Crystal structure of N,N'-bis-(pyridin-3-ylmeth-yl)cyclo-hexane-1,4-di-ammonium dichloride.

The title salt, C18H26N42+·2Cl-, was obtained by the protonation of N,N-bis-(pyridin-4-ylmeth-yl)cyclo-hexane-1,4-di-amine with hydro-chloric acid in ethanol. The asymmetric unit consists of one half of an N,N-bis-(pyridin-3-ylmeth-yl)cyclo-hexane-1,4-di-ammonium dication, with a crystallographic inversion centre located at the centre of the cyclo-hexyl ring, and a chloride anion. The central cyclo-hexyl ring in the dication adopts a chair conformation. The two trans-(4-pyridine)-CH2-NH2- moieties at the 1- and 4-positions of the central cyclo-hexyl ring occupy equatorial sites. The terminal pyridine ring is tilted by 53.72 (6)° with respect to the mean plane of the central cyclo-hexyl ring (r.m.s. deviation = 0.2413 Å). In the crystal, N+-H⋯Cl- hydrogen bonds between the dications and the chloride anions, and π-π stacking inter-actions between the pyridine rings of the dications afford a two-dimensional sheet extending parallel to the ab plane. These sheets are further connected through weak C-H⋯Cl- hydrogen bonds, resulting in the formation of a three-dimensional supra-molecular network.

Chemical context

Several dipyridyl-type ligands with or without a central section between the terminal pyridine rings have contributed greatly to the development of metal–organic coordination polymers with intriguing topologies or potential applications (Silva et al., 2015 ▸; Furukawa et al., 2014 ▸; Robin & Fromm, 2006 ▸; Robson, 2008 ▸; Leong & Vittal, 2011 ▸). Our group has also tried to prepare extended dipyridyl-type ligands with a bulky central moiety for the construction of versatile coordination polymers. Recently, we prepared the dipyridyl-type ligand containing 4-pyridine terminal groups and a cyclo­hexyl ring as a bulky central moiety, namely N,N-bis­(pyridin-4-ylmeth­yl)cyclo­hexane-1,4-di­amine, and reported the crystal structure of its chloride salt (Moon et al., 2016 ▸). As an extension of our research, we have prepared a dipyridyl-type ligand with central cyclo­hexyl ring and 3-pyridine terminal groups, namely N,N-bis­(pyridin-3-ylmeth­yl)cyclo­hexane-1,4-di­amine, synthesized by a condensation reaction between 1,4-cyclo­hexa­ne­diamine and 3-pyridine­carboxaldehyde according to the literature procedure (Huh & Lee, 2007 ▸). Herein we report on crystal structure of the title salt obtained by the protonation of both amine groups in this mol­ecule.

Structural commentary

Fig. 1 ▸ shows the mol­ecular structure of the title salt, which lies about an inversion centre located at the centre of the cyclo­hexyl ring. Therefore, the asymmetric unit comprises one half of the N,N-bis­(pyridin-3-ylmeth­yl)cyclo­hexane-1,4-di­ammo­nium dication and a chloride anion. In the dication, the central cyclo­hexyl ring displays a chair conformation and the two trans-(4-pyridine)–CH2–NH2– moieties occupy equatorial sites at the 1- and 4-positions of the central cyclo­hexyl ring. The terminal pyridine ring is tilted by 53.72 (6)° with respect to the mean plane of the cyclo­hexyl ring (r.m.s. deviation = 0.2413 Å). This tilting angle is larger than that [27.98 (5)°] of the similar dication with 4-pyridine rings as the terminal groups (Moon et al., 2016 ▸).

Figure 1

A view of the mol­ecular structure of the title salt, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radius and yellow dashed lines represent the inter­molecular N+—H⋯Cl− hydrogen bonds. [Symmetry code: (i) −x + 1, −y + 1, −z + 1.]

Supra­molecular features

In the crystal, N+–H⋯Cl− hydrogen bonds, Table 1 ▸ (yellow dashed lines in Figs. 2 ▸ and 3 ▸), between the dications and the chloride anions lead to the formation of chains along the b axis. Adjacent chains are additionally connected through inter­molecular π–π stacking inter­actions [centroid-to-centroid distance = 3.8197 (8) Å] between the pyridine rings (red dashed lines in Figs. 2 ▸ and 3 ▸), resulting in the formation of a sheet extending parallel to the ab plane. These sheets are linked by weak C–H⋯Cl− hydrogen bonds, Table 1 ▸ (black dashed lines in Fig. 3 ▸), between the dications and the chloride anions, forming a three-dimensional supra­molecular network.

