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Volume 61 
Part 8 
Pages o2727-o2729  
August 2005  

Received 15 July 2005
Accepted 25 July 2005
Online 27 July 2005

Key indicators
Single-crystal X-ray study
T = 190 K
Mean [sigma](C-C) = 0.002 Å
R = 0.032
wR = 0.069
Data-to-parameter ratio = 10.2
Details

(2R,3S,4S,5R)-Methyl 5-cyano-2,3:4,5-di-O-isopropylidene-2,3,4,5-tetrahydroxypentanoate

aChemical Crystallography, Chemical Research Laboratory, University of Oxford, Oxford OX1 3TA, England, and bDepartment of Organic Chemistry, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England
Correspondence e-mail: david.watkin@chem.ox.ac.uk

The title nitrile, C13H19NO6, a formal oxidation product, was unexpectedly isolated during hydrogenation of an azide precursor in the presence of palladium black.

Comment

The azide group is synthetically important due to its ability to be reduced under a variety of conditions, thus permitting the controlled introduction of an amine functionality (Scriven & Turnbull, 1988[Scriven, E. F. V. & Turnbull, K. (1988). Chem. Rev. 88, 297-368.]). Further reagents for the reduction of azides to form amines and amides continue to be discovered (Fazio & Wong, 2003[Fazio, F. & Wong, C.-H. (2003). Tetrahedron Lett. 44, 9083-9085.]); ruthenium(III) has been shown to be an efficient promoter for the formation of amides from azides and thioacids (Shangguan et al., 2003[Shangguan, N., Katukojvala, S., Greenberg, R. & Williams, L. J. (2003). J. Am. Chem. Soc. 125, 7754-7755.]). Although catalytic hydrogenation is a particularly useful method of azide reduction, often providing excellent yields whilst leaving other sensitive functionalities intact, surprising complications are still discovered; thus catalytic reduction of a series of bicyclic azides (RN3) resulted in the formation of a number of azoamines (RN=N-NH2) arising from simple addition of hydrogen to the terminal nitrogen of the azide (Beacham et al., 1998[Beacham, A. R., Smelt, K. H., Biggadike, K., Britten, C. J., Hackett, L., Winchester, B. G., Nash, R. J., Griffiths, R. C. & Fleet, G. W. J. (1998). Tetrahedron Lett. 39, 151-154.]). When the azido ester (1) was hydrogenated in the presence of palladium black in 1,4-dioxan, the majority of the products were derived from the amino ester (2) (Mayes, Simon et al., 2004[Mayes, B. A., Simon, L., Watkin, D. J., Ansell, C. W. G. & Fleet, G. W. J. (2004). Tetrahedron Lett. 45, 157-162.]; Mayes, Stetz, Watterson et al., 2004[Mayes, B. A., Stetz, R. J. E., Watterson, M. P., Edwards, A. A., Ansell, C. W. G., Tranter, G. E. & Fleet, G. W. J. (2004). Tetrahedron Asymmetry, 15, 627-638.]; Mayes, Stetz, Ansell & Fleet, 2004[Mayes, B. A., Stetz, R. J. E., Ansell, C. W. G. & Fleet, G. W. J. (2004). Tetrahedron Lett. 45, 153-156.]). However, significant amounts of the nitrile (3) were also formed during the reduction; this is unexpected, since the formation of the nitrile appears to be a formal oxidation occurring under reducing conditions. Although previous examples of the catalytic decomposition of primary azides to nitriles have been reported (Hayashi et al., 1976[Hayashi, H., Ohno, A. & Oka, S. (1976). Bull. Chem. Soc. Jpn, 49, 506-509.]; Kappe, 1990[Kappe, C. O. (1990). Liebigs Ann. Chem. pp. 505-507.]; Kotsuki et al., 1997[Kotsuki, H., Ohishi, T. & Araki, T. (1997). Tetrahedron Lett. 38, 2129-2132.]), this is the first example of the formation of a nitrile being formed under hydrogenation conditions. The structure of the unexpected product (3), including the relative configuration at C-5 (atom C13) bearing the nitrile, was firmly established by X-ray crystallographic analysis (Fig. 1[link]); the absolute configuration arises from the use of D-galactose as the original starting material.

