The crystal structure of
-(1,3,6,8,10,13,16,19-octaazabicyclo[6.6.6]eicosane)cobalt(III) trinitrate, [Co(C
12H
30N
8)](NO
3)
3, consists of a sepulchrate moiety that serves as a macrobicyclic nitrogen cage for the Co
3+ 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
CCDC reference: 774882
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.
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.
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).
[(1,3,6,8,10,13,16,19-octaazabicyclo[6.6.6]eicosane) cobalt(III) trinitrate
top
Crystal data top
[Co(C12H30N8)](NO3)3 | Dx = 1.773 Mg m−3 |
Mr = 531.4 | Mo Kα radiation, λ = 0.71069 Å |
Hexagonal, P6322 | Cell parameters from 7040 reflections |
Hall symbol: P 6c 2c | θ = 1.5–30.0° |
a = 8.4945 (5) Å | µ = 0.94 mm−1 |
c = 15.9195 (13) Å | T = 295 K |
V = 994.80 (12) Å3 | Prism, translucent light orange |
Z = 2 | 0.30 × 0.15 × 0.10 mm |
F(000) = 556 | |
Data collection top
MarIP mar345dtb diffractometer | 1404 independent reflections |
Radiation source: rotating anode X-ray tube | 1322 reflections with I > 3σ(I) |
Graphite monochromator | Rint = 0.025 |
Detector resolution: 0.15 pixels mm-1 | θmax = 34.8°, θmin = 3.8° |
ϕ scans | h = −10→10 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2008) | k = −11→12 |
Tmin = 0.693, Tmax = 0.747 | l = −25→25 |
49907 measured reflections | |
Refinement top
Refinement on F | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.034 | Weighting scheme based on measured s.u.'s w = 1/(σ2(F) + 0.0004F2) |
wR(F2) = 0.053 | (Δ/σ)max = 0.003 |
S = 2.25 | Δρmax = 0.46 e Å−3 |
1404 reflections | Δρmin = −0.37 e Å−3 |
62 parameters | Absolute structure: Flack (1983), with how many Friedel pairs? |
0 restraints | Absolute structure parameter: 0.13 (3) |
17 constraints | |
Crystal data top
[Co(C12H30N8)](NO3)3 | Z = 2 |
Mr = 531.4 | Mo Kα radiation |
Hexagonal, P6322 | µ = 0.94 mm−1 |
a = 8.4945 (5) Å | T = 295 K |
c = 15.9195 (13) Å | 0.30 × 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 = 0.747 | Rint = 0.025 |
49907 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.034 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.053 | Δρmax = 0.46 e Å−3 |
S = 2.25 | Δρmin = −0.37 e Å−3 |
1404 reflections | Absolute structure: Flack (1983), with how many Friedel pairs? |
62 parameters | Absolute 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 | x | y | z | Uiso*/Ueq | Occ. (<1) |
Co1 | 0.333333 | 0.666667 | 0.25 | 0.02064 (11) | |
N2 | 0.14496 (17) | 0.67296 (17) | 0.17970 (7) | 0.0325 (4) | |
C3 | 0.1397 (3) | 0.8393 (3) | 0.20274 (10) | 0.0414 (6) | |
C4 | 0.1654 (3) | 0.6537 (3) | 0.08610 (10) | 0.0531 (9) | |
N5 | 0.333333 | 0.666667 | 0.06460 (16) | 0.0548 (8) | |
N6 | 0.666667 | 0.333333 | 0.1527 (2) | 0.0548 (10) | |
O7 | 0.5048 (2) | 0.2200 (3) | 0.15316 (17) | 0.0963 (11) | |
H2 | 0.042 (3) | 0.585 (3) | 0.1876 (10) | 0.039* | |
H31 | 0.024655 | 0.825722 | 0.186568 | 0.0497* | |
H32 | 0.238755 | 0.942813 | 0.176079 | 0.0497* | |
H41 | 0.067255 | 0.539374 | 0.066901 | 0.0637* | |
H42 | 0.152599 | 0.744844 | 0.056263 | 0.0637* | |
N8 | 0.0269 (13) | 0.0106 (13) | 0.0018 (5) | 0.049 (2) | 0.1667 |
O9a | 0.0452 (13) | 0.1550 (14) | −0.0192 (5) | 0.076 (3) | 0.1667 |
O9b | 0.1344 (13) | −0.0334 (13) | −0.0212 (5) | 0.076 (5) | 0.1667 |
O9c | −0.0990 (13) | −0.0898 (14) | 0.0458 (5) | 0.076 (5) | 0.1667 |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Co1 | 0.01767 (14) | 0.01767 (14) | 0.02657 (17) | 0.00883 (7) | 0 | 0 |
N2 | 0.0267 (5) | 0.0300 (5) | 0.0422 (5) | 0.0153 (4) | −0.0056 (4) | 0.0034 (4) |
C3 | 0.0297 (7) | 0.0313 (7) | 0.0694 (8) | 0.0199 (5) | 0.0011 (7) | 0.0107 (7) |
