3-C-Methyl-d-allono-1,5-lactone

Jones, N.A.; Watkin, D.J.; Curran, L.A.; Jenkinson, S.F.; Fleet, G.W.J.

doi:10.1107/S1600536807002899

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 63| Part 2| February 2007| Pages o992-o994

https://doi.org/10.1107/S1600536807002899

3-C-Methyl-D-allono-1,5-lactone

Nigel A. Jones,^a ^* David J. Watkin,^b Louise A. Curran,^a Sarah F. Jenkinson ^a and George W. J. Fleet ^a

^aDepartment of Organic Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, England, and ^bDepartment of Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, England
^*Correspondence e-mail: nigel.jones@chem.ox.ac.uk

(Received 11 January 2007; accepted 18 January 2007; online 31 January 2007)

The relative configuration and ring size of the title compound, C₇H₁₂O₆, were established by X-ray crystallographic analysis. The absolute configuration was determined by the use of 2-C-methyl-D-ribonolactone as a starting material. Almost all unprotected carbohydrate lactones are five-membered ring 1,4-lactones; the title compound provides a very rare example of a stable six-membered ring lactone.

Comment

Although carbohydrates are the most varied of cheap chiral building blocks (Lichtenthaler & Peters, 2004 ), only recently have the first examples of branched 2-C-methylpentoses become readily available by treatment of an Amadori ketose with aqueous calcium hydroxide (Hotchkiss et al., 2007 ). The recognition of the value of a family of 2-C-methylnucleosides in the treatment of hepatitis C has led to current interest in the synthesis of 2-C-carbon-substituted sugars (Sorbera et al., 2006 ). The Kiliani reaction of ketoses and deoxyketoses with cyanide has provided an environmentally friendly procedure for the generation of a set of carbohydrate scaffolds with a branched carbon substituent at C-2 (Hotchkiss et al., 2004 ; Soengas et al., 2005 ). X-ray crystallographic analysis was vital in determining the structures of the products in these reactions (Punzo et al., 2006 ; Watkin et al., 2005 ). At present, free sugars and their lactones with a carbon branch at C-3 are essentially unknown. A 3-C-methylpentonolactone of unknown stereochemistry has been isolated from cigarette smoke (Schumacher et al., 1977 ), 3-C-methyl-D-mannose (Kwon et al., 2004 ) is one of the components of the trisaccharide repeating unit of the polysaccharide from Helicobacter pylori (Kocharova et al., 2000 ) and 3-C-methyl-L-mannose is one of the sugars in a pentasaccharide hapten of the GPL of Mycobacterium avium serovar (Fekete et al., 2006 ).

The value of the Kiliani reaction on 2-C-carbon-substituted carbohydrates in the synthesis of 3-C-hydroxymethyl branched sugars (Parker et al., 2006 ; Simone et al., 2007 ) and 3-C-methyl branched sugars (Bream et al., 2006 ) has been established. Under completely environmentally friendly aqueous conditions, the reaction of cyanide in water with 2-C-methyl-D-ribose, (2), derived from 2-C-methyl-D-ribonolactone, (1) (Hotchkiss et al., 2006 ), gave a major product which crystallized from the reaction mixture. X-ray crystallographic analysis shows (Fig. 1) that the structure is the title compound, (4), removing ambiguities as to the stereochemistry at the new C-2 chiral centre and the ring size of the lactone. The minor product is most likely the five-membered ring altrono-lactone, (3). The strain in five-membered ring lactones is generally considerably less than in six-membered ring lactones (Luisa et al., 1990 ; Brown et al., 1989 ). Compound (4) is thus a very rare example of the preferential formation of a six-membered ring lactone. Its C-2 isomer crystallizes as the 2-C-methyl-D-allono-1,4-lactone, (5), rather than the six-membered ring isomer, (6) (Harding et al., 2005 ). The absolute configuration of compound (4) was determined by the use of the D-sugar (1) as the starting material.

The isolated molecule of (4) (Fig. 1) shows no unusual bond lengths or angles, in spite of the strain mentioned above. The largest differences from the MOGUL norms (Bruno et al., 2004 ) are C6—O7 (00.01 Å; MOGUL s.u. 0.02 Å) and C3—C5—O4 (5.0°; MOGUL s.u. 2.2°).

