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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

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

CROSSMARK_Color_square_no_text.svg

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: francesco.punzo@chemistry.oxford.ac.uk

(Received 22 December 2004; accepted 7 January 2005; online 29 January 2005)

The configuration of the title azide, C9H13N3O4, prepared from an arabinonolactone, is established by the X-ray crystal structure. The methyl group on the azide-substituted C atom is in a flagpole position. There are two mol­ecules in the asymmetric unit.

Comment

The potential of the Kiliani ascension of ketoses to provide readily available branched scaffolds has been recognized (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.]). A further class of branched carbo­hydrate building blocks may be available from the reaction of cyanide on 1-deoxy­ketoses, themselves prepared by addition of organometallic reagents to sugar lactones. The Kiliani ascension of a protected 1-deoxy-D-ribulose gave the arabinonolactone, (1[link]) (Punzo et al., 2005[Punzo, F., Watkin, D. J., Jenkinson, S. F. & Fleet, G. W. J. (2005). Acta Cryst. E61, o127-o129.]). The free hydroxyl group in (1[link]) was esterified with triflic anhydride and the resulting tri­fluoro­methane­sulfonate ester treated with sodium azide in di­methyl­form­amide. An azide was formed in good yield by nucleophilic displacement of the tri­fluoro­methane­sulfonate, even though the C atom C1 in (2[link]) is tertiary and highly sterically hindered. It is possible that neighbouring group participation by oxy­gen might be involved in the reaction, but the crystal structure shows that the reaction proceeds with clean inversion of configuration to give the ribonolactone (2[link]) in a boat conformation with the methyl group on C1 in the flagpole position (Fig. 1[link]). Elaboration of (2[link]) to a novel proline derivative is in progress. There are two mol­ecules in the asymmetric unit, related by a twofold axis of pseudosymmetry, of the form (1.29 − z, 1.24 − y, 1.08 − x), lying approximately parallel to [101]. Bond lengths and angles are normal. The crystal packing is shown in Fig. 2[link].[link]

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

Experimental

The sugar was crystallized by dissolving it in diethyl ether and allowing the slow evaporation of the solvent until clear colourless crystals formed.

Crystal data
  • C9H13N3O4

  • Mr = 227.22

  • Monoclinic, P21

  • a = 6.4862 (1) Å

  • b = 27.9310 (5) Å

  • c = 6.4787 (1) Å

  • β = 109.8940 (7)°

  • V = 1103.68 (3) Å3

  • Z = 4

  • Dx = 1.367 Mg m−3

  • Mo Kα radiation

  • Cell parameters from 2156 reflections

  • θ = 5–30°

  • μ = 0.11 mm−1

  • T = 120 K

  • Block, colourless

  • 0.60 × 0.40 × 0.30 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 and R. M. Sweet, pp. 307-326. New York: Academic Press.]) Tmin = 0.96, Tmax = 0.97

  • 5531 measured reflections

  • 3200 independent reflections

  • 2511 reflections with I > 2σ(I)

  • Rint = 0.016

  • θmax = 30.0°

  • h = −9 → 9

  • k = −39 → 36

  • l = −8 → 8

Refinement
  • Refinement on F2

  • R[F2 > 2σ(F2)] = 0.045

  • wR(F2) = 0.102

  • S = 0.99

  • 3200 reflections

  • 290 parameters

  • H-atom parameters constrained

  • w = 1/[σ2(F2) + 0.04 + 0.34P], where P = [max(Fo2,0) + 2Fc2]/3

  • (Δ/σ)max < 0.001

  • Δρmax = 0.31 e Å−3

  • Δρmin = −0.33 e Å−3

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

  • Extinction coefficient: 4.7 (8) × 102

In the absence of significant anomalous scattering effects, Friedel pairs were merged. The absolute configuration is known from the synthesis. H atoms were found in a difference density synthesis. 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 = 0.97–1.00 Å), after which they were refined as riding, with Uiso(H) = 1.2Ueq(C).

