The pseudosymmetric structure of bis(pentane-1,5-diaminium) iodide tris(triiodide)

The asymmetric unit of the title compound, [H3N(CH2)5NH3]2I[I3]3 or 2C5H16N2 2+·3I3 −·I−, consists of two crystallographically independent pentane-1,5-diaminium dications and two triiodide anions in general positions besides two additional triiodide and two iodide anions located on twofold axes. The compound crystallizes in the centrosymmetric monoclinic space group P2/n. The structure refinement was handicapped by the pseudosymmetry (pseudo-centering) of the structure and by twinning. The crystal structure is composed of two alternate layers, which differ in their arrangement of the pentane-1,5-diaminium dications and the iodide/triiodide anions and which are connected via weak to medium–strong N—H⋯I hydrogen bonds, constructing a complex hydrogen-bonded network.

The asymmetric unit of the title compound, [H 3 N(CH 2 ) 5 NH 3 ] 2 I[I 3 ] 3 or 2C 5 H 16 N 2 2+ Á3I 3 À ÁI À , consists of two crystallographically independent pentane-1,5-diaminium dications and two triiodide anions in general positions besides two additional triiodide and two iodide anions located on twofold axes. The compound crystallizes in the centrosymmetric monoclinic space group P2/n. The structure refinement was handicapped by the pseudosymmetry (pseudo-centering) of the structure and by twinning. The crystal structure is composed of two alternate layers, which differ in their arrangement of the pentane-1,5-diaminium dications and the iodide/triiodide anions and which are connected via weak to medium-strong N-HÁ Á ÁI hydrogen bonds, constructing a complex hydrogen-bonded network.

