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

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Powder study of 3-aza­bi­cyclo­[3.3.1]nonane-2,4-dione form 2

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aChristopher Ingold Laboratory, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England, bSolid-State Research Group, Department of Pharmaceutical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, Scotland, and cISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, England
*Correspondence e-mail: alastair.florence@strath.ac.uk

(Received 12 May 2006; accepted 19 June 2006; online 28 June 2006)

A polycrystalline sample of a new polymorph of the title compound, C8H11NO2, was produced during a variable-temperature X-ray powder diffraction study. The crystal structure was solved at 1.67 Å resolution by simulated annealing from laboratory powder data collected at 250 K. Subsequent Rietveld refinement yielded an Rwp of 0.070 to 1.54 Å resolution. The structure contains two mol­ecules in the asymmetric unit, which form a C22(8) chain motif via N—H⋯O hydrogen bonds.

Comment

The crystal structure of the title compound, (I)[link], was solved by simulated annealing using laboratory capillary X-ray powder diffraction data. The compound crystallizes in space group P21/c with two independent mol­ecules of 3-aza­bicyclo­nonane-2,4-dione in the asymmetric unit (Fig. 1[link]).

[Scheme 1]

The crystal structure of this polymorph (form 2) is approximately a cell-doubled modification of the stable room-temperature form of 3-aza­bicyclo­nonane-2,4-dione (form 1) (Howie & Skakle, 2001[Howie, R. A. & Skakle, J. M. S. (2001). Acta Cryst. E57, o822-o824.]), with the cell doubling in the c direction [18.8867 (4) versus 9.3384 (6) Å]. Form 2 is metastable with respect to form 1 at room temperature, with full conversion taking less than 1 h. However, with rapid cooling to 250 K (the data collection temperature), form 2 is kinetically trapped and stable for over 10 h.

The basic hydrogen-bond motif in (I)[link] is a chain [graph set C22(8); Etter, 1990[Etter, M. C. (1990). Acc. Chem. Res. 23, 120-126.]] running parallel to the a axis. Each chain contains alternating independent mol­ecules linked by N—H⋯O hydrogen bonds (Table 1[link]). Form 2 packs the chains in a manner similar to form 1, with the chains lying side by side to form layers (Fig. 2[link]) parallel to the ab plane. The layers are related by the 21 screw axis and the stacking of the layers differs between the two forms, with form 1 showing an AB repeat packing and form 2 an ABCD repeat packing (Fig. 3[link]). This stacking difference can be attributed to form 2 having two symmetry-independent mol­ecules. The stacking in form 2 can be envisaged as related to that of form 1 by a translation of approximately half a unit cell parallel to the b axis of the C and D layers. With no strong inter­actions between the layers, the conversion from form 2 to form 1 would be facile and may account for the rapid conversion at room temperature.

[Figure 1]
Figure 1
The asymmetric unit of (I)[link] with the atom-numbering scheme. Displacement spheres are shown at the 50% probability level.
[Figure 2]
Figure 2
Four layers, each containing two ribbons, stacking in an ABCD repeat pattern. The view is parallel to the axis of propagation of the ribbons and the a axis.
[Figure 3]
Figure 3
Overlay of the layer stacking of form 1 (blue) and form 2 (red). The members of the uppermost layer and two bottom layers coincide, while the remaining two layers do not. Hydrogen bonds are shown as dashed lines.
[Figure 4]
Figure 4
Final observed (points), calculated (line) and difference [(yobsycalc)/σ(yobs)] profiles for the Rietveld refinement of the title compound.

Experimental

A polycrystalline sample of (I)[link] was prepared by heating a sample of the raw material (form 1) to 420 K and subsequently quenching in situ to 250 K. The sample was held in a rotating 0.7 mm borosilicate glass capillary and the temperature controlled using an Oxford Cryosystems Cryostream Plus 700 series device. Data were collected over a period of 7.5 h using a variable-counting-time scheme (Shankland et al., 1997[Shankland, K., David, W. I. F. & Sivia, D. S. (1997). J. Mater. Chem. 7, 569-572.]; Hill & Madsen, 2002[Hill, R. J. & Madsen, I. C. (2002). Structure Determination from Powder Diffraction Data, edited by W. I. F. David, K. Shankland, L. B. McCusker & Ch. Baerlocher, pp. 114-116. Oxford University Press.]) in the range 7–60° 2θ. The final data set showed no evidence of diffraction associated with the form 1 structure.