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 and 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.

Supporting information


Computing details top

Data collection: COLLECT (Nonius, 1997-2001); cell refinement: 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.

2-Azido-2-deoxy-3,4-O-isopropylidene-2-C-methyl-D-ribono-1,5-lactone top
Crystal data top
C9H13N3O4F(000) = 480
Mr = 227.22Dx = 1.367 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
a = 6.4862 (1) ÅCell parameters from 2156 reflections
b = 27.9310 (5) Åθ = 5–30°
c = 6.4787 (1) ŵ = 0.11 mm1
β = 109.8940 (7)°T = 120 K
V = 1103.68 (3) Å3Block, colourless
Z = 40.60 × 0.40 × 0.30 mm
Data collection top
Nonius KappaCCD
diffractometer
2511 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.016
ω scansθmax = 30.0°, θmin = 5.3°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
h = 99
Tmin = 0.96, Tmax = 0.97k = 3936
5531 measured reflectionsl = 88
3200 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 w = 1/[σ2(F2) + 0.04 + 0.34P],
where P = [max(Fo2,0) + 2Fc2]/3
wR(F2) = 0.102(Δ/σ)max = 0.001
S = 0.99Δρmax = 0.31 e Å3
3200 reflectionsΔρmin = 0.33 e Å3
290 parametersExtinction correction: Larson (1970), equation 22
1 restraintExtinction coefficient: 470 (80)
Primary atom site location: structure-invariant direct methods
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.4360 (4)0.27602 (10)0.6243 (4)0.0262
C20.2608 (4)0.23935 (10)0.5058 (4)0.0270
C30.0828 (4)0.25922 (10)0.2974 (5)0.0291
O40.1094 (3)0.23142 (7)0.1227 (3)0.0325
C50.2153 (4)0.18818 (10)0.2154 (4)0.0293
O60.3620 (3)0.20184 (7)0.4252 (3)0.0328
C70.0525 (6)0.15158 (12)0.2377 (6)0.0463
C80.3449 (6)0.17048 (12)0.0748 (5)0.0434
C90.1202 (5)0.31068 (11)0.2503 (5)0.0372
O100.3468 (4)0.32017 (7)0.2781 (3)0.0379
C110.5067 (5)0.30414 (10)0.4566 (5)0.0324
O120.6941 (4)0.31213 (8)0.4754 (4)0.0430
N130.6274 (4)0.25200 (10)0.7844 (4)0.0333
N140.7362 (4)0.22497 (10)0.7068 (4)0.0314
N150.8515 (4)0.19952 (10)0.6648 (4)0.0396
C160.3527 (5)0.30998 (11)0.7654 (5)0.0360
C170.8089 (4)0.46134 (10)0.6214 (5)0.0273
C180.6928 (4)0.49833 (10)0.4474 (4)0.0294
C190.4854 (5)0.47874 (10)0.2701 (5)0.0289
O200.3122 (3)0.50613 (7)0.2990 (3)0.0346
C210.4034 (5)0.54973 (10)0.4053 (5)0.0337
O220.6145 (3)0.53574 (7)0.5500 (3)0.0371
C230.4252 (6)0.58654 (12)0.2415 (6)0.0463
C240.2662 (6)0.56632 (13)0.5386 (6)0.0500
C250.4397 (5)0.42676 (10)0.2975 (5)0.0325
O260.4665 (3)0.41594 (7)0.5246 (3)0.0322
C270.6411 (5)0.43277 (10)0.6880 (5)0.0297
O280.6555 (4)0.42482 (8)0.8745 (4)0.0455
N290.9703 (4)0.48479 (10)0.8150 (4)0.0344
N300.8940 (4)0.51152 (10)0.9228 (4)0.0300
N310.8510 (4)0.53727 (10)1.0379 (4)0.0399
C320.9515 (5)0.42758 (13)0.5388 (6)0.0442
H210.19200.22690.60550.0328*
H310.06540.25580.30300.0339*
H710.13930.12320.29640.0535*
H720.01660.16560.33620.0535*
H730.05270.14590.09320.0535*
H910.07440.33220.34560.0446*
