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Volume 62 
Part 1 
Pages o321-o323  
January 2006  

Received 25 November 2005
Accepted 13 December 2005
Online 21 December 2005

Key indicators
Single-crystal X-ray study
T = 250 K
Mean [sigma](C-C) = 0.006 Å
R = 0.047
wR = 0.129
Data-to-parameter ratio = 11.3
Details

2-C-Azidomethyl-2-deoxy-3,4-O-isopropylidene-D-ribono-1,5-lactone

aDipartimento di Scienze Chimiche, Facoltà di Farmacia, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy,bDepartment of Chemical Crystallography, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, and cDepartment of Organic Chemistry, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England
Correspondence e-mail: fpunzo@unict.it

X-ray crystallographic analysis firmly establishes the ribo stereochemistry and the unusual boat conformation of the title branched carbon chain lactone, C9H13N3O4, arising from an unexpected rearrangement in the nucleophilic substitution of a trifluoromethanesulfonate. There are two molecules in the asymmetric unit.

Comment

The Kiliani reaction of ketoses with cyanide (Hotchkiss et al., 2004[Hotchkiss, D., Soengas, R., Simone, M. I., van Ameijde, J., Hunter, S., Cowley, A. R. & Fleet, G. W. J. (2004). Tetrahedron Lett. 45, 9461-9464.]; Soengas et al., 2005[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.]) provides access to a novel class of carbohydrate scaffold which contains a branched carbon chain. Such sugar building blocks have hitherto been rare and difficult to prepare in large quantities (Bols, 1996[Bols, M. (1996). Carbohydrate Building Blocks. New York: John Wiley & Sons, Inc.]; Lichtenthaler & Peters, 2004[Lichtenthaler, F. W. & Peters, S. (2004). C. R. Chim. 7, 65-90.]). However, naturally occurring ketoses restrict the branched carbon chain to a hydroxymethyl group. A further class of branched carbohydrates is available from the Kiliani ascension on 1-deoxyketoses, themselves prepared by addition of organometallic reagents to sugar lactones. Thus, reaction of cyanide with a protected 1-deoxy-D-ribulose allowed the isolation of the isopropylidene derivative of arabinono-1,5-lactone, (1) (Hotchkiss et al., 2006[Hotchkiss, D. J., Jenkinson, S. F., Storer, R., Heinz, T. & Fleet, G. W. J. (2006). Tetrahedron Lett. 47, 315-318.]), shown to crystallize in a boat conformation (Punzo, Watkin, Jenkinson & Fleet, 2005[Punzo, F., Watkin, D. J., Jenkinson, S. F. & Fleet, G. W. J. (2005). Acta Cryst. E61, o127-129.]).

[Scheme 1]

The value of protected sugar lactones such as (1) depends on being able to modify the tertiary alcohol functionality to other groups. Thus, the esterification of the free alcohol (1) with triflic anhydride in pyridine afforded the trifluoromethanesulfonate, (2), which on further reaction with sodium azide in dimethylformamide gave the ribo-azide, (3), as the major product in good yield, even though the overall reaction is a nucleophilic displacement at a very hindered position. It was possible that neighbouring group participation by an O atom might have been involved in the reaction but the X-ray crystal structure (Punzo, Watkin, Jenkinson, Cruz & Fleet, 2005[Punzo, F., Watkin, D. J., Jenkinson, S. F., Cruz, F. P. & Fleet, G. W. J. (2005). Acta Cryst. E61, o511-o512.]) showed that the reaction proceeded with inversion of configuration to give the ribonolactone (3) in a boat conformation, with the C2-methyl group in a hindered flag-pole position. A small quantity of a second crystalline azide, the title compound, (4), was also isolated.

X-ray crystal-structure analysis of (4) firmly establishes that the relative configuration of the azidomethyl branch at C2 is in a bowsprit conformation. The absolute configuration of (4) was determined by the use of D-erythronolactone as the starting material for the synthesis. Azides (3) and (4) are likely to be useful building blocks for the synthesis of novel branched prolines and pipecolic acids, respectively.

In Fig. 2[link], a pseudo-translational operator of the form (0.48 + x, 0.48 + y, +z) is clearly detectable.

[Figure 1]
Figure 1
The asymmetric unit of (4), containing two molecules, with displacement ellipsoids drawn at the 50% probability level. H-atom radii are arbitrary.
[Figure 2]
Figure 2
A packing diagram of (4), viewed down the a axis.

Experimental

The title lactone, (4) {m.p. 365-367 K; [[alpha]]D23 -168.2% (c 1.0 in MeCN)}, was crystallized by dissolving it in ethyl acetate, adding cyclohexane and allowing slow competitive evaporation of the two solvents until clear colourless crystals formed. The multi-scan technique was used to correct for changes in the illuminated volume.

