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2-C-Hydro­xymethyl-2,3-O-iso­propyl­­idene-D-ribono-1,5-lactam

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aDepartment of Chemical Crystallography, Chemistry Research Laboratory, Oxford OX1 3TA, England, bDepartment of Organic Chemistry, Chemistry Research Laboratory, Oxford OX1 3TA, England, and cEcole Normale Supérieure, Département de Chimie, UMR 8642, 24 rue Lhomond, 75231 Paris Cedex 05, France
*Correspondence e-mail: christopher.newton@new.ox.ac.uk

(Received 22 March 2004; accepted 5 April 2004; online 30 April 2004)

The title compound, C9H14NO5, was formed by catalytic hydrogenation of an azido­lactone using Pd-black in 1,4-dioxane.

Comment

The replacement of the ring O atom of a carbohydrate by nitro­gen gives a range of sugar mimics (Winchester & Fleet, 1992[Winchester, B. & Fleet, G. W. J. (1992). Glycobiology, 2, 199-210.]), many of which are natural products widely spread in plants (Asano et al., 2000[Asano, N., Nash, R. J., Molyneux, R. J. & Fleet, G. W. J. (2000). Tetrahedron Asymm. 11, 1645-1680.]). Because of the multitude of potential biological activities, interest in understanding the structures in the search for transition-state analogues continues (Heck et al., 2004[Heck, M. P., Vincent, S. P., Murray, B. W., Bellamy, F., Wong, C. H. & Mioskowski, C. (2004). J. Am. Chem. Soc. 126, 1971-1979.]). Almost all of the natural products and their synthetic analogues contain straight carbon chains; however, there are some very promising indications that carbohydrate mimics with hydroxy­methyl branches (Ichikawa & Igarashi, 1995[Ichikawa, Y. & Igarashi, Y. (1995). Tetrahedron Lett. 36, 4586.]; Ichikawa et al., 1998[Ichikawa, Y., Igarashi, Y., Ichikawa, M. & Suhara, Y. (1998). J. Am. Chem. Soc. 120, 3007-3018.]), as well as their deoxy­genated equivalents (Lillelund et al., 2003[Lillelund, V. H., Liu, H. Z., Liang, X. F., Sohoel, H. & Bols, M. (2003). Org. Biomol. Chem. 1, 282-287.]; Ostrowski et al., 2003[Ostrowski, J., Altenbach, H. J., Wischnat, R. & Brauer, D. J. (2003). Eur. J. Org. Chem. pp. 1104-1110.]), will show significant inhibition of sugar-metabolizing enzymes. However, the chemistry of simple branched sugars as starting materials is little explored. The title compound, (3[link]), is a powerful intermediate in which a stereochemical ambiguity arises from an aldol reaction; additionally, information about the conformation of both protected and unprotected lactams may help to understand the basis of their biological activity.[link]

[Scheme 1]

The azido­lactol (1[link]) was prepared from D-ribose and submitted to the key aldol branching step. Subsequent oxidation of the aldol product with bromine water gave the branched azido­lactone (2[link]). Hydro­genation of (2[link]) resulted in initial reduction of the azide to the corresponding amine which underwent subsequent isomerization to the title lactam (3[link]). The X-ray crystal structure of (3[link]) removes any ambiguity about the course of the aldol condensation.

[Figure 1]
Figure 1
The molecular structure of (3), with 50% probability displacement ellipsoids.

Experimental

2-C-Hydroxymethyl-2,3-O-isopropylidene-D-ribono-1,5-lactam was obtained on reduction of 5-azido-2,3-O-isopropylidene-D-hamamelono-1,4-lactone, (2[link]), using Pd-black and hydrogen gas in 1,4-dioxane at low reaction concentration (2.5 mg ml−1). A quantitative yield of the title compound was obtained. The title material was then recrystallized using solvent evaporation (methanol), appearing as colourless block crystals.

Crystal data
  • C9H14NO5

  • Mr = 216.21

  • Orthorhombic, P212121

  • a = 7.3137 (1) Å

  • b = 10.6657 (2) Å

  • c = 12.6476 (3) Å

  • V = 986.59 (3) Å3

  • Z = 4

  • Dx = 1.456 Mg m−3

  • Mo Kα radiation

  • Cell parameters from 1329 reflections

  • θ = 5–27°

  • μ = 0.12 mm−1

  • T = 150 K

  • Block, colourless

  • 0.20 × 0.10 × 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 = 0.976, Tmax = 0.988

  • 2272 measured reflections

  • 1315 independent reflections

  • 1195 reflections with I > 2σ(I)

  • Rint = 0.01

  • θmax = 27.5°

  • h = −9 → 9

  • k = −13 → 13

  • l = −16 → 16

Refinement
  • Refinement on F2

  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 0.087

  • S = 0.98

  • 1315 reflections

  • 136 parameters

  • H-atom parameters constrained

  • w = 1/[σ2(F*) + (0.0403p)2 + 0.549p] where p = 0.333max(Fo2,0) + 0.667Fc2

  • (Δ/σ)max < 0.001

  • Δρmax = 0.44 e Å−3

  • Δρmin = −0.25 e Å−3

Table 1
Selected geometric parameters (Å, °)

C1—C14 1.528 (3)
C1—O11 1.428 (2)
C1—C6 1.531 (3)
C1—C2 1.521 (3)
C2—O9 1.432 (2)
C2—C3 1.513 (3)
C3—O8 1.431 (2)
C3—C4 1.517 (3)
C4—N5 1.473 (3)
N5—C6 1.331 (3)
C6—O7 1.259 (3)
O9—C10 1.438 (2)
C10—C13 1.513 (3)
C10—C12 1.512 (3)
C10—O11 1.444 (2)
C14—O15 1.419 (3)
C14—C1—O11 107.00 (17)
C14—C1—C6 110.38 (17)
O11—C1—C6 107.11 (16)
C14—C1—C2 114.23 (17)
O11—C1—C2 103.03 (16)
C6—C1—C2 114.30 (16)
O9—C2—C3 110.70 (16)
O9—C2—C1 102.89 (15)
C3—C2—C1 111.33 (17)
O8—C3—C4 109.83 (16)
O8—C3—C2 111.11 (16)
C4—C3—C2 109.97 (16)
N5—C4—C3 110.11 (16)
C6—N5—C4 125.82 (18)
O7—C6—N5 122.03 (19)
O7—C6—C1 118.13 (18)
N5—C6—C1 119.79 (18)
C10—O9—C2 108.04 (15)
C13—C10—C12 114.02 (19)
C13—C10—O11 107.24 (16)
C12—C10—O11 110.31 (17)
C13—C10—O9 111.49 (18)
C12—C10—O9 107.55 (17)
O11—C10—O9 105.94 (16)
C1—O11—C10 109.05 (14)
O15—C14—C1 109.28 (17)

H atoms were placed geometrically after each cycle, at a distance of 1.0 Å; Uiso values were set to 1.2 times the Ueq value of the parent atom. The absolute configuration was assumed to be the same as that of the sugar and the Friedel pairs were merged in the final refinement.

