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

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N-Benzyl-1,3-dide­­oxy-1,3-imino-L-xylitol

aDepartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England, and bDepartment of Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England
*Correspondence e-mail: sarah.jenkinson@chem.ox.ac.uk

(Received 16 August 2011; accepted 19 August 2011; online 27 August 2011)

The structure determination confirms the stereochemistry of the title compound, C12H17NO3, which contains a four-membered azetidine ring system. The absolute configuration was determined by the use of D-glucose as the starting material. In the crystal, O—H⋯O and O—H⋯N hydrogen bonds link the mol­ecules into layers in the ab plane.

Related literature

For related literature on azetidines, see: Krämer et al. (1997[Krämer, B., Franz, T., Picasso, S., Pruschek, P. & Jäger, V. (1997). Synlett, pp. 295-297.]); Michaud et al. (1997a[Michaud, T., Chanet-Ray, J., Chou, S. & Gelas, J. (1997a). Carbohydr. Res. 299, 253-269.],b[Michaud, T., Chanet-Ray, J., Chou, S. & Gelas, J. (1997b). Carbohydr. Res. 303, 123-127.]); Dekaris & Reissig (2010[Dekaris, V. & Reissig, H.-U. (2010). Synlett, pp. 42-46.]); Soengas et al. (2011[Soengas, R. G., Segade, Y., Jiménez, C. & Rodríguez, J. (2011). Tetrahedron, 67, 2617-2622.]). For related literature on imino­sugars, see: Asano et al. (2000[Asano, N., Nash, R. J., Molyneux, R. J. & Fleet, G. W. J. (2000). Tetrahedron Asymmetry, 11, 1645-1680.]); Watson et al. (2001[Watson, A. A., Fleet, G. W. J., Asano, N., Molyneux, R. J. & Nash, R. J. (2001). Phytochemistry, 56, 265-295.]). For details of the cryostat, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]).

[Scheme 1]

Experimental

Crystal data
  • C12H17NO3

  • Mr = 223.27

  • Orthorhombic, P 21 21 21

  • a = 6.2309 (2) Å

  • b = 9.3918 (4) Å

  • c = 19.9175 (9) Å

  • V = 1165.56 (8) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 150 K

  • 0.20 × 0.10 × 0.07 mm

Data collection
  • Nonius KappaCCD diffractometer

  • 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 = 0.97, Tmax = 0.99

  • 6149 measured reflections

  • 1541 independent reflections

  • 1098 reflections with I > 2σ(I)

  • Rint = 0.065

Refinement
  • R[F2 > 2σ(F2)] = 0.045

  • wR(F2) = 0.102

  • S = 0.95

  • 1541 reflections

  • 146 parameters

  • H-atom parameters constrained

  • Δρmax = 0.49 e Å−3

  • Δρmin = −0.49 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O4—H41⋯O16i 0.84 2.18 2.825 (4) 134
O16—H161⋯O1ii 0.84 1.90 2.735 (4) 171
O1—H11⋯N6i 0.86 1.86 2.719 (4) 171
Symmetry codes: (i) [-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) [-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}].

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 & 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


Comment top

Azetidines (Michaud et al., 1997a,b; Dekaris & Reissig, 2010; Soengas et al., 2011) are a relatively unstudied class of iminosugars (Asano et al., 2000; Watson et al., 2001) but initial results (Krämer et al., 1997) have shown that they can exhibit interesting biological activity. The title compound was formed from a protected ribofuranose derived from D-glucose (Fig. 1).

The molecular structure of the title compound is shown in Fig. 2. The four-membered ring system adopts a puckered conformation. The structure consists of hydrogen bonded layers of molecules in the ab plane (Fig. 3, Fig. 4). Each molecule is a hydrgen-bond donor and acceptor for three hydrogen bonds. Only classical hydrogen bonding was considered.

