Putrescinium dichloride: a redetermination at 100 K

The crystal structure of the title compound, C₄H₁₄N₂²⁺·2Cl⁻, has been redetermined at 100 (1) K. In the room-temperature structure [Chandrasekhar & Pattabhi (1980). Acta Cryst. B36, 2486–2488], the H atoms were located but their parameters were not refined. Since the hydrogen bonds in this structure are extensive, the H-atom positions are of primary importance. The dication lies on a centre of symmetry and the N atoms are slightly displaced [0.019 (4) Å] from the plane of the four C atoms. N—H...Cl and C—H...Cl hydrogen bonds form a three-dimensional network.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.037
• wR factor = 0.085
• Data-to-parameter ratio = 14.9

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT480_ALERT_4_C Long H...A H-Bond Reported H2B    ..  CL1     ..       3.00 Ang.

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

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

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S1. Comment

Putrescine is involved in proliferation and differentiation of cells in DNA replication and membrane stabilization, in addition to being present in high intercellular concentration in carcinogenetic states of cells. The negative charge of the DNA backbone makes it target for cationic species, so positively charged putrescine and the other biogenic polyamines may interact directly with DNA (Karigiannis & Papaioannou, 2000). During our study on design and synthesis of self-assembled supramolecular architectures incorporating biogenic polyamine fragments with flexibility and strong affinity to nucleic acids, therefore displaying interesting properties and potential applications (Radecka-Paryzek et al., 2007), we isolated the crystals of putrescine dichloride.

The crystal structure of putrescinium chloride was investigated by Ashida & Hirokawa (1963) using visually estimated intensities, and then by Chandrasekhar & Pattabhi (1980). This last determination was performed at room temperature, and H atom positions and thermal parameters were not refined. R factor of this determination was also quite high, 6.4%. The hydrogen bond system is extensive in this crystal structure, so the positions of H atoms are important. We have repeated this structure determination at 100 (1) K and with the new data we were able to refine all parameters of H atoms. The overall features of the crystal structure are similar to those of Ashida & Hirokawa (1963). The elongation of the bond lengths at 100 K is probably connected with the minimalization of libration effect. The N—H···Cl and C—H···Cl hydrogen bonds connect cations and anions into layers (Fig. 2). These layers in turn by means of electrostatic interactions and weaker C—H···Cl hydrogen bonds make a three-dimensional structure with alternate cation and anion layers (Fig. 3).

Related literature

For related literature, see: Ashida & Hirokawa (1963); Karigiannis & Papaioannou (2000); Radecka-Paryzek et al. (2007).

S2. Experimental

The title compound was isolated during the slow diffusion of dioxane into a methanol solution of the lanthanum(III) chloride Schiff base complex – product of the template condensation reaction of one molecule of putrescine with two molecules of salicylaldehyde.

S3. Refinement

H atoms were located in a difference Fourier map and freely refined.

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. Anisotropic displacement ellipsoid representation at the 50% probability level (Siemens, 1989) of the title compound, with atom-numbering scheme. The H atoms are drawn as spheres of arbitrary radius. Hydrogen bonds are depicted as dashed lines [symmetry code: (i) 1 - x, 1 - y, 1 - z].
	Fig. 2. Hydrogen-bonded layer as seen along the a axis. Hydrogen bonds are depicted as dashed lines.
	Fig. 3. Crystal packing viewed along the b axis. Hydrogen bonds and weaker C—H···Cl contacts are depicted as dashed lines.

Butane-1,4-diyldiammonium dichloride

Crystal data

C4H14N2^2+·2Cl^−	F(000) = 172
Mr = 161.07	Dx = 1.314 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1321 reflections
a = 4.5625 (9) Å	θ = 3–25°
b = 8.3514 (16) Å	µ = 0.71 mm^−1
c = 10.696 (2) Å	T = 100 K
β = 92.472 (16)°	Prism, colourless
V = 407.16 (14) Å^3	0.3 × 0.15 × 0.1 mm
Z = 2

Data collection

Kuma KM4 CCD four-circle diffractometer	716 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.045
Graphite monochromator	θmax = 28.0°, θmin = 3.1°
ω scans	h = −6→5
2576 measured reflections	k = −9→11
970 independent reflections	l = −14→12