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[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); cell refinement: DENZO/SCALEPACK; data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1996); 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-C-Hydroxymethyl-2,3-O-isopropylidene-D-ribono-1,5-lactam top
Crystal data top
C9H14NO5Dx = 1.456 Mg m3
Mr = 216.21Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121Cell parameters from 1329 reflections
a = 7.3137 (1) Åθ = 5–27°
b = 10.6657 (2) ŵ = 0.12 mm1
c = 12.6476 (3) ÅT = 150 K
V = 986.59 (3) Å3Plate, colourless
Z = 40.20 × 0.10 × 0.10 mm
F(000) = 460
Data collection top
Nonius KappaCCD
diffractometer
1195 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.01
ω scansθmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1996)
h = 99
Tmin = 0.976, Tmax = 0.988k = 1313
2272 measured reflectionsl = 1616
1315 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.087 w = 1/[σ2(F*) + (0.0403p)2 + 0.549p]
where p = 0.333max(Fo2,0) + 0.667Fc2
S = 0.98(Δ/σ)max = 0.000238
1315 reflectionsΔρmax = 0.44 e Å3
136 parametersΔρmin = 0.25 e Å3
0 restraints
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.7866 (3)0.0035 (2)0.02895 (15)0.0188
C20.7198 (3)0.11166 (19)0.03931 (16)0.0193
C30.6725 (3)0.0679 (2)0.14980 (15)0.0201
C40.5206 (3)0.0288 (2)0.14517 (16)0.0229
N50.5697 (2)0.12992 (17)0.07111 (15)0.0231
C60.6915 (3)0.1217 (2)0.00682 (17)0.0206
O70.7278 (2)0.21316 (13)0.06611 (13)0.0263
O80.6178 (2)0.17082 (15)0.21510 (11)0.0246
O90.5593 (2)0.15309 (15)0.01535 (11)0.0233
C100.5842 (3)0.1282 (2)0.12615 (16)0.0202
O110.7351 (2)0.04121 (14)0.13309 (11)0.0213
C120.4107 (3)0.0679 (2)0.16656 (17)0.0270
C130.6394 (3)0.2453 (2)0.18566 (19)0.0292
C140.9941 (3)0.0134 (2)0.02935 (16)0.0218
O151.0513 (2)0.05872 (15)0.07082 (12)0.0291
H210.81290.18020.04920.0233*
H310.78380.02480.18130.0262*
H410.49800.06340.21730.0283*
H420.40590.01460.11990.0283*
H1210.42290.04890.24350.0338*
H1220.38900.01270.12690.0338*
H1230.30480.12530.15480.0338*
H1310.65550.22620.26250.0368*
H1320.75810.27800.15640.0368*
H1330.54320.31160.17720.0368*
H1411.05640.06870.04490.0264*
H1421.03050.07510.08660.0264*
H21.10000.13530.06680.0500*
H50.67670.15780.28580.0500*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0176 (10)0.0214 (9)0.0176 (9)0.0002 (8)0.0004 (8)0.0006 (8)
C20.0184 (9)0.0199 (9)0.0194 (9)0.0000 (8)0.0014 (8)0.0007 (8)
C30.0200 (9)0.0221 (10)0.0182 (9)0.0017 (8)0.0010 (8)0.0019 (8)
C40.0229 (10)0.0246 (11)0.0213 (10)0.0012 (9)0.0052 (9)0.0020 (8)
N50.0229 (8)0.0226 (8)0.0237 (8)0.0016 (8)0.0054 (8)0.0017 (8)
C60.0189 (9)0.0219 (9)0.0209 (10)0.0006 (8)0.0004 (8)0.0004 (8)
O70.0277 (8)0.0214 (7)0.0298 (8)0.0024 (7)0.0048 (7)0.0043 (6)
O80.0267 (8)0.0261 (8)0.0209 (7)0.0028 (7)0.0006 (6)0.0043 (6)
O90.0232 (7)0.0294 (8)0.0172 (7)0.0093 (7)0.0018 (6)0.0017 (6)
C100.0210 (10)0.0226 (10)0.0169 (9)0.0027 (9)0.0016 (8)0.0009 (8)
O110.0227 (7)0.0248 (7)0.0163 (6)0.0055 (7)0.0009 (6)0.0005 (6)
C120.0222 (10)0.0334 (12)0.0254 (11)0.0006 (10)0.0011 (9)0.0033 (10)
C130.0319 (12)0.0249 (11)0.0307 (11)0.0028 (10)0.0048 (10)0.0046 (10)
C140.0180 (9)0.0242 (10)0.0231 (10)0.0007 (9)0.0001 (9)0.0004 (9)
O150.0294 (8)0.0325 (8)0.0255 (8)0.0114 (7)0.0059 (7)0.0040 (7)
Geometric parameters (Å, º) top
C1—C141.528 (3)O8—H51.002
C1—O111.428 (2)O9—C101.438 (2)
C1—C61.531 (3)C10—C131.513 (3)
C1—C21.521 (3)C10—C121.512 (3)
C2—H211.007C10—O111.444 (2)
C2—O91.432 (2)C12—H1230.998
C2—C31.513 (3)C12—H1221.007
C3—H311.016C12—H1210.998
C3—O81.431 (2)C13—H1331.003
C3—C41.517 (3)C13—H1321.006
C4—H421.010C13—H1310.999
C4—H410.998C14—H1421.013
C4—N51.473 (3)C14—H1411.007
N5—C61.331 (3)C14—O151.419 (3)
C6—O71.259 (3)O15—H20.892
C14—C1—O11107.00 (17)H5—O8—C3106.752
C14—C1—C6110.38 (17)C10—O9—C2108.04 (15)
O11—C1—C6107.11 (16)C13—C10—C12114.02 (19)
C14—C1—C2114.23 (17)C13—C10—O11107.24 (16)
O11—C1—C2103.03 (16)C12—C10—O11110.31 (17)
C6—C1—C2114.30 (16)C13—C10—O9111.49 (18)
H21—C2—O9112.952C12—C10—O9107.55 (17)
H21—C2—C3105.327O11—C10—O9105.94 (16)
O9—C2—C3110.70 (16)C1—O11—C10109.05 (14)
H21—C2—C1113.805H123—C12—H122109.083
O9—C2—C1102.89 (15)H123—C12—H121109.798
C3—C2—C1111.33 (17)H122—C12—H121109.056
H31—C3—O8110.168H123—C12—C10109.863
H31—C3—C4107.155H122—C12—C10109.099
O8—C3—C4109.83 (16)H121—C12—C10109.920
H31—C3—C2108.516H133—C13—H132108.752
O8—C3—C2111.11 (16)H133—C13—H131109.264
C4—C3—C2109.97 (16)H132—C13—H131109.064
H42—C4—H41108.764H133—C13—C10109.966
H42—C4—N5109.677H132—C13—C10109.488
H41—C4—N5110.531H131—C13—C10110.279
H42—C4—C3107.994H142—C14—H141107.835
H41—C4—C3109.712H142—C14—O15109.835
N5—C4—C3110.11 (16)H141—C14—O15109.681
C6—N5—C4125.82 (18)H142—C14—C1109.874
O7—C6—N5122.03 (19)H141—C14—C1110.317
O7—C6—C1118.13 (18)O15—C14—C1109.28 (17)
N5—C6—C1119.79 (18)H2—O15—C14112.190
 