Crystal data
  • C9H13N3O4

  • Mr = 227.22

  • Monoclinic, P 21

  • a = 6.6145 (2) Å

  • b = 11.1194 (4) Å

  • c = 15.0252 (8) Å

  • [beta] = 91.6306 (13)°

  • V = 1104.65 (8) Å3

  • Z = 4

  • Dx = 1.366 Mg m-3

  • Mo K[alpha] radiation

  • Cell parameters from 2605 reflections

  • [theta] = 5-30°

  • [mu] = 0.11 mm-1

  • T = 250 K

  • Plate, colourless

  • 0.30 × 0.20 × 0.10 mm

Data collection
  • Bruker Nonius KappaCCD area-detector 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 = 0.98, Tmax = 0.99

  • 5623 measured reflections

  • 3275 independent reflections

  • 1944 reflections with I > 2[sigma](I)

  • Rint = 0.018

  • [theta]max = 29.9°

  • h = -9 [rightwards arrow] 9

  • k = -15 [rightwards arrow] 15

  • l = -21 [rightwards arrow] 21

Refinement
  • Refinement on F2

  • R[F2 > 2[sigma](F2)] = 0.047

  • wR(F2) = 0.129

  • S = 1.08

  • 3275 reflections

  • 290 parameters

  • H-atom parameters constrained

  • w = [1 - (Fo - Fc)2/36[sigma]2(F)]2/[38.7T0(x) + 61.9T1(x) + 38.9T2(x)] where Ti are Chebychev polynomials and x = Fc/Fmax (Prince, 1982[Prince, E. (1982). Mathematical Techniques in Crystallography and Materials Science. New York: Springer-Verlag.]; Watkin, 1994[Watkin, D. J. (1994). Acta Cryst. A50, 411-437.])

  • ([Delta]/[sigma])max < 0.001

  • [Delta][rho]max = 0.54 e Å-3

  • [Delta][rho]min = -0.52 e Å-3

  • Extinction correction: Larson (1970[Larson, A. C. (1970). Crystallographic Computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, pp. 291-294. Copenhagen: Munksgaard.]), eq. 22

  • Extinction coefficient: 1.0 (2) × 102

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

C5-C6 1.497 (6)
C21-C22 1.498 (6)
C2-C1-C6 111.9 (3)
C2-C1-O9 107.8 (3)
O9-C8-C11 111.4 (4)
C18-C17-C22 112.1 (3)
C18-C17-O25 107.6 (3)
C22-C17-O25 104.5 (3)
O20-C21-C22 110.4 (3)

In the absence of significant anomalous dispersion effects, Friedel pairs were merged before refinement. H atoms were seen in difference Fourier maps. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry [C-H in the range 0.93-98 Å and Uiso(H) in the range 1.2-1.5 times Ueq of the parent atom], after which their positions 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, C. 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, University of Oxford, England.]); software used to prepare material for publication: CRYSTALS.

Acknowledgements

Financial support (to FPC) provided by the Fundacao para a Ciencia e a Tecnologia, Portugal, 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] [details]
Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, C. K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487. [CrossRef] [details]
Bols, M. (1996). Carbohydrate Building Blocks. New York: John Wiley & Sons, Inc.
Hotchkiss, D. J., Jenkinson, S. F., Storer, R., Heinz, T. & Fleet, G. W. J. (2006). Tetrahedron Lett. 47, 315-318. [ISI] [CrossRef] [ChemPort]
Hotchkiss, D., Soengas, R., Simone, M. I., van Ameijde, J., Hunter, S., Cowley, A. R. & Fleet, G. W. J. (2004). Tetrahedron Lett. 45, 9461-9464. [ISI] [CrossRef] [ChemPort]
Larson, A. C. (1970). Crystallographic Computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, pp. 291-294. Copenhagen: Munksgaard.
Lichtenthaler, F. W. & Peters, S. (2004). C. R. Chim. 7, 65-90. [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.
Prince, E. (1982). Mathematical Techniques in Crystallography and Materials Science. New York: Springer-Verlag.
Punzo, F., Watkin, D. J., Jenkinson, S. F., Cruz, F. P. & Fleet, G. W. J. (2005). Acta Cryst. E61, o511-o512. [CrossRef] [details]
Punzo, F., Watkin, D. J., Jenkinson, S. F. & Fleet, G. W. J. (2005). Acta Cryst. E61, o127-129. [CrossRef] [details]
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. [ISI] [CrossRef] [ChemPort]
Watkin, D. J. (1994). Acta Cryst. A50, 411-437. [CrossRef] [details]
Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, University of Oxford, England.


Acta Cryst (2006). E62, o321-o323   [ doi:10.1107/S1600536805041632 ]