Related literature top

For related literature on azetidines, see: Krämer et al. (1997); Michaud et al. (1997a,b); Dekaris & Reissig (2010); Soengas et al. (2011). For related literature on iminosugars, see: Asano et al. (2000); Watson et al. (2001). For details of the cryostat, see: Cosier & Glazer (1986).

Experimental top

The title compound was recrystallized from methanol: [α]D25 -103.0 (c 0.23 in MeOH); m.p. 452–453 K.

Refinement top

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

The H atoms were all located in a difference map, but 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 in the range 0.93–0.98, N—H in the range 0.86–0.89 N—H to 0.86 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.

Computing details top

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); 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 (Betteridge et al., 2003).

Figures top
[Figure 1] Fig. 1. Synthetic Scheme.
[Figure 2] Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
[Figure 3] Fig. 3. Packing diagram of the compound projected along the a axis. Hydrogen bonding is denoted by dotted lines.
[Figure 4] Fig. 4. Packing diagram of the compound projected along the b axis. Hydrogen bonding is denoted by dotted lines.
N-Benzyl-1,3-dideoxy-1,3-imino-L-xylitol top
Crystal data top
C12H17NO3F(000) = 480
Mr = 223.27Dx = 1.272 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1467 reflections
a = 6.2309 (2) Åθ = 5–27°
b = 9.3918 (4) ŵ = 0.09 mm1
c = 19.9175 (9) ÅT = 150 K
V = 1165.56 (8) Å3Prism, colourless
Z = 40.20 × 0.10 × 0.07 mm
Data collection top
Nonius KappaCCD
diffractometer
1098 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.065
ω scansθmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
h = 88
Tmin = 0.97, Tmax = 0.99k = 1212
6149 measured reflectionsl = 2525
1541 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 = modified Sheldrick, w = 1/[σ2(F2) + (0.05P)2 + 0.13P],
where P = [max(Fo2,0) + 2Fc2]/3
wR(F2) = 0.102(Δ/σ)max = 0.0002627
S = 0.95Δρmax = 0.49 e Å3
1541 reflectionsΔρmin = 0.49 e Å3
146 parametersExtinction correction: Larson (1970), Equation 22
0 restraintsExtinction coefficient: 400 (70)
Primary atom site location: structure-invariant direct methods
Crystal data top
C12H17NO3V = 1165.56 (8) Å3
Mr = 223.27Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 6.2309 (2) ŵ = 0.09 mm1
b = 9.3918 (4) ÅT = 150 K
c = 19.9175 (9) Å0.20 × 0.10 × 0.07 mm
Data collection top
Nonius KappaCCD
diffractometer
1541 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
1098 reflections with I > 2σ(I)
Tmin = 0.97, Tmax = 0.99Rint = 0.065
6149 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0450 restraints
wR(F2) = 0.102H-atom parameters constrained
S = 0.95Δρmax = 0.49 e Å3
1541 reflectionsΔρmin = 0.49 e Å3
146 parameters
Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems open-flow nitrogen cryostat (Cosier & Glazer, 1986) with a nominal stability of 0.1 K.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.7910 (3)0.89266 (18)0.79718 (9)0.0257
