Disordered structure of propane-1,2-diaminium dichloride

In the title compound, C₃H₁₂N₂²⁺·2Cl⁻, the cations are disordered over two well resolved positions in a 0.525 (13):0.475 (13) ratio. The disorder involves two C atoms which assume positions that make an almost mirror-sym­metrical system. Similar disorder is observed both at room temperature and at 120 (1) K. The conformation of the NCCN chain in both components is close to trans (the torsion angles ca ±170°), while that of CCCN chain is close to gauche (±50°). In the crystal, a network of relatively strong N—H...Cl hydrogen bonds connects the cations and anions into one-cation-deep layers parallel to (001); there are R₂⁴(8) and R₂⁴(11) ring motifs within the plane. The planes are only loosely connected by van der Waals contacts and electrostatic inter­actions between cations and anions.

Key indicators

• Single-crystal X-ray study
• T = 120 K
• Mean [sigma](N-C) = 0.004 Å
• Disorder in main residue
• R factor = 0.034
• wR factor = 0.098
• Data-to-parameter ratio = 15.2

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       3.12
PLAT915_ALERT_3_C Low Friedel Pair Coverage ......................      65.99 Perc.
PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L=  0.600          9

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           75.71
           From the CIF: _reflns_number_total               1306
           Count of symmetry unique reflns          831
           Completeness (_total/calc)            157.16%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       475
           Fraction of Friedel pairs measured     0.572
           Are heavy atom types Z>Si present        yes
PLAT301_ALERT_3_G Note: Main Residue  Disorder ...................      22.00 Perc.
PLAT033_ALERT_4_G Flack x Parameter Value Deviates from Zero .....       0.09
PLAT811_ALERT_5_G No ADDSYM Analysis: Too Many Excluded Atoms ....          !

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   3 ALERT level C = Check and explain
   4 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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S1. Comment

The study of polycation structure, counterions and the nature of the interaction between low-molecular-weight salts with some electrolites in solutions are very important to understanding behaviour biogenic polyamines under normal physiological conditions. Aliphatic biogenic polyamines in biological systems exist as polycations which interact with nucleic acid polyanions. The crystal structure of the salts of these amines are therefore essential in the modeling of nucleic acids. Complexes formed from DNA and polycations containing primary amine grups are relevant because of their potential use in gene therapy, modifying the conformation and the state of aggregation of DNA (Hosseinkhani et al., 2004; Ziebarth et al., 2009; Itaka et al., 2010). During our study on metal promoted synthesis ofSchiff base complexes derived from various polyamines and salicylaldehyde we isolated the crystals of some salts of polyamines (Pospieszna-Markiewicz et al., 2006, 2007). Here we report another salt, propane-1,2-diaminium dichloride (I, Scheme 1).

It turned out that in the crystal structure the cation is heavily disordered - disorder involves two carbon atoms - between the two positions with the site occupation factors of 0.525 (13) and 0.475 (13). Both alternative positions refined quite well (anisotropically) without any kind of restraints. Fig. 1 shows one of the alternatives (most occupied) and Fig. 2 - the comparison of both disordered cations. Similar disorder is observed at room temperature with s.o.f.'s of 0.57 (4) and 0.43 (4), so this disorder is rather of statistical nature.

Both alternative cations have opposite signs of torsion angles. The conformation of N1—C2—C3—N4 chain is extended (torsion angles are 172.0 (4)° and -168.5 (4)° for more and less occupied part, respectively) while the C21—C2—C3—N4 torsion angles are 50.0 (10)° and -47.0 (11)°. Such conformation - we will call it tg - is the most popular among the simple propane-1,2-diaminium salts (for instance it was found in the structures of hydrogenarsenate (Todd & Harrison, 2005), bis(6-carboxypyridine-2-carboxylate) (Aghabozorg et al., 2008), or tetrafluoro-beryllium (Gerrard & Weller, 2002). The other possibilities are also observed, for instance in some simple hydrates (e.g. arsenate monohydrate, Lee & Harrison, 2003) the g⁺g^- combination is also reported.

