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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o1972.
Published online 2009 July 25. doi:  10.1107/S1600536809028657
PMCID: PMC2977377

5-Azido-4-benz­yloxy-2-meth­oxy-6-methyl­perhydro­pyran-3-ol

Abstract

In the title compound, C14H19N3O4, the perhydro­pyran ring adopts a chair conformation. An intra­molecular C—H(...)O hydrogen bond generates an S(6) ring motif. In the crystal packing, mol­ecules are linked by O—H(...)O hydrogen bonds, forming infinite chains along [100].

Related literature

For background to d-perosamine, see: Jacquinet (2006 [triangle]). For the synthesis of d-perosamine, see: Krishna & Agrawal (2000 [triangle]). For metabolites, see: Grond et al. (2000 [triangle]). For ring conformations, see: Cremer & Pople (1975 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 [triangle]).

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Object name is e-65-o1972-scheme1.jpg

Experimental

Crystal data

  • C14H19N3O4
  • M r = 293.32
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1972-efi1.jpg
  • a = 4.6662 (2) Å
  • b = 15.3356 (8) Å
  • c = 20.9273 (12) Å
  • V = 1497.54 (13) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 100 K
  • 0.27 × 0.11 × 0.08 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.773, T max = 0.980
  • 13029 measured reflections
  • 1742 independent reflections
  • 1334 reflections with I > 2σ(I)
  • R int = 0.096

Refinement

  • R[F 2 > 2σ(F 2)] = 0.049
  • wR(F 2) = 0.103
  • S = 1.09
  • 1742 reflections
  • 196 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.23 e Å−3
  • Δρmin = −0.20 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809028657/ng2616sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809028657/ng2616Isup2.hkl

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

Acknowledgments

HKF and WSL thank Universiti Sains Malaysia (USM) for the Research University Golden Goose Grant (1001/PFIZIK/811012). WSL thanks USM for a student assistantship.

supplementary crystallographic information

Comment

4-Amino-4,6-dideoxy-D-mannose (D-perosamine) was first discovered in the polyene macrolide antibiotic perimycin and was later recognized to be present in the lipopolysaccharide (LPS) of Vivrio cholera (Jacquinet, 2006). Methyl 3-benzyloxy-4-azido-α-D-rhamnopyranoside is an important intermediate in the synthesis of D-perosamine (Krishna & Agrawal, 2000). Rhamnopyranosides were detected as metabolites from five different strains of Streptomycetes (Grond et al., 2000).

The bond lengths (Allen et al., 1987) and angles in the molecule (Fig. 1) are within normal ranges. The perhydropyran ring adopts a chair conformation. The puckering parameters (Cremer & Pople, 1975) are Q = 0.540 (3) Å; Θ = 8.0 (3)° and [var phi] = 8.0 (2)°. Intramolecular C7—H7B···O2 hydrogen bonds formed a six-membered ring, producing an S(6) ring motif (Bernstein et al., 1995). The dihedral angle formed between the benzene (C1—C6) and perhydropyran (C8—C10/O4/C11/C12) rings is 57.32 (16)°.

In the crystal packing (Fig. 2), the molecules are linked by intermolecular O2—H1O2···O2 and O2—H1O2···O3 hydrogen bonds (Table 1) into an infinite one-dimensional chains along the [100] direction.

Experimental

To a stirred mixture of methyl 3-benzyloxy-4-methoxysulfonyl-α-D-rhamnopyranoside (0.50 g, 1.4 mmol) in DMF (5.0 ml) was added sodium azide (0.18 g, 2.8 mmol). The reaction mixture was stirred further at room temperature for 12 h. TLC (30% EtOAc/hexane, Rf-0.5) analysis showed complete conversion. The reaction mixture was concentrated under vacuum and the residue was purified by column chromatography using 25% ethylacetate in petroleum ether to get pure product as colourless crystals (yield: 300.0 mg, 71%, M.p. 376–378 K).

Refinement

Atom H1O2 was located in a difference map and was refined freely. Other H atoms were positioned geometrically [C—H = 0.93 to 0.98 Å] and was refined using a riding model, with Uiso(H) = 1.2 or 1.5 Ueq(C). A rotating-group model was applied for the methyl groups. In the absence of significant anomalous dispersion, 1187 Friedel pairs were merged for the final refinement.

