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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 60| Part 9| September 2004| Pages o1463-o1464
https://doi.org/10.1107/S1600536804018665

3-epi-Casuarine monohydrate

CROSSMARK_Color_square_no_text.svg
Christopher Newton,a Jeroen van Ameijde,b George W. J. Fleet,b Robert J. Nashc and David J. Watkina*

aDepartment of Chemical Crystallography, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, bDepartment of Organic Chemistry, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, and cMolecular Nature Ltd, Institute of Grassland and Environmental Research, Aberystwyth SY23 3EB, Dyfed, Wales
*Correspondence e-mail: david.watkin@chem.ox.ac.uk

(Received 18 June 2004; accepted 29 July 2004; online 7 August 2004)

The title compound [systematic name: (1R,2R,3S,6S,7S,7aR)-3-hydroxy­methyl-1,2,6,7-tetra­hydroxy­pyrrolizidine monohydrate or (2S,3R,4R,5R,6S,7S)-2-hydroxy­methyl-1-aza­bi­cyclo[3.3.0]octan-3,4,6,7-tetraol monohydrate], C8H15NO5·H2O, was formed in a synthetic sequence in which there were several ambiguities in the stereochemistry of the reactions. Its crystal structure was determined to resolve these ambiguities.

Comment

3-epi-Casuarine, (1[link]), is a synthetic epimer of the natural product casuarine, (2[link]) (Nash et al., 1994[Nash, R. J., Thomas, P. I., Waigh, R. D., Fleet, G. W. J., Wormald, M. R., Lilley, P. M. Q. & Watkin, D. J. (1994). Tetrahedron Lett. 35, 7849-7852.]), the most heavily oxy­genated of the poly­hydroxy­lated alkaloids which can be viewed as sugar mimics. Although the 6-α-D-glucoside of (2[link]) is also a natural product (Wormald et al., 1996[Wormald, M. R., Nash, R. J., Watson, A. A., Bhadoria, B. K., Langford, R., Sim, M. & Fleet, G. W. J. (1996). Carbohydr. Lett. 2, 169-174.]), as yet no other diastereomers of casuarine have been isolated as natural products. In contrast, since the initial isolation of alexine (3[link]) (without a hydroxyl group at C6) (Fellows et al., 1988[Fellows, L. E., Nash, R. J., Dring, J. V., Derome, A. E., Hamor, T. A., Scofield, A. M., Watkin, D. J. & Fleet, G. W. J. (1988). Tetrahedron Lett. 29, 2487-2490.]), a number of stereoisomers have been isolated (Asano et al., 2000[Asano, N., Nash, R. J., Molyneux, R. J. & Fleet, G. W. J. (2000). Tetrahedron Asymmetry, 11, 1645-1680.]).[link]

[Scheme 1]

A combination of crystal structures and NMR studies have firmly established solid-state and solution conformations of a number of stereoisomers of alexine (Wormald et al., 1998[Wormald, M. R., Nash, R. J., Hrnicar, P., White, J. D., Molyneux, R. J. & Fleet, G. W. J. (1998). Tetrahedron Asymmetry, 9, 2549-2558.]; Kato et al., 2003[Kato, A., Kano, E., Adachi, I., Molyneux, R. J., Watson, A. A., Nash, R. J., Fleet, G. W. J., Wormald, M. R., Kizu, H., Ikeda, K. & Asano, N. (2003). Tetrahedron Asymmetry, 14, 325-331.]), which may be used to rationalize their biological activity. Studies on the epimers of casuarine at present are scant (Bell et al., 1997[Bell, A. A., Pickering, L., Watson, A. A., Nash, R. J., Pan, Y. T., Elbein, A. D. & Fleet, G. W. J. (1997). Tetrahedron Lett. 38, 5869-5872.]). Since coupling constants are notoriously unreliable in assigning the relative configuration at stereogenic centres in five-membered ring systems, a crystal structure was necessary to firmly establish the structure of the title compound, (1[link]), and to allow comparison of the solution and solid-state conformation; this may allow the development of rationales for the glycosidase inhibition of casuarines.

Fig. 1[link] shows the asymmetric unit of (1[link]). The open O—H bonds shown are to one of each pair of disordered H atoms. The crystal structure consists of a three-dimensional hydrogen-bonded network. Of particular interest is the hydrogen-bonded ring shown in Fig. 2[link]. Because this ring straddles a twofold rotation axis, the hydrogen bonds in it are necessarily disordered and the H atoms have occupancy factors of exactly one-half.

[Figure 1]
Figure 1
The asymmetric unit of (1), with displacement ellipsoids drawn at the 50% probability level. H-atom radii are arbitary. Unfilled O—H bonds indicate one of each pair of disordered H-atom positions.
[Figure 2]
Figure 2
Partial packing diagram showing how the disorder in the hydrogen-bonded network results from the crystallographic twofold axis lying horizontally across the figure. The mol­ecule containing atom O14′ is generated by the symmetry code (2 − y, −x, ½ − z) and that containing atom O7′′ by (1 + x, 2 − y, z). Hydro­gen bonds are shown as dotted lines.

Experimental

The title compound (Nash et al., 2004[Nash, R. J., Thomas, P. I., Waigh, R. D., Fleet, G. W. J. & Wormald, M. R. (2004). In preparation.]) was recrystallized from 1,4-dioxane to give colourless prismatic crystals.

Crystal data

  • C8H15NO5·H2O

  • Mr = 223.23

  • Tetragonal, P41212

  • a = 7.6230 (2) Å

  • c = 33.8174 (10) Å

  • V = 1965.13 (9) Å3

  • Z = 8

  • Dx = 1.509 Mg m−3

  • Mo Kα radiation

  • Cell parameters from 1241 reflections

  • θ = 5–27°

  • μ = 0.13 mm−1

  • T = 150 K

  • Prism, colourless

  • 0.40 × 0.20 × 0.20 mm
Data collection

  • Nonius KappaCCD diffractometer

  • ω scans

  • 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 and R. M. Sweet, pp. 307-326. New York: Academic Press.]) Tmin = 0.96, Tmax = 0.97

  • 9161 measured reflections

  • 1372 independent reflections

  • 1372 reflections with I > −3σ(I)

  • Rint = 0.021

  • θmax = 27.5°

  • h = −9 → 9

  • k = −6 → 7

  • l = −42 → 43
Refinement

  • Refinement on F2

  • R[F2>2σ(F2)] = 0.047

  • wR(F2) = 0.072

  • S = 1.01

  • 1372 reflections

  • 199 parameters

  • H atoms: only coordinates refined

  • w = 1/[σ2(F) + (0.029P)2 + 0.165P], where P = [max(Fo2,0) + 2Fc2]/3

  • (Δ/σ)max < 0.001

  • Δρmax = 0.35 e Å−3

  • Δρmin = −0.34 e Å−3

Table 1
Selected geometric parameters (Å, °)

C1—C5 1.528 (3)
C1—C12 1.530 (3)
C1—N2 1.509 (2)
C3—C4 1.531 (3)
C3—C8 1.511 (3)
C3—N2 1.494 (3)
C4—C5 1.526 (3)
C4—O7 1.431 (2)
C5—O6 1.428 (2)
C8—O9 1.433 (2)
C10—C11 1.524 (3)
C10—N2 1.494 (2)
C11—C12 1.517 (3)
C11—O14 1.418 (2)
C12—O13 1.420 (2)
C5—C1—C12 116.88 (16)
C5—C1—N2 106.92 (15)
C12—C1—N2 105.52 (15)
C4—C3—C8 115.05 (17)
C4—C3—N2 105.52 (15)
C8—C3—N2 116.31 (16)
C3—C4—C5 101.50 (16)
C3—C4—O7 109.85 (17)
C5—C4—O7 109.04 (15)
C1—C5—C4 103.35 (16)
C1—C5—O6 107.24 (16)
C4—C5—O6 111.76 (15)
C3—C8—O9 109.04 (16)
C11—C10—N2 103.10 (16)
C10—C11—C12 101.71 (17)
C10—C11—O14 112.16 (18)
C12—C11—O14 114.32 (16)
C1—C12—C11 102.10 (16)
C1—C12—O13 113.73 (16)
C11—C12—O13 114.58 (17)
C1—N2—C3 106.05 (15)
C1—N2—C10 107.10 (14)
C3—N2—C10 117.00 (16)

H atoms were found in difference maps and refined with Uiso = 0.02 Å2. In the absence of significant anomalous dispersion effects, Friedel pairs were averaged.

Data collection: COLLECT (Nonius, 1997[Nonius (1997). COLLECT. Nonius BV, Deflt, The Netherlands.]); cell refinement: DENZO/SCALEPACK; data reduction: 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 and R. M. Sweet, pp. 307-326. New York: Academic Press.]); structure solution: 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.]); structure refinement: 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.]).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536804018665/cf6365sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536804018665/cf6365Isup2.hkl


Computing details top

Data collection: COLLECT (Nonius, 1997); cell refinement: DENZO/SCALEPACK; data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1996); 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.

