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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

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

(Received 1 February 2014; accepted 4 February 2014; online 8 February 2014)

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[Murray-Rust, P. (1974). J. Chem. Soc. Perkin Trans. 2, pp. 1136-1141.]). 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 site symmetry m and the other with site symmetry 2) and two H atoms] in the asymmetric unit. No directional inter­actions beyond van der Waals contacts are apparent in the crystal structure.

Related literature

For the original synthesis procedure, see: Bischoff (1898[Bischoff, C. A. (1898). Ber. Dtsch Chem. Ges.. 31 3248-3260.]). For the previous determination of the structure, see: Murray-Rust (1974[Murray-Rust, P. (1974). J. Chem. Soc. Perkin Trans. 2, pp. 1136-1141.]). For crystal structures containing the title compound as a fragment, see: Rivera et al. (2007[Rivera, A., Rios-Motta, J., Hernandez-Barragan, A. & Joseph-Nathan, P. (2007). J. Mol. Struct. 831, 180-186.]); Glister et al. (2005[Glister, J. F., Vaughan, K., Biradha, K. & Zaworotko, M. J. (2005). J. Mol. Struct. 749, 78-83.]). For a description of the Cambridge Crystallographic Database, see: Allen et al. (2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]).

[Scheme 1]

Experimental

Crystal data
  • C8H16N4

  • Mr = 168.25

  • Tetragonal, [I \overline 42m ]

  • a = 7.4065 (7) Å

  • c = 7.6235 (8) Å

  • V = 418.20 (9) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 173 K

  • 0.32 × 0.28 × 0.27 mm

Data collection
  • Stoe IPDS II two-circle diffractometer

  • Absorption correction: multi-scan (X-AREA; Stoe & Cie, 2001[Stoe & Cie (2001). X-AREA. Stoe & Cie, Darmstadt, Germany.]) Tmin = 0.973, Tmax = 0.977

  • 4336 measured reflections

  • 264 independent reflections

  • 264 reflections with I > 2σ(I)

  • Rint = 0.049

Refinement
  • R[F2 > 2σ(F2)] = 0.050

  • wR(F2) = 0.141

  • S = 1.12

  • 264 reflections

  • 18 parameters

  • H-atom parameters constrained

  • Δρmax = 0.27 e Å−3

  • Δρmin = −0.17 e Å−3

Data collection: X-AREA (Stoe & Cie, 2001[Stoe & Cie (2001). X-AREA. Stoe & Cie, Darmstadt, Germany.]); cell refinement: X-AREA; data reduction: X-AREA; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: XP in SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

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).

Related literature top

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 top

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.

Refinement top

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 absolute structure was indeterminate in the present refinement.

Computing details top

Data collection: X-AREA (Stoe & Cie, 2001); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. A view of the molecular structure of the title compound as determined by Murray-Rust (1974).
[Figure 2] Fig. 2. A view of the crystal structure of the title compound with the numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. Symmetry operators for generating equivalent atoms: (A) -y, x, -z, (B) y, -x, -z, (C) -x, -y, z.
[Figure 3] Fig. 3. Packing diagram of the title compound with view onto the ac plane.
1,3,6,8-Tetraazatricyclo[4.4.1.13,8]dodecane top
Crystal data top
C8H16N4Dx = 1.336 Mg m3
Mr = 168.25Mo Kα radiation, λ = 0.71073 Å
Tetragonal, I42mCell parameters from 11628 reflections
a = 7.4065 (7) Åθ = 3.8–27.9°
c = 7.6235 (8) ŵ = 0.09 mm1
V = 418.20 (9) Å3T = 173 K
Z = 2Block, colourless
F(000) = 1840.32 × 0.28 × 0.27 mm
Data collection top
Stoe IPDS II two-circle
diffractometer
264 reflections with I > 2σ(I)
Radiation source: Genix 3D IµS microfocus X-ray sourceRint = 0.049
ω scansθmax = 27.5°, θmin = 5.4°
Absorption correction: multi-scan
(X-AREA; Stoe & Cie, 2001)
h = 98
Tmin = 0.973, Tmax = 0.977k = 99
4336 measured reflectionsl = 99
264 independent reflections
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.050H-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 reflectionsΔρmax = 0.27 e Å3
18 parametersΔρmin = 0.17 e Å3
Crystal data top
C8H16N4Z = 2
Mr = 168.25Mo Kα radiation
Tetragonal, I42mµ = 0.09 mm1
a = 7.4065 (7) ÅT = 173 K
c = 7.6235 (8) Å0.32 × 0.28 × 0.27 mm
V = 418.20 (9) Å3
Data collection top
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 = 0.977Rint = 0.049
4336 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0500 restraints
wR(F2) = 0.141H-atom parameters constrained
S = 1.12Δρmax = 0.27 e Å3
264 reflectionsΔρmin = 0.17 e Å3
18 parameters
Special details top

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. ;

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.1352 (2)0.1352 (2)0.0995 (4)0.0373 (9)
C10.2345 (4)0.00000.00000.0406 (10)
H10.31400.06490.08320.049*
C20.0705 (4)0.0705 (4)0.2690 (5)0.0604 (14)
H20.02350.17560.33500.073*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0317 (10)0.0317 (10)0.0483 (16)0.0099 (11)0.0011 (8)0.0011 (8)
C10.0228 (14)0.0310 (16)0.068 (2)0.0000.0000.0063 (15)
C20.071 (2)0.071 (2)0.0392 (17)0.038 (2)0.0017 (11)0.0017 (11)
Geometric parameters (Å, º) top
N1—C1i1.456 (2)C1—H10.9900
N1—C11.456 (2)C2—C2iii1.477 (8)
N1—C21.459 (5)C2—H20.9900
C1—N1ii1.456 (2)
C1i—N1—C1115.0 (3)N1—C1—H1107.5
C1i—N1—C2113.66 (12)N1—C2—C2iii117.68 (18)
C1—N1—C2113.66 (12)N1—C2—H2107.9
N1ii—C1—N1119.4 (3)C2iii—C2—H2107.9
N1ii—C1—H1107.5
C1i—N1—C1—N1ii52.65 (18)C1i—N1—C2—C2iii67.1 (2)
C2—N1—C1—N1ii80.8 (2)C1—N1—C2—C2iii67.1 (2)
Symmetry codes: (i) y, x, z; (ii) y, x, z; (iii) x, y, z.

Experimental details

Crystal data
Chemical formulaC8H16N4
Mr168.25
Crystal system, space groupTetragonal, I42m
Temperature (K)173
a, c (Å)7.4065 (7), 7.6235 (8)
V3)418.20 (9)
Z2
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.32 × 0.28 × 0.27
Data collection
DiffractometerStoe IPDS II two-circle
diffractometer
Absorption correctionMulti-scan
(X-AREA; Stoe & Cie, 2001)
Tmin, Tmax0.973, 0.977
No. of measured, independent and
observed [I > 2σ(I)] reflections
4336, 264, 264
Rint0.049
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.050, 0.141, 1.12
No. of reflections264
No. of parameters18
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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

First citationAllen, F. H. (2002). Acta Cryst. B58, 380–388.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationBischoff, C. A. (1898). Ber. Dtsch Chem. Ges.. 31 3248-3260.  CrossRef CAS Google Scholar
First citationGlister, J. F., Vaughan, K., Biradha, K. & Zaworotko, M. J. (2005). J. Mol. Struct. 749, 78–83.  Web of Science CSD CrossRef CAS Google Scholar
First citationMurray-Rust, P. (1974). J. Chem. Soc. Perkin Trans. 2, pp. 1136–1141.  Google Scholar
First citationRivera, 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
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationStoe & Cie (2001). X-AREA. Stoe & Cie, Darmstadt, Germany.  Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds