organic compounds
Powder study of 3-azabicyclo[3.3.1]nonane-2,4-dione form 2
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
A polycrystalline sample of a new polymorph of the title compound, C8H11NO2, was produced during a variable-temperature X-ray powder diffraction study. The was solved at 1.67 Å resolution by simulated annealing from laboratory powder data collected at 250 K. Subsequent yielded an Rwp of 0.070 to 1.54 Å resolution. The structure contains two molecules in the which form a C22(8) chain motif via N—H⋯O hydrogen bonds.
Comment
The , was solved by simulated annealing using laboratory capillary X-ray powder diffraction data. The compound crystallizes in P21/c with two independent molecules of 3-azabicyclononane-2,4-dione in the (Fig. 1).
of the title compound, (I)The ), 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.
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, 2001The basic hydrogen-bond motif in (I) is a chain [graph set C22(8); Etter, 1990] running parallel to the a axis. Each chain contains alternating independent molecules linked by N—H⋯O hydrogen bonds (Table 1). Form 2 packs the chains in a manner similar to form 1, with the chains lying side by side to form layers (Fig. 2) 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). 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 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.
Experimental
A polycrystalline sample of (I) 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; Hill & Madsen, 2002) in the range 7–60° 2θ. The final data set showed no evidence of diffraction associated with the form 1 structure.
Crystal data
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Data collection
|
Refinement
The diffraction pattern indexed to a monoclinic cell [M(18) = 28.0, F(18) = 65.9; DICVOL91; Boultif & Louër, 1991] and P21/c was assigned from volume considerations and a statistical consideration of the (Markvardsen et al., 2001). 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; χ2Pawley = 18.50) and the structure solved using the simulated annealing (SA) global optimization procedure, described previously (David et al., 1998), that is now implemented in the DASH computer program (David et al., 2001). 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 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 χ2SA/χ2Pawley ratio of 4.5, had a chemically reasonable packing arrangement and exhibited no significant misfit to the data.
(positional and orientational). All were assigned random values at the start of the simulated annealing run. The best SA solution had a favourableThe solved structure was subsequently refined against data in the range 7.0–60.0° 2θ using a restrained Rietveld (1969) method as implemented in TOPAS (Coelho, 2003), with Rwp falling to 0.0698 during the All atomic positions (including H atoms) for the structure of (I) were refined, subject to a series of restraints on bond lengths, bond angles and planarity. A spherical harmonics (8th order) correction of intensities for was applied in the final (Järvinen, 1993). 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 are shown in Fig. 4.
Data collection: DIFFRAC plus XRD Commander (Kienle & Jacob, 2003); cell TOPAS (Coelho, 2003); data reduction: DASH (David et al., 2001); program(s) used to solve structure: DASH; program(s) used to refine structure: TOPAS; molecular graphics: MERCURY (Macrae et al., 2006) and PLATON (Spek, 2003); software used to prepare material for publication: enCIFer (Version 1.1; Allen et al., 2004).
Supporting information
https://doi.org/10.1107/S1600536806023312/cv2057sup1.cif
contains datablocks global, I. DOI:Rietveld powder data: contains datablock I. DOI: https://doi.org/10.1107/S1600536806023312/cv2057Isup2.rtv
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).
C8H11NO2 | Z = 8 |
Mr = 153.18 | F(000) = 656.0 |
Monoclinic, P21/c | Dx = 1.338 Mg m−3 |
Hall symbol: -P 2ybc | Cu Kα1 radiation, λ = 1.54056 Å |
a = 7.67102 (18) Å | µ = 0.79 mm−1 |
b = 10.5483 (2) Å | T = 250 K |
c = 18.8867 (4) Å | white |
β = 95.5800 (12)° | cylinder, 12 × 0.7 mm |
V = 1521.00 (6) Å3 | Specimen preparation: Prepared at 420 K |
Bruker AXS D8 Advance diffractometer | Data collection mode: transmission |
Radiation source: sealed X-ray tube, Bruker-AXS D8 | Scan method: step |
Primary focussing, Ge 111 monochromator | 2θmin = 7.0°, 2θmax = 60.0°, 2θstep = 0.017° |
Specimen mounting: 0.7 mm borosilicate capillary |
Least-squares matrix: selected elements only | 92 restraints |
Rp = 0.054 | 2 constraints |
Rwp = 0.070 | H atoms treated by a mixture of independent and constrained refinement |
Rexp = 0.016 | Weighting scheme based on measured s.u.'s 1/σ(Yobs)2 |
RBragg = 3.058 | (Δ/σ)max = 0.111 |
3070 data points | Background 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 |
x | y | z | Uiso*/Ueq | ||
N1 | 0.7188 (2) | 0.20485 (14) | 0.59572 (18) | 0.0380* | |
H1 | 0.8105 (12) | 0.1517 (6) | 0.5942 (4) | 0.0760* | |
C1 | 0.5536 (2) | 0.14964 (16) | 0.5933 (2) | 0.0380* | |
O1 | 0.5397 (5) | 0.0342 (2) | 0.5915 (3) | 0.0380* | |
C2 | 0.3992 (2) | 0.23660 (16) | 0.59562 (9) | 0.0380* | |
H2 | 0.3033 (12) | 0.1955 (6) | 0.5695 (4) | 0.0760* | |
C3 | 0.4373 (2) | 0.36391 (16) | 0.56342 (9) | 0.0380* | |
H3A | 0.3414 (11) | 0.4204 (6) | 0.5661 (4) | 0.0760* | |
H3B | 0.4527 (10) | 0.3553 (6) | 0.5143 (5) | 0.0760* | |
C4 | 0.6000 (2) | 0.41980 (16) | 0.60445 (9) | 0.0380* | |
H4 | 0.6326 (12) | 0.4984 (6) | 0.5846 (4) | 0.0760* | |
C5 | 0.7548 (2) | 0.33355 (17) | 0.5989 (2) | 0.0380* | |
O2 | 0.9060 (3) | 0.3689 (3) | 0.6007 (3) | 0.0380* | |
C6 | 0.5709 (2) | 0.43895 (15) | 0.68362 (8) | 0.0380* | |
H6A | 0.4815 (11) | 0.5017 (6) | 0.6831 (4) | 0.0760* | |
H6B | 0.6770 (13) | 0.4725 (6) | 0.7066 (4) | 0.0760* | |
C7 | 0.5134 (2) | 0.31638 (15) | 0.71761 (9) | 0.0380* | |
H7A | 0.6069 (11) | 0.2563 (6) | 0.7206 (5) | 0.0760* | |
H7B | 0.4810 (10) | 0.3317 (7) | 0.7643 (4) | 0.0760* | |
C8 | 0.3599 (2) | 0.25471 (16) | 0.67356 (9) | 0.0380* | |
H8A | 0.3286 (11) | 0.1746 (7) | 0.6922 (4) | 0.0760* | |
H8B | 0.2564 (12) | 0.3047 (6) | 0.6726 (4) | 0.0760* | |
N1w | 0.2227 (2) | 0.62126 (15) | 0.0902 (3) | 0.0380* | |
H1w | 0.3151 (11) | 0.5676 (6) | 0.0925 (6) | 0.0760* | |
C1w | 0.0572 (2) | 0.56668 (17) | 0.0834 (3) | 0.0380* | |
O1w | 0.0443 (5) | 0.4507 (3) | 0.0867 (4) | 0.0380* | |
C2w | −0.0968 (2) | 0.65429 (15) | 0.08651 (9) | 0.0380* | |
H2w | −0.1932 (11) | 0.6143 (6) | 0.0598 (4) | 0.0760* | |
C3w | −0.0589 (2) | 0.78378 (15) | 0.05587 (9) | 0.0380* | |
H3Aw | −0.1535 (11) | 0.8405 (6) | 0.0603 (4) | 0.0760* | |
H3Bw | −0.0449 (10) | 0.7782 (6) | 0.0064 (4) | 0.0760* | |
C4w | 0.1043 (2) | 0.83674 (16) | 0.09717 (9) | 0.0380* | |
H4w | 0.1381 (12) | 0.9151 (7) | 0.0777 (4) | 0.0760* | |
C5w | 0.2583 (2) | 0.75006 (17) | 0.0912 (2) | 0.0380* | |
O2w | 0.4093 (3) | 0.7853 (3) | 0.0928 (4) | 0.0380* | |
C6w | 0.0742 (2) | 0.85581 (15) | 0.17599 (8) | 0.0380* | |
H6Aw | −0.0119 (11) | 0.9206 (7) | 0.1752 (4) | 0.0760* | |
H6Bw | 0.1815 (12) | 0.8864 (7) | 0.1993 (4) | 0.0760* | |
C7w | 0.0097 (2) | 0.73736 (16) | 0.21080 (9) | 0.0380* | |
H7Aw | 0.1038 (12) | 0.6790 (6) | 0.2192 (5) | 0.0760* | |
H7Bw | −0.0318 (10) | 0.7583 (7) | 0.2553 (4) | 0.0760* | |
C8w | −0.1364 (2) | 0.66815 (17) | 0.16490 (9) | 0.0380* | |
H8Aw | −0.1579 (11) | 0.5853 (7) | 0.1828 (4) | 0.0760* | |
H8Bw | −0.2463 (12) | 0.7112 (6) | 0.1643 (4) | 0.0760* |
O1—C1 | 1.223 (3) | C6—H6B | 0.953 (9) |
O2—C5 | 1.216 (3) | C7—H7B | 0.953 (8) |
O1W—C1W | 1.230 (4) | C7—H7A | 0.955 (8) |
O2W—C5W | 1.214 (3) | C8—H8B | 0.952 (9) |
N1—C5 | 1.386 (2) | C8—H8A | 0.955 (8) |
N1—C1 | 1.391 (2) | C1W—C2W | 1.506 (2) |
N1—H1 | 0.902 (8) | C2W—C8W | 1.547 (2) |
N1W—C5W | 1.386 (2) | C2W—C3W | 1.523 (2) |
N1W—C1W | 1.389 (2) | C3W—C4W | 1.516 (2) |
N1W—H1W | 0.905 (8) | C4W—C5W | 1.507 (2) |
C1—C2 | 1.502 (2) | C4W—C6W | 1.542 (2) |
C2—C3 | 1.514 (2) | C6W—C7W | 1.517 (2) |
C2—C8 | 1.543 (2) | C7W—C8W | 1.534 (2) |
C3—C4 | 1.522 (2) | C2W—H2W | 0.952 (8) |
C4—C6 | 1.546 (2) | C3W—H3AW | 0.951 (8) |
C4—C5 | 1.508 (2) | C3W—H3BW | 0.953 (8) |
C6—C7 | 1.528 (2) | C4W—H4W | 0.951 (8) |
C7—C8 | 1.520 (2) | C6W—H6AW | 0.950 (8) |
C2—H2 | 0.950 (8) | C6W—H6BW | 0.951 (9) |
C3—H3B | 0.951 (8) | C7W—H7AW | 0.950 (8) |
C3—H3A | 0.952 (8) | C7W—H7BW | 0.953 (8) |
C4—H4 | 0.953 (7) | C8W—H8AW | 0.957 (8) |
C6—H6A | 0.953 (8) | C8W—H8BW | 0.957 (9) |
C1—N1—C5 | 126.06 (15) | C7—C8—H8A | 112.7 (5) |
C1—N1—H1 | 116.7 (5) | C2—C8—H8A | 108.8 (5) |
C5—N1—H1 | 117.2 (5) | C2—C8—H8B | 106.9 (5) |
C1W—N1W—C5W | 125.81 (16) | O1W—C1W—N1W | 119.0 (2) |
C5W—N1W—H1W | 117.4 (5) | N1W—C1W—C2W | 117.11 (16) |
C1W—N1W—H1W | 116.7 (5) | O1W—C1W—C2W | 122.8 (2) |
O1—C1—N1 | 119.6 (2) | C1W—C2W—C8W | 108.9 (2) |
N1—C1—C2 | 117.50 (14) | C3W—C2W—C8W | 109.98 (14) |
O1—C1—C2 | 122.8 (2) | C1W—C2W—C3W | 110.87 (16) |
C1—C2—C8 | 109.34 (19) | C2W—C3W—C4W | 108.28 (14) |
C3—C2—C8 | 109.67 (14) | C3W—C4W—C6W | 110.56 (13) |
C1—C2—C3 | 110.26 (14) | C3W—C4W—C5W | 110.62 (16) |
C2—C3—C4 | 108.64 (13) | C5W—C4W—C6W | 110.10 (18) |
C3—C4—C6 | 110.76 (13) | O2W—C5W—C4W | 124.4 (2) |
C3—C4—C5 | 110.07 (16) | N1W—C5W—C4W | 116.18 (14) |
C5—C4—C6 | 109.56 (18) | O2W—C5W—N1W | 119.1 (2) |
O2—C5—C4 | 124.7 (2) | C4W—C6W—C7W | 113.38 (13) |
N1—C5—C4 | 116.06 (14) | C6W—C7W—C8W | 113.47 (14) |
O2—C5—N1 | 119.2 (2) | C2W—C8W—C7W | 112.66 (13) |
C4—C6—C7 | 111.75 (13) | C1W—C2W—H2W | 106.2 (5) |
C6—C7—C8 | 111.85 (13) | C3W—C2W—H2W | 111.3 (4) |
C2—C8—C7 | 111.24 (13) | C8W—C2W—H2W | 109.5 (5) |
C1—C2—H2 | 106.2 (5) | C2W—C3W—H3AW | 110.8 (5) |
C3—C2—H2 | 111.5 (4) | C2W—C3W—H3BW | 111.2 (4) |
C8—C2—H2 | 109.8 (5) | C4W—C3W—H3AW | 108.8 (5) |
C2—C3—H3A | 110.7 (5) | C4W—C3W—H3BW | 111.2 (5) |
H3A—C3—H3B | 106.4 (6) | H3AW—C3W—H3BW | 106.6 (6) |
C2—C3—H3B | 110.8 (4) | C3W—C4W—H4W | 111.3 (5) |
C4—C3—H3A | 109.3 (5) | C5W—C4W—H4W | 104.7 (6) |
C4—C3—H3B | 111.1 (5) | C6W—C4W—H4W | 109.4 (5) |
C3—C4—H4 | 111.7 (5) | C4W—C6W—H6AW | 104.4 (5) |
C5—C4—H4 | 105.0 (5) | C4W—C6W—H6BW | 106.7 (5) |
C6—C4—H4 | 109.6 (5) | C7W—C6W—H6AW | 110.1 (5) |
C7—C6—H6B | 113.1 (4) | C7W—C6W—H6BW | 112.5 (5) |
H6A—C6—H6B | 109.2 (6) | H6AW—C6W—H6BW | 109.4 (7) |
C4—C6—H6A | 104.6 (5) | C6W—C7W—H7AW | 109.4 (5) |
C4—C6—H6B | 107.0 (5) | C6W—C7W—H7BW | 110.0 (5) |
C7—C6—H6A | 110.8 (5) | C8W—C7W—H7AW | 106.7 (5) |
C6—C7—H7B | 110.9 (5) | C8W—C7W—H7BW | 108.7 (5) |
H7A—C7—H7B | 108.7 (7) | H7AW—C7W—H7BW | 108.4 (7) |
C8—C7—H7A | 106.6 (5) | C2W—C8W—H8AW | 108.0 (5) |
C6—C7—H7A | 109.9 (5) | C2W—C8W—H8BW | 106.8 (5) |
C8—C7—H7B | 108.7 (5) | C7W—C8W—H8AW | 112.1 (5) |
C7—C8—H8B | 111.9 (5) | C7W—C8W—H8BW | 112.1 (5) |
H8A—C8—H8B | 105.0 (7) | H8AW—C8W—H8BW | 104.8 (7) |
D—H···A | D—H | H···A | D···A | 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) |
C2—H2···O1Wiii | 0.95 (1) | 2.56 (1) | 3.355 (4) | 141 (1) |
C3W—H3BW···O2iv | 0.95 (1) | 2.56 (1) | 3.406 (5) | 148 (1) |
C3—H3B···O2Wv | 0.95 (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, z−1/2; (iii) x, −y+1/2, z+1/2; (iv) −x+1, y+1/2, −z+1/2; (v) −x+1, y−1/2, −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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