Comment
There is a general interest in diaminiumalkane iodides and polyiodides as they are well known for having a significant influence on the redox chemistry in dye-sensitized solar cells (O′Regan & Grätzel, 1991;Yang et al., 2011). The semi-flexible, stick-shaped α,ω-diaminiumalkane dications have proved to be potent templates for crystal engineering with a wide field of application, e. g. for the synthesis of layered structures of aluminium and zinc phosphates (Feng et al., 2000;Wiebcke, 2002), for the encapsulation of hydronium cations with unusual topology in hydrogen-bonded frameworks (Frank & Reiss, 1997) and for connecting metal clusters as special spacers (Johnson et al., 2000). In the recent past several groups have also synthesized new polyiodides using stick-shaped cationic templates whose lengths and shapes fit with the structures of the polyiodides (Tebbe & Bittner, 1995;Abate et al., 2010;Meyer et al., 2010;García et al., 2011;Reiss & van Megen, 2012). This selective and robust synthetic protocol for solid polyiodides is now termed dimensional caging (Svensson et al., 2008). Especially the α,ω-diaminiumalkane dications have successfully been used for the dimensional caging of polyiodides (Reiss & Engel, 2002;Reiss & Engel, 2004). This contribution presents the crystal structure of a salt composed of pentane-1,5-diaminium dications and iodide and triiodide anions.
The asymmetric unit of the title compound consists of two crystallographically independent pentane-1,5-diaminium dications and two triiodides in general positions. In addition to that there are two more triiodides and two iodide anions all located on twofold axes. The organic dications exhibit an all-trans conformation within the experimental uncertainties.
The crystallographically independent dications are found in two different, alternate layers which are connected by weak to medium strong N-H···I hydrogen-bonds (Steiner, 2002). The pentane-1,5-diaminium dications and the different types of anions construct a complex hydrogen-bonded framework. Generally the N-H···I hydrogen bonds accepted by the iodide anions are, as expected, shorter than those accepted by the triiodide anions. However, there is also one triiodide anion which is not involved in any classical hydrogen bonding, but it is integrated in the structure by weak H···I contacts ( Fig. 1).
The basic hydrogen-bonded structural motif in both layers consists of two cations, one iodide and one triiodide arranged as a ring ( Fig. 2 and Fig. 3). In these hydrogen-bonded rings the iodide anion accepts two hydrogen bonds and the triiodide anion accepts one hydrogen bond at each terminal iodine atom (graph set: R 3 4 (22); Etter, 1990). In the A layer the iodide anion accepts two more hydrogen bonds of neighbouring aminium groups whereas the triiodide anion is not further connected (Fig. 2, Table 1). In contrast to that in layer B the iodide and the triiodide anion of the basic hydrogenbonded ring motif are not involved in further hydrogen bonding. The connection to neighbouring units in this case is performed by the aminium groups (Fig. 3, Table 1). In both layers triiodide anions (I3-I4-I5; I9-I10-I11) are arranged parallel to the rod-shaped cations. The inclusion of these triiodides can be understood as a typical encapsulation of a supplementary materials sup-2 Acta Cryst. (2012). E68, o1331-o1332 small polyiodide (Abate et al., 2010;Müller et al., 2010;García et al., 2011).
All triiodide anions in this compound are nearly linear and symmetric with bond lengths and angles in the expected ranges (Svensson & Kloo, 2003). Furthermore the Raman spectroscopic results are in excellent agreement with those of the crystal structure analysis. For a centrosymmetric triiodide anion with D ∞h symmetry one Raman active band from the centrosymmetric stretching vibration is predicted at ~110 cm -1 by selection rules (Deplano et al., 1999). The experimental Raman spectrum of the title compound shows one very strong band at 110 cm -1 .
The whole structure determination is affected by pseudosymmetry problems. The diffraction pattern shows weak superstructure reflections besides the main reflections (Fig. 4). The ADDSYM option of the PLATON programme (Spek, 2009) detects a centering of most non-hydrogen atoms which produces a B-Alert using the IUCR-CheckCif programme.
A view along [010] shows the title structure ( Fig. 5) with the true monoclinic cell (red) and the pseudo-orthorhombic cell (black). From all the non-hydrogen atom positions in the asymmetric unit, only two iodide anion positions do not fit with a face-centered description of the structure. In the projection along [010] the deviation from the higher symmetric description is marginal. Fig. 4 and Fig. 5 document the difficulties which arose during the data collection and the structure refinement. As the final structural model does not reveal any disorder, including the hydrogen atoms, a description in a higher symmetric model accepting a disorder has definitively been ruled out.
Upon slow cooling to room temperature, dark-red, shiny crystals were formed at the bottom of the reaction vessel within one to two days.
The Raman spectrum was measured using a Bruker MULTIRAM spectrometer (Nd:YAG-laser at 1064 nm; InGaAsdetector); 300-70 cm -1 : 216(w), 110(vs). -IR spectroscopic data were collected on a Digilab FT3500 spectrometer using refinement of the anisotropic displacement parameters for the nitrogen and carbon atoms only succeeded with the parameters kept roughly isotropical (ISOR option of the SHELX programme; Sheldrick, 2008). The hydrogen atoms of the CH 2 groups were included using a riding model. The U iso (H) values were set 1.2 times of their parent atoms.
Refinement of this structural model yielded all 12 missing hydrogen atom positions of the aminium groups. In the latest stages of refinement the hydrogen atom positions of these were refined with their N-H distances softly restrained with a common U value for each group. In the final refinements it was possible to omit the restraints on the anisotropic displacement parameters. For the most disagreeable reflections in the Fo/Fc statistic it was observed that the Fo value is always too large. This finding must be attributed to the fact that a small twin component added its intensity to some reflections.    Showing the basic structural motif of the A layer (symmetry code: ′ = 0.5 -x, y, 0.5 -z, displacement ellipsoids are drawn at the 70% probability level; hydrogen atoms are drawn as spheres with arbitrary radii; only classical hydrogen bonds are shown).

Figure 3
Showing the basic structural motif of the B layer (symmetry code: ′ = 0.5 -x, y, 1.5 -z, displacement ellipsoids are drawn with 70% probability; hydrogen atoms are drawn as spheres with arbitrary radii; only classical hydrogen bonds are shown).   View along [010] on the pseudosymmetric title structure; a, c: true cell (red); a′, c′: pseudosymmetric cell (black). Hydrogen site location: inferred from neighbouring sites H atoms treated by a mixture of independent and constrained refinement w = 1/[σ 2 (F o 2 ) + (0.010P) 2 + 2.P] where P = (F o 2 + 2F c 2 )/3 (Δ/σ) max = 0.002 Δρ max = 0.89 e Å −3 Δρ min = −0.85 e Å −3 Extinction correction: SHELXL97 (Sheldrick, 2008), Fc * =kFc[1+0.001xFc 2 λ 3 /sin(2θ)] -1/4 Extinction coefficient: 0.000079 (7) Special details Experimental. Absorption correction: CrysAlis PRO, Oxford Diffraction Ltd., Version 1.171.34.44. Analytical numeric absorption correction using a multifaceted crystal model (Clark & Reid, 1995). 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 F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.