Issue contents
Download PDF of article
Download CIF
3D view
Navigation
Highlighting
Dictionary of Crystallography reference
IUPAC Gold Book reference
more ...
Download citation
FormatBIBTeX
EndNote
RefMan
Refer
Medline
CIF
SGML
Plain Text
share
Previous article
Next article
Previous article
Issue contents
Download PDF of article
Download CIF
3D view
Navigation
Highlighting
Dictionary of Crystallography reference
IUPAC Gold Book reference
more ...
Download citation
FormatBIBTeX
EndNote
RefMan
Refer
Medline
CIF
SGML
Plain Text
share
Next article

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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 69| Part 12| December 2013| Page o1772
doi:10.1107/S1600536813030584

2-N-Benzyl-2,6-dide­­oxy-2,6-imino-3,4-O-iso­propyl­­idene-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 28 October 2013; accepted 7 November 2013; online 13 November 2013)

X-ray crystallography firmly established the relative stereochemistry of the title compound, C16H20N2O3. The acetonide ring adopts an envelope conformation with one of the O atoms as the flap and the piperidine ring adopts a slightly twisted boat conformation. The absolute configuration was determined by use of D-ribose as the starting material. The compound exists as O—H⋯O hydrogen-bonded chains of mol­ecules running parallel to the b axis.

CCDC reference: 970751

Related literature

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 a related α-imino­nitrile, see: Ayers et al. (2012[Ayers, B. J., Jenkinson, S. F., Fleet, G. W. J. & Thompson, A. L. (2012). Acta Cryst. E68, o1474.]). For the hydrogen-atom treatment, see; Cooper et al. (2010[Cooper, R. I., Thompson, A. L. & Watkin, D. J. (2010). J. Appl. Cryst. 43, 1100-1107.]). For details of the low temperature equipment used in the experiment, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]). For the weighting scheme, 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

  • C16H20N2O3

  • Mr = 288.35

  • Orthorhombic, P 21 21 21

  • a = 8.3978 (3) Å

  • b = 11.2689 (4) Å

  • c = 15.9210 (6) Å

  • V = 1506.67 (9) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 150 K

  • 0.4 × 0.4 × 0.2 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 = 0.91, Tmax = 0.98

  • 11529 measured reflections

  • 1970 independent reflections

  • 1422 reflections with I > 2.0σ(I)

  • Rint = 0.079
Refinement

  • R[F2 > 2σ(F2)] = 0.044

  • wR(F2) = 0.121

  • S = 0.95

  • 1970 reflections

  • 190 parameters

  • H-atom parameters constrained

  • Δρmax = 0.47 e Å−3

  • Δρmin = −0.42 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O1—H11⋯O6i 0.86 2.05 2.850 (5) 156 (1)
Symmetry code: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\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

CCDC reference: 970751

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536813030584/lh5665sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813030584/lh5665Isup2.hkl

checkCIF report


Comment top

Many polyhydroxylated piperidines have been found to display interesting biological properties (Nash et al., 2011; Watson et al., 2001). Piperidine α-iminonitrile 4 was prepared from 2,3-O-isopropylidene-5-O-toluenesulfonyl-D-ribose 3 by a tandem Strecker reaction and iminocyclization (Fig. 1). The title crystal structure establishes the relative configuration of 4. The absolute configuration is determined by use of D-ribose 1 as the starting material. The acetonide ring adopts an envelope conformation with O4 out of the plane and the piperidine ring adopts a slightly twisted boat conformation with the nitrile group in the flagpole position (Fig. 2). The compound exists as O—H···O hydrogen bonded chains of molecules running parallel to the b-axis (Fig. 3). Only classical hydrogen bonding was considered.

Related literature top

For the biological activity of polyhydroxylated piperidines, see: Nash et al. (2011); Watson et al. (2001). For a related α-iminonitrile, see: Ayers et al. (2012). For the hydrogen-atom treatment, see; Cooper et al. (2010). For details of the low temperature equipment used in the experiment, see: Cosier & Glazer (1986). For the weighting scheme, see: Prince (1982); Watkin (1994).