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯Cl1	0.891 (15)	2.237 (15)	3.1215 (10)	171.7 (12)
N1—H1B⋯Cl1i	0.876 (16)	2.287 (16)	3.1588 (10)	173.8 (13)
C3—H3⋯Cl1ii	1.00	2.76	3.7106 (11)	158
C8—H8⋯Cl1iii	0.95	2.76	3.6020 (13)	148

Symmetry codes: (i) ; (ii) ; (iii) .

Figure 2

The two-dimensional sheet of the title salt formed through inter­molecular N+—H⋯Cl− hydrogen bonds (yellow dashed lines) between the dications and the chloride anions and π–π stacking inter­actions (red dashed lines) between the pyridine rings of dications. H atoms not involved in inter­molecular inter­actions have been omitted for clarity.

Figure 3

The three-dimensional supra­molecular network of the title salt formed through inter­molecular C—H⋯Cl− hydrogen bonds (black dashed lines) between the two-dimensional sheets constructed by inter­molecular N+—H⋯Cl− hydrogen bonds (yellow dashed lines) and π–π stacking inter­actions (red dashed lines). H atoms not involved in inter­molecular inter­actions have been omitted for clarity.

Database survey

A search of the Cambridge Structural Database (Version 5.37, Feb 2016 with two updates; Groom et al., 2016 ▸) revealed only a CoII complex with the dication of the title salt as a ligand, namely catena-[bis­(μ 2-N,N′-bis­(pyridin-3-ylmeth­yl)cyclo­hexane-1,4-diaminium)(nitrato-O,O′)cobalt(II) penta­nitrate methanol solvate] (Lee & Lee, 2010 ▸). Each CoII ion in this complex is six-coordinated by two O atoms of one nitrate anion and four N atoms of four dipyridyl-type dication ligands to form a distorted octahedral geometry.

Synthesis and crystallization

N,N-bis­(pyridin-3-yl­methyl­ene)cyclo­hexane-1,4-di­amine, prepared according to a literature method (Huh & Lee, 2007 ▸), was dissolved in ethanol, and then the pH was adjusted to 4–5 with 2 M hydro­chloric acid. The resultant mixture was left to evaporate slowly over several days, resulting in the formation of X-ray quality single crystals of the title salt.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. The position of the pyridine nitro­gen atom was determined by the difference in the displacement parameters. All C-bound H atoms were positioned geometrically [with d(C—H) = 0.95 Å for Csp 2—H, 0.99 Å for methyl­ene, 1.00 Å for methine H atoms] and were refined as riding with U iso(H) = 1.2U eq(C). The N-bound H atoms involved in hydrogen bonds were located in difference Fourier maps and refined freely [N—H = 0.891 (15) and 0.876 (16) Å].

Table 2

Experimental details

Crystal data
Chemical formula	C18H26N4 2+·2Cl−
M r	369.33
Crystal system, space group	Monoclinic, P21/n
Temperature (K)	173
a, b, c (Å)	10.4637 (2), 8.1942 (2), 11.2797 (2)
β (°)	107.812 (1)
V (Å3)	920.78 (3)
Z	2
Radiation type	Mo Kα
μ (mm−1)	0.36
Crystal size (mm)	0.32 × 0.27 × 0.21
Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker 2013 ▸)
T min, T max	0.671, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	8881, 2303, 2118
R int	0.022
(sin θ/λ)max (Å−1)	0.670
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S	0.030, 0.083, 1.03
No. of reflections	2303
No. of parameters	117
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)	0.29, −0.26

Computer programs: APEX2 and SAINT (Bruker, 2013 ▸), SHELXS97 and SHELXTL (Sheldrick, 2008 ▸), SHELXL2014 (Sheldrick, 2015 ▸) and DIAMOND (Brandenburg, 2010 ▸).

Crystal structure: contains datablock(s) I, New_Global_Publ_Block. DOI: 10.1107/S2056989016017205/hg5479sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016017205/hg5479Isup2.hkl

CCDC reference: 1511616

Additional supporting information: crystallographic information; 3D view; checkCIF report

C18H26N42+·2Cl−	F(000) = 392
Mr = 369.33	Dx = 1.332 Mg m−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
a = 10.4637 (2) Å	Cell parameters from 4678 reflections
b = 8.1942 (2) Å	θ = 2.3–28.4°
c = 11.2797 (2) Å	µ = 0.36 mm−1
β = 107.812 (1)°	T = 173 K
V = 920.78 (3) Å3	Block, colourless
Z = 2	0.32 × 0.27 × 0.21 mm

Bruker APEXII CCD diffractometer	2118 reflections with I > 2σ(I)
φ and ω scans	Rint = 0.022
Absorption correction: multi-scan (SADABS; Bruker 2013)	θmax = 28.4°, θmin = 2.3°
Tmin = 0.671, Tmax = 0.746	h = −12→14
8881 measured reflections	k = −9→10
2303 independent reflections	l = −15→15

Refinement on F2	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.030	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.083	w = 1/[σ2(Fo2) + (0.0443P)2 + 0.3189P] where P = (Fo2 + 2Fc2)/3
S = 1.03	(Δ/σ)max < 0.001
2303 reflections	Δρmax = 0.29 e Å−3
117 parameters	Δρmin = −0.26 e Å−3

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

	x	y	z	Uiso*/Ueq
Cl1	0.40846 (3)	0.04783 (3)	0.28633 (2)	0.02513 (10)
N1	0.63461 (9)	0.19285 (11)	0.51048 (9)	0.01829 (19)
H1A	0.5756 (14)	0.1538 (18)	0.4416 (13)	0.021 (3)*
H1B	0.6295 (14)	0.1263 (19)	0.5696 (14)	0.026 (4)*
N2	0.83020 (13)	−0.19199 (14)	0.33231 (10)	0.0343 (3)
C1	0.54173 (12)	0.64376 (14)	0.44414 (11)	0.0240 (2)
H1C	0.6086	0.6937	0.5170	0.029*
H1D	0.5352	0.7127	0.3704	0.029*
C2	0.58760 (13)	0.47226 (14)	0.42261 (11)	0.0236 (2)
H2A	0.5242	0.4254	0.3462	0.028*
H2B	0.6773	0.4780	0.4106	0.028*
C3	0.59394 (11)	0.36313 (13)	0.53315 (10)	0.0180 (2)
H3	0.6618	0.4083	0.6089	0.022*
C4	0.77439 (12)	0.18178 (15)	0.50226 (12)	0.0265 (3)
H4A	0.8381	0.2237	0.5804	0.032*
H4B	0.7819	0.2515	0.4330	0.032*
C5	0.81211 (11)	0.00954 (14)	0.48115 (10)	0.0207 (2)
C6	0.79449 (14)	−0.04487 (16)	0.36097 (12)	0.0298 (3)
H6	0.7541	0.0278	0.2944	0.036*
C7	0.88687 (13)	−0.29136 (15)	0.42730 (12)	0.0289 (3)
H7	0.9154	−0.3959	0.4092	0.035*
C8	0.90643 (13)	−0.25138 (16)	0.54997 (12)	0.0299 (3)
H8	0.9454	−0.3275	0.6144	0.036*
C9	0.86810 (13)	−0.09778 (16)	0.57749 (11)	0.0271 (3)
H9	0.8801	−0.0667	0.6613	0.033*

	U11	U22	U33	U12	U13	U23
Cl1	0.02754 (17)	0.02485 (16)	0.02046 (15)	−0.00212 (10)	0.00355 (11)	0.00078 (9)
N1	0.0189 (5)	0.0152 (4)	0.0209 (4)	0.0013 (3)	0.0064 (4)	−0.0008 (3)
N2	0.0445 (7)	0.0312 (6)	0.0274 (5)	0.0077 (5)	0.0114 (5)	−0.0051 (4)
C1	0.0265 (6)	0.0173 (5)	0.0333 (6)	0.0025 (4)	0.0168 (5)	0.0029 (4)
C2	0.0291 (6)	0.0187 (5)	0.0291 (6)	0.0045 (4)	0.0177 (5)	0.0032 (4)
C3	0.0197 (5)	0.0141 (5)	0.0199 (5)	0.0019 (4)	0.0056 (4)	−0.0019 (4)
C4	0.0205 (6)	0.0209 (6)	0.0404 (7)	0.0008 (4)	0.0125 (5)	−0.0048 (5)
C5	0.0177 (5)	0.0197 (5)	0.0261 (5)	0.0011 (4)	0.0086 (4)	−0.0014 (4)
C6	0.0379 (7)	0.0274 (6)	0.0236 (6)	0.0089 (5)	0.0087 (5)	0.0031 (4)
C7	0.0281 (6)	0.0199 (6)	0.0407 (7)	0.0032 (5)	0.0133 (5)	−0.0032 (5)
C8	0.0289 (6)	0.0269 (6)	0.0340 (6)	0.0068 (5)	0.0097 (5)	0.0089 (5)
C9	0.0271 (6)	0.0319 (7)	0.0222 (5)	0.0042 (5)	0.0075 (4)	−0.0002 (5)