Figures

Fig. 1.
The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom numbering scheme. Intramolecular interaction is shown by dashed line.
Fig. 2.
The crystal packing of the title compound, viewed along a axis. Intermolecular hydrogen bonds are shown by dashed lines.

Crystal data

C14H19N3O4F(000) = 624
Mr = 293.32Dx = 1.301 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1880 reflections
a = 4.6662 (2) Åθ = 2.4–29.9°
b = 15.3356 (8) ŵ = 0.10 mm1
c = 20.9273 (12) ÅT = 100 K
V = 1497.54 (13) Å3Block, colourless
Z = 40.27 × 0.11 × 0.08 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer1742 independent reflections
Radiation source: fine-focus sealed tube1334 reflections with I > 2σ(I)
graphiteRint = 0.096
[var phi] and ω scansθmax = 26.0°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −5→5
Tmin = 0.773, Tmax = 0.980k = −18→17
13029 measured reflectionsl = −25→25

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.103H atoms treated by a mixture of independent and constrained refinement
S = 1.09w = 1/[σ2(Fo2) + (0.0499P)2] where P = (Fo2 + 2Fc2)/3
1742 reflections(Δ/σ)max < 0.001
196 parametersΔρmax = 0.23 e Å3
0 restraintsΔρmin = −0.20 e Å3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

xyzUiso*/Ueq
O10.0881 (4)0.40074 (13)0.13521 (10)0.0229 (5)
O20.0911 (5)0.28256 (14)0.02574 (11)0.0251 (5)
O30.3176 (5)0.39026 (14)−0.06657 (9)0.0236 (5)
O4−0.0200 (5)0.49881 (14)−0.04434 (10)0.0250 (5)
N10.3572 (6)0.56890 (17)0.10102 (12)0.0260 (7)
N20.3482 (6)0.56020 (18)0.16023 (14)0.0306 (7)
N30.3680 (9)0.5600 (2)0.21422 (15)0.0537 (11)
C10.2228 (8)0.2487 (2)0.26646 (17)0.0341 (9)
H1A0.35170.21000.24790.041*
C20.1203 (8)0.2318 (2)0.32682 (17)0.0389 (9)
H2A0.17950.18200.34850.047*
C3−0.0706 (8)0.2888 (3)0.35523 (17)0.0379 (9)
H3A−0.14050.27760.39600.045*
C4−0.1561 (9)0.3619 (2)0.32269 (16)0.0362 (9)
H4A−0.28560.40030.34130.043*
C5−0.0489 (8)0.3786 (2)0.26165 (16)0.0314 (9)
H5A−0.10510.42890.24020.038*
C60.1390 (7)0.3216 (2)0.23289 (15)0.0245 (7)
C70.2586 (8)0.3380 (2)0.16733 (16)0.0309 (9)
H7A0.45410.35900.17080.037*
H7B0.26070.28400.14310.037*
C80.1803 (7)0.4219 (2)0.07207 (14)0.0209 (7)
