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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 65| Part 9| September 2009| Page o2199
doi:10.1107/S1600536809032796

2,3-O-(S)-Benzyl­­idene-2-C-methyl-D-ribono-1,4-lactone

K. Victoria Booth,a* Sarah F. Jenkinson,a George W. J. Fleeta and David J. Watkinb

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

(Received 14 August 2009; accepted 18 August 2009; online 22 August 2009)

The crystal structure of the title compound, C13H14O5, establishes (i) the (S) – rather than (R) – configuration at the acetal carbon and (ii) that both the acetal and the lactone form five- rather than six-membered rings; the absolute configuration is determined by the use of 2-C-methyl-D-ribono-1,4-lactone as the starting material. The compound consists of hydrogen-bonded chains of mol­ecules running along the a axis; there are no unusual packing features. Only classical hydrogen bonding has been considered.

Related literature

For the synthesis of sugar lactones and their use as building blocks, see: Lundt & Madsen (2001[Lundt, I. & Madsen, R. (2001). Top. Curr. Chem. 215, 178-191.]); Hotchkiss, Soengas et al. (2007[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.]); Booth et al. (2008[Booth, K. V., da Cruz, F. P., Hotchkiss, D. J., Jenkinson, S. F., Jones, N. A., Weymouth-Wilson, A. C., Clarkson, R., Heinz, T. & Fleet, G. W. J. (2008). Tetrahedron Asymmetry 19, 2417-2424.], 2009[Booth, K. V., Jenkinson, S. F., Best, D., Nieto, F. F., Estevez, R. J., Wormald, M. R., Weymouth-Wilson, A. C. & Fleet, G. W. J. (2009). Tetrahedron Lett. 50, 5088-5093.]); Jenkinson et al. (2007[Jenkinson, S. F., Jones, N. A., Moussa, A., Stewart, A. J., Heinz, T. & Fleet, G. W. J. (2007). Tetrahedron Lett. 48, 4441-4445.]); Hotchkiss, Kato et al. (2007[Hotchkiss, D. J., Kato, A., Odell, B., Claridge, T. D. W. & Fleet, G. W. J. (2007). Tetrahedron Asymmetry 18, 500-512.]); Chen & Joullie (1984[Chen, S. Y. & Joullie, M. M. (1984). J. Org. Chem. 49, 2168-2174.]); Dho et al. (1986[Dho, J. C., Fleet, G. W. J., Peach, J. M., Prout, K. & Smith, P. W. (1986). Tetrahedron Lett. 27, 3203-3204.]); Baird et al. (1987[Baird, P. D., Dho, J. C., Fleet, G. W. J., Peach, J. M., Prout, K. & Smith, P. W. (1987). J. Chem. Soc. Perkin Trans. 1, pp. 1785-1791.]). For the structures of benzyl­idene acetals, see: Baggett et al. (1985[Baggett, N., Buchanan, J. G., Fatah, M. V., Lachut, C. H., McCullough, K. J. & Webber, J. M. (1985). J. Chem. Soc. Chem. Commun. pp. 1826-1827.]); Zinner et al. (1968[Zinner, H., Voight, H. & Voight, J. (1968). Carbohydr. Res. 7, 38-55.]).

[Scheme 1]

Experimental

Crystal data

  • C13H14O5

  • Mr = 250.25

  • Orthorhombic, P 21 21 21

  • a = 8.6170 (2) Å

  • b = 10.4615 (3) Å

  • c = 13.2693 (5) Å

  • V = 1196.18 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 150 K

  • 0.50 × 0.40 × 0.40 mm
Data collection

  • Nonius KappaCCD diffractometer

  • Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997[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.]) Tmin = 0.91, Tmax = 0.96

  • 8306 measured reflections

  • 1547 independent reflections

  • 1369 reflections with I > 2.0σ(I)

  • Rint = 0.036
Refinement

  • R[F2 > 2σ(F2)] = 0.033

  • wR(F2) = 0.075

  • S = 0.96

  • 1547 reflections

  • 163 parameters

  • H-atom parameters constrained

  • Δρmax = 0.21 e Å−3

  • Δρmin = −0.18 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O18—H181⋯O9i 0.84 2.02 2.801 (3) 153
Symmetry code: (i) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1].