The crystal structure of (4) is composed of hydrogen-bonded sheets of molecules lying parallel to the bc plane. Both the ketonic atom O8 and the hydroxyl atom O10 act as acceptors for two hydrogen bonds (Table 1 and Fig. 2).

Figure 1
The molecular structure of (4), with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radii.

Figure 2
A projection along the a axis of part of a hydrogen-bonded sheet of (I). There are no strong interactions between the sheets. Hydrogen bonds are shown as dotted lines.

Experimental

3-C-Methyl-D-allono-1,5-lactone, (4), was crystallized from a 3:1:1 mixture of ethyl acetate, methanol and cyclohexane. Analysis: m.p. 421–423 K; [α]_D²³ 63.5 (c, 0.795 in MeOH).

Crystal data

C₇H₁₂O₆
M_r = 192.17
Monoclinic, P 2₁
a = 5.6603 (2) Å
b = 8.0045 (2) Å
c = 9.3242 (3) Å
β = 103.1470 (13)°
V = 411.39 (2) Å³
Z = 2
D_x = 1.551 Mg m⁻³
Mo Kα radiation
μ = 0.14 mm⁻¹
T = 150 K
Needle, colourless
0.20 × 0.05 × 0.05 mm

Data collection

Nonius KappaCCD area-detector diffractometer
ω scans
Absorption correction: multi-scan (DENZO and SCALEPACK; Otwinowski & Minor, 1997 ) T_min = 0.75, T_max = 1.0
5511 measured reflections
1000 independent reflections
930 reflections with I > 2σ(I)
R_int = 0.050
θ_max = 27.4°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.031
wR(F²) = 0.076
S = 1.16
1000 reflections
118 parameters
H-atom parameters constrained
w = 1/[σ²(F²) + (0.02P)² + 0.12P] where P = [max(F_o²,0) + 2F_c²]/3
(Δ/σ)_max < 0.001
Δρ_max = 0.29 e Å⁻³
Δρ_min = −0.26 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O10—H7⋯O8ⁱ	0.84	2.08	2.856 (2)	153
O7—H8⋯O8ⁱⁱ	0.85	2.06	2.832 (2)	152
O11—H12⋯O10ⁱⁱⁱ	0.82	2.09	2.836 (2)	152
O12—H3⋯O10^iv	0.83	2.07	2.901 (2)	173
Symmetry codes: (i) $[-x+2, y-{\script{1\over 2}}, -z]$ ; (ii) $[-x+2, y+{\script{1\over 2}}, -z]$ ; (iii) $[-x+2, y+{\script{1\over 2}}, -z+1]$ ; (iv) x, y+1, z.

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

The relatively large ratio of minimum to maximum corrections applied in the multiscan process (1:1.33) reflects changes in the illuminated volume of the very thin needle-like crystal. These changes were kept to a minimum and were taken into account (Görbitz, 1999 ) by multiscan interframe scaling (DENZO and SCALEPACK; Otwinowski & Minor, 1997).

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

Data collection: COLLECT (Nonius, 1997–2001 ); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and 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, 4. DOI: https://doi.org/10.1107/S1600536807002899/lh2287sup1.cif

Structure factors: contains datablock 4. DOI: https://doi.org/10.1107/S1600536807002899/lh22874sup2.hkl

Computing details top

Data collection: COLLECT (Nonius, 1997–2001); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and 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.

3-C-Methyl-D-allono-1,5-lactone top

Crystal data top

C₇H₁₂O₆	F(000) = 204
M_r = 192.17	D_x = 1.551 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 976 reflections
a = 5.6603 (2) Å	θ = 5–27°
b = 8.0045 (2) Å	µ = 0.14 mm⁻¹
c = 9.3242 (3) Å	T = 150 K
β = 103.1470 (13)°	Plate, colourless
V = 411.39 (2) Å³	0.20 × 0.05 × 0.05 mm
Z = 2

