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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 5| May 2012| Page o1474
doi:10.1107/S1600536812016273

2-N-Benzyl-2,6-dide­­oxy-2,6-imino-3,4-O-iso­propyl­­idene-3-C-methyl-D-allono­nitrile

Benjamin J. Ayers,a Sarah F. Jenkinson,a* George W. J. Fleeta and Amber L. Thompsonb

aDepartment of Organic 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 12 April 2012; accepted 14 April 2012; online 21 April 2012)

X-ray crystallography firmly established the relative stereochemistry of the title compound, C17H22N2O3. The absolute configuration was determined by use of 2-C-methyl-D-ribonolactone as the starting material. The compound exists as O—H⋯N hydrogen-bonded chains of mol­ecules running parallel to the a-axis.

Related literature

For 2-C-methyl sugar lactones and their use in synthesis, see: da Cruz et al. (2011[Cruz, F. P. da, Newberry, S., Jenkinson, S. F., Wormald, M. R., Butters, T. D., Alonzi, D. S., Nakagawa, S., Becq, F., Norez, C., Nash, R. J., Kato, A. & Fleet, G. W. J. (2011). Tetrahedron Lett. 52, 219-223.]); Best et al. (2010[Best, D., Jenkinson, S. F., Saville, A. W., Alonzi, D. S., Wormald, M. R., Butters, T. D., Norez, C., Becq, F., Bleriot, Y., Adachi, I., Kato, A. & Fleet, G. W. J. (2010). Tetrahedron Lett. 51, 4170-4174.]); da Cruz & Horne (2008[Cruz, F. P. da & Horne, G. (2008). Tetrahedron Lett. 49, 6812-6815.]6); Booth et al. (2008[Booth, K. V., da Cruz, F. P., Hotchkiss, D. J., Jenkinson, S. F., Jones, N. A., Weymouth-Wilson, A. C., Clarkson, R., Heinz, T. & Fleet, G. W. J. (2008). Tetrahedron Asymmetry, 19, 2417-2424.]); Hotchkiss, Soengas et al. (2007[Hotchkiss, D. J., Soengas, R., Booth, K. V., Weymouth-Wilson, A. C., Eastwick-Field, V. & Fleet, G. W. J. (2007). Tetrahedron Lett. 48, 517-520.]); Hotchkiss, Kato et al. (2007[Hotchkiss, D. J., Kato, A., Odell, B., Claridge, T. D. W. & Fleet, G. W. J. (2007). Tetrahedron Asymmetry, 18, 500-512.]); Hotchkiss et al. (2006[Hotchkiss, D. J., Jenkinson, S. F., Storer, R., Heinz, T. & Fleet, G. W. J. (2006). Tetrahedron Lett. 47, 315-318.]); Sowden & Strobach (1960[Sowden, J. C. & Strobach, D. R. (1960). J. Am. Chem. Soc. 82, 3707-3708.]). For the biological activity of polyhy­droxy­lated piperidines, see: Nash et al. (2011[Nash, R. J., Kato, A., Yu, C.-Y. & Fleet, G. W. J. (2011). Future Med. Chem. 3, 1513-1521.]); 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 the extinction correction, see: Larson (1970[Larson, A. C. (1970). Crystallographic Computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, pp. 291-294. Copenhagen: Munksgaard.]). For the temperature controller, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]).

[Scheme 1]

Experimental

Crystal data

  • C17H22N2O3

  • Mr = 302.37

  • Orthorhombic, P 21 21 21

  • a = 8.5647 (3) Å

  • b = 10.0019 (4) Å

  • c = 18.7031 (7) Å

  • V = 1602.17 (10) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 150 K

  • 0.25 × 0.25 × 0.20 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 = 0.96, Tmax = 0.98

  • 7953 measured reflections

  • 2082 independent reflections

  • 1808 reflections with I > 2σ(I)

  • Rint = 0.042
Refinement

  • R[F2 > 2σ(F2)] = 0.041

  • wR(F2) = 0.106

  • S = 0.97

  • 2082 reflections

  • 200 parameters

  • H-atom parameters constrained

  • Δρmax = 0.22 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O1—H11⋯N4i 0.88 2.15 2.997 (3) 161
Symmetry code: (i) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1].

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

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536812016273/lh5456sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812016273/lh5456Isup2.hkl

checkCIF report


Comment top

Many polyhydroxylated piperidines have been found to display interesting biological properties (Nash et al., 2011; Watson et al., 2001). 2-C-Methyl lactones, derived from sugars (Hotchkiss, Soengas et al., 2007; Sowden & Strobach, 1960; Hotchkiss et al., 2006), have been used for the synthesis of iminosugars bearing a carbon branch (da Cruz et al., 2011; Best et al., 2010; da Cruz et al., 2008; Hotchkiss, Kato et al., 2007). In a new one-pot approach to carbon-branched piperidines, the α-iminonitrile 4 was prepared from the lactol tosylate 3, itself readily available in two steps from 2-C-methyl-D-ribonolactone 1 (Booth et al., 2008), by Strecker α-aminonitrile formation and concomitant intramolecular tosylate displacement (Fig. 1).

