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

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3-Azido-3-de­oxy-2,2′:5,6-di-O-iso­propyl­­idene-2-C-hydro­xmethyl-D-gulono-1,4-lactone

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aDepartment of Chemical Crystallography, Chemical Research Laboratory, Oxford University, Mansfield Road, Oxford OX1 3TA, England, and bDepartment of Organic Chemistry, Chemical Research Laboratory, Oxford University, Mansfield Road, Oxford OX1 3TA, England
*Correspondence e-mail: christopher.harding@seh.ox.ac.uk

(Received 22 October 2004; accepted 10 November 2004; online 20 November 2004)

The title azido­lactone, C13H19O6N3, formed by SN2 displacement of the tri­fluoro­methane­sulfonate with sodium azide, is the first example of a branched β-sugar amino acid scaffold.

Comment

Gellman (Lai & Gellman, 2003[Lai, J. R. & Gellman, S. H. (2003). Protein Sci. 12, 560-566.]; Hayen et al., 2004[Hayen, A., Schmitt, M. A., Ngassa, F. N., Thomasson, K. A. & Gellman, S. H. (2004). Angew. Chem. Int. Ed. 43, 505-510.]) and Seebach (Lelais & Seebach, 2003[Lelais, G. & Seebach, D. (2003). Helv. Chim. Acta, 86, 4152-4168.]; Rueping et al., 2004[Rueping, M., Mahajan, Y. R., Jaun, B. & Seebach, D. (2004). Chem. Eur. J. 10, 1607-1615.]) have pioneered studies on the exploitation of β-amino acids in their adoption of secondary structural features in short chains. Although sugar amino acids (SAA) have been extensively investigated as peptidomimetics and dipeptide isosteres (Schweizer, 2002[Schweizer, F. (2002). Angew. Chem. Int. Ed. 41, 230-253.]; Chakraborty et al., 2004[Chakraborty, T. K., Srinivasi, P., Tapadar, S. & Mohan, B. K. (2004). J. Chem. Sci. 116, 187-207.]), there have been very few studies of β-SAAs (Jenkinson & Fleet, 2004[Jenkinson, S. F. & Fleet, G. W. J. (2004). Tetrahedron Asymmetry, 15, 2667-2679.]; Johnson et al., 2004[Johnson, S. W., Jenkinson, S. F., Angus, D., Taillefumier, C., Jones, J. H. & Fleet, G. W. J. (2004). Tetrahedron Asymmetry, 15, 2681-2686.]), even though some oxetane-derived β-SAAs exhibited novel helical structures (Barker et al., 2001[Barker, S. F., Angus, D., Taillefumier, C., Probert, M. R., Watkin, D. J., Watterson, M. P., Claridge, T. D. W., Hungerford, N. L. & Fleet, G. W. J. (2001). Tetrahedron Lett. 42, 4247-4250.]). This paper reports the structure of the β-azido­lactone, (4[link]), which is a novel β-SAA scaffold containing a branched carbon chain.

[Scheme 1]

D-Fructose may be readily converted into the diacetonide (2[link]) (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. In the press.]); esterification of (2[link]) with triflic anhydride gave the corresponding stable tri­fluoro­methane­sulfonate. Reaction of (3[link]) with sodium azide in DMF gave an organic azide in good yield. The structure of this azide is fraught with uncertainties; the tri­fluoro­methane­sulfonate in (3[link]) has two β-O atoms and the adjacent α-C atom is trisubstituted, so the efficiency of the SN2 reaction is surprising. There is considerable ambiguity in the stereochemistry of the product, since there may well be neighbouring group participation by the O atom; it is also possible that some rearrangement that maintained the same connectivity of CH atoms may have occurred. However, X-ray crystallographic analysis of the product of the reaction showed that the anticipated inverted azide, (4[link]), had indeed been produced.