H920.03210.31690.09810.0446*
H1610.46330.33540.83080.0466*
H1620.21370.32540.67950.0466*
H1630.32470.29170.88620.0466*
H1810.79890.51180.38510.0354*
H1910.48690.48480.11600.0359*
H2310.49420.61600.32080.0526*
H2320.27370.59270.14260.0526*
H2330.51400.57420.15460.0526*
H2510.28570.41970.20930.0398*
H2520.53590.40640.24870.0398*
H3211.01550.40170.64820.0571*
H3221.07510.44590.52210.0571*
H3230.86640.41320.39480.0571*
H810.42120.13990.13740.0518*
H820.45600.19510.07300.0518*
H830.24320.16470.07830.0518*
H2410.32710.59700.61490.0587*
H2420.11180.57160.43930.0587*
H2430.26880.54130.65000.0587*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0277 (12)0.0304 (14)0.0235 (13)0.0038 (11)0.0126 (10)0.0058 (11)
C20.0260 (12)0.0299 (14)0.0262 (13)0.0026 (11)0.0103 (10)0.0032 (11)
C30.0275 (12)0.0303 (15)0.0289 (14)0.0063 (11)0.0088 (11)0.0031 (11)
O40.0349 (10)0.0304 (11)0.0271 (10)0.0090 (8)0.0042 (8)0.0011 (8)
C50.0286 (12)0.0264 (14)0.0266 (14)0.0011 (11)0.0014 (10)0.0003 (11)
O60.0318 (10)0.0228 (9)0.0348 (11)0.0029 (8)0.0002 (8)0.0028 (8)
C70.0476 (18)0.0388 (18)0.0447 (19)0.0134 (15)0.0056 (15)0.0077 (15)
C80.0477 (18)0.0397 (17)0.0416 (18)0.0159 (14)0.0138 (14)0.0023 (14)
C90.0503 (18)0.0293 (15)0.0322 (15)0.0091 (13)0.0143 (13)0.0011 (12)
O100.0610 (14)0.0283 (11)0.0302 (11)0.0060 (10)0.0229 (11)0.0004 (9)
C110.0433 (15)0.0241 (13)0.0365 (16)0.0068 (12)0.0225 (13)0.0119 (12)
O120.0464 (12)0.0360 (12)0.0594 (14)0.0108 (10)0.0348 (11)0.0077 (10)
N130.0266 (11)0.0462 (15)0.0276 (12)0.0015 (10)0.0098 (9)0.0085 (11)
N140.0249 (11)0.0415 (15)0.0253 (12)0.0080 (11)0.0052 (9)0.0041 (11)
N150.0278 (12)0.0488 (16)0.0424 (15)0.0020 (12)0.0124 (11)0.0072 (13)
C160.0450 (16)0.0381 (16)0.0315 (15)0.0014 (13)0.0217 (13)0.0069 (13)
C170.0242 (12)0.0318 (15)0.0275 (14)0.0035 (10)0.0107 (11)0.0004 (11)
C180.0306 (13)0.0328 (15)0.0250 (13)0.0038 (11)0.0097 (11)0.0028 (11)
C190.0325 (13)0.0280 (14)0.0258 (14)0.0006 (11)0.0095 (11)0.0008 (11)
O200.0300 (10)0.0289 (11)0.0398 (12)0.0005 (8)0.0052 (9)0.0097 (9)
C210.0318 (13)0.0253 (14)0.0341 (16)0.0016 (11)0.0015 (12)0.0030 (12)
O220.0408 (11)0.0235 (10)0.0333 (11)0.0037 (9)0.0054 (9)0.0047 (8)
C230.0531 (19)0.0325 (16)0.045 (2)0.0098 (15)0.0057 (16)0.0094 (14)
C240.0519 (19)0.0393 (18)0.056 (2)0.0026 (16)0.0146 (17)0.0203 (16)
C250.0354 (14)0.0306 (15)0.0336 (15)0.0011 (12)0.0146 (12)0.0016 (12)
O260.0347 (10)0.0284 (10)0.0371 (11)0.0004 (8)0.0167 (9)0.0038 (9)
C270.0371 (14)0.0231 (13)0.0336 (16)0.0055 (11)0.0183 (12)0.0030 (11)
O280.0691 (15)0.0387 (13)0.0342 (12)0.0038 (11)0.0246 (11)0.0051 (10)
N290.0269 (11)0.0446 (15)0.0295 (13)0.0083 (11)0.0067 (10)0.0002 (11)
N300.0262 (11)0.0381 (14)0.0235 (12)0.0027 (10)0.0058 (9)0.0061 (10)
N310.0418 (14)0.0483 (16)0.0297 (14)0.0034 (12)0.0125 (11)0.0000 (12)
C320.0372 (15)0.0495 (19)0.0491 (19)0.0117 (14)0.0186 (14)0.0092 (15)
Geometric parameters (Å, º) top
