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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 8| August 2012| Page o2410
https://doi.org/10.1107/S1600536812030656

N-Benzyl-3,5-dide­­oxy-3,5-imino-1,2-O-iso­propyl­­idene-β-L-lyxo­furan­ose

David S. Edgeley,a Sarah F. Jenkinson,b* Gabriel Lenagh-Snow,b Catherine Rutherford,b George W. J. Fleetb and Amber L. Thompsona

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

(Received 30 June 2012; accepted 4 July 2012; online 10 July 2012)

X-ray crystallography confirmed the formation, structure and relative stereochemistry of the title compound, C15H19NO3, which contains a sterically congested four-membered azetidine ring system. The absolute configuration was determined by the use of L-arabinose as the starting material.

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. 95-97.]); 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.]); Jenkinson et al. (2011[Jenkinson, S. F., Lenagh-Snow, G. M. J., Fleet, G. W. J. & Thompson, A. L. (2011). Acta Cryst. E67, o2452.]); Lenagh-Snow et al. (2011[Lenagh-Snow, G. M. J., Araujo, N., Jenkinson, S. F., Rutherford, C., Nakagawa, S., Kato, A., Yu, C.-Y., Weymouth-Wilson, A. C. & Fleet, G. W. J. (2011). Org. Lett. 13, 5834-5837.], 2012[Lenagh-Snow, G. M. J., Araujo, N., Jenkinson, S. F., Martinez, R. F., Shimada, Y., Yu, C.-Y., Kato, A. & Fleet, G. W. J. (2012). Org. Lett. 14, 2142-2145.]); Lee et al. (2012[Lee, J. C., Francis, S., Dutta, D., Gupta, V., Yang, Y., Zhu, J.-Y., Tash, J. S., Schonbrunn, E. & Georg, G. I. (2012). J. Org. Chem. 77, 3082-3098.]). For related literature on imino­sugars, see: Asano et al. (2000[Asano, N., Nash, R. J., Molyneuxl, 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.]). For details of hydrogen refinement, see: Cooper et al. (2010[Cooper, R. I., Thompson, A. L. & Watkin, D. J. (2010). J. Appl. Cryst. 43, 1100-1107.]). For references to the Chebychev polynomial, see: Prince (1982[Prince, E. (1982). In Mathematical Techniques in Crystallography and Materials Science. New York: Springer-Verlag.]); Watkin (1994[Watkin, D. (1994). Acta Cryst. A50, 411-437.]).

[Scheme 1]

Experimental

Crystal data

  • C15H19NO3

  • Mr = 261.32

  • Monoclinic, P 21

  • a = 9.1674 (2) Å

  • b = 5.7551 (1) Å

  • c = 13.1112 (3) Å

  • β = 106.9544 (8)°

  • V = 661.67 (2) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 150 K

  • 0.24 × 0.23 × 0.07 mm
Data collection

  • Nonius KappaCCD diffractometer

  • Absorption correction: multi-scan (DENZO and 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 = 0.94, Tmax = 0.99

  • 13110 measured reflections

  • 1638 independent reflections

  • 1544 reflections with I > 2σ(I)

  • Rint = 0.014
Refinement

  • R[F2 > 2σ(F2)] = 0.033

  • wR(F2) = 0.087

  • S = 0.94

  • 1638 reflections

  • 172 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.17 e Å−3

  • Δρmin = −0.18 e Å−3

Data collection: COLLECT (Nonius, 2001[Nonius (2001). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: DENZO and 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 and 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

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536812030656/lh5500sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812030656/lh5500Isup2.hkl

checkCIF report


Comment top

Azetidines (Michaud et al., 1997a; Michaud et al., 1997b; Dekaris & Reissig, 2010; Soengas et al., 2011) are a relatively unstudied class of iminosugars (Asano et al., 2000; Watson et al., 2001, Michaud et al., 1997a; Michaud et al., 1997b; Dekaris & Reissig, 2010; Soengas et al., 2011) but initial results (Krämer et al., 1997; Lee et al., 2012) have shown some interesting biological activity.

Azetidine formation can be achieved by the double displacement of ditriflates with amines (Jenkinson et al., 2011; Lenagh-Snow et al., 2011; Lenagh-Snow et al., 2012). X-Ray crystallography confirmed the structure and relative stereochemistry of the formation of the title compound 3 (Fig. 1) from the displacement of a 3,5-O-ditriflate 2 with benzylamine. The absolute stereochemistry was determined by the use of L-arabinose as the starting material.

The five membered rings adopt envelope conformations with O7 and C10 out of the plane, and the azetidine ring adopts a puckered conformation (Fig. 2, Fig. 3).

