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organic compounds
2,3-O-(S)-Benzylidene-2-C-methyl-D-ribono-1,4-lactone
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
The 13H14O5, 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 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.
of the title compound, CRelated literature
For the synthesis of sugar ); 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 see: Baggett et al. (1985
); Zinner et al. (1968
).
Experimental
Crystal data
|
Refinement
|
|
Data collection: COLLECT (Nonius, 1997-2001).; cell 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
10.1107/S1600536809032796/lh2882sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809032796/lh2882Isup2.hkl
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).
In the absence of significant
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.
Data collection: COLLECT (Nonius, 1997-2001).; cell
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).C13H14O5 | F(000) = 528 |
Mr = 250.25 | Dx = 1.390 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 1493 reflections |
a = 8.6170 (2) Å | θ = 5–27° |
b = 10.4615 (3) Å | µ = 0.11 mm−1 |
c = 13.2693 (5) Å | T = 150 K |
V = 1196.18 (6) Å3 | Block, colourless |
Z = 4 | 0.50 × 0.40 × 0.40 mm |
Nonius KappaCCD diffractometer | 1369 reflections with I > 2.0σ(I) |
Graphite monochromator | Rint = 0.036 |
ω scans | θmax = 27.4°, θmin = 5.1° |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | h = −11→11 |
Tmin = 0.91, Tmax = 0.96 | k = −13→13 |
8306 measured reflections | l = −17→17 |
1547 independent reflections |
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)] = 0.033 | H-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 reflections | Δρmax = 0.21 e Å−3 |
163 parameters | Δρmin = −0.18 e Å−3 |
0 restraints |
C13H14O5 | V = 1196.18 (6) Å3 |
Mr = 250.25 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 8.6170 (2) Å | µ = 0.11 mm−1 |
b = 10.4615 (3) Å | T = 150 K |
c = 13.2693 (5) Å | 0.50 × 0.40 × 0.40 mm |
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 = 0.96 | Rint = 0.036 |
8306 measured reflections |
R[F2 > 2σ(F2)] = 0.033 | 0 restraints |
wR(F2) = 0.075 | H-atom parameters constrained |
S = 0.96 | Δρmax = 0.21 e Å−3 |
1547 reflections | Δρmin = −0.18 e Å−3 |
163 parameters |
x | y | z | Uiso*/Ueq | ||
O1 | 0.20180 (16) | 0.58639 (12) | 0.35659 (10) | 0.0315 | |
C2 | 0.0428 (2) | 0.53792 (18) | 0.36504 (15) | 0.0308 | |
C3 | 0.0572 (2) | 0.41273 (17) | 0.42367 (14) | 0.0290 | |
O4 | 0.07235 (15) | 0.30513 (13) | 0.35853 (12) | 0.0348 | |
C5 | 0.2332 (2) | 0.27989 (17) | 0.34757 (14) | 0.0282 | |
O6 | 0.30017 (15) | 0.31402 (12) | 0.44177 (10) | 0.0292 | |
C7 | 0.2137 (2) | 0.42186 (16) | 0.47876 (13) | 0.0271 | |
C8 | 0.2876 (2) | 0.54172 (17) | 0.43333 (14) | 0.0284 | |
O9 | 0.41116 (16) | 0.58753 (14) | 0.45530 (11) | 0.0382 | |
C10 | 0.2143 (3) | 0.4195 (2) | 0.59243 (14) | 0.0403 | |
C11 | 0.2581 (2) | 0.14034 (17) | 0.32652 (14) | 0.0278 | |
