organic compounds
Redetermination of 1,3,6,8-tetraazatricyclo[4.4.1.13,8]dodecane
aUniversidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Departamento de Química, Cra 30 No.45-03, Bogotá, Código Postal 111321, Colombia, and bInstitut für Anorganische Chemie, J. W. Goethe-Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
*Correspondence e-mail: ariverau@unal.edu.co
The structure of the title compound, C8H16N4, which consists of four fused seven-membered rings, has been redetermined at 173 K. This redetermination corrects the orientation of two H atoms, which were located at unrealistic positions in the original room-temperature study [Murray-Rust (1974). J. Chem. Soc. Perkin Trans. 2, pp. 1136–1141]. The complete molecule is generated by -42m symmetry, with one quarter of a molecule [one N atom (site symmetry m), two C atoms (one with m and the other with 2) and two H atoms] in the No directional interactions beyond van der Waals contacts are apparent in the crystal structure.
CCDC reference: 985132
Related literature
For the original synthesis procedure, see: Bischoff (1898). For the previous determination of the structure, see: Murray-Rust (1974). For crystal structures containing the title compound as a fragment, see: Rivera et al. (2007); Glister et al. (2005). For a description of the Cambridge Crystallographic Database, see: Allen et al. (2002).
Experimental
Crystal data
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Data collection: X-AREA (Stoe & Cie, 2001); cell X-AREA; data reduction: X-AREA; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97.
Supporting information
CCDC reference: 985132
10.1107/S1600536814002608/hb7192sup1.cif
contains datablocks I, New_Global_Publ_Block. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814002608/hb7192Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814002608/hb7192Isup3.cml
1,3,6,8-tetraazatricyclo[4.4.1.1^3,8^]dodecane (TATD) was synthesized from formaldehyde and diaminoethane as described in the literature (Bischoff, 1898) and recrystallized from 1,4-dioxane solution as colourless blocks.
All H atoms were located in a difference map. Nevertheless, they were geometrically placed and refined using a riding model, with C—H = 0.99 Å and with Uiso(H) = 1.2Ueq(C). The
was indeterminate in the present refinement.Data collection: X-AREA (Stoe & Cie, 2001); cell
X-AREA (Stoe & Cie, 2001); data reduction: X-AREA (Stoe & Cie, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).C8H16N4 | Dx = 1.336 Mg m−3 |
Mr = 168.25 | Mo Kα radiation, λ = 0.71073 Å |
Tetragonal, I42m | Cell parameters from 11628 reflections |
a = 7.4065 (7) Å | θ = 3.8–27.9° |
c = 7.6235 (8) Å | µ = 0.09 mm−1 |
V = 418.20 (9) Å3 | T = 173 K |
Z = 2 | Block, colourless |
F(000) = 184 | 0.32 × 0.28 × 0.27 mm |
Stoe IPDS II two-circle diffractometer | 264 reflections with I > 2σ(I) |
Radiation source: Genix 3D IµS microfocus X-ray source | Rint = 0.049 |
ω scans | θmax = 27.5°, θmin = 5.4° |
Absorption correction: multi-scan (X-AREA; Stoe & Cie, 2001) | h = −9→8 |
Tmin = 0.973, Tmax = 0.977 | k = −9→9 |
4336 measured reflections | l = −9→9 |
264 independent reflections |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.050 | H-atom parameters constrained |
wR(F2) = 0.141 | w = 1/[σ2(Fo2) + (0.0809P)2 + 0.2587P] where P = (Fo2 + 2Fc2)/3 |
S = 1.12 | (Δ/σ)max < 0.001 |
264 reflections | Δρmax = 0.27 e Å−3 |
18 parameters | Δρmin = −0.17 e Å−3 |
C8H16N4 | Z = 2 |
Mr = 168.25 | Mo Kα radiation |
Tetragonal, I42m | µ = 0.09 mm−1 |
a = 7.4065 (7) Å | T = 173 K |
c = 7.6235 (8) Å | 0.32 × 0.28 × 0.27 mm |
V = 418.20 (9) Å3 |
Stoe IPDS II two-circle diffractometer | 264 independent reflections |
Absorption correction: multi-scan (X-AREA; Stoe & Cie, 2001) | 264 reflections with I > 2σ(I) |
Tmin = 0.973, Tmax = 0.977 | Rint = 0.049 |
4336 measured reflections |
R[F2 > 2σ(F2)] = 0.050 | 0 restraints |
wR(F2) = 0.141 | H-atom parameters constrained |
S = 1.12 | Δρmax = 0.27 e Å−3 |
264 reflections | Δρmin = −0.17 e Å−3 |
18 parameters |
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. ; |
x | y | z | Uiso*/Ueq | ||
N1 | 0.1352 (2) | 0.1352 (2) | 0.0995 (4) | 0.0373 (9) | |
C1 | 0.2345 (4) | 0.0000 | 0.0000 | 0.0406 (10) | |
H1 | 0.3140 | 0.0649 | −0.0832 | 0.049* | |
C2 | 0.0705 (4) | 0.0705 (4) | 0.2690 (5) | 0.0604 (14) | |
H2 | 0.0235 | 0.1756 | 0.3350 | 0.073* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0317 (10) | 0.0317 (10) | 0.0483 (16) | −0.0099 (11) | 0.0011 (8) | 0.0011 (8) |
C1 | 0.0228 (14) | 0.0310 (16) | 0.068 (2) | 0.000 | 0.000 | 0.0063 (15) |
C2 | 0.071 (2) | 0.071 (2) | 0.0392 (17) | −0.038 (2) | −0.0017 (11) | −0.0017 (11) |
N1—C1i | 1.456 (2) | C1—H1 | 0.9900 |
N1—C1 | 1.456 (2) | C2—C2iii | 1.477 (8) |
N1—C2 | 1.459 (5) | C2—H2 | 0.9900 |
C1—N1ii | 1.456 (2) | ||
C1i—N1—C1 | 115.0 (3) | N1—C1—H1 | 107.5 |
C1i—N1—C2 | 113.66 (12) | N1—C2—C2iii | 117.68 (18) |
C1—N1—C2 | 113.66 (12) | N1—C2—H2 | 107.9 |
N1ii—C1—N1 | 119.4 (3) | C2iii—C2—H2 | 107.9 |
N1ii—C1—H1 | 107.5 | ||
C1i—N1—C1—N1ii | −52.65 (18) | C1i—N1—C2—C2iii | 67.1 (2) |
C2—N1—C1—N1ii | 80.8 (2) | C1—N1—C2—C2iii | −67.1 (2) |
Symmetry codes: (i) −y, x, −z; (ii) y, −x, −z; (iii) −x, −y, z. |
Experimental details
Crystal data | |
Chemical formula | C8H16N4 |
Mr | 168.25 |
Crystal system, space group | Tetragonal, I42m |
Temperature (K) | 173 |
a, c (Å) | 7.4065 (7), 7.6235 (8) |
V (Å3) | 418.20 (9) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.32 × 0.28 × 0.27 |
Data collection | |
Diffractometer | Stoe IPDS II two-circle diffractometer |
Absorption correction | Multi-scan (X-AREA; Stoe & Cie, 2001) |
Tmin, Tmax | 0.973, 0.977 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4336, 264, 264 |
Rint | 0.049 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.050, 0.141, 1.12 |
No. of reflections | 264 |
No. of parameters | 18 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.27, −0.17 |
Computer programs: X-AREA (Stoe & Cie, 2001), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP in SHELXTL (Sheldrick, 2008).
Acknowledgements
We acknowledge the Dirección de Investigaciones, Sede Bogotá (DIB) de la Universidad Nacional de Colombia, for financial support of this work.
References
Allen, F. H. (2002). Acta Cryst. B58, 380–388. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Bischoff, C. A. (1898). Ber. Dtsch Chem. Ges.. 31 3248-3260. CrossRef CAS Google Scholar
Glister, J. F., Vaughan, K., Biradha, K. & Zaworotko, M. J. (2005). J. Mol. Struct. 749, 78–83. Web of Science CSD CrossRef CAS Google Scholar
Murray-Rust, P. (1974). J. Chem. Soc. Perkin Trans. 2, pp. 1136–1141. Google Scholar
Rivera, A., Rios-Motta, J., Hernandez-Barragan, A. & Joseph-Nathan, P. (2007). J. Mol. Struct. 831, 180–186. Web of Science CSD CrossRef CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Stoe & Cie (2001). X-AREA. Stoe & Cie, Darmstadt, Germany. Google Scholar
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The crystal structure of the title compound, a fully saturated cage-like molecule, was first reported (Murray-Rust, 1974) at room temperature. This heterocyclic system is of considerable conformational interest. While by now the structure of the molecule would seem well established, the position of some hydrogen atoms is rather strange (Fig. 1). Both H atoms bonded to C1 almost lie in a common plane with the two N atoms attached to C1 (r.m.s. deviation for all five atoms 0.050 Å). The dihedral angle between the NC2 plane and the CH2 plane is 10.7°. However, the CH2 plane should be more or less perpendicular to the CN2 plane.
Our interest in the title compound prompted the present re-investigation carrying out the data collection at 173 (2) K which provides more regular positions for the H atoms (Fig. 2).
The re-determination of the crystal structure is consistent with the observation that TATD belongs to the D2d point group as pointed out Murray-Rust. The only significant difference is the localization of the H atoms. The largest difference between the two determinations pertains to the C—C distance of the ethylene bridge. In the original study this distance was determined as 1.534 (8) Å, whereas it is 1.477 (8) Å in this study. Taking the displacement ellipsoid which is elongated perpendicular to the N—C—C—N moiety into account, the shortened bond length might be due to a slight disorder of C2.
Concerning the H atoms, the orientation of the methylene group connecting two N atoms in particular is corrected: in the structure of Murray-Rust the orientation of the H atoms is such that both C—H bonds are in the same plane with the N—C bonds, with a dihedral angle of 10.7° between the NC2 plane and the CH2 plane. In the redetermination, the dihedral angle between these planes is exactly 90°.
The title molecule is composed of four seven-membered rings which have exactly the same conformation due to the molecular symmetry. The conformation can be described as a chair. A search in the Cambridge Crystallographic Database (CSD, Version 5.35 of 2013, plus two updates; Allen 2002) yielded three structures containing the title compound as a fragment, namely the structure determination of Murray-Rust (1974), the title compound as a co-crystal with hydroquinone (Rivera et al., 2007), the title compound substituted with a cyclohexane ring at the C—C bonds (Glister et al., 2005). The conformation of the seven-membered rings is a chair in all cases which is not surprising since the the molecule is rigid.
Concerning the crystal packing, molecules of the title compound are located at the origin and at the centre of the unit cell. Thus, the crystal packing can be regarded as two sets of layers. The molecules in neighbouring layers are displaced by the symmetry operation 1/2 + x, 1/2 + y, 1/2 + z (Fig. 3).