3-Aza­bi­cyclo­[3.3.1]­nonane-2,4-dione: CSP2001 structure prediction test case No. 1

Features of the structure of the title compound, C₈H₁₁NO₂, are the near planar arrangement of the dicarbox­imide fragment and the C atoms α to it and the molecular non-crystallographic C_s mirror symmetry. N—H...O hydrogen bonds link the mol­ecules to form zigzag chains propagated in the a direction and sheets parallel to (001) are formed by replication of the chains by cell translation in the b direction. The sheets, related to one another by the operation of crystallographic centres of symmetry, are stacked in the c direction.

Key indicators

• Single-crystal X-ray study
• T = 297 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.044
• wR factor = 0.123
• Data-to-parameter ratio = 19.0

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

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S1. Comment

The structure of the title compound, (I), was undertaken initially simply because suitable crystals were available. It is gratifying that the compound was later found suitable for use as a case study for structure prediction.

Fig. 1 is a general view of the molecule of (I) showing the atom labels used in the X-ray structure analysis. Noted here is the near planar arrangement of the dicarboximide fragment of the molecule (N1, C1, O1, C5 and O2 including the α C atoms, C2 and C4). The greatest displacement from the least squares plane so defined is that of O1 at 0.0391 (7) Å, while that of H1 (attached to N1) is only 0.005 (13) Å. Fig. 2 is another view of the molecule in which its non-crystallographic C_s mirror symmetry is clearly evident and seen to extend even as far as the H atoms. Bond distances and angles in various categories are summarized as ranges in Table 1. They are more or less as anticipated for a molecule of this kind and are not discussed further.

The arrangement of the molecules in the cell, particularly in the context of structure prediction, is worthy of discussion. The molecules are arranged in layers parallel to (001). One such layer, with the centroids of the molecules close to z = 1/4, is shown in Fig. 3. Here intermolecular H-bonds of the form N1—H1.·O1 (Table 2) interconnect the molecules to form zigzag chains propagated in the a direction in which each molecule is related to its neighbours by the operation of the a-glide of the space group P2₁/a. The chains are then related one to another by cell translation in the b direction creating in the process further intermolecular contacts of the form C6—H6A···O2 (Table 2).

These layers are then stacked in the c direction as shown in Fig. 4 where they are viewed along a and therefore seen edge on. The layers are now related to one another by the operation of crystallographic centres of symmetry resulting in displacement of the molecules in the ab plane from one layer to the next and creating two cases. First, because of the choice of origin used in the structure analysis, the dicarboximide `fronts' of the molecules are opposed to one another across interfaces at z = 0 and z = 1 creating intermolecular contacts of the form C3—H3B.·O2 (Table 2). Second, in a similar manner, the alkyl `backs' of the molecules are juxtaposed at z = 1/2 at van der Waals distances of which H7···H7ⁱ [symmetery code: (i) 1 - x, 1 - y, 1 - z] at 2.28 (2) Å is the shortest.

S2. Experimental

The material from which the sample crystal was taken was kindly supplied by H. K. Hall and so its provenance is limited. The synthesis of (I) has however been described by Hall (1958) and more recently by Poloński et al. (1996).

S3. Refinement

In the later stages of refinement, H atoms were found in a difference map and refined freely.

Computing details

Data collection: SMART (Bruker, 1999); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. The molecule of (I) showing the atom labels. Non-H atoms are shown as 20% probability ellipsoids and H atoms are shown as small circles.
	Fig. 2. The molecule of (I) viewed edge-on to the plane defined by N1, C3 and C7 with C3 directed down into the page. Non-H atoms are now shown as 50% probability ellipsoids.
	Fig. 3. The view down c of a portion of a single layer of molecules of (I) whose centroids are close to z = 1/4. The representation is the same as in Fig. 2 except that only selected H atoms are now labelled in order to identify intermolecular contacts (dashed lines) which are discussed in more detail in the text.
	Fig. 4. The unit cell of (I) viewed along a showing the stacking of the layers exemplified in Fig. 3 and in the same representation.

3-Aza-bicyclo[3.3.1]nonane-2,4-dione

Crystal data

C8H11NO2	F(000) = 328
Mr = 153.18	Dx = 1.338 Mg m^−3
Monoclinic, P21/a	Mo Kα radiation, λ = 0.71073 Å
a = 7.7046 (5) Å	Cell parameters from 2072 reflections
b = 10.6062 (7) Å	θ = 2.2–30.3°
c = 9.3384 (6) Å	µ = 0.10 mm^−1
β = 95.033 (2)°	T = 297 K
V = 760.16 (9) Å^3	Block, colourless
Z = 4	0.30 × 0.20 × 0.20 mm

Data collection

Bruker SMART CCD area-detector diffractometer	2736 independent reflections
Radiation source: fine-focus sealed tube	1584 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.026
ϕ–ω scans	θmax = 32.5°, θmin = 2.9°
Absorption correction: multi-scan (SADABS; Bruker, 1999)	h = −11→11
Tmin = 0.972, Tmax = 0.981	k = −16→7
7616 measured reflections	l = −14→13

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.044	Hydrogen site location: difference Fourier map
wR(F^2) = 0.123	All H-atom parameters refined
S = 0.90	w = 1/[σ^2(Fo^2) + (0.0713P)^2] where P = (Fo^2 + 2Fc^2)/3
2736 reflections	(Δ/σ)max < 0.001
144 parameters	Δρmax = 0.24 e Å^−3
0 restraints	Δρmin = −0.20 e Å^−3

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

In this refinement, all H atoms were located from the difference Fourier map and refined freely

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
N1	0.47604 (11)	0.41167 (9)	0.19143 (11)	0.0385 (2)
H1	0.5638 (18)	0.3594 (15)	0.1944 (14)	0.050 (4)*
C1	0.31183 (13)	0.35911 (11)	0.19361 (12)	0.0382 (3)
O1	0.29710 (11)	0.24477 (8)	0.19994 (12)	0.0609 (3)
C2	0.15972 (13)	0.44791 (11)	0.19189 (13)	0.0385 (3)
H2	0.0576 (18)	0.4025 (14)	0.1402 (15)	0.053 (4)*
C3	0.19984 (16)	0.57024 (13)	0.11776 (14)	0.0444 (3)
H3A	0.1010 (18)	0.6311 (14)	0.1206 (15)	0.055 (4)*
H3B	0.2158 (19)	0.5561 (13)	0.0134 (16)	0.054 (4)*
C4	0.36180 (16)	0.62782 (11)	0.19735 (14)	0.0422 (3)
H4	0.396 (2)	0.7013 (16)	0.1533 (16)	0.065 (5)*
C5	0.51396 (14)	0.53949 (10)	0.19270 (12)	0.0366 (2)
O2	0.66431 (11)	0.57333 (9)	0.19198 (11)	0.0541 (3)
C6	0.32967 (17)	0.65664 (13)	0.35390 (15)	0.0496 (3)
H6A	0.235 (2)	0.7262 (16)	0.3468 (17)	0.068 (5)*
H6B	0.440 (2)	0.6914 (14)	0.4008 (15)	0.060 (4)*
C7	0.26614 (16)	0.54282 (15)	0.43251 (14)	0.0501 (3)
H7A	0.362 (2)	0.4814 (14)	0.4494 (14)	0.052 (4)*
H7B	0.229 (2)	0.5673 (16)	0.523 (2)	0.075 (5)*
C8	0.11724 (14)	0.47485 (14)	0.34682 (14)	0.0458 (3)
H8A	0.0860 (18)	0.3940 (16)	0.3915 (15)	0.053 (4)*
H8B	0.0121 (19)	0.5233 (14)	0.3405 (14)	0.049 (4)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0256 (4)	0.0312 (5)	0.0591 (6)	0.0018 (3)	0.0054 (4)	−0.0022 (4)
C1	0.0283 (5)	0.0336 (6)	0.0526 (7)	−0.0021 (4)	0.0025 (4)	−0.0024 (5)
O1	0.0378 (4)	0.0326 (5)	0.1127 (9)	−0.0042 (4)	0.0093 (5)	−0.0038 (5)
C2	0.0246 (4)	0.0417 (6)	0.0484 (6)	0.0014 (4)	−0.0018 (4)	−0.0027 (5)
C3	0.0409 (6)	0.0468 (7)	0.0450 (7)	0.0114 (5)	0.0009 (5)	0.0063 (5)
C4	0.0433 (6)	0.0280 (5)	0.0561 (7)	0.0028 (5)	0.0092 (5)	0.0061 (5)
C5	0.0356 (5)	0.0326 (6)	0.0424 (6)	−0.0027 (4)	0.0084 (4)	−0.0008 (4)
O2	0.0377 (4)	0.0472 (5)	0.0791 (6)	−0.0119 (4)	0.0157 (4)	−0.0063 (5)
C6	0.0410 (6)	0.0452 (7)	0.0628 (8)	0.0027 (5)	0.0061 (6)	−0.0172 (6)
C7	0.0386 (6)	0.0710 (10)	0.0411 (7)	0.0028 (6)	0.0063 (5)	−0.0051 (6)
C8	0.0294 (5)	0.0553 (7)	0.0539 (7)	0.0011 (5)	0.0103 (5)	0.0038 (6)

Geometric parameters (Å, º)

N1—C1	1.3843 (13)	C4—C6	1.5348 (19)
N1—C5	1.3866 (14)	C4—H4	0.929 (17)
N1—H1	0.873 (15)	C5—O2	1.2133 (13)
C1—O1	1.2199 (14)	C6—C7	1.516 (2)
C1—C2	1.5025 (15)	C6—H6A	1.038 (16)
C2—C3	1.5151 (18)	C6—H6B	0.992 (15)
C2—C8	1.5379 (17)	C7—C8	1.5215 (18)
C2—H2	1.009 (14)	C7—H7A	0.990 (15)
C3—C4	1.5231 (18)	C7—H7B	0.952 (18)
C3—H3A	1.001 (14)	C8—H8A	0.993 (16)
C3—H3B	1.004 (14)	C8—H8B	0.957 (15)
C4—C5	1.5042 (16)
C1—N1—C5	125.86 (9)	C6—C4—H4	109.2 (10)
C1—N1—H1	116.8 (10)	O2—C5—N1	119.32 (10)
C5—N1—H1	117.3 (10)	O2—C5—C4	124.25 (11)
O1—C1—N1	119.35 (10)	N1—C5—C4	116.42 (9)
O1—C1—C2	123.22 (10)	C7—C6—C4	112.86 (10)
N1—C1—C2	117.41 (10)	C7—C6—H6A	109.9 (9)
C1—C2—C3	110.58 (9)	C4—C6—H6A	104.7 (9)
C1—C2—C8	109.67 (9)	C7—C6—H6B	112.5 (9)
C3—C2—C8	109.85 (10)	C4—C6—H6B	107.0 (9)
C1—C2—H2	106.3 (8)	H6A—C6—H6B	109.7 (12)
C3—C2—H2	111.8 (8)	C6—C7—C8	112.53 (11)
C8—C2—H2	108.5 (8)	C6—C7—H7A	109.3 (8)
C2—C3—C4	108.16 (10)	C8—C7—H7A	107.0 (8)
C2—C3—H3A	110.8 (8)	C6—C7—H7B	110.3 (10)
C4—C3—H3A	108.7 (8)	C8—C7—H7B	109.2 (10)
C2—C3—H3B	111.3 (8)	H7A—C7—H7B	108.4 (12)
C4—C3—H3B	111.6 (8)	C7—C8—C2	111.71 (9)
H3A—C3—H3B	106.3 (12)	C7—C8—H8A	112.8 (8)
C5—C4—C3	110.09 (10)	C2—C8—H8A	108.3 (8)
C5—C4—C6	110.05 (10)	C7—C8—H8B	111.9 (9)
C3—C4—C6	110.55 (10)	C2—C8—H8B	106.9 (8)
C5—C4—H4	105.1 (10)	H8A—C8—H8B	104.7 (11)
C3—C4—H4	111.7 (9)
C5—N1—C1—O1	−176.09 (11)	C1—N1—C5—C4	0.21 (16)
C5—N1—C1—C2	2.33 (16)	C3—C4—C5—O2	148.85 (12)
O1—C1—C2—C3	−154.08 (12)	C6—C4—C5—O2	−89.06 (14)
N1—C1—C2—C3	27.57 (14)	C3—C4—C5—N1	−32.16 (14)
O1—C1—C2—C8	84.64 (14)	C6—C4—C5—N1	89.93 (12)
N1—C1—C2—C8	−93.72 (12)	C5—C4—C6—C7	−67.62 (13)
C1—C2—C3—C4	−58.23 (13)	C3—C4—C6—C7	54.19 (14)
C8—C2—C3—C4	62.95 (12)	C4—C6—C7—C8	−48.23 (15)
C2—C3—C4—C5	60.72 (13)	C6—C7—C8—C2	49.82 (15)
C2—C3—C4—C6	−61.07 (13)	C1—C2—C8—C7	63.92 (14)
C1—N1—C5—O2	179.25 (11)	C3—C2—C8—C7	−57.80 (14)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^i	0.873 (15)	2.107 (15)	2.9739 (12)	172.2 (14)
C3—H3B···O2^ii	1.004 (14)	2.594 (15)	3.5088 (16)	151.5 (11)
C6—H6A···O2^iii	1.038 (16)	2.601 (17)	3.4313 (17)	136.7 (11)

Symmetry codes: (i) x+1/2, −y+1/2, z; (ii) −x+1, −y+1, −z; (iii) x−1/2, −y+3/2, z.