[Figure 1]
Figure 1
The title mol­ecule at 120 K, with displacement ellipsoids drawn at the 50% probability level. The large ellipsoids at atoms 07, C9 and C10 are discussed in the text. H atoms are shown as spheres of arbitrary radii.
[Figure 2]
Figure 2
The disordered fragment of the title mol­ecule at 120 K, displayed as a `split atom' model. Even with firm anisotropic displacement parameter similarity restraints, the ellipsoids do not conform to any reasonable physical model.
[Figure 3]
Figure 3
Fo electron density map viewed perpendicular to the line through atoms O7a and O7b, computed excluding phasing information derived from these two partial atoms. There are no distinct lobes near the two atom positions proposed by the `split atom' refinement, suggesting that there still remains substantial dynamic disorder.
[Figure 4]
Figure 4
Packing diagram of the title compound, viewed along the b axis.

Experimental

The full preparative method is not available for publication as yet. The sample was crystallized from diethyl ether by inward diffusion of n-hexane to give lath-shaped colourless crystals.

Crystal data
  • C13H19N3O6

  • Mr = 313.31

  • Monoclinic, P21

  • a = 8.7755 (2) Å

  • b = 7.6452 (2) Å

  • c = 12.2232 (3) Å

  • β = 106.9659 (11)°

  • V = 784.37 (3) Å3

  • Z = 2

  • Dx = 1.326 Mg m−3

  • Mo Kα radiation

  • Cell parameters from 1734 reflections

  • θ = 5–27°

  • μ = 0.11 mm−1

  • T = 120 K

  • Lath, colourless

  • 0.30 × 0.20 × 0.10 mm

Data collection
  • Nonius KappaCCD diffractometer

  • ω 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

  • 3320 measured reflections

  • 1869 independent reflections

  • 1655 reflections with I > 2σ(I)

  • Rint = 0.015

  • θmax = 27.5°

  • h = −11 → 11

  • k = −9 → 9

  • l = −15 → 15

Refinement
  • Refinement on F2

  • R[F2 > 2σ(F2)] = 0.045

  • wR(F2) = 0.109

  • S = 0.93

  • 1866 reflections

  • 200 parameters

  • H-atom parameters constrained

  • w = 1/[σ2(F) + (0.0522p)2 + 0.571p], where p = [max(Fo2,0) + 2Fc2]/3

  • (Δ/σ)max < 0.001

  • Δρmax = 0.65 e Å−3

  • Δρmin = −0.42 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.])

  • Extinction coefficient: 3.0 (5) × 102

Table 1
Selected interatomic distances (Å)

O5—C6 1.433 (3)
C6—O7 1.370 (5)
C6—C9 1.503 (6)
C6—C10 1.486 (7)
O7—C8 1.384 (4)

An initial data set was collected at 190 K. This gave reasonable refinement [Nmeasured = 2766, Rint = 0.02, Nref = 1748, Rw(2σ) = 0.081, R(2σ) = 0.034], though atoms O7, C9 and C10 had very elongated displacement ellipsoids. It was unclear whether the C6/O7/C9/C10 fragment should be modelled with large anisotropic displacement parameters (ADPs) or with `split atoms'. Refinement was continued with this fragment represented by `split atoms'. However, the ADPs could not be explained by a rational physical model. As with the unsplit model, the bond lengths deviated unacceptably from averages drawn by MOGUL (Bruno et al., 2004[Bruno, I. J., Cole, J. C., Kessler, M., Luo, J., Motherwell, W. D. S., Purkis, L. H., Smith, B. R., Taylor, R., Cooper, R. I., Harris, S. E. & Orpen, A. G. (2004). J. Chem. Inf. Comput. Sci. In the press.]) from the Cambridge Structural Database (CSD; Version 5.25; Allen, 2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]), even with the application of firm bond length similarity restraints.

In order to resolve this issue, data were recollected at 120 K. It is the result of this refinement that is reported in the CIF. Even at this temperature, the ADPs of the problematic group remained large, though not as large as in the 190 K data set. Both the large ADP and the `split atom' refinements continued to give unacceptable bond lengths and ellipsoids (see Fig. 2[link]). Fig. 3[link], plotted with MCE (Hušák & Kratochvíl, 2003[Hušák, M. & Kratochvíl, B. (2003). J. Appl. Cryst. 36, 1104.]), shows the observed electron density perpendicular to the line connecting atoms O7a and O7b. The map is phased by all of the structure except these two atoms, which are included for illustrative purposes at the positions they refine to in the `split atom' model. There is a smooth transition in electron density between the two sites, with no evident build-up of density at either site.