C12 | 0.3486 (2) | 0.10164 (19) | 0.24540 (15) | 0.0314 | |
C13 | 0.3662 (2) | −0.0280 (2) | 0.22427 (16) | 0.0349 | |
C14 | 0.2945 (3) | −0.11716 (19) | 0.28505 (15) | 0.0358 | |
C15 | 0.2066 (2) | −0.07955 (18) | 0.36660 (15) | 0.0345 | |
C16 | 0.1874 (2) | 0.04930 (19) | 0.38769 (15) | 0.0314 | |
C17 | −0.0516 (2) | 0.63951 (19) | 0.41789 (16) | 0.0359 | |
O18 | 0.02305 (17) | 0.66472 (14) | 0.51139 (11) | 0.0385 | |
H21 | 0.0028 | 0.5221 | 0.2934 | 0.0368* | |
H31 | −0.0301 | 0.4024 | 0.4712 | 0.0369* | |
H51 | 0.2780 | 0.3352 | 0.2917 | 0.0355* | |
H101 | 0.3207 | 0.4225 | 0.6174 | 0.0626* | |
H103 | 0.1573 | 0.4942 | 0.6146 | 0.0621* | |
H102 | 0.1635 | 0.3404 | 0.6145 | 0.0620* | |
H121 | 0.3978 | 0.1652 | 0.2045 | 0.0380* | |
H131 | 0.4316 | −0.0556 | 0.1653 | 0.0416* | |
H141 | 0.3061 | −0.2081 | 0.2710 | 0.0428* | |
H151 | 0.1588 | −0.1422 | 0.4102 | 0.0424* | |
H161 | 0.1248 | 0.0765 | 0.4455 | 0.0371* | |
H172 | −0.0541 | 0.7167 | 0.3741 | 0.0456* | |
H171 | −0.1605 | 0.6071 | 0.4292 | 0.0454* | |
H181 | −0.0132 | 0.7294 | 0.5413 | 0.0598* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0387 (7) | 0.0245 (6) | 0.0313 (7) | −0.0037 (6) | 0.0002 (6) | 0.0025 (5) |
C2 | 0.0337 (9) | 0.0244 (9) | 0.0343 (10) | 0.0014 (8) | −0.0037 (8) | −0.0015 (8) |
C3 | 0.0286 (9) | 0.0233 (9) | 0.0352 (10) | −0.0005 (8) | −0.0006 (8) | −0.0020 (8) |
O4 | 0.0290 (7) | 0.0240 (7) | 0.0513 (9) | 0.0010 (6) | −0.0099 (7) | −0.0079 (6) |
C5 | 0.0307 (9) | 0.0232 (9) | 0.0306 (10) | −0.0008 (7) | −0.0024 (8) | −0.0019 (7) |
O6 | 0.0303 (6) | 0.0239 (6) | 0.0335 (7) | 0.0014 (6) | −0.0054 (6) | −0.0044 (5) |
C7 | 0.0296 (9) | 0.0226 (8) | 0.0290 (9) | −0.0003 (8) | 0.0000 (8) | −0.0009 (7) |
C8 | 0.0335 (10) | 0.0226 (8) | 0.0292 (9) | −0.0013 (8) | 0.0028 (8) | −0.0053 (7) |
O9 | 0.0341 (7) | 0.0322 (7) | 0.0482 (8) | −0.0095 (6) | −0.0005 (7) | −0.0095 (7) |
C10 | 0.0500 (12) | 0.0428 (12) | 0.0282 (10) | 0.0028 (11) | 0.0006 (9) | 0.0014 (9) |
C11 | 0.0312 (9) | 0.0217 (8) | 0.0307 (9) | −0.0016 (7) | −0.0040 (8) | −0.0008 (7) |
C12 | 0.0320 (9) | 0.0276 (9) | 0.0345 (10) | −0.0016 (8) | 0.0004 (8) | 0.0022 (8) |
C13 | 0.0372 (10) | 0.0314 (10) | 0.0360 (11) | 0.0031 (9) | 0.0022 (9) | −0.0041 (8) |
C14 | 0.0418 (11) | 0.0245 (9) | 0.0411 (11) | 0.0017 (9) | −0.0031 (10) | −0.0014 (8) |
C15 | 0.0414 (10) | 0.0251 (9) | 0.0370 (10) | −0.0042 (9) | −0.0013 (9) | 0.0017 (8) |
C16 | 0.0350 (10) | 0.0283 (9) | 0.0308 (9) | −0.0015 (8) | 0.0014 (8) | 0.0013 (8) |
C17 | 0.0382 (10) | 0.0291 (10) | 0.0406 (11) | 0.0050 (9) | −0.0079 (10) | −0.0051 (9) |
O18 | 0.0442 (8) | 0.0326 (7) | 0.0385 (8) | 0.0078 (6) | −0.0058 (7) | −0.0091 (6) |
O1—C2 | 1.465 (2) | C10—H103 | 0.968 |
O1—C8 | 1.342 (2) | C10—H102 | 0.981 |
C2—C3 | 1.528 (3) | C11—C12 | 1.390 (3) |
C2—C17 | 1.511 (3) | C11—C16 | 1.392 (3) |
C2—H21 | 1.025 | C12—C13 | 1.394 (3) |
C3—O4 | 1.425 (2) | C12—H121 | 0.957 |
C3—C7 | 1.537 (3) | C13—C14 | 1.379 (3) |