Data collection: COLLECT (Nonius, 1997-2001[Nonius (1997-2001). COLLECT. Nonius BV, Delft, The Netherlands.]).; cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997[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.]); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994[Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.]); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003[Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.]); molecular graphics: CAMERON (Watkin et al., 1996[Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON, Chemical Crystallography Laboratory, Oxford, UK.]); software used to prepare material for publication: CRYSTALS.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809032796/lh2882sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809032796/lh2882Isup2.hkl

checkCIF report


Comment top

Lactones have been widely used for the enantiospecific synthesis of complex chiral targets (Lundt & Madsen, 2001). 2-C-Methyl-D-ribono-1,4-lactone 3 (Fig. 1) has recently become a readily available starting material (Hotchkiss, Soengas et al., 2007; Booth et al., 2008) and has been used in the synthesis of doubly branched sugars (Booth et al., 2009), 2-C-methyl nucleosides (Jenkinson et al., 2007) and complex piperidines (Hotchkiss, Kato et al., 2007). D-Ribono-1,4-lactone 5 with benzaldehyde and concentrated aqueous hydrochloric acid forms a 5 ring benzylidene acetal - 6-ring lactone 6 (Fig. 1). The structure of 6 was established by X-ray crystallographic analysis (Baggett et al., 1985) which corrected the original erroneous 6 ring benzylidene acetal - 5-ring lactone structure proposed (Zinner et al., 1968). The protected 1,5-lactone 6 leaves only the C-2 OH unprotected and has been widely used as a chiron (Chen & Joullie, 1984; Dho et al., 1986; Baird et al., 1987). It was hoped that the analogous reaction with 2-C-methyl lactone 3 would form the analogous lactone 4; however, treatment of 3 with benzaldehyde and concentrated aqueous hydrochloric acid gave as the major product a mixture of epimeric 1,4-lactones 1 and 2; although it was not possible to separate 1 and 2 by chromatography, suitable crystals of the major component 1 were obtained and the structure of a 5 ring benzylidene acetal - 5-ring lactone, together with the (S) stereochemistry at the acetal carbon, was firmly established (Fig. 2).

The compound consists of H—O···H hydrogen bonded chains of molecules running along the a-axis (Fig. 3); there are no unusual packing features. Only classical hydrogen bonding has been considered.

Related literature top

For the synthesis of sugar lactones and their use as building blocks, see: Lundt & Madsen (2001); Hotchkiss, Soengas et al. (2007); Booth et al. (2008, 2009); Jenkinson et al. (2007); Hotchkiss, Kato et al. (2007); Chen & Joullie (1984); Dho et al. (1986); Baird et al. (1987). For the structures of benzylidene acetals, see: Baggett et al. (1985); Zinner et al. (1968).

Experimental top

The title compound was recrystallized from a mixture of diethyl ether and petrol by slow evaporation: m.p. 369–372 K; [α]D18 -38.7 (c, 0.86 in CHCl3).

Refinement top

In the absence of significant anomalous scattering, Friedel pairs were merged.

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 Uiso(H) (in the range 1.2–1.5 times Ueq of the parent atom), after which the positions were refined with riding constraints.

Computing details top

Data collection: COLLECT (Nonius, 1997-2001).; 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 (Betteridge et al., 2003).