C4 | 0.0604 (12) | 0.0633 (12) | 0.0382 (7) | 0.0328 (10) | −0.0168 (7) | 0.0001 (7) |
N5 | 0.0675 (12) | 0.0675 (12) | 0.0294 (8) | 0.0338 (6) | 0 | 0 |
N6 | 0.0396 (8) | 0.0396 (8) | 0.085 (2) | 0.0198 (4) | 0 | 0 |
O7 | 0.0380 (8) | 0.0574 (12) | 0.180 (2) | 0.0136 (7) | 0.0155 (10) | −0.0131 (11) |
N8 | 0.049 (2) | 0.051 (4) | 0.043 (2) | 0.0230 (19) | −0.0083 (19) | −0.0063 (18) |
O9a | 0.056 (5) | 0.059 (4) | 0.107 (4) | 0.025 (3) | −0.014 (3) | 0.006 (3) |
O9b | 0.091 (6) | 0.106 (8) | 0.055 (5) | 0.068 (6) | 0.007 (4) | 0.011 (4) |
O9c | 0.080 (3) | 0.058 (9) | 0.073 (4) | 0.022 (4) | 0.017 (3) | −0.009 (4) |
Geometric parameters (Å, º) top
Co1—N2 | 1.9752 (15) | C3—C3iii | 1.515 (2) |
Co1—N2i | 1.9752 (19) | C4—N5 | 1.417 (3) |
Co1—N2ii | 1.9752 (13) | N6—O7 | 1.2222 (17) |
Co1—N2iii | 1.9752 (15) | N6—O7vi | 1.222 (4) |
Co1—N2iv | 1.9752 (19) | N6—O7vii | 1.222 (2) |
Co1—N2v | 1.9752 (13) | N8—O9a | 1.204 (17) |
N2—C3 | 1.482 (3) | N8—O9b | 1.204 (18) |
N2—C4 | 1.518 (2) | N8—O9c | 1.204 (11) |
N2—H2 | 0.83 (2) | | |
| | | |
N2—Co1—N2i | 91.05 (6) | N2—C3—C3iii | 107.47 (17) |
N2—Co1—N2ii | 91.05 (6) | N2—C4—N5 | 113.19 (18) |
N2—Co1—N2iii | 87.06 (6) | C4—N5—C4i | 114.36 (13) |
N2—Co1—N2iv | 177.32 (5) | C4—N5—C4ii | 114.36 (17) |
N2—Co1—N2v | 90.89 (6) | C4i—N5—C4ii | 114.36 (17) |
Co1—N2—C3 | 107.26 (10) | O7—N6—O7vi | 120.00 (18) |
Co1—N2—C4 | 114.53 (14) | O7—N6—O7vii | 120.0 (2) |
Co1—N2—H2 | 113.1 (19) | O7vi—N6—O7vii | 120.0 (2) |
C3—N2—C4 | 113.91 (14) | O9a—N8—O9b | 120.0 |
C3—N2—H2 | 108 (2) | O9a—N8—O9c | 120.0 |
C4—N2—H2 | 100.2 (12) | O9b—N8—O9c | 120.0 |
Symmetry codes: (i) −y+1, x−y+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, x−y+1, −z+1/2; (vi) −y+1, x−y, z; (vii) −x+y+1, −x+1, z. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O7viii | 0.83 (2) | 2.463 (19) | 3.231 (3) | 154 (2) |
Symmetry code: (viii) −y, x−y, z. |
Experimental details
Crystal data |
Chemical formula | [Co(C12H30N8)](NO3)3 |
Mr | 531.4 |
Crystal system, space group | Hexagonal, P6322 |
Temperature (K) | 295 |
a, c (Å) | 8.4945 (5), 15.9195 (13) |
V (Å3) | 994.80 (12) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.94 |
Crystal size (mm) | 0.30 × 0.15 × 0.10 |
|
Data collection |
Diffractometer | MarIP mar345dtb diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2008) |
Tmin, Tmax | 0.693, 0.747 |
No. of measured, independent and observed [I > 3σ(I)] reflections | 49907, 1404, 1322 |
Rint | 0.025 |
(sin θ/λ)max (Å−1) | 0.802 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.034, 0.053, 2.25 |
No. of reflections | 1404 |
No. of parameters | 62 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.46, −0.37 |
Absolute structure | Flack (1983), with how many Friedel pairs? |
Absolute structure parameter | 0.13 (3) |
Selected geometric parameters (Å, º) topCo1—N2 | 1.9752 (15) | C3—C3i | 1.515 (2) |
N2—C3 | 1.482 (3) | C4—N5 | 1.417 (3) |
N2—C4 | 1.518 (2) | N6—O7 | 1.2222 (17) |
N2—H2 | 0.83 (2) | N8—O9a | 1.204 (17) |
| | | |
N2—Co1—N2ii | 91.05 (6) | N2—C4—N5 | 113.19 (18) |
N2—Co1—N2iii | 90.89 (6) | C4—N5—C4ii | 114.36 (13) |
C3—N2—C4 | 113.91 (14) | | |
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. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O7iv | 0.83 (2) | 2.463 (19) | 3.231 (3) | 154 (2) |
Symmetry code: (iv) −y, x−y, 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. topO—N—Oiv | 109.1 (5) | O—N—Oxi | 109.1 (5) |
O—N—Oxiv | 99.3 (5) | O—N—Oxiii | 149.0 (7) |
Oxiv—N—Oiv | 149.0 (7) | Oxiii—N—Oxi | 99.3 (7) |
Symmetry codes: (iv) -y, x - y, z;
(xi) -x + y, -x, z;
(xiii) x - y, -y, -z;
(xiv) y, x, -z. |
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.