One interpretation of these observations is that neither the split atom model nor the large ADP model really represents what is occurring in this structure. It is clearly something more complicated than simply having the envelope flap (O7/O7a) distributed over two sites on opposite sides of a plane through the other ring atoms. Of 29 structures in the CSD containing this moiety some clearly have the atom corresponding to O7 as the `flap', some have C6 as the flap, but there are also a number in which no four atoms form a convincing plane. It seems that, even in the solid state, there is a continuum between an O-flap and a C-flap geometry. The amount of material available was insufficient to enable low-temperature solid-state NMR measurements to be carried out.

For the large ADP model, all H atoms were seen in the difference electron density map (even those on the highly anisotropic C9 and C10). Their positions and Uiso(H) values were regularized by several cycles of refinement using slack restraints, after which the refinement was completed using `riding' constraints and all reflections with I > −3σ(I). Fig. 4[link] is a packing diagram showing an alternation of highly mobile and highly ordered groups lying in a plane at approximately c/2.

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); 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.

Supporting information


Computing details top

Data collection: COLLECT (Nonius, 1997–2001); cell refinement: DENZO/SCALEPACK; data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: User-defined structure solution (reference?); 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.

3-Azido-3-deoxy-2,2':5,6-di-O-isopropylidene-2-C-hydroxmethyl-D– gulono-1,4-lactone top
Crystal data top
C13H19N3O6F(000) = 332
Mr = 313.31Dx = 1.326 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
a = 8.7755 (2) ÅCell parameters from 1734 reflections
b = 7.6452 (2) Åθ = 5–27°
c = 12.2232 (3) ŵ = 0.11 mm1
β = 106.9659 (11)°T = 120 K
V = 784.37 (3) Å3Plate, colourless
Z = 20.30 × 0.20 × 0.10 mm
Data collection top
Nonius KappaCCD
diffractometer
1655 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.015
ω scansθmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan
DENZO/SCALEPACK (Otwinowski & Minor, 1997)
h = 1111
Tmin = 0.98, Tmax = 0.99k = 99
3320 measured reflectionsl = 1515
1869 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.045 Method: SHELXL97 (Sheldrick, 1997); w = 1/[σ2(f) + (0.0522p)2 + 0.571p],
where p = [max(F02,0) + 2Fc2]/3
wR(F2) = 0.109(Δ/σ)max = 0.000326
S = 0.93Δρmax = 0.65 e Å3
1866 reflectionsΔρmin = 0.42 e Å3
200 parametersExtinction correction: Larson 1970 Crystallographic Computing eq 22
1 restraintExtinction coefficient: 300 (50)