Figures top
[Figure 1] Fig. 1. Synthetic Scheme
[Figure 2] Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
[Figure 3] Fig. 3. Packing diagram for the title compound projected along the c-axis. Hydrogen bonds are indicated by dotted lines.
(I) top
Crystal data top
C13H14O5F(000) = 528
Mr = 250.25Dx = 1.390 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1493 reflections
a = 8.6170 (2) Åθ = 5–27°
b = 10.4615 (3) ŵ = 0.11 mm−1
c = 13.2693 (5) ÅT = 150 K
V = 1196.18 (6) Å3Block, colourless
Z = 40.50 × 0.40 × 0.40 mm
Data collection top
Nonius KappaCCD
diffractometer		1369 reflections with I > 2.0σ(I)
Graphite monochromatorRint = 0.036
ω scansθmax = 27.4°, θmin = 5.1°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		h = −11→11
Tmin = 0.91, Tmax = 0.96k = −13→13
8306 measured reflectionsl = −17→17
1547 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033H-atom parameters constrained
wR(F2) = 0.075 Method = Modified Sheldrick w = 1/[σ2(F2) + ( 0.04P)2 + 0.33P] ,
where P = (max(Fo2,0) + 2Fc2)/3
S = 0.96(Δ/σ)max = 0.000267
1547 reflectionsΔρmax = 0.21 e Å−3
163 parametersΔρmin = −0.18 e Å−3
0 restraints
Crystal data top
C13H14O5V = 1196.18 (6) Å3
Mr = 250.25Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 8.6170 (2) ŵ = 0.11 mm−1
b = 10.4615 (3) ÅT = 150 K
c = 13.2693 (5) Å0.50 × 0.40 × 0.40 mm
Data collection top
Nonius KappaCCD
diffractometer		1547 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		1369 reflections with I > 2.0σ(I)
Tmin = 0.91, Tmax = 0.96Rint = 0.036
8306 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0330 restraints
wR(F2) = 0.075H-atom parameters constrained
S = 0.96Δρmax = 0.21 e Å−3
1547 reflectionsΔρmin = −0.18 e Å−3
163 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.20180 (16)0.58639 (12)0.35659 (10)0.0315
C20.0428 (2)0.53792 (18)0.36504 (15)0.0308
C30.0572 (2)0.41273 (17)0.42367 (14)0.0290
O40.07235 (15)0.30513 (13)0.35853 (12)0.0348
C50.2332 (2)0.27989 (17)0.34757 (14)0.0282
O60.30017 (15)0.31402 (12)0.44177 (10)0.0292
C70.2137 (2)0.42186 (16)0.47876 (13)0.0271
C80.2876 (2)0.54172 (17)0.43333 (14)0.0284
O90.41116 (16)0.58753 (14)0.45530 (11)0.0382
C100.2143 (3)0.4195 (2)0.59243 (14)0.0403
C110.2581 (2)0.14034 (17)0.32652 (14)0.0278
C120.3486 (2)0.10164 (19)0.24540 (15)0.0314
C130.3662 (2)−0.0280 (2)0.22427 (16)0.0349
C140.2945 (3)−0.11716 (19)0.28505 (15)0.0358
C150.2066 (2)−0.07955 (18)0.36660 (15)0.0345
C160.1874 (2)0.04930 (19)0.38769 (15)0.0314
C17−0.0516 (2)0.63951 (19)0.41789 (16)0.0359
O180.02305 (17)0.66472 (14)0.51139 (11)0.0385
H210.00280.52210.29340.0368*
H31−0.03010.40240.47120.0369*
H510.27800.33520.29170.0355*
H1010.32070.42250.61740.0626*
H1030.15730.49420.61460.0621*
H1020.16350.34040.61450.0620*
H1210.39780.16520.20450.0380*
H1310.4316−0.05560.16530.0416*
H1410.3061−0.20810.27100.0428*
H1510.1588−0.14220.41020.0424*
H1610.12480.07650.44550.0371*
H172−0.05410.71670.37410.0456*
H171−0.16050.60710.42920.0454*
H181−0.01320.72940.54130.0598*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0387 (7)0.0245 (6)0.0313 (7)−0.0037 (6)0.0002 (6)0.0025 (5)
C20.0337 (9)0.0244 (9)0.0343 (10)0.0014 (8)−0.0037 (8)−0.0015 (8)
C30.0286 (9)0.0233 (9)0.0352 (10)−0.0005 (8)−0.0006 (8)−0.0020 (8)
O40.0290 (7)0.0240 (7)0.0513 (9)0.0010 (6)−0.0099 (7)−0.0079 (6)
C50.0307 (9)0.0232 (9)0.0306 (10)−0.0008 (7)−0.0024 (8)−0.0019 (7)
O60.0303 (6)0.0239 (6)0.0335 (7)0.0014 (6)−0.0054 (6)−0.0044 (5)
C70.0296 (9)0.0226 (8)0.0290 (9)−0.0003 (8)0.0000 (8)−0.0009 (7)
C80.0335 (10)0.0226 (8)0.0292 (9)−0.0013 (8)0.0028 (8)−0.0053 (7)
O90.0341 (7)0.0322 (7)0.0482 (8)−0.0095 (6)−0.0005 (7)−0.0095 (7)
