Cadaverinium dichloride: A case of centro-non-centrosymmetric ambiguity

Article abstract of DOI:10.1107/S0108270106018397

In the title salt, also known as pentane-1,5-diammonium dichloride, C ₅H₁₆N₂²⁺·2Cl^-, the cation exists in an ideal fully extended conformation and lies on a mirror plane in the space group Pbam. In the crystal structure, layers of cations are hydrogen bonded with Cl^- anions, which occupy the space between the layers. This kind of packing leads to a short unit-cell parameter of 4.463 (1) A. This structure is another case of centro-non-centrosymmetric ambiguity; the best results were obtained in a centrosymmetric space group, with the disordered NH₃ groups accounting for the non-centrosymmetric 'component'.

Full text of DOI:10.1107/S0108270106018397

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
of cadaverinium dichloride trihydrate has been reported to
date (Ramaswamy & Murthy, 1992; R factor of 0.101, no H
atoms reported, three doubtful water O atoms). During our
systematic investigations of the coordination template effect
of various metal ions in generating new supramolecular
macrocyclic and acyclic Schiff base systems derived from
biogenic and biogenic-like diamines, we obtained crystals of
cadaverine dichloride, (I), and decided to determine the
crystal structure of this missing member of the family. In the
course of these studies, we have found another case of one of
the primary crystallographic problems, namely centro±non-
centrosymmetric ambiguity (see, for example, Schomaker &
Marsh, 1979; Marsh, 1999; Kubicki et al., 2003, and references
therein).
ISSN 0108-2701
Cadaverinium dichloride: a case
of centro±non-centrosymmetric
ambiguity
Izabela Pospieszna-Markiewicz, Wanda Radecka-Paryzek
and Maciej Kubicki*
Department of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780
The symmetric absences allowed the orthorhombic space
groups Pbam and Pba2; the former, centrosymmetric, space
group was chosen on the basis of the statistics of the |E|-value
distribution. The probability that the structure is centrosym-
metric, based on this distribution, is as high as 90%. The
re®nement was straightforward until the determination of the
H atoms of the NH3 groups. They could not be reasonably
determined from the Fourier maps and were placed in idea-
lized positions, but with the possibility of a `rigid body' rota-
tion of the whole set around the CÐN bond (AFIX137 in
SHELXL97; Sheldrick, 1997). Both NH3 groups were opti-
mized in the disordered dispositions, in which two sets of H
atoms were connected by the mirror plane. Analysis of the
hydrogen-bond network shows that the rational description of
this network demands that consecutive molecules have alter-
native dispositions of H atoms, just as in the case without a
mirror plane, i.e. in the space group Pba2. Attempts to re®ne
the structure in that space group were not conclusive. The R
Â
Poznan, Poland
Correspondence e-mail: mkubicki@amu.edu.pl
Received 4 April 2006
Accepted 17 May 2006
Online 15 June 2006
In the title salt, also known as pentane-1,5-diammonium
2+
dichloride, C5H16N2 Á2Cl , the cation exists in an ideal fully
extended conformation and lies on a mirror plane in the space
group Pbam. In the crystal structure, layers of cations are
hydrogen bonded with Cl anions, which occupy the space
between the layers. This kind of packing leads to a short unit-
Ê
cell parameter of 4.463 (1) A. This structure is another case of
centro±non-centrosymmetric ambiguity; the best results were
obtained in a centrosymmetric space group, with the
disordered NH3 groups accounting for the non-centrosym-
metric `component'.
Comment
Polyamines play a major role in many cellular and genetic
processes, such as DNA synthesis, gene expression, cell divi-
sion, protein synthesis and plant response to abiotic stress.
One of these compounds is cadaverine, which is derived from
the amino acid lysine by decarboxylation catalysed by lysine
decarboxylase. Cadaverine is naturally present in decaying
corpses and in the roots of certain plants. Under normal
physiological conditions, polyamines exist as polycations.
Natural polyamines bind to polyanions, for example, to DNA,
and induce various changes in their secondary structure
(Karigiannis & Papaioannou, 2000).
Figure 1
A view of the title salt, (I), with the atom-labelling scheme. Displacement
ellipsoids are drawn at the 50% probability level and H atoms are shown
as spheres of arbitrary radii. Dashed lines indicate the hydrogen bonds.
Flexible molecules (dications) of ꢀ,!-diammonioalkanes
are also used in the crystal engineering of different layered
structures, either organic or organometallic. Therefore,
knowledge of the packing modes of these compounds is crucial
for the rational design of the new materials. Some crystal
structures of halides of ꢀ,!-diammonioalkanes, of the general
formula [NH3±(CH2)n±NH3]2+Á2Cl , are known for n = 1±8,
with a gap at n = 5. For n = 5, only the poorly de®ned structure
Figure 2
A packing scheme for (I), viewed approximately along the [010]
direction. Hydrogen bonds are depicted as dashed lines. For clarity, only
H atoms involved in hydrogen bonds are shown.
Acta Cryst. (2006). C62, o399±o401
DOI: 10.1107/S0108270106018397
# 2006 International Union of Crystallography o399