Acknowledgements

Financial support (to MIS), provided through the European Community's Human Potential Programme under contract HPRN-CT-2002-00173, 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 citationAsano, N., Nash, R. J., Molyneux, R. J. & Fleet, G. W. J. (2000). Tetrahedron Asymm. 11, 1645–1680.  Web of Science CrossRef CAS 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 citationHeck, M. P., Vincent, S. P., Murray, B. W., Bellamy, F., Wong, C. H. & Mioskowski, C. (2004). J. Am. Chem. Soc. 126, 1971–1979.  Web of Science CrossRef PubMed CAS Google Scholar
First citationIchikawa, Y. & Igarashi, Y. (1995). Tetrahedron Lett. 36, 4586.  Google Scholar
First citationIchikawa, Y., Igarashi, Y., Ichikawa, M. & Suhara, Y. (1998). J. Am. Chem. Soc. 120, 3007–3018.  Web of Science CrossRef CAS Google Scholar
First citationLillelund, V. H., Liu, H. Z., Liang, X. F., Sohoel, H. & Bols, M. (2003). Org. Biomol. Chem. 1, 282–287.  Web of Science CrossRef PubMed CAS Google Scholar
First citationNonius (1997–2001). COLLECT. Nonius BV, Delft, The Netherlands.  Google Scholar
First citationOstrowski, J., Altenbach, H. J., Wischnat, R. & Brauer, D. J. (2003). Eur. J. Org. Chem. pp. 1104–1110.  CSD CrossRef Google Scholar
First citationOtwinowski, 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.  Google Scholar
First citationWatkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England.  Google Scholar
First citationWinchester, B. & Fleet, G. W. J. (1992). Glycobiology, 2, 199–210.  CrossRef PubMed CAS Web of Science Google Scholar

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