Crystal data
  • C8H11NO2

  • Mr = 153.18

  • Monoclinic, P 21 /c

  • a = 7.67102 (18) Å

  • b = 10.5483 (2) Å

  • c = 18.8867 (4) Å

  • β = 95.5800 (12)°

  • V = 1521.00 (6) Å3

  • Z = 8

  • Dx = 1.338 Mg m−3

  • Cu Kα1 radiation

  • μ = 0.79 mm−1

  • T = 250 K

  • Specimen shape: cylinder

  • 12 × 0.7 × 0.7 mm

  • Specimen prepared at 420 K

  • Particle morphology: polycrystalline mass, white

Data collection
  • Bruker AXS D8 Advance diffractometer

  • Specimen mounting: 0.7 mm borosilicate capillary

  • Specimen mounted in transmission mode

  • Scan method: step

  • Absorption correction: none

  • 2θmin = 7.0, 2θmax = 60.0°

  • Increment in 2θ = 0.017°

Refinement
  • Rp = 0.054

  • Rwp = 0.070

  • Rexp = 0.016

  • RB = 3.058

  • S = 4.31

  • Profile function: Fundamental parameters with axial divergence correction.

  • 142 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • w = 1/σ(Yobs)2

  • (Δ/σ)max = 0.111

  • Preferred orientation correction: a spherical harmonics-based preferred orientation correction (Järvinen, 1993[Järvinen, M. (1993). J. Appl. Cryst. 26, 525-531.]) was applied with TOPAS (Coelho, 2003[Coelho, A. A. (2003). TOPAS. Version 3.1 User Manual. Bruker AXS GmbH, Karlsruhe, Germany.]) during the Rietveld refinement.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O1wi 0.90 (1) 2.11 (1) 3.006 (4) 172 (1)
N1w—H1w⋯O1ii 0.91 (1) 2.03 (1) 2.931 (4) 172 (1)
Symmetry codes: (i) [x+1, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (ii) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}].

The diffraction pattern indexed to a monoclinic cell [M(18) = 28.0, F(18) = 65.9; DICVOL91; Boultif & Louër, 1991[Boultif, A. & Louër, D. (1991). J. Appl. Cryst. 24, 987-993.]] and space group P21/c was assigned from volume considerations and a statistical consideration of the systematic absences (Markvardsen et al., 2001[Markvardsen, A. J., David, W. I. F., Johnson, J. C. & Shankland, K. (2001). Acta Cryst. A57, 47-54.]). P21/a and P21/n were discounted as they did not account for the peak attributable to form 2 at 15.63° 2θ.

The data were background subtracted and truncated to 54.8° 2θ for Pawley fitting (Pawley, 1981[Pawley, G. S. (1981). J. Appl. Cryst. 14, 357-361.]; χ2Pawley = 18.50) and the structure solved using the simulated annealing (SA) global optimization procedure, described previously (David et al., 1998[David, W. I. F., Shankland, K. & Shankland, N. (1998). Chem. Commun. pp. 931-932.]), that is now implemented in the DASH computer program (David et al., 2001[David, W. I. F., Shankland, K., Cole, J., Maginn, S., Motherwell, W. D. S. & Taylor, R. (2001). DASH. Version 3.0 User Manual. Cambridge Crystallographic Data Centre, Cambridge, England.]). The inter­nal coordinate description (including H atoms) of the mol­ecules was constructed from standard bond lengths, bond angles and bond torsions where appropriate. The structure was solved using data to 54.8° 2θ, comprising 402 reflections. The structure was refined against data in the range 7.0–60.0° 2θ (448 reflections). The restraints were set such that bonds and angles did not deviate more than 0.01 Å and 1°, respectively, from their initial values during the refinement. Atoms C1, C5, C4, C2, O1, N1, O2 and H1 (first mol­ecule) and atoms C1w, C5w, C4w, C1w, O1w, N1w, O2w and H1w (second mol­ecule) of 3-aza­bicyclo­[3.3.1]nonane-2,4-dione were restrained to be coplanar.

The SA structure solution involved the optimization of two independent mol­ecules totaling 12 degrees of freedom (positional and orientational). All degrees of freedom were assigned random values at the start of the simulated annealing run. The best SA solution had a favourable χ2SA/χ2Pawley ratio of 4.5, had a chemically reasonable packing arrangement and exhibited no significant misfit to the data.

The solved structure was subsequently refined against data in the range 7.0–60.0° 2θ using a restrained Rietveld (1969[Rietveld, H. M. (1969). J. Appl. Cryst. 2, 65-71.]) method as implemented in TOPAS (Coelho, 2003[Coelho, A. A. (2003). TOPAS. Version 3.1 User Manual. Bruker AXS GmbH, Karlsruhe, Germany.]), with Rwp falling to 0.0698 during the refinement. All atomic positions (including H atoms) for the structure of (I)[link] were refined, subject to a series of restraints on bond lengths, bond angles and planarity. A spherical harmonics (8th order) correction of intensities for preferred orientation was applied in the final refinement (Järvinen, 1993[Järvinen, M. (1993). J. Appl. Cryst. 26, 525-531.]). An 8th order correction yielded a significant improvement in Rwp compared with lower orders. The need for such a high level of correction is most likely due to the effect of the in situ method of sample preparation on particle morphology. The observed and calculated diffraction patterns for the refined crystal structure are shown in Fig. 4[link].

Data collection: DIFFRAC plus XRD Commander (Kienle & Jacob, 2003[Kienle, M. & Jacob, M. (2003). DIFFRAC plus XRD Commander. Version 2.3. Bruker AXS GmbH, Karlsruhe, Germany.]); cell refinement: TOPAS (Coelho, 2003[Coelho, A. A. (2003). TOPAS. Version 3.1 User Manual. Bruker AXS GmbH, Karlsruhe, Germany.]); data reduction: DASH (David et al., 2001[David, W. I. F., Shankland, K., Cole, J., Maginn, S., Motherwell, W. D. S. & Taylor, R. (2001). DASH. Version 3.0 User Manual. Cambridge Crystallographic Data Centre, Cambridge, England.]); program(s) used to solve structure: DASH; program(s) used to refine structure: TOPAS; molecular graphics: MERCURY (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]) and PLATON (Spek, 2003[Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.]); software used to prepare material for publication: enCIFer (Version 1.1; Allen et al., 2004[Allen, F. H., Johnson, O., Shields, G. P., Smith, B. R. & Towler, M. (2004). J. Appl. Cryst. 37, 335-338.]).

Supporting information


Computing details top

Data collection: DIFFRAC plus XRD Commander (Kienle & Jacob, 2003); data reduction: DASH (David et al., 2001); program(s) used to solve structure: DASH; program(s) used to refine structure: TOPAS (Coelho, 2003); software used to prepare material for publication: enCIFer (Version 1.1; Allen et al., 2004).

3-Azabicyclo[3.3.1]nonane-2,4-dione top
Crystal data top
C8H11NO2Z = 8
Mr = 153.18F(000) = 656.0
Monoclinic, P21/cDx = 1.338 Mg m3
Hall symbol: -P 2ybcCu Kα1 radiation, λ = 1.54056 Å
a = 7.67102 (18) ŵ = 0.79 mm1
b = 10.5483 (2) ÅT = 250 K
c = 18.8867 (4) Åwhite
β = 95.5800 (12)°cylinder, 12 × 0.7 mm
V = 1521.00 (6) Å3Specimen preparation: Prepared at 420 K
Data collection top
Bruker AXS D8 Advance
diffractometer
Data collection mode: transmission
Radiation source: sealed X-ray tube, Bruker-AXS D8Scan method: step
Primary focussing, Ge 111 monochromator2θmin = 7.0°, 2θmax = 60.0°, 2θstep = 0.017°
Specimen mounting: 0.7 mm borosilicate capillary
Refinement top
Least-squares matrix: selected elements only92 restraints
Rp = 0.0542 constraints
Rwp = 0.070H atoms treated by a mixture of independent and constrained refinement
Rexp = 0.016Weighting scheme based on measured s.u.'s 1/σ(Yobs)2
RBragg = 3.058(Δ/σ)max = 0.111
3070 data pointsBackground function: Chebyshev polynomial
Profile function: Fundamental parameters with axial divergence correction.Preferred orientation correction: A spherical harmonics-based preferred orientation correction (Järvinen, 1993) was applied with Topas during the Rietveld refinement.
142 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.7188 (2)0.20485 (14)0.59572 (18)0.0380*
H10.8105 (12)0.1517 (6)0.5942 (4)0.0760*
C10.5536 (2)0.14964 (16)0.5933 (2)0.0380*
O10.5397 (5)0.0342 (2)0.5915 (3)0.0380*
C20.3992 (2)0.23660 (16)0.59562 (9)0.0380*
H20.3033 (12)0.1955 (6)0.5695 (4)0.0760*
C30.4373 (2)0.36391 (16)0.56342 (9)0.0380*
H3A0.3414 (11)0.4204 (6)0.5661 (4)0.0760*
H3B0.4527 (10)0.3553 (6)0.5143 (5)0.0760*
C40.6000 (2)0.41980 (16)0.60445 (9)0.0380*
H40.6326 (12)0.4984 (6)0.5846 (4)0.0760*
C50.7548 (2)0.33355 (17)0.5989 (2)0.0380*
O20.9060 (3)0.3689 (3)0.6007 (3)0.0380*
C60.5709 (2)0.43895 (15)0.68362 (8)0.0380*
H6A0.4815 (11)0.5017 (6)0.6831 (4)0.0760*
H6B0.6770 (13)0.4725 (6)0.7066 (4)0.0760*
C70.5134 (2)0.31638 (15)0.71761 (9)0.0380*
H7A0.6069 (11)0.2563 (6)0.7206 (5)0.0760*
H7B0.4810 (10)0.3317 (7)0.7643 (4)0.0760*
C80.3599 (2)0.25471 (16)0.67356 (9)0.0380*
H8A0.3286 (11)0.1746 (7)0.6922 (4)0.0760*
H8B0.2564 (12)0.3047 (6)0.6726 (4)0.0760*
N1w0.2227 (2)0.62126 (15)0.0902 (3)0.0380*
H1w0.3151 (11)0.5676 (6)0.0925 (6)0.0760*
C1w0.0572 (2)0.56668 (17)0.0834 (3)0.0380*
O1w0.0443 (5)0.4507 (3)0.0867 (4)0.0380*
C2w0.0968 (2)0.65429 (15)0.08651 (9)0.0380*
H2w0.1932 (11)0.6143 (6)0.0598 (4)0.0760*
C3w0.0589 (2)0.78378 (15)0.05587 (9)0.0380*
H3Aw0.1535 (11)0.8405 (6)0.0603 (4)0.0760*
H3Bw0.0449 (10)0.7782 (6)0.0064 (4)0.0760*
C4w0.1043 (2)0.83674 (16)0.09717 (9)0.0380*
H4w0.1381 (12)0.9151 (7)0.0777 (4)0.0760*
C5w0.2583 (2)0.75006 (17)0.0912 (2)0.0380*
O2w0.4093 (3)0.7853 (3)0.0928 (4)0.0380*
C6w0.0742 (2)0.85581 (15)0.17599 (8)0.0380*
H6Aw0.0119 (11)0.9206 (7)0.1752 (4)0.0760*
H6Bw0.1815 (12)0.8864 (7)0.1993 (4)0.0760*
C7w0.0097 (2)0.73736 (16)0.21080 (9)0.0380*
H7Aw0.1038 (12)0.6790 (6)0.2192 (5)0.0760*
H7Bw0.0318 (10)0.7583 (7)0.2553 (4)0.0760*
C8w0.1364 (2)0.66815 (17)0.16490 (9)0.0380*
H8Aw0.1579 (11)0.5853 (7)0.1828 (4)0.0760*
H8Bw0.2463 (12)0.7112 (6)0.1643 (4)0.0760*
Geometric parameters (Å, º) top
O1—C11.223 (3)C6—H6B0.953 (9)
O2—C51.216 (3)C7—H7B0.953 (8)
O1W—C1W1.230 (4)C7—H7A0.955 (8)
O2W—C5W1.214 (3)C8—H8B0.952 (9)
N1—C51.386 (2)C8—H8A0.955 (8)
N1—C11.391 (2)C1W—C2W1.506 (2)
N1—H10.902 (8)C2W—C8W1.547 (2)
N1W—C5W1.386 (2)C2W—C3W1.523 (2)
N1W—C1W1.389 (2)C3W—C4W1.516 (2)
N1W—H1W0.905 (8)C4W—C5W1.507 (2)
C1—C21.502 (2)C4W—C6W1.542 (2)
C2—C31.514 (2)C6W—C7W1.517 (2)
C2—C81.543 (2)C7W—C8W1.534 (2)
C3—C41.522 (2)C2W—H2W0.952 (8)
C4—C61.546 (2)C3W—H3AW0.951 (8)
C4—C51.508 (2)C3W—H3BW0.953 (8)
C6—C71.528 (2)C4W—H4W0.951 (8)
C7—C81.520 (2)C6W—H6AW0.950 (8)
C2—H20.950 (8)C6W—H6BW0.951 (9)
C3—H3B0.951 (8)C7W—H7AW0.950 (8)
C3—H3A0.952 (8)C7W—H7BW0.953 (8)
C4—H40.953 (7)C8W—H8AW0.957 (8)
C6—H6A0.953 (8)C8W—H8BW0.957 (9)
C1—N1—C5126.06 (15)C7—C8—H8A112.7 (5)
C1—N1—H1116.7 (5)C2—C8—H8A108.8 (5)
C5—N1—H1117.2 (5)C2—C8—H8B106.9 (5)
C1W—N1W—C5W125.81 (16)O1W—C1W—N1W119.0 (2)
C5W—N1W—H1W117.4 (5)N1W—C1W—C2W117.11 (16)
C1W—N1W—H1W116.7 (5)O1W—C1W—C2W122.8 (2)
O1—C1—N1119.6 (2)C1W—C2W—C8W108.9 (2)
N1—C1—C2117.50 (14)C3W—C2W—C8W109.98 (14)
O1—C1—C2122.8 (2)C1W—C2W—C3W110.87 (16)
C1—C2—C8109.34 (19)C2W—C3W—C4W108.28 (14)
C3—C2—C8109.67 (14)C3W—C4W—C6W110.56 (13)
C1—C2—C3110.26 (14)C3W—C4W—C5W110.62 (16)
C2—C3—C4108.64 (13)C5W—C4W—C6W110.10 (18)
C3—C4—C6110.76 (13)O2W—C5W—C4W124.4 (2)
C3—C4—C5110.07 (16)N1W—C5W—C4W116.18 (14)
C5—C4—C6109.56 (18)O2W—C5W—N1W119.1 (2)
O2—C5—C4124.7 (2)C4W—C6W—C7W113.38 (13)
N1—C5—C4116.06 (14)C6W—C7W—C8W113.47 (14)
O2—C5—N1119.2 (2)C2W—C8W—C7W112.66 (13)
C4—C6—C7111.75 (13)C1W—C2W—H2W106.2 (5)
C6—C7—C8111.85 (13)C3W—C2W—H2W111.3 (4)
C2—C8—C7111.24 (13)C8W—C2W—H2W109.5 (5)
C1—C2—H2106.2 (5)C2W—C3W—H3AW110.8 (5)
C3—C2—H2111.5 (4)C2W—C3W—H3BW111.2 (4)
C8—C2—H2109.8 (5)C4W—C3W—H3AW108.8 (5)
C2—C3—H3A110.7 (5)C4W—C3W—H3BW111.2 (5)
H3A—C3—H3B106.4 (6)H3AW—C3W—H3BW106.6 (6)
C2—C3—H3B110.8 (4)C3W—C4W—H4W111.3 (5)
C4—C3—H3A109.3 (5)C5W—C4W—H4W104.7 (6)
C4—C3—H3B111.1 (5)C6W—C4W—H4W109.4 (5)
C3—C4—H4111.7 (5)C4W—C6W—H6AW104.4 (5)
C5—C4—H4105.0 (5)C4W—C6W—H6BW106.7 (5)
C6—C4—H4109.6 (5)C7W—C6W—H6AW110.1 (5)
C7—C6—H6B113.1 (4)C7W—C6W—H6BW112.5 (5)
H6A—C6—H6B109.2 (6)H6AW—C6W—H6BW109.4 (7)
C4—C6—H6A104.6 (5)C6W—C7W—H7AW109.4 (5)
C4—C6—H6B107.0 (5)C6W—C7W—H7BW110.0 (5)
C7—C6—H6A110.8 (5)C8W—C7W—H7AW106.7 (5)
C6—C7—H7B110.9 (5)C8W—C7W—H7BW108.7 (5)
H7A—C7—H7B108.7 (7)H7AW—C7W—H7BW108.4 (7)
C8—C7—H7A106.6 (5)C2W—C8W—H8AW108.0 (5)
C6—C7—H7A109.9 (5)C2W—C8W—H8BW106.8 (5)
C8—C7—H7B108.7 (5)C7W—C8W—H8AW112.1 (5)
C7—C8—H8B111.9 (5)C7W—C8W—H8BW112.1 (5)
H8A—C8—H8B105.0 (7)H8AW—C8W—H8BW104.8 (7)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1Wi0.90 (1)2.11 (1)3.006 (4)172 (1)
N1W—H1W···O1ii0.91 (1)2.03 (1)2.931 (4)172 (1)
C2—H2···O1Wiii0.95 (1)2.56 (1)3.355 (4)141 (1)
C3W—H3BW···O2iv0.95 (1)2.56 (1)3.406 (5)148 (1)
C3—H3B···O2Wv0.95 (1)2.49 (1)3.384 (7)158 (1)
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x, y+1/2, z1/2; (iii) x, y+1/2, z+1/2; (iv) x+1, y+1/2, z+1/2; (v) x+1, y1/2, z+1/2.
 

Acknowledgements

We thank the Basic Technology programme of the UK Research Councils for funding under the project Control and Prediction of the Organic Solid State (https://www.cposs.org.uk). We also thank the EPSRC for grant GR/N07462/01.

References

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