C1—C21.528 (4)C17—C181.526 (4)
C1—C111.532 (4)C17—C271.525 (4)
C1—N131.480 (4)C17—N291.485 (4)
C1—C161.538 (4)C17—C321.539 (4)
C2—C31.550 (4)C18—C191.541 (4)
C2—O61.426 (3)C18—O221.422 (4)
C2—H210.967C18—H1810.983
C3—O41.431 (3)C19—O201.423 (3)
C3—C91.506 (4)C19—C251.504 (4)
C3—H310.979C19—H1911.016
O4—C51.418 (3)O20—C211.425 (3)
C5—O61.420 (3)C21—O221.426 (3)
C5—C71.512 (4)C21—C231.518 (5)
C5—C81.517 (4)C21—C241.508 (5)
C7—H710.972C23—H2310.992
C7—H720.977C23—H2320.988
C7—H730.965C23—H2330.994
C8—H811.000C24—H2411.000
C8—H821.000C24—H2421.000
C8—H831.000C24—H2431.000
C9—O101.443 (4)C25—O261.453 (4)
C9—H910.979C25—H2510.987
C9—H920.972C25—H2520.974
O10—C111.340 (4)O26—C271.345 (4)
C11—O121.200 (4)C27—O281.201 (4)
N13—N141.250 (3)N29—N301.235 (4)
N14—N151.130 (3)N30—N311.137 (4)
C16—H1610.996C32—H3211.000
C16—H1620.983C32—H3220.988
C16—H1631.002C32—H3230.994
C2—C1—C11109.8 (2)C18—C17—C27110.1 (2)
C2—C1—N13110.6 (2)C18—C17—N29110.8 (2)
C11—C1—N13110.3 (2)C27—C17—N29111.0 (2)
C2—C1—C16111.2 (2)C18—C17—C32111.2 (2)
C11—C1—C16110.9 (2)C27—C17—C32110.4 (2)
N13—C1—C16104.1 (2)N29—C17—C32103.3 (2)
C1—C2—C3113.8 (2)C17—C18—C19113.3 (2)
C1—C2—O6108.7 (2)C17—C18—O22108.5 (2)
C3—C2—O6104.1 (2)C19—C18—O22104.4 (2)
C1—C2—H21109.8C17—C18—H181108.9
C3—C2—H21109.6C19—C18—H181112.7
O6—C2—H21110.7O22—C18—H181108.8
C2—C3—O4103.9 (2)C18—C19—O20103.8 (2)
C2—C3—C9113.2 (2)C18—C19—C25114.3 (2)
O4—C3—C9106.7 (2)O20—C19—C25107.9 (2)
C2—C3—H31112.4C18—C19—H191112.1
O4—C3—H31111.1O20—C19—H191108.1
C9—C3—H31109.3C25—C19—H191110.2
C3—O4—C5107.4 (2)C19—O20—C21107.8 (2)
O4—C5—O6104.3 (2)O20—C21—O22103.4 (2)
O4—C5—C7111.3 (2)O20—C21—C23111.3 (2)
O6—C5—C7110.6 (2)O22—C21—C23110.4 (3)
O4—C5—C8108.1 (2)O20—C21—C24108.1 (2)
O6—C5—C8109.5 (2)O22—C21—C24109.2 (2)
C7—C5—C8112.6 (3)C23—C21—C24113.9 (3)
C2—O6—C5107.8 (2)C21—O22—C18108.1 (2)
C5—C7—H71105.0C21—C23—H231109.4
C5—C7—H72106.4C21—C23—H232105.2
H71—C7—H72113.9H231—C23—H232111.4
C5—C7—H73107.7C21—C23—H233111.7
H71—C7—H73111.7H231—C23—H233109.5
H72—C7—H73111.6H232—C23—H233109.5
C5—C8—H81109.5C21—C24—H241109.6
C5—C8—H82109.3C21—C24—H242109.5
H81—C8—H82109.5H241—C24—H242109.5
C5—C8—H83109.6C21—C24—H243109.3
H81—C8—H83109.5H241—C24—H243109.5
H82—C8—H83109.5H242—C24—H243109.5
C3—C9—O10112.2 (2)C19—C25—O26111.1 (2)
C3—C9—H91110.8C19—C25—H251109.0
O10—C9—H91108.9O26—C25—H251107.1
C3—C9—H92107.3C19—C25—H252110.6
O10—C9—H92108.4O26—C25—H252109.8
H91—C9—H92109.2H251—C25—H252109.3
C9—O10—C11120.2 (2)C25—O26—C27120.2 (2)
C1—C11—O10116.9 (2)C17—C27—O26116.8 (2)
C1—C11—O12124.1 (3)C17—C27—O28124.2 (3)
O10—C11—O12119.0 (3)O26—C27—O28119.0 (3)
C1—N13—N14116.5 (2)C17—N29—N30116.2 (2)
N13—N14—N15170.9 (3)N29—N30—N31171.2 (3)
C1—C16—H161110.2C17—C32—H321110.5
C1—C16—H162111.9C17—C32—H322109.1
H161—C16—H162108.5H321—C32—H322107.3
C1—C16—H163110.1C17—C32—H323111.6
H161—C16—H163109.1H321—C32—H323109.6
H162—C16—H163106.9H322—C32—H323108.7
 