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); Jenkinson et al. (2011); Lenagh-Snow et al. (2011, 2012); Lee et al. (2012). For related literature on iminosugars, see: Asano et al. (2000); Watson et al. (2001). For details of the cryostat, see: Cosier & Glazer (1986). For details of hydrogen refinement, see: Cooper et al. (2010). For related literature, see: Prince (1982); Watkin (1994).

Experimental top

The title compound was recrystallized from cyclohexane/pentane. [α]D25 +76.0 (c 0.50 in CHCl3); m.p. 337–339 K.

Refinement top

In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from the starting material.

The H atoms were all located in a difference map, but those attached to carbon 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 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 (Cooper et al., 2010).

Structure description top

Azetidines (Michaud et al., 1997a; Michaud et al., 1997b; Dekaris & Reissig, 2010; Soengas et al., 2011) are a relatively unstudied class of iminosugars (Asano et al., 2000; Watson et al., 2001, Michaud et al., 1997a; Michaud et al., 1997b; Dekaris & Reissig, 2010; Soengas et al., 2011) but initial results (Krämer et al., 1997; Lee et al., 2012) have shown some interesting biological activity.

Azetidine formation can be achieved by the double displacement of ditriflates with amines (Jenkinson et al., 2011; Lenagh-Snow et al., 2011; Lenagh-Snow et al., 2012). X-Ray crystallography confirmed the structure and relative stereochemistry of the formation of the title compound 3 (Fig. 1) from the displacement of a 3,5-O-ditriflate 2 with benzylamine. The absolute stereochemistry was determined by the use of L-arabinose as the starting material.

The five membered rings adopt envelope conformations with O7 and C10 out of the plane, and the azetidine ring adopts a puckered conformation (Fig. 2, Fig. 3).

For related literature on azetidines, see: Krämer et al. (1997); Michaud et al. (1997a,b); Dekaris & Reissig (2010); Soengas et al. (2011); Jenkinson et al. (2011); Lenagh-Snow et al. (2011, 2012); Lee et al. (2012). For related literature on iminosugars, see: Asano et al. (2000); Watson et al. (2001). For details of the cryostat, see: Cosier & Glazer (1986). For details of hydrogen refinement, see: Cooper et al. (2010). For related literature, see: Prince (1982); Watkin (1994).

