.0344	0.0429*
H163	0.4378	0.3414	1.1921	0.0431*
H5	0.1952	0.0124	1.2084	0.0458*
H14	0.5420	0.1310	0.9170	0.0361*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0201 (11)	0.0210 (14)	0.0170 (13)	−0.0016 (11)	0.0011 (10)	−0.0006 (11)
C2	0.0193 (11)	0.0194 (13)	0.0219 (14)	−0.0025 (11)	0.0016 (9)	−0.0030 (12)
C3	0.0213 (12)	0.0166 (13)	0.0245 (14)	−0.0003 (11)	−0.0030 (10)	0.0021 (12)
O4	0.0276 (8)	0.0221 (10)	0.0227 (10)	0.0063 (8)	0.0027 (7)	0.0030 (8)
C5	0.0315 (13)	0.0271 (15)	0.0203 (14)	0.0050 (13)	0.0058 (11)	0.0033 (13)
O6	0.0806 (17)	0.0499 (15)	0.0216 (11)	0.0378 (14)	0.0091 (11)	0.0060 (11)
C7	0.0299 (13)	0.0251 (15)	0.0260 (15)	0.0049 (13)	0.0060 (11)	0.0031 (13)
C8	0.0337 (14)	0.048 (2)	0.0341 (17)	−0.0084 (16)	−0.0006 (13)	0.0133 (17)
C9	0.0393 (14)	0.0369 (18)	0.0295 (16)	−0.0079 (15)	−0.0010 (13)	0.0073 (16)
O10	0.0182 (8)	0.0204 (10)	0.0261 (10)	−0.0005 (8)	−0.0011 (7)	0.0039 (8)
C11	0.0177 (10)	0.0200 (14)	0.0246 (15)	0.0029 (11)	0.0038 (10)	0.0013 (12)
C12	0.0198 (11)	0.0214 (14)	0.0232 (14)	0.0026 (11)	−0.0005 (10)	0.0039 (12)
O13	0.0205 (8)	0.0270 (10)	0.0376 (11)	0.0013 (8)	−0.0011 (8)	0.0139 (10)
O14	0.0204 (8)	0.0224 (10)	0.0361 (11)	−0.0016 (9)	0.0004 (8)	0.0061 (9)
O15	0.0210 (8)	0.0241 (10)	0.0215 (10)	0.0052 (8)	0.0008 (7)	0.0002 (9)
C16	0.0241 (12)	0.0303 (16)	0.0251 (15)	−0.0078 (13)	−0.0032 (11)	−0.0030 (13)

Geometric parameters (Å, º)

C1—C2	1.526 (3)	C8—H81	0.952
C1—C12	1.534 (4)	C8—H82	0.967
C1—O15	1.423 (3)	C8—H83	0.974
C1—C16	1.521 (3)	C9—H91	0.975
C2—C3	1.507 (4)	C9—H92	0.961
C2—O10	1.465 (3)	C9—H93	0.970
C2—H21	1.011	O10—C11	1.339 (3)
C3—O4	1.436 (3)	C11—C12	1.523 (3)
C3—C7	1.527 (4)	C11—O14	1.206 (3)
C3—H31	0.993	C12—O13	1.401 (3)
O4—C5	1.436 (3)	C12—H121	1.002
C5—O6	1.431 (4)	O13—H5	0.848
C5—C8	1.518 (4)	O15—H14	0.825
C5—C9	1.506 (4)	C16—H161	0.978
O6—C7	1.422 (3)	C16—H162	0.969
C7—H71	0.971	C16—H163	0.987
C7—H72	0.989
C2—C1—C12	99.13 (18)	H71—C7—H72	110.9
C2—C1—O15	106.35 (19)	C5—C8—H81	107.7
C12—C1—O15	108.9 (2)	C5—C8—H82	109.7
C2—C1—C16	114.2 (2)	H81—C8—H82	109.8
C12—C1—C16	114.2 (2)	C5—C8—H83	108.8
O15—C1—C16	112.96 (19)	H81—C8—H83	109.1
C1—C2—C3	116.6 (2)	H82—C8—H83	111.7
C1—C2—O10	104.5 (2)	C5—C9—H91	106.6
C3—C2—O10	109.98 (19)	C5—C9—H92	108.8
C1—C2—H21	107.1	H91—C9—H92	108.4
C3—C2—H21	109.9	C5—C9—H93	110.7
O10—C2—H21	108.4	H91—C9—H93	110.6
C2—C3—O4	108.1 (2)	H92—C9—H93	111.5
C2—C3—C7	118.7 (2)	C2—O10—C11	108.93 (17)
O4—C3—C7	101.98 (19)	O10—C11—C12	109.7 (2)
C2—C3—H31	108.7	O10—C11—O14	122.6 (2)
O4—C3—H31	109.9	C12—C11—O14	127.6 (2)
C7—C3—H31	109.1	C1—C12—C11	101.1 (2)
C3—O4—C5	107.09 (19)	C1—C12—O13	113.38 (19)
O4—C5—O6	105.1 (2)	C11—C12—O13	114.2 (2)
O4—C5—C8	110.4 (2)	C1—C12—H121	110.1
O6—C5—C8	109.6 (2)	C11—C12—H121	107.5
O4—C5—C9	108.6 (2)	O13—C12—H121	110.0
O6—C5—C9	109.5 (3)	C12—O13—H5	113.2
C8—C5—C9	113.3 (2)	C1—O15—H14	105.7
C5—O6—C7	109.8 (2)	C1—C16—H161	109.4
C3—C7—O6	104.8 (2)	C1—C16—H162	111.8
C3—C7—H71	109.9	H161—C16—H162	108.8
O6—C7—H71	111.3	C1—C16—H163	110.0
C3—C7—H72	107.9	H161—C16—H163	106.0
O6—C7—H72	111.9	H162—C16—H163	110.6

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O13—H5···O4^i	0.85	1.95	2.787 (2)	170
O15—H14···O14^ii	0.83	2.05	2.848 (2)	163

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