[Scheme 1]

The crystal structure of (3) is unexceptional, consisting of layers of molecules lying parallel to the ab plane (Fig. 2[link]). One face of the layer is relatively flat and consists of nitrile and methyl groups facing an identical face of the next layer. The other face of the layer is pleated, with the methyl carboxylate groups of one layer interleaving with the corresponding groups on the adjacent face. There are no unexpectedly short O-methyl or N-methyl contacts.

[Figure 1]
Figure 1
The title compound with displacement ellipsoids drawn at the 50% probability level. The H atoms are shown as spheres of arbitary radius.
[Figure 2]
Figure 2
Packing diagram of (3), viewed along the b axis.

Experimental

The azide ester (1) was hydrogenated in the presence of palladium black in 1,4-dioxan (Mayes, Simon et al., 2004[Mayes, B. A., Simon, L., Watkin, D. J., Ansell, C. W. G. & Fleet, G. W. J. (2004). Tetrahedron Lett. 45, 157-162.]) and the title material crystallized from ethyl acetate/hexane.

Crystal data
  • C13H19NO6

  • Mr = 285.30

  • Monoclinic, P 21

  • a = 10.4312 (3) Å

  • b = 5.4469 (1) Å

  • c = 13.0536 (5) Å

  • [beta] = 93.4825 (10)°

  • V = 740.31 (4) Å3

  • Z = 2

  • Dx = 1.280 Mg m-3

  • Mo K[alpha] radiation

  • Cell parameters from 1417 reflections

  • [theta] = 3-27°

  • [mu] = 0.10 mm-1

  • T = 190 K

  • Block, colourless

  • 0.80 × 0.50 × 0.30 mm

Data collection
  • Nonius KappaCCD diffractometer

  • [omega] scans

  • 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 = 0.87, Tmax = 0.97

  • 4978 measured reflections

  • 1848 independent reflections

  • 1848 reflections with I > -3[sigma](I)

  • Rint = 0.020

  • [theta]max = 27.5°

  • h = -13 [rightwards arrow] 13

  • k = -6 [rightwards arrow] 7

  • l = -16 [rightwards arrow] 16

Refinement
  • Refinement on F2

  • R[F2 > 2[sigma](F2)] = 0.032

  • wR(F2) = 0.069

  • S = 0.99

  • 1848 reflections

  • 182 parameters

  • H-atom parameters constrained

  • w = 1/[[sigma]2(F2) + (0.03P)2 + 0.15P] where P = [max(Fo2,0) + 2Fc2]/3

  • ([Delta]/[sigma])max < 0.001

  • [Delta][rho]max = 0.18 e Å-3

  • [Delta][rho]min = -0.15 e Å-3

  • Extinction correction: Larson (1970), equation 22

  • Extinction coefficient: 1.6 (3) × 102

Table 1
Selected geometric parameters (Å, °)[link]

