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Acta Crystallogr Sect E Struct Rep Online. 2010 May 1; 66(Pt 5): o1221–o1222.
Published online 2010 April 30. doi:  10.1107/S160053681001500X
PMCID: PMC2979260

2-Azido-2-de­oxy-3,4-O-isopropyl­idene-2-C-methyl-d-talono-1,5-lactone

Abstract

The relative stereochemistry of the title compound, C10H15N3O5, was confirmed by the crystal structure determin­ation. The absolute configuration was determined from the use of d-lyxonolactone as the starting material. The six-membered ring adopts a boat conformation with the larger azide group, rather than the methyl group, in the bowsprit position. In the crystal structure, a bifurcated inter­molecular O—H(...)O/O—H(...)N hydrogen bond links mol­ecules into chains running parallel to the b axis.

Related literature

For carbohydrates as chirons, see: Lichtenthaler & Peters (2004 [triangle]); Fechter et al. (1999 [triangle]); Fleet (1989 [triangle]). For branched sugars and their use as chirons, see: Rao et al. (2008 [triangle]); Jones et al. (2008 [triangle]); Booth et al. (2008 [triangle]); Hotchkiss, Kato et al. (2007 [triangle]); da Cruz et al. (2008 [triangle]); Soengas et al. (2005 [triangle]). For the structures of similar sugars, see: Chesterton et al. (2006 [triangle]); Booth et al. (2007 [triangle]); Hotchkiss, Jenkinson et al. (2007 [triangle]); Baird et al. (1987 [triangle]); Bruce et al. (1990 [triangle]); Punzo et al. (2005 [triangle]). For the extinction correction, see: Larson (1970 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o1221-scheme1.jpg

Experimental

Crystal data

  • C10H15N3O5
  • M r = 257.25
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1221-efi1.jpg
  • a = 5.9481 (3) Å
  • b = 13.3427 (7) Å
  • c = 15.6351 (9) Å
  • V = 1240.86 (12) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 150 K
  • 0.20 × 0.15 × 0.05 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 [triangle]) T min = 0.89, T max = 0.99
  • 10775 measured reflections
  • 1647 independent reflections
  • 1170 reflections with I > 2σ(I)
  • R int = 0.077

Refinement

  • R[F 2 > 2σ(F 2)] = 0.038
  • wR(F 2) = 0.087
  • S = 0.88
  • 1647 reflections
  • 164 parameters
  • H-atom parameters constrained
  • Δρmax = 0.53 e Å−3
  • Δρmin = −0.45 e Å−3

Data collection: COLLECT (Nonius, 2001 [triangle]).; cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994 [triangle]); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 [triangle]); molecular graphics: CAMERON (Watkin et al., 1996 [triangle]); software used to prepare material for publication: CRYSTALS.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053681001500X/lh5031sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053681001500X/lh5031Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Comment

Carbohydrates are a diverse set of chirons for the synthesis of complex amino acids and iminosugars (Lichtenthaler & Peters, 2004; Fechter et al., 1999; Fleet, 1989). 2-C-Methyl branched sugars constitute a class of rare sugars with chemotherapeutic potential (Rao et al., 2008; Jones et al., 2008; Booth et al., 2008) and can be used as building blocks in the synthesis of biologically active compounds (da Cruz et al., 2008; Hotchkiss, Kato et al., 2007; Soengas et al., 2005).

The azidolactone 3 (Fig. 1) would be a key intermediate for the synethsis of branched pyrrolidines, piperidines and prolines derived from D-lyxonolactone. Nucleophilic displacement of a triflate leaving group at the tertiary centre by azide was confirmed by X-ray crystallography to have proceeded with overall inversion of configuration (Booth et al. 2007; Hotchkiss, Jenkinson et al. 2007). The 6-membered lactone ring adopts a boat conformation, as is common with 3,4-O-isopropylidene-1,5-lactones (Baird et al., 1987; Bruce et al., 1990; Punzo et al., 2005), with the larger azide group, rather than the methyl, in the bowsprit position (Fig. 2). The absolute configuration was determined from the use of D-lyxonolactone as the starting material. As is common with these materials the azide is non linear [N7 - N8 - N9 = 172.4 (3) °] (Chesterton et al., 2006), with the anisotropic atomic displacement parameter of the central atom lowered with respect to its neighbours. The compound exists as hydrogen bonded chains of molecules running parallel to the b-axis (Fig. 3). The hydrogen bond is bifurcated. Only classical hydrogen bonding is considered.

Experimental

The title compound was recrystallised by slow evaporation from a mixture of diethyl ether and cyclohexane: m.p. 397-403 K, [α]D25 +112.4 (c, 1.145 in CHCl3).

Refinement

In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from the use of D-lyonolactone as the starting material.

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.

Figures

Fig. 1.
Synthetic Scheme
Fig. 2.
The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
Fig. 3.
Packing diagram for the title compound projected along the a-axis. Hydrogen bonds are shown by dotted lines.

Crystal data

C10H15N3O5F(000) = 544
Mr = 257.25Dx = 1.377 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1637 reflections
a = 5.9481 (3) Åθ = 5–27°
b = 13.3427 (7) ŵ = 0.11 mm1
c = 15.6351 (9) ÅT = 150 K
V = 1240.86 (12) Å3Plate, colourless
Z = 40.20 × 0.15 × 0.05 mm

Data collection

Nonius KappaCCD diffractometer1170 reflections with I > 2σ(I)
graphiteRint = 0.077
ω scansθmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)h = −7→7
Tmin = 0.89, Tmax = 0.99k = −17→17
10775 measured reflectionsl = −20→20
1647 independent reflections

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.038 Method = Modified Sheldrick w = 1/[σ2(F2) + ( 0.05P)2 + 0.16P], where P = [max(Fo2,0) + 2Fc2]/3
wR(F2) = 0.087(Δ/σ)max = 0.0003
S = 0.88Δρmax = 0.53 e Å3
1647 reflectionsΔρmin = −0.45 e Å3
164 parametersExtinction correction: Larson (1970), Equation 22
0 restraintsExtinction coefficient: 460 (60)
Primary atom site location: structure-invariant direct methods

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

xyzUiso*/Ueq
O10.4977 (3)0.87439 (12)0.79200 (10)0.0276
C20.5736 (5)0.85325 (19)0.87769 (16)0.0297
O30.7326 (3)0.77432 (13)0.86551 (10)0.0334
C40.8307 (4)0.78267 (17)0.78210 (15)0.0258
C50.6901 (4)0.86484 (17)0.73767 (14)0.0250
C60.6110 (4)0.83522 (18)0.64929 (15)0.0247
N70.4436 (4)0.91275 (16)0.62475 (14)0.0317
N80.3742 (4)0.90581 (16)0.55031 (15)0.0313
N90.2976 (4)0.90888 (18)0.48383 (15)0.0443
C100.4914 (4)0.73333 (18)0.65603 (15)0.0243
O110.3123 (3)0.71606 (13)0.62348 (11)0.0323
O120.5913 (3)0.66364 (12)0.70449 (11)0.0256
C130.8169 (4)0.68186 (17)0.73740 (16)0.0250
C140.8716 (5)0.59403 (17)0.79413 (17)0.0309
O150.8866 (3)0.50433 (11)0.74599 (11)0.0351
C160.8056 (4)0.83600 (19)0.58502 (16)0.0303
C170.6857 (5)0.9437 (2)0.91665 (18)0.0385
C180.3762 (5)0.8142 (2)0.92680 (19)0.0459
H410.99050.80320.78720.0311*
H510.77400.92840.73500.0310*
H1310.92350.68130.68880.0288*
H1411.01800.60750.82090.0398*
H1420.75520.58730.83880.0391*
H1610.74610.81670.52920.0461*
H1620.87070.90270.58180.0463*
H1630.92190.78930.60240.0460*
H1720.73910.92580.97300.0598*
H1710.57430.99720.92060.0603*
H1730.81130.96350.87970.0603*
H1820.42600.79570.98450.0690*
H1810.26040.86550.92970.0694*
H1830.31740.75590.89750.0688*
H1510.75910.47780.74530.0532*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0272 (9)0.0348 (9)0.0207 (8)0.0036 (8)−0.0008 (8)0.0009 (7)
C20.0358 (14)0.0323 (13)0.0209 (12)0.0025 (12)−0.0027 (11)−0.0011 (12)
O30.0480 (11)0.0305 (9)0.0217 (9)0.0089 (9)−0.0031 (8)0.0004 (8)
C40.0254 (13)0.0278 (12)0.0241 (13)−0.0041 (11)−0.0031 (10)0.0007 (11)
C50.0249 (12)0.0250 (12)0.0252 (12)0.0006 (10)−0.0006 (11)0.0016 (11)
C60.0253 (12)0.0255 (12)0.0233 (13)0.0057 (11)−0.0011 (11)0.0031 (10)
N70.0361 (12)0.0337 (11)0.0253 (11)0.0090 (10)−0.0035 (10)−0.0003 (10)
N80.0309 (12)0.0300 (11)0.0330 (13)0.0066 (10)0.0013 (11)0.0030 (11)
N90.0446 (14)0.0544 (16)0.0340 (14)0.0089 (13)−0.0105 (12)0.0052 (12)
C100.0210 (12)0.0297 (13)0.0221 (11)0.0039 (11)0.0023 (11)−0.0047 (11)
O110.0255 (9)0.0391 (10)0.0322 (10)−0.0029 (9)−0.0047 (8)−0.0022 (9)
O120.0228 (8)0.0246 (8)0.0293 (9)−0.0005 (7)−0.0023 (7)0.0012 (8)
C130.0192 (11)0.0267 (12)0.0292 (14)0.0008 (10)−0.0021 (11)0.0020 (11)
C140.0327 (14)0.0247 (12)0.0351 (14)0.0018 (12)−0.0044 (12)0.0045 (12)
O150.0297 (9)0.0248 (9)0.0509 (12)0.0035 (8)0.0037 (9)0.0003 (9)
C160.0318 (13)0.0317 (13)0.0274 (13)0.0010 (12)0.0036 (11)0.0049 (11)
C170.0484 (17)0.0374 (15)0.0297 (14)0.0015 (14)−0.0060 (14)−0.0059 (12)
C180.0446 (17)0.063 (2)0.0300 (16)−0.0052 (15)0.0033 (13)0.0041 (15)