X-ray crystallography firmly established the relative stereochemistry of the title compound 4. The absolute configuration was determined by the use of 2-C-methyl-D-ribonolactone 1 as the starting material. The acetonide ring adopts an envelope conformation with C16 out of the plane and the piperidine ring adopts a chair conformation (Fig. 2). The compound exists as O—H···N hydrogen-bonded chains of molecules running parallel to the a-axis (Fig. 3). Only classical hydrogen-bonding was considered.

Related literature top

For 2-C-methyl sugar lactones and their use in synthesis, see: da Cruz et al. (2011); Best et al. (2010); da Cruz & Horne (20086); Booth et al. (2008); Hotchkiss, Soengas et al. (2007); Hotchkiss, Kato et al. (2007); Hotchkiss et al. (2006); Sowden & Strobach (1960). For the biological activity of polyhydroxylated piperidines, see: Nash et al. (2011); Watson et al. (2001). For the extinction correction, see: Larson (1970). For the temperature controller, see: Cosier & Glazer (1986).

Experimental top

α-Iminonitrile 4 was recrystallized by diffusion from a mixture of ethyl acetate and cyclohexane: m.p. 394–395 K; [α]D20 +39.7 (c 5.5, methanol).

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, 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 for the crystal projected along the b-axis. Hydrogen bonds are shown as dotted lines.
2-N-Benzyl-2,6-dideoxy-2,6-imino-3,4-O-isopropylidene- 3-C-methyl-D-allononitrile top
Crystal data top
C17H22N2O3F(000) = 648
Mr = 302.37Dx = 1.253 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1959 reflections
a = 8.5647 (3) Åθ = 5–27°
b = 10.0019 (4) ŵ = 0.09 mm−1
c = 18.7031 (7) ÅT = 150 K
V = 1602.17 (10) Å3Block, colourless
Z = 40.25 × 0.25 × 0.20 mm
Data collection top
Nonius KappaCCD
diffractometer		1808 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.042
ω scansθmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		h = −11→11
Tmin = 0.96, Tmax = 0.98k = −12→12
7953 measured reflectionsl = −24→24
2082 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.041 Method = Modified Sheldrick w = 1/[σ2(F2) + (0.07P)2 + 0.23P],
where P = (max(Fo2,0) + 2Fc2)/3
wR(F2) = 0.106(Δ/σ)max = 0.0002994
S = 0.97Δρmax = 0.22 e Å−3
2082 reflectionsΔρmin = −0.22 e Å−3
200 parametersExtinction correction: Larson (1970), Equation 22
0 restraintsExtinction coefficient: 280 (110)
Primary atom site location: structure-invariant direct methods
Crystal data top
C17H22N2O3V = 1602.17 (10) Å3
Mr = 302.37Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 8.5647 (3) ŵ = 0.09 mm−1
b = 10.0019 (4) ÅT = 150 K
c = 18.7031 (7) Å0.25 × 0.25 × 0.20 mm
Data collection top
Nonius KappaCCD
diffractometer		2082 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		1808 reflections with I > 2σ(I)
Tmin = 0.96, Tmax = 0.98Rint = 0.042
7953 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0410 restraints
wR(F2) = 0.106H-atom parameters constrained
S = 0.97Δρmax = 0.22 e Å−3
2082 reflectionsΔρmin = −0.22 e Å−3
200 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
O10.28415 (17)0.66972 (14)0.47877 (7)0.0285
C20.3904 (2)0.7319 (2)0.52685 (10)0.0240
C30.4656 (2)0.62006 (19)0.56970 (10)0.0245
