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The crystal structure of [Lambda]-(1,3,6,8,10,13,16,19-octa­aza­bi­cyclo­[6.6.6]eicosane)cobalt(III) trinitrate, [Co(C12H30N8)](NO3)3, consists of a sepulchrate moiety that serves as a macrobicyclic nitro­gen cage for the Co3+ cation, which is six-coordinated by N atoms, and three nitrate anions. The Co-sepulchrate group lies on a threefold axis (site symmetry 32), as do two symmetry-related and ordered nitrate groups (site symmetry 3), with which it is connected via N-H...O hydrogen bonds [Co-N = 5.1452 (12) Å]. The third nitrate group is disordered as a result of symmetry requirements around the origin (site symmetry 32), and is further away from the Co-sepulchrate cage [Co-N = 6.3160 (8) Å]. The structure is described by applying orientational disorder over six equivalent orientations for the disordered nitrate group, which is considered as an ideal planar mol­ecule of regular trigonal geometry with its mol­ecular plane rotated out of the ab plane and the mol­ecular centre of gravity slightly shifted away from the origin. This new model for disorder clearly improves a previous crystal structure determination.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270110005755/su3043sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270110005755/su3043Isup2.hkl
Contains datablock I

CCDC reference: 774882

Comment top

Λ-Cobalt(III) sepulchrate trinitrate, (I), crystallizes at room temperature in space group P6322 (Dubicki et al., 1980) (Fig. 1). Applying spectroscopic measurements, phase transitions have been observed at T1 = 133 K and at T2 = 106 K (Dubicki et al., 1984). By single-crystal neutron diffraction upon cooling, the appearance of satellite reflections in the diffraction pattern at T1 = 133 K was discovered, indicating the development of a modulated structure (Larsen et al., 1988). Additional phase transitions have been observed at T2 = 107 K and T3 = 98 K. In the course of investigations of the phase transitions of Λ-Cobalt(III) sepulchrate trinitrate, we have developed an improved model for its room-temperature crystal structure, which is presented here. The present description of the orientational disorder of one of the three nitrate groups is essentially different from that of Dubicki et al. (1980). It will form the basis for structure models of the incommensurate phases, which involve ordering of this nitrate group. Furthermore, Dubicki et al. (1980) have presented only a picture of the crystal structure and they did not give structural parameters. Here we present accurate structural parameters for all atoms.

The Co3+ ion is located on the 32 site at (2/3, 1/3, -1/4), conforming to the 32 geometry of the Co(sep)3+ cation. It also follows that the capping atom N5 of the sepulchrate group lies on the threefold axis. The chiral atoms N2 have an S configuration (Fig. 2). All interatomic distances and angles are in good agreement with the published data of related structures (Mikami et al., 1979; Dubicki et al., 1980; Bacchi et al., 1993a,b, 1996). The three N—C bonds in the sepulchrate cage, N2lig—C3en, N2lig—C4ap and N5ap—C4ap, have different lengths (see scheme and Table 1). The packing consists of layers of hydrogen-bonded Co(sep)3+ cations and ordered nitrate groups (Table 2), with each Co(sep)3+ cation connected to six NO3- anions and each NO3- anion to three Co(sep)3+ cations. These layers are separated by layers of disordered nitrate groups (Fig. 1).

Dubicki et al. (1980) placed atom N8 of the disordered nitrate anion at the origin with site symmetry 32. Disorder was described by one atom O9 at a general position (x, y, z) with site symmetry 1 and occupancy 1/2, spread over six equivalent positions around the origin. In the present work the crystal structure was solved using SUPERFLIP (Palatinus & Chapuis, 2007) and refined with JANA2006 (Petříček et al., 2006). The position of atom O9 converged to (0.035826, 0.147196, -0.025571) (Fig. 3). As already mentioned by Dubicki et al. (1984), due to symmetry the disorder `should be orientational in character' with six orientations of the nitrate group, each with its normal to the molecular plane tilted with respect to the crystal c axis by about 30°. However, this description results in chemically meaningless geometries of the NO3- anions (Table 3). In addition, the NO3- groups would be non-planar; atom N8 is ±0.102 (1) Å out of the plane defined by the three corresponding O atoms.

For a proper description of the disordered nitrate group, orientational disorder of the complete NO3- group as a rigid body has been applied. Due to its rotation out of the ab plane, the threefold axis of the molecule does not coincide with the threefold axis of the space group. Therefore, it is not appropriate to fix the nitrate group on the origin. Thus, the molecular centre of gravity (represented by the central atom N8) was shifted slightly away from the origin and then refined. In the final model atom N8 converged to a position at [0.0269 (13), 0.0106 (13), 0.0018 (5)], which is displaced from the origin by ca 0.2 Å. As the site symmetry of the origin is 32, five additional equivalent positions are generated for the NO3- rigid body, leading in total to six equivalent N positions and 18 equivalent O positions. By applying this model of orientational disorder, 62 instead of 60 parameters have to be refined, but now the disordered nitrate group can be defined as planar with O—N—O angles of 120°. The proper geometry is also reflected in smaller anisotropic displacement parameters for atoms N8 and O9 (Fig. 3). In addition, all statistical refinement parameters are onsiderably improved: S from 2.48 to 2.25, Robs from 0.038 to 0.034, and wRobs from 0.058 to 0.052.