H8A0.38370.40730.06750.025*
C90.1415 (7)0.51995 (19)0.06387 (14)0.0193 (7)
H9A−0.04980.53610.07910.023*
C100.1727 (7)0.5493 (2)−0.00515 (14)0.0215 (7)
H10A0.37030.5397−0.01930.026*
C110.0416 (7)0.4086 (2)−0.04432 (15)0.0241 (8)
H11A−0.09650.3794−0.07230.029*
C120.0088 (7)0.37161 (19)0.02287 (15)0.0214 (7)
H12A−0.19410.37540.03470.026*
C130.3436 (8)0.4054 (3)−0.13393 (15)0.0361 (9)
H13A0.53090.3880−0.14800.054*
H13B0.31590.4662−0.14270.054*
H13C0.20120.3720−0.15620.054*
C140.0949 (9)0.6437 (2)−0.01442 (16)0.0364 (9)
H14A0.11460.6588−0.05870.055*
H14B0.22030.67950.01070.055*
H14C−0.09970.6530−0.00120.055*
H1O2−0.060 (8)0.251 (2)0.0151 (15)0.028 (10)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0225 (12)0.0219 (12)0.0243 (11)0.0014 (10)0.0055 (10)0.0037 (10)
O20.0200 (12)0.0185 (12)0.0368 (13)−0.0030 (11)0.0015 (11)−0.0055 (10)
O30.0222 (11)0.0283 (13)0.0205 (11)0.0038 (11)−0.0013 (10)−0.0046 (10)
O40.0249 (12)0.0218 (12)0.0282 (12)0.0030 (11)−0.0041 (10)−0.0033 (10)
N10.0301 (16)0.0255 (17)0.0224 (16)−0.0079 (14)0.0009 (14)−0.0004 (12)
N20.0360 (17)0.0250 (17)0.0307 (19)−0.0096 (14)−0.0032 (15)−0.0024 (13)
N30.084 (3)0.049 (2)0.0274 (18)−0.028 (2)−0.0075 (19)−0.0015 (15)
C10.036 (2)0.032 (2)0.035 (2)0.0072 (17)0.0014 (17)0.0053 (17)
C20.044 (2)0.032 (2)0.040 (2)0.003 (2)0.000 (2)0.0127 (18)
C30.040 (2)0.045 (2)0.0295 (19)−0.002 (2)0.0026 (18)0.0106 (18)
C40.040 (2)0.036 (2)0.0329 (19)0.0034 (19)0.0131 (19)0.0041 (17)
C50.038 (2)0.0257 (19)0.0300 (19)0.0002 (18)0.0039 (18)0.0061 (16)
C60.0246 (18)0.0220 (18)0.0267 (17)−0.0019 (16)−0.0029 (16)0.0018 (15)
C70.0305 (19)0.031 (2)0.0315 (19)0.0135 (17)0.0029 (16)0.0033 (16)
C80.0170 (16)0.0213 (18)0.0244 (17)−0.0001 (15)0.0013 (15)0.0015 (14)
C90.0197 (16)0.0150 (16)0.0233 (16)0.0001 (14)0.0031 (15)−0.0037 (13)
C100.0238 (17)0.0185 (17)0.0224 (16)−0.0001 (15)0.0005 (15)−0.0037 (14)
C110.0224 (16)0.0213 (18)0.0286 (18)−0.0019 (15)−0.0045 (15)−0.0047 (15)
C120.0153 (15)0.0157 (16)0.0333 (18)0.0017 (14)0.0013 (15)−0.0062 (14)
C130.035 (2)0.052 (2)0.0214 (17)0.004 (2)−0.0043 (18)−0.0014 (17)
C140.052 (2)0.028 (2)0.0291 (19)0.0020 (19)0.0024 (19)0.0017 (16)