Experimental top

α-Iminonitrile 4 was recrystallized by diffusion from a mixture of ethyl acetate and cyclohexane: m.p. 342–344 K; [α]D20 +20.3 (c 1.75, methanol).

Refinement top

In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from the use of D-ribose as 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, 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 (Cooper et al., 2010).

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 a-axis. Hydrogen bonds are shown as dotted lines.
2-N-Benzyl-2,6-dideoxy-2,6-imino-3,4-O-isopropylidene-D-allononitrile top
Crystal data top
C16H20N2O3F(000) = 616
Mr = 288.35Dx = 1.271 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1934 reflections
a = 8.3978 (3) Åθ = 5–27°
b = 11.2689 (4) ŵ = 0.09 mm−1
c = 15.9210 (6) ÅT = 150 K
V = 1506.67 (9) Å3Plate, colourless
Z = 40.4 × 0.4 × 0.2 mm
Data collection top
Nonius KappaCCD
diffractometer		1422 reflections with I > 2.0σ(I)
Graphite monochromatorRint = 0.079
ω scansθmax = 27.5°, θmin = 5.1°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		h = −10→10
Tmin = 0.91, Tmax = 0.98k = −14→14
11529 measured reflectionsl = −20→20
1970 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)] = 0.044H-atom parameters constrained
wR(F2) = 0.121 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: 9.51 13.9 7.19 2.01
S = 0.95(Δ/σ)max = 0.0000939
1970 reflectionsΔρmax = 0.47 e Å−3
190 parametersΔρmin = −0.42 e Å−3
0 restraints
Crystal data top
C16H20N2O3V = 1506.67 (9) Å3
Mr = 288.35Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 8.3978 (3) ŵ = 0.09 mm−1
b = 11.2689 (4) ÅT = 150 K
c = 15.9210 (6) Å0.4 × 0.4 × 0.2 mm
Data collection top
Nonius KappaCCD
diffractometer		1970 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		1422 reflections with I > 2.0σ(I)
Tmin = 0.91, Tmax = 0.98Rint = 0.079
11529 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0440 restraints
wR(F2) = 0.121H-atom parameters constrained
S = 0.95Δρmax = 0.47 e Å−3
1970 reflectionsΔρmin = −0.42 e Å−3
190 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
O10.6465 (3)0.06340 (19)0.37776 (14)0.0305
C20.5963 (4)0.1832 (3)0.37195 (18)0.0259
C30.6544 (4)0.2450 (3)0.29350 (18)0.0245
O40.5816 (3)0.19584 (18)0.21979 (12)0.0272
C50.5779 (4)0.2890 (3)0.15876 (18)0.0261
O60.5489 (3)0.39518 (18)0.20739 (13)0.0271
C70.6006 (4)0.3759 (3)0.29150 (18)0.0256
C80.4595 (4)0.4018 (3)0.35050 (19)0.0263
N90.3478 (3)0.3035 (2)0.34958 (16)0.0261
C100.4160 (4)0.1919 (3)0.38247 (19)0.0270
C110.1968 (4)0.3292 (3)0.3920 (2)0.0318
C120.1021 (4)0.4285 (3)0.35313 (19)0.0274
C130.0911 (5)0.4450 (3)0.26682 (19)0.0315
C14−0.0032 (5)0.5344 (3)0.23328 (19)0.0323
C15−0.0876 (4)0.6088 (3)0.2858 (2)0.0308
C16−0.0756 (5)0.5947 (3)0.3724 (2)0.0343
C170.0182 (4)0.5058 (3)0.4056 (2)0.0292
C180.5178 (5)0.4307 (3)0.4370 (2)0.0328
N190.5612 (5)0.4487 (3)0.50421 (18)0.0470