Footnotes

Visiting Scientist at the Department of Chemical Crystallography, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England

Acknowledgements

Financial support (to FPC) provided by the Fundacao para a Ciencia e a Tecnologia of Portugal is gratefully acknowledged.

References

First citationAltomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.  CrossRef Web of Science IUCr Journals Google Scholar
First citationBetteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.  Web of Science CrossRef IUCr Journals Google Scholar
First citationHotchkiss, D., Soengas, R., Simone, M. I., van Ameijde, J., Hunter, S., Cowley, A. R. & Fleet, G. W. J. (2004). Tetrahedron Lett. 45, 9461–9464.  Web of Science CrossRef CAS Google Scholar
First citationLarson, A. C. (1970). Crystallographic Computing, edited by F. R. Ahmed, S. R. Hall and C. P. Huber, pp. 291–294. Copenhagen: Munksgaard.  Google Scholar
First citationNonius (2001). COLLECT. Nonius BV, Delft, The Netherlands.  Google Scholar
First citationOtwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr and R. M. Sweet, pp. 307–326. New York: Academic Press.  Google Scholar
First citationPunzo, F., Watkin, D. J., Jenkinson, S. F. & Fleet, G. W. J. (2005). Acta Cryst. E61, o127–o129.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationWatkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England.  Google Scholar

© International Union of Crystallography. Prior permission is not required to reproduce short quotations, tables and figures from this article, provided the original authors and source are cited. For more information, click here.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds