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

In the title salt, also known as pentane-1,5-diammonium dichloride, C₅H₁₆N₂²⁺·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) Å. 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'.

S1. Comment

Polyamines play a major role in many cellular and genetic processes, such as DNA synthesis, gene expression, cell division, 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).

Flexible molecules (dications) of α,ω-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 α,ω-diammonioalkanes, of the general formula [NH₃—(CH₂)_n—NH₃]²⁺·2Cl⁻, are known for n = 1–8, with a gap at n = 5. For n = 5, only the poorly defined structure 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 we 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–noncentrosymmetric ambiguity (see, for example, Schomaker & Marsh, 1979; Marsh, 1999; Kubicki et al., 2003, and references therein).

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 centrosymmetric, based on this distribution, is as high as 90%. The refinement 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 idealized positions, but with the possibility of a `rigid body' rotation of the whole set around the C—N bond (AFIX137 in SHELXL97; Sheldrick, 1997). Both NH₃ groups were optimized 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 alternative dispositions of H atoms, just as in the case without a mirror plane, i.e. in the space group Pba2. A ttempts to refine the structure in that space group were not conclusive. The R factors, residual maps etc. were comparable with the centrosymmetric refinement, but, due to the large correlations between parameters related by a pseudo-mirror plane of symmetry, the refinement 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 centrosymmetric (this is further confirmed 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 refined 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).

Fig. 1 shows a perspective view of the salt molecule, together with the labelling scheme. The cation is symmetrical, C_s, and it lies on a mirror plane in space group Pbam. Bond lengths and angles (Table 1) are typical (Reference for standard values?). Due to symmetry requirements, the cation is in a fully extended conformation and all torsion angles along the aliphatic chain are 180°. The terminal NH₃ groups are disordered and there are two sets of (symmetry-equivalent) positions of the H atoms.

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 the present case, c) is short, ca 4.5 Å. Such a unit-cell parameter can be found in many analogous α,ω-diammonioalkane halogenates, for example ethylenediammonium dichloride (4.419 Å; Bujak et al., 2000), 1,3-diammoniumpropyl dibromide (4.579 Å; Dou et al., 1995), putrescinium (tetramethylenediammonium) dichloride (4.589 Å; Chandrasekhar & Pattabhi, 1980), hexamethylenediammonium dichloride (4.594 Å; Borkakoti et al., 1978), etc. The structure of a layer is shown in Fig. 3. This structure is created by N—H···Cl and relatively strong C—H···Cl hydrogen bonds (Table 2).

It may be noted that C—H···Cl 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: R²₄(10), R³₆(17) and R²₄(20). This structure is to some extent exceptional; in the majority of the structures of other α,ω-diammonioalkane halogenates, the characteristic motif R²₄(8) is present.

S2. Experimental

Crystals of cadaverine dichloride were obtained by slow diffusion of dioxane into a methanol solution of the cadaverine complex with yttrium chloride. [Quantities, concentrations, volumes?]

Computing details

Data collection: CrysAlis CCD (Oxford Diffraction, 2002); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Stereochemical Workstation Operation Manual (Siemens, 1989); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 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.
	Fig. 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.
	Fig. 3. The structure of a layer of (I), together with graph-set designators. Hydrogen bonds are depicted as dashed lines.

Pentane-1,5-diammonium dichloride

Crystal data

C5H16N2^2+·2Cl^−	F(000) = 376
Mr = 175.10	Dx = 1.198 Mg m^−3
Orthorhombic, Pbam	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2 2ab	Cell parameters from 2608 reflections
a = 11.9697 (13) Å	θ = 4–22°
b = 18.180 (2) Å	µ = 0.60 mm^−1
c = 4.4626 (5) Å	T = 295 K
V = 971.10 (19) Å^3	Prism, colourless
Z = 4	0.35 × 0.2 × 0.12 mm

Data collection

Kuma KM4 CCD four-circle diffractometer	1079 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.030
Graphite monochromator	θmax = 29.1°, θmin = 2.8°
ω scans	h = −14→16
5851 measured reflections	k = −23→21
1386 independent reflections	l = −4→6

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.037	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.109	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ^2(Fo^2) + (0.07P)^2] where P = (Fo^2 + 2Fc^2)/3
1386 reflections	(Δ/σ)max = 0.001
79 parameters	Δρmax = 0.43 e Å^−3
0 restraints	Δρmin = −0.23 e Å^−3