C200.4377 (4)0.2689 (3)0.1017 (2)0.0328
C210.7352 (5)0.3002 (4)0.1127 (2)0.0385
H210.64690.22600.42010.0308*
H310.77170.23990.28920.0303*
H710.69190.42910.30370.0311*
H810.40520.47240.32890.0310*
H1010.39120.18420.44270.0319*
H1020.36910.12650.35010.0317*
H1110.21870.34780.45190.0382*
H1120.13180.25710.38950.0380*
H1310.15020.39630.23020.0381*
H141−0.00940.54420.17540.0379*
H151−0.15360.66910.26320.0372*
H161−0.13250.64610.40820.0410*
H1710.02550.49570.46420.0353*
H2010.42760.33510.06340.0489*
H2020.34080.26370.13460.0490*
H2030.45270.19720.06980.0487*
H2120.73220.36830.07480.0564*
H2130.82150.31080.15270.0572*
H2110.75410.22750.08040.0572*
H110.59950.02360.33930.0472*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0390 (13)0.0236 (11)0.0289 (11)0.0062 (10)−0.0064 (10)0.0008 (9)
C20.0334 (17)0.0206 (14)0.0237 (14)0.0016 (14)−0.0040 (13)0.0000 (12)
C30.0305 (15)0.0222 (13)0.0208 (13)0.0006 (14)−0.0048 (14)0.0002 (12)
O40.0383 (13)0.0206 (9)0.0227 (10)−0.0004 (11)−0.0020 (10)0.0007 (9)
C50.0354 (17)0.0203 (13)0.0225 (14)−0.0022 (14)0.0008 (14)0.0010 (12)
O60.0408 (13)0.0194 (9)0.0210 (10)−0.0008 (10)−0.0012 (10)−0.0008 (8)
C70.0325 (16)0.0229 (14)0.0214 (14)−0.0036 (13)−0.0041 (14)0.0010 (12)
C80.0354 (18)0.0217 (14)0.0218 (13)−0.0011 (14)−0.0012 (13)0.0010 (12)
N90.0293 (13)0.0201 (12)0.0289 (12)0.0013 (11)0.0032 (12)0.0036 (11)
C100.0359 (17)0.0205 (14)0.0247 (14)0.0011 (14)0.0014 (14)0.0061 (12)
C110.0353 (19)0.0314 (17)0.0285 (16)0.0043 (15)0.0085 (15)0.0053 (14)
C120.0306 (17)0.0264 (15)0.0253 (14)−0.0003 (14)0.0030 (13)0.0033 (13)
C130.0408 (19)0.0280 (15)0.0257 (14)0.0045 (16)0.0066 (15)0.0009 (13)
C140.042 (2)0.0315 (16)0.0236 (15)−0.0002 (16)−0.0002 (15)0.0040 (13)
C150.0306 (17)0.0283 (15)0.0336 (16)0.0003 (15)−0.0043 (15)0.0030 (14)
C160.0340 (19)0.0366 (18)0.0323 (16)0.0076 (16)−0.0012 (15)−0.0040 (14)
C170.0304 (18)0.0315 (17)0.0258 (15)0.0027 (14)0.0001 (14)−0.0024 (13)
C180.046 (2)0.0235 (15)0.0292 (16)0.0004 (16)0.0010 (15)−0.0013 (13)
N190.072 (3)0.0403 (17)0.0285 (15)−0.0022 (19)−0.0039 (16)−0.0078 (13)
C200.0394 (19)0.0299 (17)0.0289 (16)−0.0040 (15)−0.0061 (16)0.0013 (13)
C210.040 (2)0.0405 (19)0.0349 (19)0.0005 (18)0.0091 (16)0.0004 (18)
Geometric parameters (Å, º) top
O1—C21.418 (4)C11—C121.506 (5)
O1—H110.855C11—H1110.993
C2—C31.511 (4)C11—H1120.980
C2—C101.527 (5)C12—C131.390 (4)
C2—H211.000C12—C171.397 (4)
C3—O41.434 (4)C13—C141.388 (5)
C3—C71.543 (4)C13—H1310.942
C3—H310.990C14—C151.381 (5)
O4—C51.431 (3)C14—H1410.929
C5—O61.446 (4)C15—C161.392 (5)
C5—C201.504 (5)C15—H1510.948
C5—C211.516 (5)C16—C171.379 (5)
O6—C71.424 (3)C16—H1610.943
C7—C81.540 (5)C17—H1710.943
C7—H710.992C18—N191.148 (4)
C8—N91.452 (4)C20—H2010.968
C8—C181.498 (4)C20—H2020.970
C8—H810.980C20—H2030.963
N9—C101.477 (4)C21—H2120.976
N9—C111.466 (4)C21—H2130.972
C10—H1010.986C21—H2110.981
C10—H1020.982
C2—O1—H11108.4N9—C10—H102107.3