In the crystal structure the strong N—H···Cl hydrogen bond connects molecules into two-dimensional, one-molecule deep layers parallel to (001) plane (Fig. 3). The motifs formed can be described, using graph set notations, as rings R₂⁴(8) and R₂⁴(11). It might be noted that for both alternatives the hydrogen atoms involved in these interactions are practically in the same positions. Each chloride anion accepts three hydrogen bonds, in flattened trigonal pyramid coordination. The layers in turn are loosely connected probably by electrostatic interactions between the charged species (Fig. 4).

Related literature

For general literature on polyamines, see, for example: Hosseinkhani et al. (2004); Pospieszna-Markiewicz et al. (2006, 2007); Ziebarth & Wang (2009); Itaka et al. (2010). For the crystal structures of simple salts of propane-1,2-diaminium, see: Aghabozorg et al. (2008); Gerrard & Weller (2002); Lee & Harrison (2003); Todd & Harrison (2005).

S2. Experimental

To a methanol solution (10 ml) of salicylaldehyde (0.043 ml, 0.4 mmol) a methanol solution (10 ml) of 1,2-diaminepropane (0.017 ml, 0.2 mmol) was added dropwise with stirring. After 5 minutes a methanol solution (20 ml) of ErCl₃.6H₂O (0.0764 g, 0.2 mmol) was added. The reaction was carried out at room temperature for 75 minutes. The solution volume was than reduced to 10 ml by roto-evaporation and after 7–14 days of slow diffusion of THF into the solution at 6 °C white crystals suitable for X-ray were formed.

S3. Refinement

Hydrogen atoms were located geometrically (C(methyl)-H 0.98 Å, C2—H 1.00 Å, C3—H 0.99 Å, N—H 0.91 Å) and refined in a riding model approximation; the U_iso values of H atoms were set at 1.2 (1.5 for CH₃ and NH₃ groups) times U_eq of their carrier atom.

Computing details

Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell refinement: CrysAlis PRO (Oxford Diffraction, 2009); data reduction: CrysAlis PRO (Oxford Diffraction, 2009); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures

	Fig. 1. Anisotropic ellipsoid representation of I together with atom labelling scheme. The ellipsoids are drawn at 50% probability level, hydrogen atoms are depicted as spheres with arbitrary radii; hydrogen bonds are shown as dashed lines. Only major part of the disordered cation is shown.
	Fig. 2. The disordered cation in I: the major part is drawn with solid lines, the minor one - with open lines.
	Fig. 3. The single layer as seen along direction [100]. Only the cations of major part are shown. Hydrogen bonds are depicted as dashed lines.
	Fig. 4. The crystal packing as seen along direction [001]. Only the cations of major part are shown. Hydrogen bonds are depicted as dashed lines.

propane-1,2-diaminium dichloride

Crystal data

C3H12N2^2+·2Cl^−	F(000) = 312
Mr = 147.05	Dx = 1.295 Mg m^−3
Orthorhombic, Pna21	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2c -2n	Cell parameters from 2191 reflections
a = 10.985 (3) Å	θ = 4.0–75.5°
b = 7.079 (2) Å	µ = 6.95 mm^−1
c = 9.698 (2) Å	T = 120 K
V = 754.1 (3) Å^3	Block, colourless
Z = 4	0.25 × 0.1 × 0.05 mm