organic compounds
Ê
the present case, c) is short, ca 4.5 A. Such a unit-cell para-
meter can be found in many analogous ꢀ,!-diammonioalkane
halogenates, for example, ethylenediammonium dichloride
factors, residual maps, etc., were comparable with the centro-
symmetric re®nement, but, due to the large correlations
between parameters related by a pseudo-mirror plane of
symmetry, the re®nement was unstable and hardly converged
(more or less constant shifts as large as 0.7 were observed).
In our opinion, the best results were obtained on the
assumption that the main skeleton of the structure is centro-
symmetric (this is further con®rmed by the regular shapes of
the anisotropic displacement ellipsoids; see Fig. 1), and it is
only slightly distorted by the positions of the terminal H
atoms. Following this assumption, we re®ned the structure in
the centrosymmetric space group Pbam, but the terminal H
atoms were assumed to be disordered over two alternative
positions with site-occupancy factors equal to 0.5. It may be
noted that these occupancies have to be exactly equal to 0.5 in
order to produce a consistent hydrogen-bond network. Similar
reasons were used, for example, in evaluating the ratio of the
tautomeric mixture found in a given crystal (e.g. Gdaniec et al.,
1995; Kubicki 2004, and references therein).
Ê
(4.419 A; Bujak et al., 2000), 1,3-diammoniopropyl dibromide
Ê
(4.579 A; Dou et al., 1995), putrescinium (tetramethylenedi-
Ê
ammonium) dichloride (4.589 A; Chandrasekhar & Pattabhi,
Ê
1980), hexamethylenediammonium dichloride (4.594 A;
Borkakoti et al., 1978), etc. The structure of a layer is shown in
Fig. 3. This structure is created by NÐHÁ Á ÁCl and relatively
strong CÐHÁ Á ÁCl hydrogen bonds (Table 2).
It may be noted that CÐHÁ Á ÁCl contacts are short and
linear, and their role is important. Using Etter's graph-set
notation (Etter et al., 1990; Bernstein et al., 1995), there are
three kinds of higher-order rings, viz. R24(10), R63(17) and
R24(20). This structure is to some extent exceptional; in the
majority of the structures of other ꢀ,!-diammonioalkane
halogenates, the characteristic motif R24(8) is present.
Fig. 1 shows a perspective view of the salt molecule, toge-
ther with the labelling scheme. The cation is symmetrical and
lies on a mirror plane in the space group Pbam. Bond lengths
and angles (Table 1) are typical (International Tables for
Crystallography, 1995, Vol. C). The cation is in a fully
extended conformation and all torsion angles along the
aliphatic chain are 180ꢀ. The terminal NH3 groups are disor-
dered and there are two sets of (symmetry-equivalent) posi-
tions of the H atoms.
Experimental