C100.0500 (12)0.0428 (12)0.0282 (10)0.0028 (11)0.0006 (9)0.0014 (9)
C110.0312 (9)0.0217 (8)0.0307 (9)−0.0016 (7)−0.0040 (8)−0.0008 (7)
C120.0320 (9)0.0276 (9)0.0345 (10)−0.0016 (8)0.0004 (8)0.0022 (8)
C130.0372 (10)0.0314 (10)0.0360 (11)0.0031 (9)0.0022 (9)−0.0041 (8)
C140.0418 (11)0.0245 (9)0.0411 (11)0.0017 (9)−0.0031 (10)−0.0014 (8)
C150.0414 (10)0.0251 (9)0.0370 (10)−0.0042 (9)−0.0013 (9)0.0017 (8)
C160.0350 (10)0.0283 (9)0.0308 (9)−0.0015 (8)0.0014 (8)0.0013 (8)
C170.0382 (10)0.0291 (10)0.0406 (11)0.0050 (9)−0.0079 (10)−0.0051 (9)
O180.0442 (8)0.0326 (7)0.0385 (8)0.0078 (6)−0.0058 (7)−0.0091 (6)
Geometric parameters (Å, º) top
O1—C21.465 (2)C10—H1030.968
O1—C81.342 (2)C10—H1020.981
C2—C31.528 (3)C11—C121.390 (3)
C2—C171.511 (3)C11—C161.392 (3)
C2—H211.025C12—C131.394 (3)
C3—O41.425 (2)C12—H1210.957
C3—C71.537 (3)C13—C141.379 (3)
C3—H310.988C13—H1311.007
O4—C51.418 (2)C14—C151.379 (3)
C5—O61.422 (2)C14—H1410.974
C5—C111.502 (2)C15—C161.387 (3)
C5—H511.016C15—H1510.967
O6—C71.438 (2)C16—H1610.981
C7—C81.530 (2)C17—O181.422 (2)
C7—C101.508 (2)C17—H1720.995
C8—O91.203 (2)C17—H1711.009
C10—H1010.975O18—H1810.844
C2—O1—C8109.66 (14)C7—C10—H103106.8
O1—C2—C3105.05 (15)H101—C10—H103110.3
O1—C2—C17107.19 (15)C7—C10—H102108.1
C3—C2—C17114.22 (17)H101—C10—H102110.2
O1—C2—H21107.4H103—C10—H102111.3
C3—C2—H21111.2C5—C11—C12120.49 (16)
C17—C2—H21111.3C5—C11—C16119.63 (17)
C2—C3—O4112.06 (15)C12—C11—C16119.86 (17)
C2—C3—C7105.08 (15)C11—C12—C13120.03 (18)
O4—C3—C7104.91 (14)C11—C12—H121119.0
C2—C3—H31110.9C13—C12—H121120.9
O4—C3—H31111.8C12—C13—C14119.47 (19)
C7—C3—H31111.8C12—C13—H131119.8
C3—O4—C5107.37 (13)C14—C13—H131120.8
O4—C5—O6105.05 (15)C13—C14—C15120.82 (19)
O4—C5—C11109.85 (15)C13—C14—H141120.1
O6—C5—C11110.45 (15)C15—C14—H141119.0
O4—C5—H51109.9C14—C15—C16120.09 (18)
O6—C5—H51110.1C14—C15—H151120.7
C11—C5—H51111.3C16—C15—H151119.2
C5—O6—C7106.65 (13)C11—C16—C15119.71 (18)
C3—C7—O6104.08 (14)C11—C16—H161119.9
C3—C7—C8103.21 (15)C15—C16—H161120.4
O6—C7—C8107.03 (14)C2—C17—O18106.96 (16)
C3—C7—C10118.52 (17)C2—C17—H172108.2
O6—C7—C10109.08 (16)O18—C17—H172111.6
C8—C7—C10113.95 (16)C2—C17—H171109.5
C7—C8—O1110.80 (15)O18—C17—H171110.7
C7—C8—O9126.80 (18)H172—C17—H171109.8
O1—C8—O9122.17 (17)C17—O18—H181113.1
C7—C10—H101110.0
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C10—H103···O180.972.533.233 (3)130
C13—H131···O9i1.012.583.289 (3)128
C14—H141···O1ii0.972.593.340 (3)134
O18—H181···O9iii0.842.022.801 (3)153
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) x, y−1, z; (iii) x−1/2, −y+3/2, −z+1.

Experimental details

Crystal data
Chemical formulaC13H14O5
Mr250.25
Crystal system, space groupOrthorhombic, P212121
Temperature (K)150
a, b, c (Å)8.6170 (2), 10.4615 (3), 13.2693 (5)
V (Å3)1196.18 (6)
Z4
Radiation typeMo Kα
µ (mm−1)0.11
Crystal size (mm)0.50 × 0.40 × 0.40
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
Tmin, Tmax0.91, 0.96
No. of measured, independent and
observed [I > 2.0σ(I)] reflections		8306, 1547, 1369
Rint0.036
(sin θ/λ)max (Å−1)0.647
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.075, 0.96
No. of reflections1547
No. of parameters163
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.21, −0.18

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

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O18—H181···O9i0.842.022.801 (3)153
Symmetry code: (i) x−1/2, −y+3/2, −z+1.
 

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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ISSN: 2056-9890
Volume 65| Part 9| September 2009| Page o2199
doi:10.1107/S1600536809032796
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