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) = 0.085	All H-atom parameters refined
S = 1.06	w = 1/[σ^2(Fo^2) + (0.041P)^2] where P = (Fo^2 + 2Fc^2)/3
970 reflections	(Δ/σ)max < 0.001
65 parameters	Δρmax = 0.52 e Å^−3
0 restraints	Δρmin = −0.43 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
N1	0.6183 (4)	0.1691 (3)	0.37234 (18)	0.0161 (4)
H1A	0.516 (5)	0.089 (3)	0.345 (2)	0.013 (6)*
H1B	0.714 (6)	0.209 (3)	0.307 (2)	0.033 (7)*
H1C	0.751 (6)	0.141 (3)	0.426 (3)	0.029 (7)*
C2	0.4232 (5)	0.2942 (3)	0.4245 (2)	0.0149 (5)
H2A	0.275 (5)	0.325 (3)	0.356 (2)	0.013 (5)*
H2B	0.319 (5)	0.247 (3)	0.492 (2)	0.019 (6)*
C3	0.6007 (5)	0.4371 (3)	0.4727 (2)	0.0156 (5)
H3A	0.713 (5)	0.483 (3)	0.399 (2)	0.019 (6)*
H3B	0.754 (5)	0.397 (3)	0.538 (2)	0.020 (6)*
Cl1	0.87455 (11)	0.10103 (6)	0.65756 (5)	0.01548 (18)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0167 (10)	0.0156 (10)	0.0160 (9)	−0.0009 (8)	0.0007 (8)	−0.0012 (8)
C2	0.0149 (11)	0.0153 (11)	0.0147 (10)	0.0021 (9)	0.0014 (8)	−0.0008 (9)
C3	0.0142 (11)	0.0184 (13)	0.0141 (11)	−0.0006 (9)	0.0011 (8)	−0.0007 (9)
Cl1	0.0164 (3)	0.0166 (3)	0.0135 (3)	0.0006 (2)	0.00115 (17)	−0.0010 (2)

Geometric parameters (Å, º)

N1—C2	1.496 (3)	C2—H2A	1.01 (2)
N1—H1A	0.86 (2)	C2—H2B	0.97 (2)
N1—H1B	0.90 (3)	C3—C3^i	1.528 (4)
N1—H1C	0.85 (3)	C3—H3A	1.03 (2)
C2—C3	1.520 (3)	C3—H3B	1.02 (2)
C2—N1—H1A	110.6 (16)	N1—C2—H2B	108.2 (15)
C2—N1—H1B	110.3 (17)	C3—C2—H2B	109.9 (14)
H1A—N1—H1B	107 (2)	H2A—C2—H2B	108.1 (18)
C2—N1—H1C	110.8 (19)	C2—C3—C3^i	110.4 (2)
H1A—N1—H1C	112 (2)	C2—C3—H3A	108.0 (13)
H1B—N1—H1C	106 (2)	C3^i—C3—H3A	111.3 (14)
N1—C2—C3	110.96 (17)	C2—C3—H3B	108.4 (14)
N1—C2—H2A	107.4 (13)	C3^i—C3—H3B	111.7 (14)
C3—C2—H2A	112.2 (13)	H3A—C3—H3B	107.0 (18)
N1—C2—C3—C3^i	−179.2 (2)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1C···Cl1	0.85 (3)	2.53 (3)	3.269 (2)	145 (2)
C3—H3B···Cl1	1.02 (2)	2.83 (2)	3.624 (2)	135.0 (17)
N1—H1A···Cl1^ii	0.86 (2)	2.38 (3)	3.192 (2)	156 (2)
N1—H1B···Cl1^iii	0.90 (3)	2.39 (3)	3.250 (2)	159 (2)
C3—H3A···Cl1^iii	1.03 (2)	2.80 (2)	3.659 (2)	140.2 (17)
N1—H1C···Cl1^iv	0.85 (3)	2.82 (3)	3.258 (2)	114 (2)
C2—H2A···Cl1^v	1.01 (2)	2.81 (2)	3.816 (2)	177.0 (17)
C2—H2B···Cl1^vi	0.97 (2)	3.00 (2)	3.952 (2)	166.3 (17)

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