To a mixture of yttrium(III) chloride (30 mg, 0.1 mmol) in methanol
(10 ml), cadaverine (23 mg, 0.2 mmol) in ethanol (10 ml) was added
dropwise with stirring. The reaction was carried out for 4 h. The
solution volume was then reduced to 5 ml by rotary evaporation.
Yellow single crystals suitable for X-ray diffraction analysis were
formed by slow diffusion of dioxan (1 ml) into a methanol solution of
the complex (1 ml) with yttrium chloride at room temperature over a
period of a few days.
In the crystal structure of (I), there are layers of cations
parallel to the ab plane and the Cl anions, hydrogen bonded
to cations, occupy the space between the layers (Fig. 2). As a
result of this packing stabilized by electrostatic interactions,
one unit-cell parameter, perpendicular to the layer plane (in
Crystal data
2+
C5H16N2 Á2Cl
Z = 4
Dx = 1.198 Mg m
Mo Kꢀ radiation
ꢁ = 0.60 mm
T = 295 (1) K
Prism, colourless
0.35 Â 0.2 Â 0.12 mm
3
Mr = 175.10
Orthorhombic, Pbam
Ê
a = 11.9697 (13) A
1
Ê
b = 18.180 (2) A
Ê
c = 4.4626 (5) A
3
Ê
V = 971.10 (19) A
Data collection
Kuma KM-4 CCD four-circle
diffractometer
! scans
5851 measured re¯ections
1386 independent re¯ections
1079 re¯ections with I > 2ꢂ(I)
Rint = 0.030
ꢃmax = 29.1ꢀ
Re®nement
Re®nement on F2
R[F2 > 2ꢂ(F2)] = 0.037
wR(F2) = 0.109
S = 1.06
1386 re¯ections
79 parameters
H atoms treated by a mixture of
independent and constrained
re®nement
w = 1/[ꢂ2(Fo2) + (0.07P)2]
2
where P = (Fo + 2Fc2)/3
(Á/ꢂ)max = 0.001
3
Ê
Áꢄmax = 0.43 e A
3
Ê
0.23 e A
Áꢄmin
=
Table 1
Selected geometric parameters (A, ).
ꢀ
Ê
N1ÐC2
C2ÐC3
C3ÐC4
1.479 (3)
1.482 (3)
1.527 (3)
C4ÐC5
C5ÐC6
C6ÐN7
1.503 (4)
1.510 (3)
1.484 (3)
N1ÐC2ÐC3
C2ÐC3ÐC4
C5ÐC4ÐC3
113.4 (2)
112.7 (2)
113.1 (2)
C4ÐC5ÐC6
N7ÐC6ÐC5
112.6 (2)
111.8 (2)
Figure 3
The structure of a layer of (I), together with graph-set designators.
Hydrogen bonds are depicted as dashed lines.
2+
C5H16N2 Á2Cl
ꢁ
o400 Pospieszna-Markiewicz et al.
Acta Cryst. (2006). C62, o399±o401

organic compounds
Table 2
Hydrogen-bond geometry (A, ).
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: DN3013). Services for accessing these data are
described at the back of the journal.
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N1ÐH1CÁ Á ÁCl1i
N1ÐH1BÁ Á ÁCl1ii
N1ÐH1CÁ Á ÁCl2iii
N1ÐH1AÁ Á ÁCl2iv
C2ÐH2Á Á ÁCl2v
C4ÐH4Á Á ÁCl2v
C5ÐH5Á Á ÁCl1
0.89
0.89
0.89
0.89
0.94 (2)
0.98 (2)
0.97 (2)
0.97 (2)
0.89
2.48
2.34
2.75
2.45
2.90 (2)
3.18 (2)
3.19 (2)
3.20 (2)
2.31
3.2133 (14)
3.2133 (14)
3.2342 (13)
3.2342 (13)
3.7446 (19)
4.037 (2)
141
167
115
147
150.8 (15)
146.9 (14)
133.4 (16)
117.6 (13)
167
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2+
C5H16N2 Á2Cl
ꢁ
Acta Cryst. (2006). C62, o399±o401
Pospieszna-Markiewicz et al.
o401