Primary atom site location: structure-invariant direct methods
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.8173 (3)0.1205 (4)0.8704 (2)0.0207
C20.8728 (3)0.0356 (4)0.9895 (2)0.0197
C30.7808 (3)0.1387 (4)1.0574 (2)0.0214
C40.8684 (3)0.1553 (4)1.1835 (2)0.0253
O50.8788 (3)0.0165 (3)1.22982 (16)0.0306
C60.8328 (4)0.0098 (5)1.3330 (3)0.0349
O70.7463 (5)0.1409 (5)1.3271 (3)0.0777
C80.7788 (4)0.2612 (4)1.2524 (3)0.0345
C90.9801 (6)0.0021 (9)1.4333 (3)0.0762
C100.7390 (8)0.1702 (9)1.3373 (5)0.0891
O110.7642 (2)0.3122 (3)1.00698 (16)0.0251
C120.7805 (3)0.3076 (4)0.8996 (2)0.0234
O130.7649 (3)0.4350 (3)0.84141 (18)0.0315
N140.8584 (3)0.1555 (3)0.9887 (2)0.0219
N150.7245 (3)0.2124 (4)0.9845 (2)0.0267
N160.6106 (4)0.2828 (4)0.9831 (3)0.0454
O170.6748 (2)0.0412 (3)0.80306 (15)0.0223
C180.6968 (3)0.0131 (4)0.6948 (2)0.0246
O190.8643 (2)0.0228 (3)0.71573 (16)0.0250
C200.9322 (3)0.1103 (4)0.7966 (2)0.0252
C210.6301 (4)0.1943 (5)0.6674 (3)0.0338
C220.6235 (4)0.1233 (5)0.6046 (3)0.0408
H210.98480.06401.02290.0240*
H310.67120.08841.04450.0251*
H410.97530.20391.19480.0304*
H810.84970.35281.29670.0438*
H820.67890.31231.20550.0432*
H910.94080.00931.50090.0912*
H921.04380.10571.43700.0913*
H931.04440.10731.42510.0920*
H1010.71050.16591.40940.1170*
H1020.80530.27501.33280.1173*
H1030.64130.15631.27030.1167*
H2011.04000.07780.84110.0321*
H2020.93260.22180.75730.0317*
H2110.65430.23490.59790.0399*
H2120.67850.27420.73000.0403*
H2130.51510.19240.65280.0409*
H2210.64050.10210.53000.0487*
H2220.66030.24310.62790.0489*
H2230.50760.12060.59220.0491*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0206 (13)0.0191 (13)0.0222 (12)0.0012 (11)0.0061 (10)0.0002 (11)
C20.0206 (13)0.0182 (13)0.0199 (12)0.0019 (11)0.0051 (10)0.0009 (10)
C30.0215 (13)0.0186 (15)0.0256 (13)0.0009 (11)0.0090 (10)0.0002 (11)
C40.0289 (15)0.0252 (16)0.0223 (12)0.0017 (12)0.0084 (11)0.0032 (12)
O50.0445 (12)0.0282 (11)0.0235 (9)0.0034 (10)0.0166 (9)0.0017 (9)
C60.0495 (19)0.0342 (17)0.0279 (14)0.0014 (17)0.0220 (13)0.0011 (14)
O70.118 (3)0.069 (2)0.080 (2)0.051 (2)0.082 (2)0.0350 (19)
C80.0481 (19)0.0326 (18)0.0262 (14)0.0028 (15)0.0161 (14)0.0044 (13)
C90.086 (3)0.109 (5)0.0317 (18)0.019 (4)0.013 (2)0.001 (3)
C100.120 (5)0.089 (5)0.080 (4)0.047 (4)0.064 (4)0.009 (3)
O110.0307 (11)0.0208 (11)0.0253 (9)0.0038 (9)0.0106 (8)0.0001 (8)
C120.0244 (14)0.0229 (15)0.0225 (12)0.0005 (12)0.0063 (10)0.0013 (12)
O130.0395 (12)0.0238 (11)0.0315 (11)0.0066 (10)0.0106 (9)0.0059 (9)
N140.0187 (12)0.0206 (12)0.0266 (11)0.0017 (10)0.0069 (9)0.0019 (10)
N150.0279 (13)0.0217 (12)0.0320 (13)0.0018 (11)0.0109 (10)0.0010 (10)
N160.0334 (15)0.0299 (16)0.078 (2)0.0116 (13)0.0236 (15)0.0071 (16)
O170.0209 (9)0.0272 (11)0.0189 (8)0.0018 (8)0.0057 (7)0.0032 (8)