Data collection top

Nonius KappaCCD area-detector diffractometer	930 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.050
ω scans	θ_max = 27.4°, θ_min = 5.1°
Absorption correction: multi-scan (DENZO and SCALEPACK; Otwinowski & Minor, 1997)	h = −7→7
T_min = 0.75, T_max = 1.0	k = −10→10
5511 measured reflections	l = −12→12
1000 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)] = 0.031	H-atom parameters constrained
wR(F²) = 0.076	w = 1/[σ²(F²) + (0.02P)² + 0.12P] where P = [max(F_o²,0) + 2F_c²]/3
S = 1.16	(Δ/σ)_max = 0.000084
1000 reflections	Δρ_max = 0.29 e Å⁻³
118 parameters	Δρ_min = −0.26 e Å⁻³
1 restraint

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

	x	y	z	U_iso*/U_eq
C1	0.6617 (4)	0.4808 (3)	0.2422 (2)	0.0134
C2	0.6307 (4)	0.3130 (3)	0.3137 (2)	0.0144
C3	0.8396 (4)	0.1948 (3)	0.3069 (2)	0.0144
O4	0.9188 (3)	0.2017 (2)	0.16759 (17)	0.0190
C5	0.8645 (4)	0.3256 (3)	0.0704 (2)	0.0144
C6	0.6588 (4)	0.4432 (3)	0.0802 (2)	0.0139
O7	0.6577 (3)	0.5857 (2)	−0.00803 (17)	0.0179
O8	0.9762 (3)	0.3333 (2)	−0.02633 (17)	0.0206
C9	0.7731 (4)	0.0148 (3)	0.3243 (3)	0.0177
O10	0.9679 (3)	−0.0981 (2)	0.31742 (18)	0.0192
O11	0.6110 (3)	0.3279 (2)	0.46166 (17)	0.0194
O12	0.8962 (3)	0.5429 (2)	0.31334 (18)	0.0169
C13	0.4618 (4)	0.6024 (3)	0.2552 (3)	0.0182
H21	0.4822	0.2623	0.2567	0.0171*
H31	0.9819	0.2273	0.3868	0.0172*
H61	0.5078	0.3822	0.0397	0.0173*
H91	0.7331	0.0010	0.4205	0.0226*
H92	0.6307	−0.0120	0.2449	0.0220*
H131	0.4845	0.7025	0.2044	0.0266*
H132	0.4745	0.6262	0.3588	0.0270*
H133	0.3052	0.5519	0.2097	0.0273*
H7	0.9904	−0.0831	0.2322	0.0289*
H8	0.7965	0.6309	0.0147	0.0280*
H12	0.7302	0.3786	0.5065	0.0306*
H3	0.9046	0.6468	0.3116	0.0251*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0109 (10)	0.0127 (12)	0.0165 (10)	−0.0016 (9)	0.0027 (8)	−0.0021 (9)
C2	0.0183 (11)	0.0133 (12)	0.0128 (10)	−0.0013 (10)	0.0060 (8)	0.0008 (11)
C3	0.0192 (11)	0.0143 (13)	0.0113 (10)	0.0001 (10)	0.0071 (8)	0.0015 (10)
O4	0.0272 (9)	0.0143 (9)	0.0187 (8)	0.0060 (8)	0.0120 (6)	0.0038 (8)
C5	0.0178 (11)	0.0119 (12)	0.0134 (10)	−0.0017 (10)	0.0031 (8)	−0.0016 (10)
C6	0.0161 (10)	0.0110 (12)	0.0145 (10)	−0.0006 (9)	0.0037 (8)	0.0023 (10)
O7	0.0180 (8)	0.0153 (9)	0.0201 (8)	−0.0007 (7)	0.0034 (6)	0.0066 (7)
O8	0.0257 (9)	0.0199 (10)	0.0199 (9)	0.0030 (8)	0.0127 (7)	0.0022 (8)
C9	0.0210 (12)	0.0134 (13)	0.0190 (11)	0.0010 (10)	0.0054 (10)	0.0014 (10)
O10	0.0285 (10)	0.0130 (9)	0.0170 (8)	0.0045 (8)	0.0068 (7)	0.0022 (7)
O11	0.0235 (9)	0.0215 (10)	0.0154 (7)	−0.0034 (8)	0.0092 (6)	−0.0007 (8)
O12	0.0170 (8)	0.0113 (9)	0.0208 (9)	−0.0030 (7)	0.0012 (7)	−0.0006 (7)
C13	0.0188 (12)	0.0145 (12)	0.0224 (11)	0.0021 (10)	0.0070 (9)	−0.0007 (11)