C1-O2 1.456 (2)
O2-C3 1.3378 (18)
C3-O4 1.1996 (19)
C3-C5 1.521 (2)
C5-O6 1.4178 (18)
C5-C11 1.523 (2)
O6-C7 1.438 (2)
C7-C8 1.516 (2)
C7-C9 1.510 (2)
C7-O10 1.4461 (19)
O10-C11 1.4222 (18)
C11-C12 1.530 (2)
C12-C13 1.522 (2)
C12-O20 1.4235 (19)
C13-C14 1.490 (2)
C13-O16 1.420 (2)
C14-N15 1.136 (2)
O16-C17 1.443 (2)
C17-C18 1.513 (2)
C17-C19 1.510 (2)
C17-O20 1.439 (2)
C1-O2-C3 115.80 (12)
O2-C3-O4 123.87 (15)
O2-C3-C5 110.05 (12)
O4-C3-C5 126.05 (14)
C3-C5-O6 112.57 (12)
C3-C5-C11 113.63 (13)
O6-C5-C11 103.27 (12)
C5-O6-C7 109.03 (12)
O6-C7-C8 110.98 (15)
O6-C7-C9 108.91 (15)
C8-C7-C9 112.88 (15)
O6-C7-O10 105.41 (13)
C8-C7-O10 108.12 (13)
C9-C7-O10 110.29 (13)
C7-O10-C11 109.36 (12)
C5-C11-O10 103.10 (11)
C5-C11-C12 111.47 (12)
O10-C11-C12 110.98 (12)
C11-C12-C13 111.06 (12)
C11-C12-O20 110.43 (12)
C13-C12-O20 102.95 (11)
C12-C13-C14 112.31 (15)
C12-C13-O16 103.07 (13)
C14-C13-O16 111.41 (13)
C13-C14-N15 179.74 (19)
C13-O16-C17 107.76 (13)
O16-C17-C18 111.13 (16)
O16-C17-C19 108.22 (16)
C18-C17-C19 113.72 (16)
O16-C17-O20 104.95 (13)
C18-C17-O20 108.84 (14)
C19-C17-O20 109.61 (14)
C17-O20-C12 110.26 (12)

In the absence of significant anomalous scattering, Friedel pairs were merged, and the absolute configuration is arbitrarily assigned. The relatively large ratio of minimum to maximum corrections applied in the multiscan process (1:1.11) reflect changes in the illuminated volume of the crystal. 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 (C-H = 0.93-0.98 Å) and displacement parameters [Uiso(H) = 1.2-1.5Ueq(parent atom)], after which they were refined with riding constraints.

Data collection: COLLECT (Nonius, 2001[Nonius (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, England.]); software used to prepare material for publication: CRYSTALS.

References

Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435. [details]
Beacham, A. R., Smelt, K. H., Biggadike, K., Britten, C. J., Hackett, L., Winchester, B. G., Nash, R. J., Griffiths, R. C. & Fleet, G. W. J. (1998). Tetrahedron Lett. 39, 151-154. [CrossRef] [ChemPort]
Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487. [details]
Fazio, F. & Wong, C.-H. (2003). Tetrahedron Lett. 44, 9083-9085. [CrossRef] [ChemPort]
Hayashi, H., Ohno, A. & Oka, S. (1976). Bull. Chem. Soc. Jpn, 49, 506-509. [ChemPort]
Kappe, C. O. (1990). Liebigs Ann. Chem. pp. 505-507.
Kotsuki, H., Ohishi, T. & Araki, T. (1997). Tetrahedron Lett. 38, 2129-2132. [CrossRef] [ChemPort]
Mayes, B. A., Simon, L., Watkin, D. J., Ansell, C. W. G. & Fleet, G. W. J. (2004). Tetrahedron Lett. 45, 157-162. [ISI] [CSD] [CrossRef] [ChemPort]
Mayes, B. A., Stetz, R. J. E., Ansell, C. W. G. & Fleet, G. W. J. (2004). Tetrahedron Lett. 45, 153-156. [ISI] [CrossRef] [ChemPort]
Mayes, B. A., Stetz, R. J. E., Watterson, M. P., Edwards, A. A., Ansell, C. W. G., Tranter, G. E. & Fleet, G. W. J. (2004). Tetrahedron Asymmetry, 15, 627-638. [CrossRef] [ChemPort]
Nonius (2001). COLLECT. Nonius BV, Delft, The Netherlands.
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.
Scriven, E. F. V. & Turnbull, K. (1988). Chem. Rev. 88, 297-368. [CrossRef] [ChemPort] [ISI]
Shangguan, N., Katukojvala, S., Greenberg, R. & Williams, L. J. (2003). J. Am. Chem. Soc. 125, 7754-7755. [CrossRef] [PubMed] [ChemPort]
Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England.


Acta Cryst (2005). E61, o2727-o2729   [ doi:10.1107/S1600536805023834 ]