Experimental top

Λ-Cobalt(III) sepulchrate trinitrate crystals were prepared at the Research School of Chemistry, Australian National University, Canberra, Australia, and a sample was supplied by Professor Alan M. Sargeson (Creaser et al., 1982). A crystal suitable for X-ray analysis was selected directly from the sample as prepared and fixed on a glass fibre. As the crystals are stable in air, no special coating was necessary.

Refinement top

In the first step all H atoms were positioned geometrically and refined using a riding model, with N—H = 0.87 Å and C—H = 0.96 Å, and with Uiso(H) = 1.2Ueq(C,N). In the next step the position of atom H2, which is involved in hydrogen bonding, was released and freely refined, to give N—H = 0.83 (2) Å.

The crystal is twinned by merohedry, containing two twin domains related to each other by inversion. The refined volume fractions converged to V1 = 0.87 (3) and V2 = 0.13 (3) for the first and second domains, respectively.

The disordered nitrate group is described with a rigid-body refinement. In the first step atoms N8 and O9 were refined independently, as proposed by Dubicki et al. (1980). The occupancy factor of atom O9 was 1/2. As atom N8 lies at the origin, only two anisotropic displacement parameters can be refined for N8. With the (3 + 6) parameters of atom O9, in total 11 parameters are involved. In the next step an ideal `model molecule' was created by one N and one O atom, with N—O = 1.22 Å and ideal molecular symmetry 321 (generating an ideal planar NO3 group with three O—N—O angles of 120° each). The position of the model O atom was made refinable, according to the restrictions of the local 321 point symmetry (one parameter). Atoms N8 and O9 were then replaced by the model molecule and the position and orientation of this rigid body were refined (three parameters for displacement and three for orientation), together with the position of the model O atom. Any attempt to apply TLS refinement for the rigid body as well resulted in singularities with blocked parameters, large correlations and a non-converging refinement. Therefore, the anisotropic displacement parameters of the atoms in the model molecule were refined independently (two for the N atom and four for the O atom). In total, 13 parameters are applied to this part of the structure.

Computing details top

Data collection: MAR345DTB (Klein, 2003); cell refinement: PEAKREF (Schreurs, 1999); data reduction: EVAL15 (Schreurs et al., 2010) and SADABS (Sheldrick, 2008); program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis, 2007); program(s) used to refine structure: JANA2006 (Petříček et al., 2006); molecular graphics: DIAMOND (Brandenburg, 2009); software used to prepare material for publication: JANA2006 (Petříček et al., 2006).