N1—C4	1.4963 (14)	C3—C1i	1.5188 (15)
N1—C3	1.5033 (13)	C3—H3	1.0000
N1—H1A	0.891 (15)	C4—C5	1.5040 (16)
N1—H1B	0.876 (16)	C4—H4A	0.9900
N2—C6	1.3309 (17)	C4—H4B	0.9900
N2—C7	1.3319 (17)	C5—C9	1.3813 (17)
C1—C3i	1.5188 (15)	C5—C6	1.3848 (16)
C1—C2	1.5283 (15)	C6—H6	0.9500
C1—H1C	0.9900	C7—C8	1.3750 (18)
C1—H1D	0.9900	C7—H7	0.9500
C2—C3	1.5193 (15)	C8—C9	1.3847 (18)
C2—H2A	0.9900	C8—H8	0.9500
C2—H2B	0.9900	C9—H9	0.9500
C4—N1—C3	113.56 (9)	C1i—C3—H3	109.0
C4—N1—H1A	110.8 (9)	C2—C3—H3	109.0
C3—N1—H1A	109.0 (9)	N1—C4—C5	112.05 (9)
C4—N1—H1B	107.3 (10)	N1—C4—H4A	109.2
C3—N1—H1B	111.2 (10)	C5—C4—H4A	109.2
H1A—N1—H1B	104.6 (13)	N1—C4—H4B	109.2
C6—N2—C7	116.57 (11)	C5—C4—H4B	109.2
C3i—C1—C2	110.35 (9)	H4A—C4—H4B	107.9
C3i—C1—H1C	109.6	C9—C5—C6	117.55 (11)
C2—C1—H1C	109.6	C9—C5—C4	122.80 (11)
C3i—C1—H1D	109.6	C6—C5—C4	119.62 (11)
C2—C1—H1D	109.6	N2—C6—C5	124.49 (12)
H1C—C1—H1D	108.1	N2—C6—H6	117.8
C3—C2—C1	110.35 (9)	C5—C6—H6	117.8
C3—C2—H2A	109.6	N2—C7—C8	123.82 (12)
C1—C2—H2A	109.6	N2—C7—H7	118.1
C3—C2—H2B	109.6	C8—C7—H7	118.1
C1—C2—H2B	109.6	C7—C8—C9	118.55 (11)
H2A—C2—H2B	108.1	C7—C8—H8	120.7
N1—C3—C1i	108.79 (9)	C9—C8—H8	120.7
N1—C3—C2	110.50 (8)	C5—C9—C8	118.99 (11)
C1i—C3—C2	110.60 (9)	C5—C9—H9	120.5
N1—C3—H3	109.0	C8—C9—H9	120.5
C3i—C1—C2—C3	−57.46 (14)	C7—N2—C6—C5	−0.2 (2)
C4—N1—C3—C1i	−172.97 (9)	C9—C5—C6—N2	−1.4 (2)
C4—N1—C3—C2	65.43 (12)	C4—C5—C6—N2	176.74 (13)
C1—C2—C3—N1	178.12 (9)	C6—N2—C7—C8	1.7 (2)
C1—C2—C3—C1i	57.60 (14)	N2—C7—C8—C9	−1.5 (2)
C3—N1—C4—C5	179.29 (9)	C6—C5—C9—C8	1.50 (18)
N1—C4—C5—C9	−88.08 (14)	C4—C5—C9—C8	−176.57 (11)
N1—C4—C5—C6	93.89 (13)	C7—C8—C9—C5	−0.16 (19)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···Cl1	0.891 (15)	2.237 (15)	3.1215 (10)	171.7 (12)
N1—H1B···Cl1ii	0.876 (16)	2.287 (16)	3.1588 (10)	173.8 (13)
C3—H3···Cl1iii	1.00	2.76	3.7106 (11)	158
C8—H8···Cl1iv	0.95	2.76	3.6020 (13)	148