(1R,2R,3S,6S,7S,7aR)-3-Hydroxymethyl-1,2,6,7- tetrahydroxypyrrolizidine monohydrate or (2S,3R,4R,5R,6S,7S)-2-Hydroxymethyl- 1-azabicyclo[3.3.0]-octan-3,4,6,7-tetraol monohydrate top
Crystal data top
C8H15NO5·H2ODx = 1.509 Mg m−3
Mr = 223.23Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P41212Cell parameters from 1241 reflections
a = 7.6230 (2) Åθ = 5–27°
c = 33.8174 (10) ŵ = 0.13 mm−1
V = 1965.13 (9) Å3T = 150 K
Z = 8Prism, colourless
F(000) = 9600.40 × 0.20 × 0.20 mm
Data collection top
Nonius KappaCCD
diffractometer		1372 reflections with I > −3σ(I)
Graphite monochromatorRint = 0.021
ω scansθmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan
DENZO/SCALEPACK (Otwinowski & Minor, 1997)		h = −9→9
Tmin = 0.96, Tmax = 0.97k = −6→7
9161 measured reflectionsl = −42→43
1372 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)] = 0.047Only H-atom coordinates refined
wR(F2) = 0.072 w = 1/[σ2(F) + (0.029P)2 + 0.165P],
where P = [max(Fo2,0) + 2Fc2]/3
S = 1.01(Δ/σ)max = 0.000220
1372 reflectionsΔρmax = 0.35 e Å−3
199 parametersΔρmin = −0.34 e Å−3
48 restraints
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
C10.5890 (3)0.6822 (3)0.32134 (5)0.0133
C30.4333 (3)0.9335 (3)0.34563 (5)0.0126
C40.3029 (3)0.8110 (3)0.32505 (5)0.0147
C50.3967 (3)0.6348 (3)0.32832 (5)0.0134
C80.3964 (3)1.1270 (3)0.34060 (5)0.0147
C100.6936 (3)0.9642 (3)0.29892 (5)0.0159
C110.7902 (3)0.8174 (3)0.27746 (5)0.0153
C120.6562 (3)0.6704 (3)0.27879 (5)0.0144
N20.6108 (2)0.8718 (2)0.33311 (4)0.0123
O11.0215 (3)0.4208 (2)0.30776 (4)0.0344
O60.38422 (19)0.56342 (18)0.36727 (4)0.0166
O70.2878 (2)0.8576 (2)0.28420 (4)0.0193
O90.5046 (2)1.2241 (2)0.36747 (4)0.0208
O130.7232 (2)0.5026 (2)0.26855 (4)0.0224
O140.8418 (2)0.8671 (2)0.23878 (4)0.0223
H110.664 (2)0.607 (2)0.3385 (4)0.0200*
H310.423 (2)0.909 (2)0.3747 (4)0.0200*
H410.188 (2)0.813 (2)0.3375 (4)0.0200*
H510.352 (2)0.550 (2)0.3088 (4)0.0200*
H610.296 (2)0.592 (3)0.3792 (6)0.0200*
H710.243 (5)0.779 (4)0.2713 (9)0.0200*0.5000
H720.241 (6)0.952 (4)0.2811 (13)0.0200*0.5000
H810.272 (2)1.145 (2)0.3473 (5)0.0200*
H820.417 (2)1.166 (2)0.3136 (4)0.0200*
H910.468 (3)1.328 (2)0.3688 (6)0.0200*
H1010.775 (2)1.056 (2)0.3078 (5)0.0200*
H1020.604 (2)1.017 (2)0.2816 (5)0.0200*
H1110.895 (2)0.779 (2)0.2922 (4)0.0200*
H1210.562 (2)0.702 (2)0.2606 (5)0.0200*
H1310.800 (4)0.473 (6)0.2828 (11)0.0200*0.5000
H1320.663 (5)0.447 (5)0.2536 (11)0.0200*0.5000
H1410.761 (4)0.885 (6)0.2234 (10)0.0200*0.5000
H1420.930 (7)0.815 (6)0.2300 (12)0.0200*0.5000
H10010.926 (3)0.426 (7)0.2982 (13)0.0200*0.5000
H10021.010 (3)0.375 (3)0.3294 (5)0.0200*
H10031.053 (6)0.343 (5)0.2936 (11)0.0200*0.5000
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0161 (11)0.0120 (11)0.0116 (8)0.0011 (9)−0.0005 (8)0.0002 (8)
C30.0128 (11)0.0135 (11)0.0114 (8)0.0018 (9)0.0009 (8)−0.0009 (8)
C40.0159 (11)0.0163 (11)0.0118 (8)0.0004 (9)−0.0007 (9)0.0000 (8)
C50.0164 (11)0.0124 (11)0.0114 (9)−0.0010 (9)0.0006 (8)−0.0008 (8)