N40.58010 (19)0.67473 (16)0.62140 (8)0.0237
C50.6509 (2)0.5619 (2)0.66204 (10)0.0290
C60.7562 (2)0.47284 (19)0.61857 (10)0.0252
C70.9075 (2)0.5134 (2)0.60165 (11)0.0298
C81.0092 (3)0.4276 (2)0.56690 (11)0.0356
C90.9612 (3)0.2999 (2)0.54895 (12)0.0377
C100.8116 (3)0.2586 (2)0.56503 (13)0.0377
C110.7094 (3)0.3444 (2)0.59975 (12)0.0317
C120.4923 (2)0.7579 (2)0.67274 (10)0.0258
C130.5940 (3)0.8056 (2)0.73119 (12)0.0349
N140.6690 (3)0.8455 (3)0.77702 (12)0.0563
C150.4085 (2)0.8802 (2)0.63836 (10)0.0258
C160.3102 (2)0.8340 (2)0.57458 (10)0.0251
O170.17610 (16)0.77936 (14)0.60920 (7)0.0267
C180.1432 (2)0.8661 (2)0.66828 (11)0.0322
O190.29237 (16)0.92224 (14)0.68874 (8)0.0293
C200.0777 (3)0.7836 (3)0.72865 (12)0.0435
C210.0377 (3)0.9798 (3)0.64619 (15)0.0503
C220.5170 (3)0.9967 (2)0.62255 (12)0.0337
H210.47440.77260.49990.0256*
H310.52180.55920.53640.0293*
H320.38380.56840.59580.0277*
H510.56410.51200.68210.0339*
H520.71380.60410.70090.0357*
H710.94260.59850.61480.0359*
H811.11190.45910.55620.0416*
H911.03040.24150.52590.0458*
H1010.78210.16900.55300.0463*
H1110.60560.31660.61180.0379*
H1210.41000.70950.69530.0311*
H1610.28290.91450.54540.0290*
H2030.05840.83810.76980.0637*
H202−0.02090.74570.71230.0635*
H2010.15210.71430.74170.0639*
H2110.02201.04170.68760.0718*
H212−0.06210.93720.63180.0712*
H2130.08381.03190.60670.0702*
H2230.45631.06310.59690.0499*
H2220.60190.96350.59280.0502*
H2210.55781.04060.66650.0511*
H110.24170.73010.45040.0457*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0278 (7)0.0332 (7)0.0244 (6)0.0012 (7)−0.0070 (6)−0.0039 (6)
C20.0225 (10)0.0293 (10)0.0201 (8)−0.0011 (8)−0.0021 (8)−0.0007 (8)
C30.0242 (9)0.0254 (9)0.0239 (9)0.0009 (8)−0.0016 (8)0.0003 (8)
N40.0231 (8)0.0267 (8)0.0215 (7)0.0005 (7)−0.0002 (7)−0.0002 (7)
C50.0277 (10)0.0346 (11)0.0249 (9)0.0025 (9)−0.0021 (8)0.0032 (9)
C60.0253 (9)0.0272 (10)0.0233 (9)0.0004 (8)−0.0041 (8)0.0050 (8)
C70.0295 (10)0.0318 (10)0.0281 (10)−0.0015 (9)−0.0036 (9)0.0040 (9)
C80.0264 (11)0.0433 (12)0.0370 (11)0.0009 (10)0.0014 (9)0.0064 (10)
C90.0368 (12)0.0367 (12)0.0397 (12)0.0081 (10)0.0054 (10)0.0025 (10)
C100.0386 (12)0.0288 (10)0.0457 (12)0.0000 (10)−0.0020 (11)−0.0007 (10)
C110.0254 (10)0.0320 (10)0.0377 (11)−0.0020 (10)−0.0031 (9)0.0022 (9)
C120.0202 (9)0.0347 (10)0.0226 (8)−0.0004 (9)−0.0014 (8)−0.0006 (8)
C130.0287 (10)0.0480 (13)0.0280 (10)0.0089 (10)−0.0025 (9)−0.0087 (10)
N140.0397 (12)0.0796 (16)0.0496 (13)0.0170 (13)−0.0156 (10)−0.0290 (13)
C150.0225 (9)0.0295 (10)0.0254 (9)−0.0005 (9)0.0015 (8)−0.0028 (8)
C160.0233 (9)0.0274 (9)0.0246 (9)0.0006 (8)−0.0010 (7)0.0000 (8)
O170.0214 (7)0.0322 (7)0.0266 (7)−0.0012 (6)0.0021 (6)−0.0085 (6)
C180.0240 (10)0.0411 (12)0.0314 (11)0.0006 (9)−0.0023 (9)−0.0138 (9)
O190.0219 (7)0.0362 (8)0.0297 (7)−0.0004 (6)0.0010 (6)−0.0104 (6)
C200.0300 (12)0.0660 (16)0.0346 (11)−0.0147 (12)0.0082 (10)−0.0152 (12)
C210.0372 (13)0.0574 (16)0.0563 (15)0.0182 (13)−0.0146 (12)−0.0231 (13)
C220.0346 (11)0.0305 (10)0.0362 (11)−0.0075 (10)0.0036 (10)−0.0040 (9)
Geometric parameters (Å, º) top
O1—C21.422 (2)C11—H1110.958
O1—H110.882C12—C131.477 (3)
C2—C31.519 (3)C12—C151.557 (3)
C2—C161.521 (3)C12—H1210.954
C2—H210.968C13—N141.143 (3)
C3—N41.482 (2)C15—C161.531 (3)