C20.8327 (4)0.7498 (3)0.81847 (12)0.0246
C30.9587 (4)0.6675 (3)0.76640 (12)0.0212
O41.1771 (3)0.71531 (19)0.75988 (9)0.0261
C50.8472 (4)0.6736 (3)0.69895 (12)0.0206
N60.9436 (3)0.5853 (2)0.64366 (9)0.0198
C71.0678 (4)0.6647 (3)0.59325 (12)0.0248
C81.1061 (4)0.5768 (3)0.53082 (12)0.0252
C91.2467 (4)0.4615 (3)0.53077 (13)0.0286
C101.2791 (5)0.3829 (3)0.47302 (15)0.0384
C111.1727 (5)0.4177 (3)0.41474 (14)0.0366
C121.0312 (5)0.5309 (3)0.41392 (14)0.0373
C130.9984 (5)0.6088 (3)0.47187 (13)0.0313
C140.7214 (4)0.5438 (3)0.62186 (13)0.0277
C150.6349 (4)0.5921 (3)0.69017 (12)0.0245
O160.6117 (3)0.48138 (19)0.73784 (9)0.0277
H220.91010.75350.86240.0291*
H210.69640.70000.82650.0280*
H310.97160.56450.78060.0250*
H510.83490.77190.68430.0251*
H721.20570.68710.61390.0252*
H710.99160.75370.58140.0268*
H911.32070.43630.57010.0319*
H1011.37190.30750.47390.0480*
H1111.19950.36460.37610.0436*
H1210.95570.55470.37470.0440*
H1310.90090.68600.47100.0365*
H1410.71040.43970.61450.0348*
H1420.66700.59390.58300.0324*
H1510.51140.65240.68810.0289*
H411.16280.80400.76230.0399*
H1610.48640.44990.73140.0409*
H110.87890.94680.81870.0398*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0245 (9)0.0213 (9)0.0312 (9)0.0011 (8)0.0042 (8)0.0039 (9)
C20.0288 (15)0.0219 (14)0.0231 (13)0.0006 (12)0.0021 (11)0.0021 (11)
C30.0174 (12)0.0210 (13)0.0251 (13)0.0022 (11)0.0003 (11)0.0004 (12)
O40.0193 (9)0.0254 (10)0.0336 (10)0.0013 (8)0.0012 (8)0.0025 (9)
C50.0242 (13)0.0189 (12)0.0187 (11)0.0011 (11)0.0015 (11)0.0004 (11)
N60.0205 (10)0.0233 (11)0.0157 (10)0.0008 (10)0.0005 (9)0.0030 (10)
C70.0226 (13)0.0283 (15)0.0236 (13)0.0042 (13)0.0003 (12)0.0009 (12)
C80.0246 (14)0.0304 (15)0.0206 (12)0.0055 (13)0.0004 (11)0.0012 (12)
C90.0224 (13)0.0402 (17)0.0232 (13)0.0039 (13)0.0016 (12)0.0029 (13)
C100.0325 (16)0.0423 (18)0.0404 (16)0.0075 (15)0.0068 (15)0.0048 (16)
C110.0372 (16)0.0458 (19)0.0267 (14)0.0000 (16)0.0051 (14)0.0056 (15)
C120.0399 (17)0.0489 (19)0.0232 (14)0.0010 (17)0.0029 (14)0.0025 (14)
C130.0350 (16)0.0333 (16)0.0256 (13)0.0041 (14)0.0033 (12)0.0017 (14)
C140.0212 (13)0.0347 (16)0.0273 (14)0.0005 (13)0.0055 (12)0.0009 (13)
C150.0174 (12)0.0286 (15)0.0275 (12)0.0059 (12)0.0002 (11)0.0017 (13)
O160.0215 (9)0.0282 (10)0.0335 (10)0.0042 (8)0.0010 (9)0.0070 (9)
Geometric parameters (Å, º) top
O1—C21.431 (3)C8—C91.393 (4)
O1—H110.862C8—C131.385 (4)
C2—C31.513 (3)C9—C101.382 (4)
C2—H221.000C9—H910.939
C2—H210.982C10—C111.376 (4)
C3—O41.439 (3)C10—H1010.914
C3—C51.514 (3)C11—C121.381 (4)
C3—H311.011C11—H1110.932
O4—H410.839C12—C131.382 (4)
C5—N61.504 (3)C12—H1210.939
C5—C151.538 (3)C13—H1310.945
C5—H510.971C14—C151.532 (3)
N6—C71.471 (3)C14—H1410.991
N6—C141.503 (3)C14—H1420.967
C7—C81.512 (3)C15—O161.416 (3)
C7—H720.976C15—H1510.956
C7—H710.990O16—H1610.844
C2—O1—H11106.9C7—C8—C13120.2 (2)
O1—C2—C3111.7 (2)C9—C8—C13118.2 (2)
O1—C2—H22108.3C8—C9—C10120.5 (3)
C3—C2—H22111.6C8—C9—H91120.3
O1—C2—H21109.7C10—C9—H91119.2