Special details

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 F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
N1	0.83570 (15)	0.41648 (10)	0.0000	0.0455 (4)
H1A	0.9031	0.4035	−0.0655	0.073 (7)*	0.50
H1B	0.7837	0.3975	−0.1199	0.073 (7)*	0.50
H1C	0.8259	0.3996	0.1854	0.073 (7)*	0.50
C2	0.8264 (2)	0.49758 (12)	0.0000	0.0511 (6)
H2	0.8641 (15)	0.5140 (10)	0.172 (5)	0.070 (6)*
C3	0.7094 (2)	0.52425 (13)	0.0000	0.0535 (6)
H3	0.6711 (14)	0.5031 (11)	0.172 (5)	0.074 (7)*
C4	0.7013 (2)	0.60809 (13)	0.0000	0.0492 (5)
H4	0.7470 (16)	0.6291 (10)	0.161 (5)	0.080 (7)*
C5	0.5830 (2)	0.63572 (13)	0.0000	0.0531 (6)
H5	0.5415 (17)	0.6152 (12)	0.168 (6)	0.081 (7)*
C6	0.5761 (2)	0.71865 (13)	0.0000	0.0496 (5)
H6	0.6085 (16)	0.7386 (11)	0.182 (5)	0.073 (6)*
N7	0.45874 (16)	0.74487 (11)	0.0000	0.0470 (5)
H7A	0.4562	0.7907	0.0700	0.073 (8)*	0.50
H7B	0.4176	0.7157	0.1161	0.073 (8)*	0.50
H7C	0.4321	0.7439	−0.1861	0.073 (8)*	0.50
Cl1	0.31659 (6)	0.66177 (4)	0.5000	0.0638 (2)
Cl2	0.48078 (4)	0.87194 (3)	0.5000	0.04160 (19)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0456 (10)	0.0408 (10)	0.0501 (11)	0.0035 (8)	0.000	0.000
C2	0.0490 (14)	0.0366 (12)	0.0678 (17)	−0.0016 (9)	0.000	0.000
C3	0.0470 (14)	0.0409 (11)	0.0726 (17)	0.0023 (10)	0.000	0.000
C4	0.0434 (12)	0.0410 (11)	0.0632 (15)	0.0020 (10)	0.000	0.000
C5	0.0479 (13)	0.0419 (12)	0.0696 (17)	0.0028 (10)	0.000	0.000
C6	0.0455 (13)	0.0398 (12)	0.0634 (15)	0.0039 (9)	0.000	0.000
N7	0.0473 (11)	0.0423 (10)	0.0512 (11)	0.0024 (8)	0.000	0.000
Cl1	0.0619 (4)	0.0873 (5)	0.0422 (3)	−0.0366 (3)	0.000	0.000
Cl2	0.0441 (3)	0.0430 (3)	0.0376 (3)	0.00063 (19)	0.000	0.000

Geometric parameters (Å, º)

N1—C2	1.479 (3)	C4—H4	0.98 (2)
N1—H1A	0.8900	C5—C6	1.510 (3)
N1—H1B	0.8900	C5—H5	0.97 (2)
N1—H1C	0.8900	C6—N7	1.484 (3)
C2—C3	1.482 (3)	C6—H6	0.97 (2)
C2—H2	0.94 (2)	N7—H7A	0.8900
C3—C4	1.527 (3)	N7—H7B	0.8900
C3—H3	0.97 (2)	N7—H7C	0.8900
C4—C5	1.503 (4)
C2—N1—H1A	109.5	C3—C4—H4	111 (1)
C2—N1—H1B	109.5	C4—C5—C6	112.6 (2)
H1A—N1—H1B	109.5	C4—C5—H5	111 (1)
C2—N1—H1C	109.5	C6—C5—H5	111 (1)
H1A—N1—H1C	109.5	N7—C6—C5	111.8 (2)
H1B—N1—H1C	109.5	N7—C6—H6	105 (1)
N1—C2—C3	113.4 (2)	C5—C6—H6	111 (1)
N1—C2—H2	106 (1)	C6—N7—H7A	109.5
C3—C2—H2	111 (1)	C6—N7—H7B	109.5
C2—C3—C4	112.7 (2)	H7A—N7—H7B	109.5
C2—C3—H3	108 (1)	C6—N7—H7C	109.5
C4—C3—H3	111 (1)	H7A—N7—H7C	109.5
C5—C4—C3	113.1 (2)	H7B—N7—H7C	109.5
C5—C4—H4	113 (1)
N1—C2—C3—C4	180.0	C3—C4—C5—C6	180.0
C2—C3—C4—C5	180.0	C4—C5—C6—N7	180.0

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1C···Cl1^i	0.89	2.48	3.2133 (14)	141
N1—H1B···Cl1^ii	0.89	2.34	3.2133 (14)	167
N1—H1C···Cl2^iii	0.89	2.75	3.2342 (13)	115
N1—H1A···Cl2^iv	0.89	2.45	3.2342 (13)	147
C2—H2···Cl2^v	0.94 (2)	2.90 (2)	3.7446 (19)	150.8 (15)
C4—H4···Cl2^v	0.98 (2)	3.18 (2)	4.037 (2)	146.9 (14)
C5—H5···Cl1	0.97 (2)	3.19 (2)	3.920 (2)	133.4 (16)
C6—H6···Cl2	0.97 (2)	3.20 (2)	3.7480 (18)	117.6 (13)
N7—H7B···Cl1	0.89	2.31	3.1869 (14)	167
N7—H7C···Cl1^vi	0.89	2.47	3.1869 (14)	138
N7—H7A···Cl2	0.89	2.44	3.2225 (15)	147
N7—H7C···Cl2^vi	0.89	2.78	3.2225 (15)	112

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+1, −y+1, −z; (iii) −x+3/2, y−1/2, z; (iv) −x+3/2, y−1/2, z−1; (v) x+1/2, −y+3/2, −z+1; (vi) x, y, z−1.