C3—H310.994C15—O191.433 (2)
C3—H320.998C15—C221.519 (3)
N4—C51.490 (2)C16—O171.427 (2)
N4—C121.477 (2)C16—H1610.999
C5—C61.506 (3)O17—C181.433 (2)
C5—H510.971C18—O191.447 (2)
C5—H520.998C18—C201.507 (3)
C6—C71.394 (3)C18—C211.510 (3)
C6—C111.391 (3)C20—H2030.958
C7—C81.385 (3)C20—H2020.975
C7—H710.935C20—H2010.972
C8—C91.383 (3)C21—H2111.000
C8—H810.956C21—H2120.992
C9—C101.380 (4)C21—H2130.987
C9—H910.937C22—H2230.971
C10—C111.387 (3)C22—H2220.974
C10—H1010.958C22—H2210.995
C2—O1—H11110.2N4—C12—H121112.2
O1—C2—C3106.45 (16)C13—C12—H121105.8
O1—C2—C16112.06 (16)C15—C12—H121103.9
C3—C2—C16112.12 (15)C12—C13—N14177.7 (2)
O1—C2—H21109.3C12—C15—C16109.79 (16)
C3—C2—H21105.6C12—C15—O19106.20 (15)
C16—C2—H21111.0C16—C15—O19102.67 (15)
C2—C3—N4110.68 (15)C12—C15—C22113.61 (16)
C2—C3—H31109.0C16—C15—C22114.56 (16)
N4—C3—H31108.3O19—C15—C22109.11 (16)
C2—C3—H32110.0C15—C16—C2114.30 (16)
N4—C3—H32109.6C15—C16—O17101.79 (14)
H31—C3—H32109.2C2—C16—O17111.85 (16)
C3—N4—C5108.84 (15)C15—C16—H161108.1
C3—N4—C12107.17 (15)C2—C16—H161109.1
C5—N4—C12107.60 (14)O17—C16—H161111.5
N4—C5—C6114.61 (15)C16—O17—C18106.03 (14)
N4—C5—H51105.9O17—C18—O19105.37 (15)
C6—C5—H51111.3O17—C18—C20108.63 (18)
N4—C5—H52105.7O19—C18—C20110.04 (17)
C6—C5—H52108.7O17—C18—C21111.28 (18)
H51—C5—H52110.5O19—C18—C21107.97 (18)
C5—C6—C7120.47 (18)C20—C18—C21113.3 (2)
C5—C6—C11120.68 (19)C18—O19—C15108.96 (14)
C7—C6—C11118.6 (2)C18—C20—H203110.8
C6—C7—C8120.7 (2)C18—C20—H202107.5
C6—C7—H71120.2H203—C20—H202108.8
C8—C7—H71119.0C18—C20—H201109.6
C7—C8—C9120.0 (2)H203—C20—H201108.5
C7—C8—H81118.2H202—C20—H201111.7
C9—C8—H81121.8C18—C21—H211109.6
C8—C9—C10120.0 (2)C18—C21—H212105.4
C8—C9—H91120.0H211—C21—H212111.2
C10—C9—H91120.1C18—C21—H213111.3
C9—C10—C11120.2 (2)H211—C21—H213107.9
C9—C10—H101118.3H212—C21—H213111.6
C11—C10—H101121.5C15—C22—H223107.1
C6—C11—C10120.5 (2)C15—C22—H222107.8
C6—C11—H111118.4H223—C22—H222110.5
C10—C11—H111121.1C15—C22—H221113.1
N4—C12—C13111.28 (16)H223—C22—H221107.1
N4—C12—C15114.13 (15)H222—C22—H221111.1
C13—C12—C15108.91 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C22—H222···O1i0.972.453.405 (3)167
O1—H11···N4ii0.882.152.997 (3)161
Symmetry codes: (i) x+1/2, −y+3/2, −z+1; (ii) x−1/2, −y+3/2, −z+1.

Experimental details

Crystal data
Chemical formulaC17H22N2O3
Mr302.37
Crystal system, space groupOrthorhombic, P212121
Temperature (K)150
a, b, c (Å)8.5647 (3), 10.0019 (4), 18.7031 (7)
V (Å3)1602.17 (10)
Z4
Radiation typeMo Kα
µ (mm−1)0.09
Crystal size (mm)0.25 × 0.25 × 0.20
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
Tmin, Tmax0.96, 0.98
No. of measured, independent and
observed [I > 2σ(I)] reflections		7953, 2082, 1808
Rint0.042
(sin θ/λ)max (Å−1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.106, 0.97
No. of reflections2082
No. of parameters200
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.22, −0.22

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
O1—H11···N4i0.882.152.997 (3)161
Symmetry code: (i) x−1/2, −y+3/2, −z+1.
 

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ISSN: 2056-9890
Volume 68| Part 5| May 2012| Page o1474
doi:10.1107/S1600536812016273
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