Geometric parameters (Å, °)

O1—C71.418 (4)C5—H5A0.9300
O1—C81.427 (4)C6—C71.502 (4)
O2—C121.420 (3)C7—H7A0.9700
O2—H1O20.88 (4)C7—H7B0.9700
O3—C111.398 (4)C8—C121.515 (4)
O3—C131.434 (4)C8—C91.524 (4)
O4—C111.412 (4)C8—H8A0.9800
O4—C101.443 (4)C9—C101.520 (4)
N1—N21.247 (4)C9—H9A0.9800
N1—C91.477 (4)C10—C141.505 (4)
N2—N31.134 (4)C10—H10A0.9800
C1—C21.375 (5)C11—C121.524 (4)
C1—C61.376 (5)C11—H11A0.9800
C1—H1A0.9300C12—H12A0.9800
C2—C31.382 (5)C13—H13A0.9600
C2—H2A0.9300C13—H13B0.9600
C3—C41.371 (5)C13—H13C0.9600
C3—H3A0.9300C14—H14A0.9600
C4—C51.396 (5)C14—H14B0.9600
C4—H4A0.9300C14—H14C0.9600
C5—C61.378 (5)
C7—O1—C8115.1 (2)N1—C9—C10106.5 (2)
C12—O2—H1O2107 (2)N1—C9—C8111.2 (3)
C11—O3—C13111.9 (2)C10—C9—C8112.8 (2)
C11—O4—C10113.5 (2)N1—C9—H9A108.7
N2—N1—C9116.5 (3)C10—C9—H9A108.7
N3—N2—N1171.1 (4)C8—C9—H9A108.7
C2—C1—C6121.5 (3)O4—C10—C14107.0 (3)
C2—C1—H1A119.2O4—C10—C9108.8 (2)
C6—C1—H1A119.2C14—C10—C9112.6 (3)
C1—C2—C3120.0 (3)O4—C10—H10A109.5
C1—C2—H2A120.0C14—C10—H10A109.5
C3—C2—H2A120.0C9—C10—H10A109.5
C4—C3—C2119.4 (3)O3—C11—O4112.6 (3)
C4—C3—H3A120.3O3—C11—C12109.0 (3)
C2—C3—H3A120.3O4—C11—C12110.2 (3)
C3—C4—C5120.1 (3)O3—C11—H11A108.3
C3—C4—H4A120.0O4—C11—H11A108.3
C5—C4—H4A120.0C12—C11—H11A108.3
C6—C5—C4120.7 (3)O2—C12—C8108.5 (2)
C6—C5—H5A119.6O2—C12—C11111.7 (2)
C4—C5—H5A119.6C8—C12—C11112.6 (3)
C1—C6—C5118.3 (3)O2—C12—H12A107.9
C1—C6—C7119.8 (3)C8—C12—H12A107.9
C5—C6—C7121.9 (3)C11—C12—H12A107.9
O1—C7—C6109.8 (3)O3—C13—H13A109.5
O1—C7—H7A109.7O3—C13—H13B109.5
C6—C7—H7A109.7H13A—C13—H13B109.5
O1—C7—H7B109.7O3—C13—H13C109.5
C6—C7—H7B109.7H13A—C13—H13C109.5
H7A—C7—H7B108.2H13B—C13—H13C109.5
O1—C8—C12110.8 (2)C10—C14—H14A109.5
O1—C8—C9107.0 (2)C10—C14—H14B109.5
C12—C8—C9111.3 (3)H14A—C14—H14B109.5
O1—C8—H8A109.2C10—C14—H14C109.5
C12—C8—H8A109.2H14A—C14—H14C109.5
C9—C8—H8A109.2H14B—C14—H14C109.5
C9—N1—N2—N3−177 (2)C12—C8—C9—C10−47.1 (4)
C6—C1—C2—C3−0.2 (6)C11—O4—C10—C14175.5 (3)
C1—C2—C3—C40.0 (6)C11—O4—C10—C9−62.7 (3)
C2—C3—C4—C5−0.5 (6)N1—C9—C10—O4176.0 (2)
C3—C4—C5—C61.2 (6)C8—C9—C10—O453.7 (3)
C2—C1—C6—C50.9 (5)N1—C9—C10—C14−65.6 (3)
C2—C1—C6—C7179.4 (3)C8—C9—C10—C14172.2 (3)
C4—C5—C6—C1−1.4 (5)C13—O3—C11—O4−70.6 (3)
C4—C5—C6—C7−179.8 (3)C13—O3—C11—C12166.9 (2)
C8—O1—C7—C6−179.9 (3)C10—O4—C11—O3−59.5 (3)
C1—C6—C7—O1163.7 (3)C10—O4—C11—C1262.4 (3)
C5—C6—C7—O1−17.8 (5)O1—C8—C12—O2−71.0 (3)
C7—O1—C8—C1298.3 (3)C9—C8—C12—O2170.1 (3)
C7—O1—C8—C9−140.2 (3)O1—C8—C12—C11164.8 (2)
N2—N1—C9—C10173.4 (3)C9—C8—C12—C1145.9 (3)
N2—N1—C9—C8−63.3 (4)O3—C11—C12—O2−51.3 (3)
O1—C8—C9—N172.2 (3)O4—C11—C12—O2−175.3 (2)
C12—C8—C9—N1−166.7 (2)O3—C11—C12—C871.1 (3)
O1—C8—C9—C10−168.2 (2)O4—C11—C12—C8−52.9 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H1O2···O2i0.88 (4)1.91 (3)2.757 (2)161 (3)
O2—H1O2···O3i0.88 (3)2.49 (3)3.063 (3)124 (3)
C7—H7B···O20.972.583.180 (4)120

Symmetry codes: (i) x−1/2, −y+1/2, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NG2616).

References

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  • Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst.19, 105–107.
  • Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc.97, 1354–1358.
  • Grond, S., Langer, H. J., Henne, P., Sattler, I., Thiericke, R., Grabley, S., Zähner, H. & Zeeck, A. (2000). Eur. J. Chem. pp. 929–937.
  • Jacquinet, J. C. (2006). Carbohydr. Res.341, 1630–1644. [PubMed]
  • Krishna, N. R. & Agrawal, P. K. (2000). Adv. Carbohydr. Chem. Biochem.56, 201–234. [PubMed]
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  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

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