Figures top
[Figure 1] Fig. 1. Crystal packing of (I), illustrating the N—H···O hydrogen bonding involving the Co(sepulchrate) cage and the two ordered nitrate groups (shown as dashed lines; see Table 2 for details). The third nitrate group at the origin is represented as a disordered moiety.
[Figure 2] Fig. 2. The molecular structure of (I), showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms have been omitted for clarity. [Symmetry codes: (i) -y + 1, -x + 1, -z + 1/2; (ii) -y + 1, x - y + 1, z; (iii) x, x - y + 1, -z + 1/2; (v) -x + y, x - 1, z; (vi) -x + y, y, -z + 1/2; (vii) -x + y + 1, -x + 1, z; (viii) -y + 1, x - y, z; (ix) x, x - y, -z + 1/2; (x) -x + y + 1, y, -z + 1/2.]
[Figure 3] Fig. 3. (a) and (b) Comparison of the model proposed by Dubicki et al. (1980), employing the refined parameters, and the present data. (c) and (d) The rigid-body model for the disordered nitrate group, viewed along the c and b axes, respectively. All figures are at the same scale. For clarity, the generated disordered positions in (c) and (d) are shown paler. [Symmetry codes: (iv) -y, x - y, z; (xi) -x + y, -x, z; (xii) -x, -x + y, -z; (xiii) x - y, -y, -z; (xiv) y, x, -z.]
[(1,3,6,8,10,13,16,19-octaazabicyclo[6.6.6]eicosane) cobalt(III) trinitrate top
Crystal data top
[Co(C12H30N8)](NO3)3Dx = 1.773 Mg m3
Mr = 531.4Mo Kα radiation, λ = 0.71069 Å
Hexagonal, P6322Cell parameters from 7040 reflections
Hall symbol: P 6c 2cθ = 1.5–30.0°
a = 8.4945 (5) ŵ = 0.94 mm1
c = 15.9195 (13) ÅT = 295 K
V = 994.80 (12) Å3Prism, translucent light orange
Z = 20.30 × 0.15 × 0.10 mm
F(000) = 556
Data collection top
MarIP mar345dtb
diffractometer
1404 independent reflections
Radiation source: rotating anode X-ray tube1322 reflections with I > 3σ(I)
Graphite monochromatorRint = 0.025
Detector resolution: 0.15 pixels mm-1θmax = 34.8°, θmin = 3.8°
ϕ scansh = 1010
Absorption correction: multi-scan
(SADABS; Sheldrick, 2008)
k = 1112
Tmin = 0.693, Tmax = 0.747l = 2525
49907 measured reflections
Refinement top
Refinement on FH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.034Weighting scheme based on measured s.u.'s w = 1/(σ2(F) + 0.0004F2)
wR(F2) = 0.053(Δ/σ)max = 0.003
S = 2.25Δρmax = 0.46 e Å3
1404 reflectionsΔρmin = 0.37 e Å3
62 parametersAbsolute structure: Flack (1983), with how many Friedel pairs?
0 restraintsAbsolute structure parameter: 0.13 (3)
17 constraints
Crystal data top
[Co(C12H30N8)](NO3)3Z = 2
Mr = 531.4Mo Kα radiation
Hexagonal, P6322µ = 0.94 mm1
a = 8.4945 (5) ÅT = 295 K
c = 15.9195 (13) Å0.30 × 0.15 × 0.10 mm
V = 994.80 (12) Å3
Data collection top
MarIP mar345dtb
diffractometer
1404 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2008)
1322 reflections with I > 3σ(I)
Tmin = 0.693, Tmax = 0.747Rint = 0.025
49907 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.034H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.053Δρmax = 0.46 e Å3
S = 2.25Δρmin = 0.37 e Å3
1404 reflectionsAbsolute structure: Flack (1983), with how many Friedel pairs?
62 parametersAbsolute structure parameter: 0.13 (3)
0 restraints
Special details top

Refinement. The crystal is twinned by merohedry and it contains two twin domains. The twinning matrix for the second domain is: -1.000 0.000 0.000 , 0.000 -1.000 0.000 , 0.000 0.000 -1.000 . The refined volume fractions are v1=0.87 (3) and v2=0.13 (3) for the first and second domains, respectively. The restriction v1+v2=1 was applied.

It is noted, that the GoF is S = 2.25, larger than 2. This is due to the fact that the structure is refined with Jana2006 and this program does not make any adjustment of the weighting scheme to force S to 1. ————————————————————————

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Co10.3333330.6666670.250.02064 (11)
N20.14496 (17)0.67296 (17)0.17970 (7)0.0325 (4)
C30.1397 (3)0.8393 (3)0.20274 (10)0.0414 (6)
C40.1654 (3)0.6537 (3)0.08610 (10)0.0531 (9)
N50.3333330.6666670.06460 (16)0.0548 (8)
N60.6666670.3333330.1527 (2)0.0548 (10)
O70.5048 (2)0.2200 (3)0.15316 (17)0.0963 (11)
H20.042 (3)0.585 (3)0.1876 (10)0.039*
H310.0246550.8257220.1865680.0497*
H320.2387550.9428130.1760790.0497*
H410.0672550.5393740.0669010.0637*
H420.1525990.7448440.0562630.0637*
N80.0269 (13)0.0106 (13)0.0018 (5)0.049 (2)0.1667
O9a0.0452 (13)0.1550 (14)0.0192 (5)0.076 (3)0.1667
O9b0.1344 (13)0.0334 (13)0.0212 (5)0.076 (5)0.1667
O9c0.0990 (13)0.0898 (14)0.0458 (5)0.076 (5)0.1667
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Co10.01767 (14)0.01767 (14)0.02657 (17)0.00883 (7)00
N20.0267 (5)0.0300 (5)0.0422 (5)0.0153 (4)0.0056 (4)0.0034 (4)
C30.0297 (7)0.0313 (7)0.0694 (8)0.0199 (5)0.0011 (7)0.0107 (7)
C40.0604 (12)0.0633 (12)0.0382 (7)0.0328 (10)0.0168 (7)0.0001 (7)
N50.0675 (12)0.0675 (12)0.0294 (8)0.0338 (6)00
N60.0396 (8)0.0396 (8)0.085 (2)0.0198 (4)00
O70.0380 (8)0.0574 (12)0.180 (2)0.0136 (7)0.0155 (10)0.0131 (11)
N80.049 (2)0.051 (4)0.043 (2)0.0230 (19)0.0083 (19)0.0063 (18)
O9a0.056 (5)0.059 (4)0.107 (4)0.025 (3)0.014 (3)0.006 (3)
O9b0.091 (6)0.106 (8)0.055 (5)0.068 (6)0.007 (4)0.011 (4)
O9c0.080 (3)0.058 (9)0.073 (4)0.022 (4)0.017 (3)0.009 (4)
Geometric parameters (Å, º) top
Co1—N21.9752 (15)C3—C3iii1.515 (2)
Co1—N2i1.9752 (19)C4—N51.417 (3)
Co1—N2ii1.9752 (13)N6—O71.2222 (17)
Co1—N2iii1.9752 (15)N6—O7vi1.222 (4)
Co1—N2iv1.9752 (19)N6—O7vii1.222 (2)
Co1—N2v1.9752 (13)N8—O9a1.204 (17)
N2—C31.482 (3)N8—O9b1.204 (18)
N2—C41.518 (2)N8—O9c1.204 (11)
N2—H20.83 (2)
N2—Co1—N2i91.05 (6)N2—C3—C3iii107.47 (17)
N2—Co1—N2ii91.05 (6)N2—C4—N5113.19 (18)
N2—Co1—N2iii87.06 (6)C4—N5—C4i114.36 (13)
N2—Co1—N2iv177.32 (5)C4—N5—C4ii114.36 (17)
N2—Co1—N2v90.89 (6)C4i—N5—C4ii114.36 (17)
Co1—N2—C3107.26 (10)O7—N6—O7vi120.00 (18)
Co1—N2—C4114.53 (14)O7—N6—O7vii120.0 (2)
Co1—N2—H2113.1 (19)O7vi—N6—O7vii120.0 (2)
C3—N2—C4113.91 (14)O9a—N8—O9b120.0
C3—N2—H2108 (2)O9a—N8—O9c120.0
C4—N2—H2100.2 (12)O9b—N8—O9c120.0
Symmetry codes: (i) y+1, xy+1, z; (ii) x+y, x+1, z; (iii) y+1, x+1, z+1/2; (iv) x+y, y, z+1/2; (v) x, xy+1, z+1/2; (vi) y+1, xy, z; (vii) x+y+1, x+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O7viii0.83 (2)2.463 (19)3.231 (3)154 (2)
Symmetry code: (viii) y, xy, z.

Experimental details

Crystal data
Chemical formula[Co(C12H30N8)](NO3)3
Mr531.4
Crystal system, space groupHexagonal, P6322
Temperature (K)295
a, c (Å)8.4945 (5), 15.9195 (13)
V3)994.80 (12)
Z2
Radiation typeMo Kα
µ (mm1)0.94
Crystal size (mm)0.30 × 0.15 × 0.10
Data collection
DiffractometerMarIP mar345dtb
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2008)
Tmin, Tmax0.693, 0.747
No. of measured, independent and
observed [I > 3σ(I)] reflections
49907, 1404, 1322
Rint0.025
(sin θ/λ)max1)0.802
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.034, 0.053, 2.25
No. of reflections1404
No. of parameters62
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.46, 0.37
Absolute structureFlack (1983), with how many Friedel pairs?
Absolute structure parameter0.13 (3)

Computer programs: MAR345DTB (Klein, 2003), PEAKREF (Schreurs, 1999), EVAL15 (Schreurs et al., 2010) and SADABS (Sheldrick, 2008), SUPERFLIP (Palatinus & Chapuis, 2007), JANA2006 (Petříček et al., 2006), DIAMOND (Brandenburg, 2009).

Selected geometric parameters (Å, º) top
Co1—N21.9752 (15)C3—C3i1.515 (2)
N2—C31.482 (3)C4—N51.417 (3)
N2—C41.518 (2)N6—O71.2222 (17)
N2—H20.83 (2)N8—O9a1.204 (17)
N2—Co1—N2ii91.05 (6)N2—C4—N5113.19 (18)
N2—Co1—N2iii90.89 (6)C4—N5—C4ii114.36 (13)
C3—N2—C4113.91 (14)
Symmetry codes: (i) y+1, x+1, z+1/2; (ii) y+1, xy+1, z; (iii) x, xy+1, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O7iv0.83 (2)2.463 (19)3.231 (3)154 (2)
Symmetry code: (iv) y, xy, z.
Interatomic angles (°) in the disordered NO3 group derived from the model proposed by Dubicki et al. (1980). Angles are given for two out of the six possible orientations. top
O—N—Oiv109.1 (5)O—N—Oxi109.1 (5)
O—N—Oxiv99.3 (5)O—N—Oxiii149.0 (7)
Oxiv—N—Oiv149.0 (7)Oxiii—N—Oxi99.3 (7)
Symmetry codes: (iv) -y, x - y, z; (xi) -x + y, -x, z; (xiii) x - y, -y, -z; (xiv) y, x, -z.
 

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