Computing details top

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and 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 arbitrary radius.
[Figure 3] Fig. 3. Packing diagram of the title compound projected along the b-axis.
N-Benzyl-3,5-dideoxy-3,5-imino-1,2-O-isopropylidene- β-L-lyxofuranose top
Crystal data top
C15H19NO3F(000) = 280
Mr = 261.32Dx = 1.312 Mg m−3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 1627 reflections
a = 9.1674 (2) Åθ = 5–27°
b = 5.7551 (1) ŵ = 0.09 mm−1
c = 13.1112 (3) ÅT = 150 K
β = 106.9544 (8)°Plate, colourless
V = 661.67 (2) Å30.24 × 0.23 × 0.07 mm
Z = 2
Data collection top
Nonius KappaCCD
diffractometer		1544 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.014
ω scansθmax = 27.4°, θmin = 5.4°
Absorption correction: multi-scan
(DENZO and SCALEPACK; Otwinowski & Minor, 1997)		h = −11→11
Tmin = 0.94, Tmax = 0.99k = −7→6
13110 measured reflectionsl = −16→16
1638 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.033H-atom parameters constrained
wR(F2) = 0.087 Method, part 1, Chebychev polynomial, (Watkin, 1994, Prince, 1982) [weight] = 1.0/[A0*T0(x) + A1*T1(x) ··· + An-1]*Tn-1(x)]
where Ai are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] * [1-(deltaF/6*sigmaF)2]2 Ai are: 22.1 34.0 17.6 5.07
S = 0.94(Δ/σ)max = 0.0003
1638 reflectionsΔρmax = 0.17 e Å−3
172 parametersΔρmin = −0.18 e Å−3
1 restraint
Crystal data top
C15H19NO3V = 661.67 (2) Å3
Mr = 261.32Z = 2
Monoclinic, P21Mo Kα radiation
a = 9.1674 (2) ŵ = 0.09 mm−1
b = 5.7551 (1) ÅT = 150 K
c = 13.1112 (3) Å0.24 × 0.23 × 0.07 mm
β = 106.9544 (8)°
Data collection top
Nonius KappaCCD
diffractometer		1638 independent reflections
Absorption correction: multi-scan
(DENZO and SCALEPACK; Otwinowski & Minor, 1997)		1544 reflections with I > 2σ(I)
Tmin = 0.94, Tmax = 0.99Rint = 0.014
13110 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0331 restraint
wR(F2) = 0.087H-atom parameters constrained
S = 0.94Δρmax = 0.17 e Å−3
1638 reflectionsΔρmin = −0.18 e Å−3
172 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
O10.09793 (13)0.5625 (2)0.84062 (10)0.0269
C20.25050 (17)0.6293 (3)0.89568 (13)0.0260
C30.35745 (18)0.6618 (3)0.82587 (13)0.0262
N40.31206 (15)0.5481 (3)0.72006 (11)0.0264
C50.45568 (19)0.4116 (4)0.74729 (15)0.0318
C60.48402 (19)0.4783 (3)0.86494 (14)0.0292
O70.42651 (14)0.3113 (3)0.92411 (10)0.0319
C80.31601 (19)0.4200 (3)0.96665 (14)0.0284
O90.19278 (13)0.2728 (3)0.96037 (10)0.0313
C100.07349 (18)0.3246 (3)0.86343 (14)0.0274
C110.0820 (2)0.1650 (3)0.77364 (14)0.0306
C12−0.07829 (19)0.3058 (4)0.88768 (15)0.0333
C130.2813 (2)0.6967 (3)0.62624 (14)0.0309
C140.2617 (2)0.5526 (4)0.52659 (14)0.0288
C150.3343 (2)0.6152 (4)0.45124 (14)0.0320
C160.3150 (2)0.4828 (4)0.35950 (14)0.0353
C170.2236 (2)0.2866 (4)0.34202 (15)0.0346
C180.1518 (2)0.2208 (4)0.41731 (16)0.0379
C190.1714 (2)0.3523 (4)0.50899 (15)0.0343
H210.24890.77220.93650.0300*
H310.39620.82320.82660.0305*
H510.44160.24800.73050.0388*
H520.53130.47790.71480.0374*
H610.58710.53250.90420.0348*
H810.36660.46391.04300.0337*
H1120.06780.00540.79310.0457*
H1130.00020.20590.70920.0453*
H1110.18070.17820.76120.0454*
H121−0.09090.14890.91120.0506*
H123−0.15890.34440.82200.0494*
H122−0.07820.41560.94540.0507*
H1320.18710.78720.62080.0373*
H1310.36790.80670.63100.0372*
H1510.39770.75070.46300.0386*
H1610.36460.52900.30640.0422*
H1710.21000.20000.27820.0423*
H1810.08960.08540.40670.0458*
H1910.12080.30770.55890.0420*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0214 (5)0.0238 (6)0.0331 (6)0.0007 (5)0.0041 (4)0.0028 (5)
C20.0234 (7)0.0239 (8)0.0291 (7)−0.0006 (6)0.0051 (6)−0.0014 (7)
C30.0234 (7)0.0242 (8)0.0299 (7)−0.0018 (6)0.0063 (6)−0.0014 (6)
N40.0255 (6)0.0246 (7)0.0293 (7)−0.0002 (6)0.0081 (5)−0.0014 (6)
C50.0287 (8)0.0290 (9)0.0385 (9)0.0023 (7)0.0108 (7)−0.0040 (8)
C60.0225 (7)0.0289 (9)0.0349 (8)−0.0002 (7)0.0063 (6)−0.0003 (7)
O70.0293 (6)0.0270 (6)0.0393 (6)0.0054 (5)0.0100 (5)0.0060 (6)
C80.0251 (7)0.0274 (9)0.0313 (8)0.0014 (7)0.0058 (6)0.0036 (7)
O90.0264 (6)0.0333 (7)0.0311 (6)−0.0017 (5)0.0034 (5)0.0078 (5)
C100.0248 (7)0.0257 (8)0.0299 (8)−0.0007 (7)0.0054 (6)0.0049 (7)
C110.0291 (8)0.0254 (8)0.0361 (8)−0.0019 (7)0.0077 (7)0.0013 (7)
C120.0264 (7)0.0366 (10)0.0376 (8)−0.0030 (8)0.0105 (6)0.0037 (8)
C130.0365 (8)0.0249 (8)0.0318 (8)−0.0035 (8)0.0106 (7)−0.0007 (7)
C140.0268 (7)0.0279 (9)0.0307 (8)0.0010 (7)0.0066 (6)−0.0015 (7)
C150.0289 (8)0.0330 (10)0.0326 (8)−0.0028 (8)0.0069 (6)0.0022 (7)
C160.0307 (8)0.0430 (12)0.0337 (9)0.0009 (8)0.0116 (7)0.0003 (8)
C170.0306 (8)0.0374 (10)0.0342 (8)0.0042 (8)0.0070 (7)−0.0071 (8)
C180.0374 (9)0.0322 (10)0.0447 (10)−0.0062 (8)0.0129 (8)−0.0080 (9)
C190.0357 (9)0.0317 (10)0.0379 (9)−0.0066 (8)0.0147 (7)−0.0034 (8)
Geometric parameters (Å, º) top
O1—C21.4271 (19)C11—H1120.972
O1—C101.433 (2)C11—H1130.981
C2—C31.535 (2)C11—H1110.967
C2—C81.534 (2)C12—H1210.972
C2—H210.984C12—H1230.983
C3—N41.480 (2)C12—H1220.985
C3—C61.542 (2)C13—C141.513 (2)
C3—H310.994C13—H1320.993
N4—C51.484 (2)C13—H1311.003
N4—C131.457 (2)C14—C151.390 (2)
C5—C61.536 (2)C14—C191.399 (3)
C5—H510.967C15—C161.391 (3)
C5—H520.990C15—H1510.957
C6—O71.429 (2)C16—C171.385 (3)
C6—H610.986C16—H1610.974
O7—C81.435 (2)C17—C181.389 (3)
C8—O91.395 (2)C17—H1710.950
C8—H811.005C18—C191.387 (3)
O9—C101.4456 (19)C18—H1810.952
C10—C111.513 (3)C19—H1910.941
C10—C121.519 (2)
C2—O1—C10109.99 (13)O9—C10—C12107.79 (14)
O1—C2—C3115.67 (13)O1—C10—C12108.68 (15)
O1—C2—C8104.34 (14)C11—C10—C12112.21 (15)
C3—C2—C8104.59 (14)C10—C11—H112109.1
O1—C2—H21109.4C10—C11—H113108.9
C3—C2—H21109.7H112—C11—H113109.0
C8—C2—H21113.1C10—C11—H111110.3
C2—C3—N4116.83 (13)H112—C11—H111108.8
C2—C3—C6105.56 (14)H113—C11—H111110.7
N4—C3—C689.27 (13)C10—C12—H121109.5
C2—C3—H31113.4C10—C12—H123107.6
N4—C3—H31115.1H121—C12—H123111.0
C6—C3—H31113.9C10—C12—H122108.6
C3—N4—C591.22 (12)H121—C12—H122109.0
C3—N4—C13117.65 (15)H123—C12—H122111.1
C5—N4—C13116.97 (14)N4—C13—C14110.62 (16)
N4—C5—C689.30 (13)N4—C13—H132108.6
N4—C5—H51114.2C14—C13—H132110.1
C6—C5—H51116.3N4—C13—H131111.3
N4—C5—H52112.1C14—C13—H131107.0
C6—C5—H52113.7H132—C13—H131109.2
H51—C5—H52109.9C13—C14—C15120.71 (17)
C3—C6—C586.95 (13)C13—C14—C19120.65 (16)
C3—C6—O7106.25 (13)C15—C14—C19118.64 (17)
C5—C6—O7113.33 (15)C14—C15—C16120.39 (18)
C3—C6—H61118.1C14—C15—H151119.4
C5—C6—H61117.3C16—C15—H151120.3
O7—C6—H61112.3C15—C16—C17120.55 (17)
C6—O7—C8109.39 (14)C15—C16—H161120.0
C2—C8—O7107.62 (14)C17—C16—H161119.4
C2—C8—O9105.91 (13)C16—C17—C18119.59 (18)
O7—C8—O9111.33 (16)C16—C17—H171119.4
C2—C8—H81113.1C18—C17—H171121.0
O7—C8—H81108.9C17—C18—C19119.92 (19)
O9—C8—H81110.0C17—C18—H181120.5
C8—O9—C10108.58 (13)C19—C18—H181119.6
O9—C10—O1104.85 (14)C14—C19—C18120.89 (17)
O9—C10—C11111.18 (15)C14—C19—H191119.8
O1—C10—C11111.77 (14)C18—C19—H191119.3
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C11—H111···N40.972.583.266 (3)128

Experimental details

Crystal data
Chemical formulaC15H19NO3
Mr261.32
Crystal system, space groupMonoclinic, P21
Temperature (K)150
a, b, c (Å)9.1674 (2), 5.7551 (1), 13.1112 (3)
β (°) 106.9544 (8)
V (Å3)661.67 (2)
Z2
Radiation typeMo Kα
µ (mm−1)0.09
Crystal size (mm)0.24 × 0.23 × 0.07
Data collection
DiffractometerNonius KappaCCD
Absorption correctionMulti-scan
(DENZO and SCALEPACK; Otwinowski & Minor, 1997)
Tmin, Tmax0.94, 0.99
No. of measured, independent and
observed [I > 2σ(I)] reflections		13110, 1638, 1544
Rint0.014
(sin θ/λ)max (Å−1)0.648
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.087, 0.94
No. of reflections1638
No. of parameters172
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.17, −0.18

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

 

References

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Volume 68| Part 8| August 2012| Page o2410
https://doi.org/10.1107/S1600536812030656
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