C3—C2—H21108.5C9—C10—C11120.3 (3)
H22—C2—H21106.9C9—C10—H101119.4
C2—C3—O4113.2 (2)C11—C10—H101120.3
C2—C3—C5110.5 (2)C10—C11—C12120.0 (3)
O4—C3—C5110.0 (2)C10—C11—H111118.9
C2—C3—H31109.8C12—C11—H111121.1
O4—C3—H31104.4C11—C12—C13119.5 (3)
C5—C3—H31108.7C11—C12—H121120.9
C3—O4—H41101.8C13—C12—H121119.6
C3—C5—N6116.5 (2)C8—C13—C12121.4 (3)
C3—C5—C15118.5 (2)C8—C13—H131119.5
N6—C5—C1589.19 (17)C12—C13—H131119.1
C3—C5—H51109.8N6—C14—C1589.48 (18)
N6—C5—H51109.6N6—C14—H141111.2
C15—C5—H51111.8C15—C14—H141113.5
C5—N6—C7115.48 (19)N6—C14—H142115.3
C5—N6—C1489.22 (17)C15—C14—H142116.3
C7—N6—C14114.8 (2)H141—C14—H142109.7
N6—C7—C8111.6 (2)C5—C15—C1486.89 (19)
N6—C7—H72106.5C5—C15—O16112.1 (2)
C8—C7—H72109.0C14—C15—O16114.5 (2)
N6—C7—H71109.8C5—C15—H151113.7
C8—C7—H71109.9C14—C15—H151114.9
H72—C7—H71109.9O16—C15—H151112.5
C7—C8—C9121.6 (2)C15—O16—H161104.4
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C11—H111···O4i0.932.553.457 (4)164
C15—H151···O4ii0.962.593.377 (4)139
O4—H41···O16iii0.842.182.825 (4)134
O16—H161···O1iv0.841.902.735 (4)171
O1—H11···N6iii0.861.862.719 (4)171
Symmetry codes: (i) x+5/2, y+1, z1/2; (ii) x1, y, z; (iii) x+2, y+1/2, z+3/2; (iv) x+1, y1/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC12H17NO3
Mr223.27
Crystal system, space groupOrthorhombic, P212121
Temperature (K)150
a, b, c (Å)6.2309 (2), 9.3918 (4), 19.9175 (9)
V3)1165.56 (8)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.20 × 0.10 × 0.07
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
Tmin, Tmax0.97, 0.99
No. of measured, independent and
observed [I > 2σ(I)] reflections
6149, 1541, 1098
Rint0.065
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.045, 0.102, 0.95
No. of reflections1541
No. of parameters146
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.49, 0.49

Computer programs: COLLECT (Nonius, 2001), DENZO/SCALEPACK (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H41···O16i0.842.182.825 (4)134
O16—H161···O1ii0.841.902.735 (4)171
O1—H11···N6i0.861.862.719 (4)171
Symmetry codes: (i) x+2, y+1/2, z+3/2; (ii) x+1, y1/2, z+3/2.
 

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 Asymmetry, 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
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First citationMichaud, T., Chanet-Ray, J., Chou, S. & Gelas, J. (1997b). Carbohydr. Res. 303, 123–127.  CrossRef CAS Web of Science 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 & R. M. Sweet, pp. 307–326. New York: Academic Press.  Google Scholar
First citationSoengas, R. G., Segade, Y., Jiménez, C. & Rodríguez, J. (2011). Tetrahedron, 67, 2617–2622.  Web of Science CSD CrossRef CAS Google Scholar
First citationWatkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England.  Google Scholar
First citationWatson, A. A., Fleet, G. W. J., Asano, N., Molyneux, R. J. & Nash, R. J. (2001). Phytochemistry, 56, 265–295.  Web of Science CrossRef PubMed CAS Google Scholar

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