C3—H31 | 0.988 | C13—H131 | 1.007 |
O4—C5 | 1.418 (2) | C14—C15 | 1.379 (3) |
C5—O6 | 1.422 (2) | C14—H141 | 0.974 |
C5—C11 | 1.502 (2) | C15—C16 | 1.387 (3) |
C5—H51 | 1.016 | C15—H151 | 0.967 |
O6—C7 | 1.438 (2) | C16—H161 | 0.981 |
C7—C8 | 1.530 (2) | C17—O18 | 1.422 (2) |
C7—C10 | 1.508 (2) | C17—H172 | 0.995 |
C8—O9 | 1.203 (2) | C17—H171 | 1.009 |
C10—H101 | 0.975 | O18—H181 | 0.844 |
C2—O1—C8 | 109.66 (14) | C7—C10—H103 | 106.8 |
O1—C2—C3 | 105.05 (15) | H101—C10—H103 | 110.3 |
O1—C2—C17 | 107.19 (15) | C7—C10—H102 | 108.1 |
C3—C2—C17 | 114.22 (17) | H101—C10—H102 | 110.2 |
O1—C2—H21 | 107.4 | H103—C10—H102 | 111.3 |
C3—C2—H21 | 111.2 | C5—C11—C12 | 120.49 (16) |
C17—C2—H21 | 111.3 | C5—C11—C16 | 119.63 (17) |
C2—C3—O4 | 112.06 (15) | C12—C11—C16 | 119.86 (17) |
C2—C3—C7 | 105.08 (15) | C11—C12—C13 | 120.03 (18) |
O4—C3—C7 | 104.91 (14) | C11—C12—H121 | 119.0 |
C2—C3—H31 | 110.9 | C13—C12—H121 | 120.9 |
O4—C3—H31 | 111.8 | C12—C13—C14 | 119.47 (19) |
C7—C3—H31 | 111.8 | C12—C13—H131 | 119.8 |
C3—O4—C5 | 107.37 (13) | C14—C13—H131 | 120.8 |
O4—C5—O6 | 105.05 (15) | C13—C14—C15 | 120.82 (19) |
O4—C5—C11 | 109.85 (15) | C13—C14—H141 | 120.1 |
O6—C5—C11 | 110.45 (15) | C15—C14—H141 | 119.0 |
O4—C5—H51 | 109.9 | C14—C15—C16 | 120.09 (18) |
O6—C5—H51 | 110.1 | C14—C15—H151 | 120.7 |
C11—C5—H51 | 111.3 | C16—C15—H151 | 119.2 |
C5—O6—C7 | 106.65 (13) | C11—C16—C15 | 119.71 (18) |
C3—C7—O6 | 104.08 (14) | C11—C16—H161 | 119.9 |
C3—C7—C8 | 103.21 (15) | C15—C16—H161 | 120.4 |
O6—C7—C8 | 107.03 (14) | C2—C17—O18 | 106.96 (16) |
C3—C7—C10 | 118.52 (17) | C2—C17—H172 | 108.2 |
O6—C7—C10 | 109.08 (16) | O18—C17—H172 | 111.6 |
C8—C7—C10 | 113.95 (16) | C2—C17—H171 | 109.5 |
C7—C8—O1 | 110.80 (15) | O18—C17—H171 | 110.7 |
C7—C8—O9 | 126.80 (18) | H172—C17—H171 | 109.8 |
O1—C8—O9 | 122.17 (17) | C17—O18—H181 | 113.1 |
C7—C10—H101 | 110.0 |
D—H···A | D—H | H···A | D···A | D—H···A |
C10—H103···O18 | 0.97 | 2.53 | 3.233 (3) | 130 |
C13—H131···O9i | 1.01 | 2.58 | 3.289 (3) | 128 |
C14—H141···O1ii | 0.97 | 2.59 | 3.340 (3) | 134 |
O18—H181···O9iii | 0.84 | 2.02 | 2.801 (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 formula | C13H14O5 |
Mr | 250.25 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 150 |
a, b, c (Å) | 8.6170 (2), 10.4615 (3), 13.2693 (5) |
V (Å3) | 1196.18 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.50 × 0.40 × 0.40 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.91, 0.96 |
No. of measured, independent and observed [I > 2.0σ(I)] reflections | 8306, 1547, 1369 |
Rint | 0.036 |
(sin θ/λ)max (Å−1) | 0.647 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.033, 0.075, 0.96 |
No. of reflections | 1547 |
No. of parameters | 163 |
H-atom treatment | H-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).
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−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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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.