C80.0158 (11)0.0145 (11)0.0137 (8)−0.0005 (9)−0.0025 (9)−0.0004 (8)
C100.0165 (11)0.0163 (12)0.0150 (9)−0.0017 (9)0.0021 (9)0.0015 (8)
C110.0152 (11)0.0196 (12)0.0112 (9)0.0005 (9)0.0013 (8)0.0024 (9)
C120.0134 (11)0.0165 (11)0.0132 (9)0.0039 (9)−0.0004 (8)−0.0023 (8)
N20.0128 (9)0.0114 (9)0.0127 (7)0.0003 (8)0.0004 (7)0.0000 (7)
O10.0557 (13)0.0293 (11)0.0182 (8)0.0015 (10)−0.0030 (9)0.0012 (7)
O60.0176 (8)0.0165 (8)0.0158 (7)0.0029 (7)0.0053 (6)0.0030 (6)
O70.0231 (9)0.0196 (9)0.0153 (7)0.0012 (8)−0.0061 (7)0.0009 (7)
O90.0291 (10)0.0113 (8)0.0219 (7)0.0017 (7)−0.0074 (7)−0.0043 (7)
O130.0246 (10)0.0187 (9)0.0240 (8)0.0048 (8)0.0022 (7)−0.0084 (7)
O140.0229 (9)0.0303 (10)0.0136 (7)0.0024 (8)0.0049 (7)0.0030 (7)
Geometric parameters (Å, º) top
C1—C51.528 (3)C10—H1010.983 (15)
C1—C121.530 (3)C10—H1020.985 (15)
C1—N21.509 (2)C11—C121.517 (3)
C1—H110.993 (15)C11—O141.418 (2)
C3—C41.531 (3)C11—H1110.986 (15)
C3—C81.511 (3)C12—O131.420 (2)
C3—N21.494 (3)C12—H1210.974 (14)
C3—H311.003 (14)O1—H10010.800 (18)
C4—C51.526 (3)O1—H10020.815 (15)
C4—O71.431 (2)O1—H10030.801 (18)
C4—H410.975 (15)O6—H610.814 (15)
C5—O61.428 (2)O7—H710.814 (18)
C5—H510.985 (15)O7—H720.812 (19)
C8—O91.433 (2)O9—H910.838 (15)
C8—H810.985 (15)O13—H1310.791 (18)
C8—H820.973 (14)O13—H1320.804 (17)
C10—C111.524 (3)O14—H1410.816 (18)
C10—N21.494 (2)O14—H1420.83 (5)
C5—C1—C12116.88 (16)C11—C10—H102110.5 (10)
C5—C1—N2106.92 (15)N2—C10—H102111.0 (10)
C12—C1—N2105.52 (15)H101—C10—H102109.1 (12)
C5—C1—H11109.0 (10)C10—C11—C12101.71 (17)
C12—C1—H11108.8 (9)C10—C11—O14112.16 (18)
N2—C1—H11109.5 (10)C12—C11—O14114.32 (16)
C4—C3—C8115.05 (17)C10—C11—H111111.7 (10)
C4—C3—N2105.52 (15)C12—C11—H111108.2 (10)
C8—C3—N2116.31 (16)O14—C11—H111108.6 (9)
C4—C3—H31106.5 (10)C1—C12—C11102.10 (16)
C8—C3—H31105.9 (10)C1—C12—O13113.73 (16)
N2—C3—H31107.0 (10)C11—C12—O13114.58 (17)
C3—C4—C5101.50 (16)C1—C12—H121109.5 (10)
C3—C4—O7109.85 (17)C11—C12—H121106.9 (10)
C5—C4—O7109.04 (15)O13—C12—H121109.6 (10)
C3—C4—H41112.1 (10)C1—N2—C3106.05 (15)
C5—C4—H41114.1 (10)C1—N2—C10107.10 (14)
O7—C4—H41109.9 (9)C3—N2—C10117.00 (16)
C1—C5—C4103.35 (16)H1001—O1—H1002107 (4)
C1—C5—O6107.24 (16)H1001—O1—H100394 (5)
C4—C5—O6111.76 (15)H1002—O1—H1003104 (4)
C1—C5—H51112.6 (10)C5—O6—H61114.2 (15)
C4—C5—H51111.5 (10)C4—O7—H71112 (3)
O6—C5—H51110.2 (9)C4—O7—H72112 (3)
C3—C8—O9109.04 (16)H71—O7—H72113 (4)
C3—C8—H81106.8 (10)C8—O9—H91109.2 (14)
O9—C8—H81109.6 (10)C12—O13—H131112 (3)
C3—C8—H82111.9 (10)C12—O13—H132115 (3)
O9—C8—H82110.1 (10)H131—O13—H132131 (5)
H81—C8—H82109.3 (12)C11—O14—H141115 (3)
C11—C10—N2103.10 (16)C11—O14—H142115 (3)
C11—C10—H101111.5 (10)H141—O14—H142117 (4)
N2—C10—H101111.5 (9)
 

References

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ISSN: 2056-9890
Volume 60| Part 9| September 2004| Pages o1463-o1464
https://doi.org/10.1107/S1600536804018665
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