organic compounds
Disordered structure of propane-1,2-diaminium dichloride
aDepartment of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland
*Correspondence e-mail: mkubicki@amu.edu.pl
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.
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).
Experimental
Crystal data
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Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell CrysAlis PRO; data reduction: CrysAlis PRO; 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.
Supporting information
10.1107/S1600536811001036/cv5036sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811001036/cv5036Isup2.hkl
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.
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 Uiso values of H atoms were set at 1.2 (1.5 for CH3 and NH3 groups) times Ueq of their carrier atom.
Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell
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).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. |
C3H12N22+·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) Å3 | Block, colourless |
Z = 4 | 0.25 × 0.1 × 0.05 mm |
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 on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.034 | H-atom parameters constrained |
wR(F2) = 0.098 | w = 1/[σ2(Fo2) + (0.0669P)2 + 0.1755P] where P = (Fo2 + 2Fc2)/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) |
C3H12N22+·2Cl− | V = 754.1 (3) Å3 |
Mr = 147.05 | Z = 4 |
Orthorhombic, Pna21 | Cu Kα radiation |
a = 10.985 (3) Å | µ = 6.95 mm−1 |
b = 7.079 (2) Å | T = 120 K |
c = 9.698 (2) Å | 0.25 × 0.1 × 0.05 mm |
Oxford Diffraction Xcalibur Eos diffractometer | 1306 independent reflections |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) | 1265 reflections with I > 2σ(I) |
Tmin = 0.640, Tmax = 1.000 | Rint = 0.032 |
2817 measured reflections |
R[F2 > 2σ(F2)] = 0.034 | H-atom parameters constrained |
wR(F2) = 0.098 | Δρmax = 0.33 e Å−3 |
S = 1.13 | Δρmin = −0.34 e Å−3 |
1306 reflections | Absolute structure: Flack (1983), 473 Friedel pairs |
86 parameters | Absolute structure parameter: 0.09 (3) |
1 restraint |
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. |
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) |
U11 | U22 | U33 | U12 | U13 | U23 | |
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) |
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) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1D···Cl1i | 0.91 | 2.25 | 3.161 (3) | 175 |
N1—H1E···Cl2ii | 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···Cl1iii | 0.91 | 2.27 | 3.136 (3) | 160 |
N4—H4C···Cl2iv | 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. |
Experimental details
Crystal data | |
Chemical formula | C3H12N22+·2Cl− |
Mr | 147.05 |
Crystal system, space group | Orthorhombic, Pna21 |
Temperature (K) | 120 |
a, b, c (Å) | 10.985 (3), 7.079 (2), 9.698 (2) |
V (Å3) | 754.1 (3) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 6.95 |
Crystal size (mm) | 0.25 × 0.1 × 0.05 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur Eos diffractometer |
Absorption correction | Multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) |
Tmin, Tmax | 0.640, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2817, 1306, 1265 |
Rint | 0.032 |
(sin θ/λ)max (Å−1) | 0.629 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.034, 0.098, 1.13 |
No. of reflections | 1306 |
No. of parameters | 86 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.33, −0.34 |
Absolute structure | Flack (1983), 473 Friedel pairs |
Absolute structure parameter | 0.09 (3) |
Computer programs: CrysAlis PRO (Oxford Diffraction, 2009), SIR92 (Altomare et al., 1993), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1D···Cl1i | 0.91 | 2.25 | 3.161 (3) | 175 |
N1—H1E···Cl2ii | 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···Cl1iii | 0.91 | 2.27 | 3.136 (3) | 160 |
N4—H4C···Cl2iv | 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. |
References
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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).