Geometric parameters (Å, °)

O1—C21.442 (3)C10—O121.338 (3)
O1—C51.431 (3)O12—C131.458 (3)
C2—O31.428 (3)C13—C141.505 (3)
C2—C171.508 (4)C13—H1310.989
C2—C181.496 (4)C14—O151.417 (3)
O3—C41.433 (3)C14—H1410.983
C4—C51.544 (3)C14—H1420.987
C4—C131.518 (3)O15—H1510.837
C4—H410.993C16—H1610.977
C5—C61.512 (3)C16—H1620.972
C5—H510.985C16—H1630.969
C6—N71.486 (3)C17—H1720.967
C6—C101.538 (3)C17—H1710.976
C6—C161.533 (3)C17—H1730.981
N7—N81.238 (3)C18—H1820.981
N8—N91.136 (3)C18—H1810.972
C10—O111.203 (3)C18—H1830.969
C2—O1—C5106.47 (18)C4—C13—O12111.08 (19)
O1—C2—O3103.17 (18)C4—C13—C14114.0 (2)
O1—C2—C17110.9 (2)O12—C13—C14106.09 (19)
O3—C2—C17110.6 (2)C4—C13—H131109.0
O1—C2—C18107.4 (2)O12—C13—H131108.6
O3—C2—C18109.4 (2)C14—C13—H131108.0
C17—C2—C18114.7 (2)C13—C14—O15111.0 (2)
C2—O3—C4109.49 (17)C13—C14—H141107.5
O3—C4—C5104.14 (19)O15—C14—H141109.0
O3—C4—C13109.17 (18)C13—C14—H142109.6
C5—C4—C13113.14 (19)O15—C14—H142110.1
O3—C4—H41109.8H141—C14—H142109.7
C5—C4—H41111.0C14—O15—H151107.9
C13—C4—H41109.5C6—C16—H161108.1
C4—C5—O1103.26 (17)C6—C16—H162110.0
C4—C5—C6113.20 (19)H161—C16—H162109.8
O1—C5—C6108.46 (18)C6—C16—H163110.5
C4—C5—H51110.9H161—C16—H163109.9
O1—C5—H51110.7H162—C16—H163108.6
C6—C5—H51110.1C2—C17—H172108.4
C5—C6—N7105.21 (19)C2—C17—H171108.1
C5—C6—C10108.20 (19)H172—C17—H171110.3
N7—C6—C10108.84 (18)C2—C17—H173108.3
C5—C6—C16111.2 (2)H172—C17—H173110.7
N7—C6—C16109.39 (19)H171—C17—H173111.0
C10—C6—C16113.6 (2)C2—C18—H182108.8
C6—N7—N8114.5 (2)C2—C18—H181109.6
N7—N8—N9172.4 (3)H182—C18—H181110.4
C6—C10—O11123.4 (2)C2—C18—H183108.6
C6—C10—O12116.6 (2)H182—C18—H183110.0
O11—C10—O12120.0 (2)H181—C18—H183109.4
C10—O12—C13119.50 (19)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C5—H51···O15i0.992.283.141 (4)146
C13—H131···O11ii0.992.573.473 (4)152
C16—H161···O11iii0.982.463.333 (4)149
C16—H163···O11ii0.972.543.465 (4)159
O15—H151···O1iv0.842.142.930 (4)157
O15—H151···N7iv0.842.523.072 (4)125

Symmetry codes: (i) −x+2, y+1/2, −z+3/2; (ii) x+1, y, z; (iii) x+1/2, −y+3/2, −z+1; (iv) −x+1, y−1/2, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH5031).

References

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