Data collection

Oxford Diffraction Xcalibur Eos diffractometer	1306 independent reflections
Radiation source: Enhance (Mo) X-ray Source	1265 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.032
Detector resolution: 16.1544 pixels mm^-1	θmax = 75.7°, θmin = 7.4°
ω scans	h = −12→13
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)	k = −8→8
Tmin = 0.640, Tmax = 1.000	l = −11→12
2817 measured reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.034	H-atom parameters constrained
wR(F^2) = 0.098	w = 1/[σ^2(Fo^2) + (0.0669P)^2 + 0.1755P] where P = (Fo^2 + 2Fc^2)/3
S = 1.13	(Δ/σ)max = 0.001
1306 reflections	Δρmax = 0.33 e Å^−3
86 parameters	Δρmin = −0.34 e Å^−3
1 restraint	Absolute structure: Flack (1983), 473 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.09 (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	0.2839 (2)	0.7068 (3)	0.5952 (3)	0.0290 (5)
H1A	0.2462	0.7953	0.5422	0.043*	0.525 (13)
H1B	0.2269	0.6348	0.6386	0.043*	0.525 (13)
H1C	0.3313	0.7653	0.6592	0.043*	0.525 (13)
H1D	0.2547	0.8030	0.5424	0.043*	0.475 (13)
H1E	0.2252	0.6685	0.6552	0.043*	0.475 (13)
H1F	0.3501	0.7474	0.6432	0.043*	0.475 (13)
C2	0.3589 (9)	0.5771 (12)	0.5034 (11)	0.027 (2)	0.525 (13)
H2	0.4390	0.6396	0.4858	0.032*	0.525 (13)
C21	0.2954 (9)	0.5541 (8)	0.3682 (7)	0.034 (2)	0.525 (13)
H21A	0.2133	0.5043	0.3838	0.051*	0.525 (13)
H21B	0.3412	0.4660	0.3101	0.051*	0.525 (13)
H21C	0.2899	0.6769	0.3219	0.051*	0.525 (13)
C2A	0.3142 (10)	0.5396 (15)	0.5026 (12)	0.027 (2)	0.475 (13)
H2A	0.2358	0.4795	0.4737	0.032*	0.475 (13)
C21A	0.3753 (8)	0.6147 (11)	0.3760 (8)	0.035 (2)	0.475 (13)
H21D	0.4024	0.5091	0.3184	0.052*	0.475 (13)
H21E	0.4458	0.6913	0.4028	0.052*	0.475 (13)
H21F	0.3178	0.6929	0.3241	0.052*	0.475 (13)
C3	0.3821 (3)	0.4007 (4)	0.5893 (4)	0.0328 (7)
H3A	0.3024	0.3566	0.6246	0.039*	0.525 (13)
H3B	0.4341	0.4308	0.6697	0.039*	0.525 (13)
H3C	0.4454	0.4649	0.6448	0.039*	0.475 (13)
H3D	0.3222	0.3452	0.6540	0.039*	0.475 (13)
N4	0.4396 (2)	0.2468 (3)	0.5090 (3)	0.0253 (5)
H4A	0.5061	0.2925	0.4640	0.038*
H4B	0.3854	0.2007	0.4466	0.038*
H4C	0.4629	0.1526	0.5672	0.038*
Cl1	0.18604 (6)	0.05885 (8)	0.42805 (6)	0.0279 (2)
Cl2	0.52155 (6)	0.91848 (8)	0.70308 (9)	0.0328 (2)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0357 (13)	0.0183 (12)	0.0329 (12)	0.0056 (9)	0.0017 (10)	−0.0040 (9)
C2	0.036 (5)	0.009 (4)	0.035 (4)	0.005 (3)	−0.003 (4)	0.000 (3)
C21	0.053 (5)	0.015 (3)	0.034 (4)	0.007 (3)	−0.014 (3)	0.002 (2)
C2A	0.033 (5)	0.014 (5)	0.033 (4)	0.004 (4)	0.009 (4)	−0.002 (3)
C21A	0.049 (5)	0.022 (3)	0.033 (3)	0.015 (3)	0.008 (3)	0.011 (3)
C3	0.0530 (18)	0.0185 (13)	0.0269 (14)	0.0108 (12)	0.0001 (13)	0.0005 (10)
N4	0.0319 (12)	0.0141 (11)	0.0298 (12)	0.0028 (9)	−0.0006 (9)	−0.0012 (8)
Cl1	0.0323 (3)	0.0199 (3)	0.0314 (3)	0.0026 (2)	−0.0011 (3)	−0.0003 (2)
Cl2	0.0350 (4)	0.0252 (3)	0.0383 (4)	−0.0001 (2)	−0.0050 (3)	0.0103 (3)

Geometric parameters (Å, º)