Geometric parameters (Å, º) top

C1—C2	1.527 (3)	C6—O7	1.405 (3)
C1—C6	1.536 (3)	C6—H61	0.982
C1—O12	1.431 (3)	O7—H8	0.847
C1—C13	1.518 (3)	C9—O10	1.439 (3)
C2—C3	1.527 (3)	C9—H91	0.980
C2—O11	1.415 (3)	C9—H92	0.987
C2—H21	0.975	O10—H7	0.842
C3—O4	1.469 (3)	O11—H12	0.816
C3—C9	1.507 (3)	O12—H3	0.833
C3—H31	0.999	C13—H131	0.954
O4—C5	1.332 (3)	C13—H132	0.972
C5—C6	1.516 (3)	C13—H133	0.979
C5—O8	1.215 (3)

C2—C1—C6	106.28 (19)	C1—C6—C5	110.15 (18)
C2—C1—O12	106.85 (19)	C1—C6—O7	114.48 (19)
C6—C1—O12	108.97 (17)	C5—C6—O7	111.67 (17)
C2—C1—C13	111.55 (18)	C1—C6—H61	106.8
C6—C1—C13	111.25 (18)	C5—C6—H61	106.3
O12—C1—C13	111.7 (2)	O7—C6—H61	106.9
C1—C2—C3	111.12 (18)	C6—O7—H8	108.7
C1—C2—O11	113.2 (2)	C3—C9—O10	112.54 (19)
C3—C2—O11	109.01 (18)	C3—C9—H91	108.8
C1—C2—H21	107.4	O10—C9—H91	108.0
C3—C2—H21	107.4	C3—C9—H92	108.0
O11—C2—H21	108.5	O10—C9—H92	109.5
C2—C3—O4	114.06 (18)	H91—C9—H92	110.1
C2—C3—C9	111.93 (18)	C9—O10—H7	103.6
O4—C3—C9	105.38 (18)	C2—O11—H12	107.6
C2—C3—H31	108.0	C1—O12—H3	112.9
O4—C3—H31	107.0	C1—C13—H131	108.2
C9—C3—H31	110.3	C1—C13—H132	108.5
C3—O4—C5	124.10 (18)	H131—C13—H132	109.9
O4—C5—C6	118.87 (18)	C1—C13—H133	108.6
O4—C5—O8	117.6 (2)	H131—C13—H133	110.0
C6—C5—O8	123.4 (2)	H132—C13—H133	111.5

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O10—H7···O8ⁱ	0.84	2.08	2.856 (2)	153
O7—H8···O8ⁱⁱ	0.85	2.06	2.832 (2)	152
O11—H12···O10ⁱⁱⁱ	0.82	2.09	2.836 (2)	152
O12—H3···O10^iv	0.83	2.07	2.901 (2)	173

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

Acknowledgements

The generous gift of 2-C-methyl-D-ribonolactone from Novartis Pharma AG, Basel, is gratefully acknowledged.

References

Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435. CrossRef Web of Science IUCr Journals Google Scholar
Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487. Web of Science CrossRef IUCr Journals Google Scholar
Bream, R., Watkin, D., Soengas, R., Eastwick-Field, V. & Fleet, G. W. J. (2006). Acta Cryst. E62, o977–o979. CSD CrossRef IUCr Journals Google Scholar
Brown, J. M., Conn, A. D., Pilcher, G., Leitao, M. L. P. & Yang, M. Y. (1989). J. Chem. Soc. Chem. Commun. pp. 1817–1819. CrossRef Google Scholar
Bruno, I. J., Cole, J. C., Kessler, M., Luo, J., Motherwell, W. D. S., Purkis, L. H., Smith, B. R., Taylor, R., Cooper, R. I., Harris, S. E. & Orpen, A. G. (2004). J. Chem. Inf. Comput. Sci. 44, 2133–2144. Web of Science CSD CrossRef PubMed CAS Google Scholar
Fekete, A., Gyergyoi, K., Kover, K. E., Bajza, I. & Liptak, A. (2006). Carbohydr. Res. 341, 1312–1321. Web of Science CrossRef PubMed CAS Google Scholar
Görbitz, C. H. (1999). Acta Cryst. B55, 1090–1098. Web of Science CSD CrossRef IUCr Journals Google Scholar
Harding, C. C., Watkin, D. J., Sawyer, N. K., Jenkinson, S. F. & Fleet, G. W. J. (2005). Acta Cryst. E61, o1472–o1474. Web of Science CSD CrossRef IUCr Journals Google Scholar
Hotchkiss, D. J., Jenkinson, S. F., Storer, R., Heinz, T. & Fleet, G. W. J. (2006). Tetrahedron Lett. 47, 315–318. Web of Science CrossRef CAS Google Scholar
Hotchkiss, D. J., Soengas, R., Booth, K. V., Weymouth-Wilson, A. C., Eastwick-Field, V. & Fleet, G. W. J. (2007). Tetrahedron Lett. 48, 517–520. Web of Science CrossRef CAS Google Scholar
Hotchkiss, D. J., Soengas, R., Simone, M. I., van Ameijde, J., Hunter, S., Cowley, A. R. & Fleet, G. W. J. (2004). Tetrahedron Lett. 45, 9461–9464. Web of Science CrossRef CAS Google Scholar
Kocharova, N. A., Knirel, Y. A., Widmalm, G., Jansson, P. E. & Moran, A. P. (2000). Biochemistry, 39, 4755–4760. Web of Science CrossRef PubMed CAS Google Scholar
Kwon, Y. T., Lee, Y. J., Lee, K. & Kim, K. S. (2004). Org. Lett. 6, 3901–3904. Web of Science CrossRef PubMed CAS Google Scholar
Lichtenthaler, F. W. & Peters, S. (2004). C. R. Chim. 7, 65–90. Web of Science CrossRef CAS Google Scholar
Luisa, M., Pilcher, G., Yang, M. Y., Brown, J. M. & Conn, A. D. (1990). J. Chem. Thermodyn. 22, 885–891. CrossRef Google Scholar
Nonius (1997–2001). COLLECT. Nonius BV, Delft, The Netherlands. Google Scholar
Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press. Google Scholar
Parker, S. G., Watkin, D. J., Simone, M. I. & Fleet, G. W. J. (2006). Acta Cryst. E62, o3961–o3963. Web of Science CSD CrossRef IUCr Journals Google Scholar
Punzo, F., Watkin, D. J., Hotchkiss, D. & Fleet, G. W. J. (2006). Acta Cryst. E62, o98–o100. Web of Science CSD CrossRef IUCr Journals Google Scholar
Schumacher, J. N., Green, C. R., Best, F. W. & Newell, M. P. (1977). J. Agric. Food Chem. 25, 310–320. CrossRef CAS PubMed Web of Science Google Scholar
Simone, M. I., Fleet, G. W. J. & Watkin, D. J. (2007). Acta Cryst. E63, o799–o801. Web of Science CSD CrossRef IUCr Journals Google Scholar
Soengas, R., Izumori, K., Simone, M. I., Watkin, D. J., Skytte, U. P., Soetaert, W. & Fleet, G. W. J. (2005). Tetrahedron Lett. 46, 5755–5759. Web of Science CrossRef CAS Google Scholar
Sorbera, L. A., Castaner, J. & Leeson, P. A. (2006). Drugs Future 31, 320–324. Web of Science CrossRef CAS Google Scholar
Watkin, D. J., Parry, L. L., Hotchkiss, D. J., Eastwick-Field, V. & Fleet, G. W. J. (2005). Acta Cryst. E61, o3302–o3303. Web of Science CSD CrossRef IUCr Journals Google Scholar
Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, University of Oxford, England. Google Scholar

© International Union of Crystallography. Prior permission is not required to reproduce short quotations, tables and figures from this article, provided the original authors and source are cited. For more information, click here.