C180.0245 (13)0.0301 (15)0.0186 (11)0.0025 (13)0.0053 (10)0.0021 (12)
O190.0254 (10)0.0270 (11)0.0236 (9)0.0018 (9)0.0089 (7)0.0026 (8)
C200.0287 (14)0.0239 (14)0.0259 (13)0.0041 (13)0.0125 (11)0.0043 (12)
C210.0341 (16)0.0377 (19)0.0289 (14)0.0073 (15)0.0084 (12)0.0114 (14)
C220.0436 (18)0.054 (2)0.0262 (14)0.0194 (18)0.0116 (13)0.0104 (15)
Geometric parameters (Å, º) top
C1—C21.538 (4)C9—H931.004
C1—C121.531 (4)C10—H1010.984
C1—O171.417 (3)C10—H1021.001
C1—C201.539 (3)C10—H1031.004
C2—C31.533 (4)O11—C121.362 (3)
C2—N141.466 (4)C12—O131.190 (4)
C2—H210.973N14—N151.240 (3)
C3—C41.514 (4)N15—N161.131 (4)
C3—O111.452 (3)O17—C181.452 (3)
C3—H311.005C18—O191.419 (3)
C4—O51.423 (4)C18—C211.504 (5)
C4—C81.538 (4)C18—C221.518 (4)
C4—H410.981O19—C201.422 (3)
O5—C61.433 (3)C20—H2010.976
C6—O71.370 (5)C20—H2020.979
C6—C91.503 (6)C21—H2110.984
C6—C101.486 (7)C21—H2120.974
O7—C81.384 (4)C21—H2130.973
C8—H810.987C22—H2210.980
C8—H820.979C22—H2220.985
C9—H910.985C22—H2230.984
C9—H920.989
C2—C1—C12101.8 (2)C6—C9—H93109.937
C2—C1—O17110.6 (2)H91—C9—H93112.584
C12—C1—O17109.0 (2)H92—C9—H93110.192
C2—C1—C20116.9 (2)C6—C10—H101107.044
C12—C1—C20113.8 (2)C6—C10—H102108.749
O17—C1—C20104.8 (2)H101—C10—H102112.303
C1—C2—C3102.9 (2)C6—C10—H103103.516
C1—C2—N14114.3 (2)H101—C10—H103110.346
C3—C2—N14117.3 (2)H102—C10—H103114.253
C1—C2—H21107.763C3—O11—C12111.1 (2)
C3—C2—H21106.585C1—C12—O11109.7 (2)
N14—C2—H21107.444C1—C12—O13128.4 (2)
C2—C3—C4113.8 (2)O11—C12—O13121.9 (3)
C2—C3—O11104.1 (2)C2—N14—N15115.4 (2)
C4—C3—O11108.3 (2)N14—N15—N16172.0 (3)
C2—C3—H31110.457C1—O17—C18108.8 (2)
C4—C3—H31111.708O17—C18—O19104.9 (2)
O11—C3—H31108.048O17—C18—C21108.6 (2)
C3—C4—O5106.4 (2)O19—C18—C21107.9 (2)
C3—C4—C8114.4 (2)O17—C18—C22109.0 (2)
O5—C4—C8104.6 (2)O19—C18—C22111.4 (2)
C3—C4—H41110.832C21—C18—C22114.6 (3)
O5—C4—H41110.245C18—O19—C20106.8 (2)
C8—C4—H41110.109C1—C20—O19103.3 (2)
C4—O5—C6108.4 (2)C1—C20—H201112.385
O5—C6—O7106.2 (3)O19—C20—H201110.314
O5—C6—C9108.9 (3)C1—C20—H202109.886
O7—C6—C9108.9 (4)O19—C20—H202110.026
O5—C6—C10107.6 (3)H201—C20—H202110.659
O7—C6—C10113.0 (4)C18—C21—H211108.339
C9—C6—C10112.0 (4)C18—C21—H212110.490
C6—O7—C8112.1 (2)H211—C21—H212109.050
C4—C8—O7104.4 (3)C18—C21—H213110.056
C4—C8—H81109.437H211—C21—H213108.699
O7—C8—H81109.119H212—C21—H213110.158
C4—C8—H82113.777C18—C22—H221114.558
O7—C8—H82109.278C18—C22—H222113.225
H81—C8—H82110.606H221—C22—H222107.285
C6—C9—H91105.028C18—C22—H223107.279
C6—C9—H92109.043H221—C22—H223106.580
H91—C9—H92109.895H222—C22—H223107.508
 

Acknowledgements

Financial support (to RS) provided through the European Community's Human Potential Programme under contract HPRN-CT-2002-00173 is gratefully acknowledged.

References

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