N1—C2	1.522 (10)	C2A—C3	1.493 (12)
N1—C2A	1.523 (10)	C2A—C21A	1.496 (14)
N1—H1A	0.9100	C2A—H2A	1.0000
N1—H1B	0.9100	C21A—H21D	0.9800
N1—H1C	0.9101	C21A—H21E	0.9800
N1—H1D	0.9101	C21A—H21F	0.9800
N1—H1E	0.9100	C3—N4	1.481 (4)
N1—H1F	0.9100	C3—H3A	0.9900
C2—C21	1.495 (13)	C3—H3B	0.9900
C2—C3	1.523 (10)	C3—H3C	0.9900
C2—H2	1.0000	C3—H3D	0.9899
C21—H21A	0.9800	N4—H4A	0.9100
C21—H21B	0.9800	N4—H4B	0.9100
C21—H21C	0.9800	N4—H4C	0.9100
C2—N1—H1A	109.3	C2A—C21A—H21D	109.5
C2A—N1—H1A	107.5	C2A—C21A—H21E	109.5
C2—N1—H1B	107.7	H21D—C21A—H21E	109.5
C2A—N1—H1B	89.3	C2A—C21A—H21F	109.5
H1A—N1—H1B	109.5	H21D—C21A—H21F	109.5
C2—N1—H1C	111.3	H21E—C21A—H21F	109.5
C2A—N1—H1C	129.1	N4—C3—C2A	113.7 (5)
H1A—N1—H1C	109.5	N4—C3—C2	112.8 (4)
H1B—N1—H1C	109.5	N4—C3—H3A	109.1
C2A—N1—H1D	109.0	C2A—C3—H3A	87.7
C2A—N1—H1E	107.5	C2—C3—H3A	107.4
H1D—N1—H1E	109.5	N4—C3—H3B	109.0
C2A—N1—H1F	111.9	C2A—C3—H3B	126.1
H1D—N1—H1F	109.5	C2—C3—H3B	110.5
H1E—N1—H1F	109.5	H3A—C3—H3B	107.8
C21—C2—N1	109.0 (7)	N4—C3—H3C	108.8
C21—C2—C3	118.0 (7)	C2A—C3—H3C	110.7
N1—C2—C3	105.4 (7)	N4—C3—H3D	109.0
C21—C2—H2	108.0	C2A—C3—H3D	106.6
N1—C2—H2	108.0	H3C—C3—H3D	107.7
C3—C2—H2	108.0	C3—N4—H4A	109.5
C3—C2A—C21A	118.2 (8)	C3—N4—H4B	109.5
C3—C2A—N1	106.8 (7)	H4A—N4—H4B	109.5
C21A—C2A—N1	107.8 (8)	C3—N4—H4C	109.5
C3—C2A—H2A	107.9	H4A—N4—H4C	109.5
C21A—C2A—H2A	107.9	H4B—N4—H4C	109.5
N1—C2A—H2A	107.9
C2A—N1—C2—C21	54.9 (18)	C21A—C2A—C3—C2	45.2 (16)
C2A—N1—C2—C3	−72.6 (19)	N1—C2A—C3—C2	−76.3 (19)
C2—N1—C2A—C3	78.5 (19)	C21—C2—C3—N4	50.0 (10)
C2—N1—C2A—C21A	−49.4 (17)	N1—C2—C3—N4	172.0 (4)
C21A—C2A—C3—N4	−47.0 (11)	C21—C2—C3—C2A	−47.0 (17)
N1—C2A—C3—N4	−168.5 (4)	N1—C2—C3—C2A	74.9 (18)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1D···Cl1^i	0.91	2.25	3.161 (3)	175
N1—H1E···Cl2^ii	0.91	2.37	3.192 (3)	151
N1—H1F···Cl2	0.91	2.31	3.187 (3)	161
N4—H4B···Cl1	0.91	2.42	3.186 (3)	142
N4—H4A···Cl1^iii	0.91	2.27	3.136 (3)	160
N4—H4C···Cl2^iv	0.91	2.21	3.123 (2)	178

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