O1—C2—C3113.4 (3)H101—C10—H102111.1
O1—C2—C10110.4 (3)N9—C11—C12114.5 (3)
C3—C2—C10112.4 (3)N9—C11—H111108.9
O1—C2—H21106.4C12—C11—H111109.6
C3—C2—H21105.9N9—C11—H112107.4
C10—C2—H21107.8C12—C11—H112107.8
C2—C3—O4111.2 (2)H111—C11—H112108.5
C2—C3—C7111.3 (3)C11—C12—C13122.8 (3)
O4—C3—C7103.1 (2)C11—C12—C17118.9 (3)
C2—C3—H31110.6C13—C12—C17118.3 (3)
O4—C3—H31110.2C12—C13—C14121.0 (3)
C7—C3—H31110.2C12—C13—H131119.9
C3—O4—C5106.4 (2)C14—C13—H131119.1
O4—C5—O6104.3 (2)C13—C14—C15120.0 (3)
O4—C5—C20108.4 (3)C13—C14—H141120.0
O6—C5—C20108.4 (3)C15—C14—H141120.0
O4—C5—C21111.8 (3)C14—C15—C16119.6 (3)
O6—C5—C21109.7 (3)C14—C15—H151120.3
C20—C5—C21113.8 (3)C16—C15—H151120.1
C5—O6—C7109.0 (2)C15—C16—C17120.3 (3)
C3—C7—O6104.8 (2)C15—C16—H161119.4
C3—C7—C8113.2 (3)C17—C16—H161120.3
O6—C7—C8108.1 (3)C12—C17—C16120.8 (3)
C3—C7—H71110.3C12—C17—H171118.9
O6—C7—H71109.1C16—C17—H171120.3
C8—C7—H71111.1C8—C18—N19177.4 (4)
C7—C8—N9110.3 (2)C5—C20—H201109.5
C7—C8—C18110.5 (3)C5—C20—H202109.9
N9—C8—C18112.8 (3)H201—C20—H202108.3
C7—C8—H81107.4C5—C20—H203110.1
N9—C8—H81108.4H201—C20—H203109.0
C18—C8—H81107.3H202—C20—H203110.1
C8—N9—C10113.3 (3)C5—C21—H212110.0
C8—N9—C11113.8 (3)C5—C21—H213110.1
C10—N9—C11109.9 (2)H212—C21—H213109.1
C2—C10—N9113.6 (3)C5—C21—H211109.0
C2—C10—H101108.1H212—C21—H211109.6
N9—C10—H101109.8H213—C21—H211109.0
C2—C10—H102107.0
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H11···O6i0.862.052.850 (5)156 (1)
Symmetry code: (i) −x+1, y−1/2, −z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H11···O6i0.8552.0492.850 (5)155.57 (8)
Symmetry code: (i) −x+1, y−1/2, −z+1/2.
 

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 citationAyers, B. J., Jenkinson, S. F., Fleet, G. W. J. & Thompson, A. L. (2012). Acta Cryst. E68, o1474.  CSD CrossRef IUCr Journals 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 citationCooper, R. I., Thompson, A. L. & Watkin, D. J. (2010). J. Appl. Cryst. 43, 1100–1107.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationCosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107.  CrossRef CAS Web of Science IUCr Journals Google Scholar
 First citationNash, R. J., Kato, A., Yu, C.-Y. & Fleet, G. W. J. (2011). Future Med. Chem. 3, 1513–1521.  Web of Science CrossRef CAS PubMed 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 citationPrince, E. (1982). In Mathematical Techniques in Crystallography and Materials Science. New York: Springer-Verlag.  Google Scholar
 First citationWatkin, D. (1994). Acta Cryst. A50, 411–437.  CrossRef CAS Web of Science IUCr Journals 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

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 69| Part 12| December 2013| Page o1772
doi:10.1107/S1600536813030584
Follow Acta Cryst. E
Sign up for e-alerts
E-alerts
Follow Acta Cryst. on Twitter
Twitter
Follow us on facebook
Facebook
Sign up for RSS feeds
RSS