trans-2,5-Di­methyl­piperazine-1,4-diium bis(perchlorate) dihydrate: crystal structure and Hirshfeld surface analysis

Ben Mleh, C.; Roisnel, T.; Marouani, H.

doi:10.1107/S205698901600520X

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Volume 72| Part 4| April 2016| Pages 593-596

https://doi.org/10.1107/S205698901600520X

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trans-2,5-Dimethylpiperazine-1,4-diium bis(perchlorate) dihydrate: crystal structure and Hirshfeld surface analysis

Cherifa Ben Mleh,^a ^* Thierry Roisnel ^b and Houda Marouani ^a

^aLaboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, 7021 Zarzouna Bizerte, Université de Carthage, Tunisia, and ^bCentre de Diffractométrie X, UMR 6226 CNRS, Unité Sciences Chimiques de Rennes, Université de Rennes I, 263 Avenue du, Général Leclerc, 35042 Rennes, France
^*Correspondence e-mail: cherifa_benmleh@hotmail.com

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 27 March 2016; accepted 27 March 2016; online 31 March 2016)

The asymmetric unit of the title hydrated molecular salt, C₆H₁₆N₂²⁺·2ClO₄⁻·2H₂O, contains a half dication (completed by inversion symmetry), a perchlorate anion and a water molecule. The extended structure consists of infinite chains of formula [(ClO₄)H₂O]_nⁿ⁻ ions extending along the b axis linked by O_w—H⋯O (w = water) hydrogen bonds. These chains are cross-linked by the dications via N—H⋯O_w and weak C—H⋯O hydrogen bonds, thus forming a three-dimensional supramolecular network. Three-dimensional Hirshfeld surface analysis and two-dimensional fingerprint maps reveal that the structure is dominated by H⋯O/O⋯H and H⋯H contacts.

Keywords: crystal structure; piperazine derivative; molecular salt; hydrogen bonding; Hirshfeld surface analysis.

CCDC reference: 1470800

1. Chemical context

Piperazine (C₄H₁₀N₂) and its derivatives are a family of strongly basic amines able to form dications, in which all of the N—H bonds are generally active in hydrogen-bond formation. They are used in pharmacology and found in biologically active compounds across a number of different therapeutic areas, displaying antibacterial, antifungal, antimalarial, antipsychotic, antidepressant and antitumor activity (Brockunier et al., 2004 ; Bogatcheva et al., 2006 ).

In this work, as part of our studies in this area, we report the preparation and structural investigation of a new hydrated perchlorate salt, C₆H₁₆N₂²⁺·2ClO₄⁻·2H₂O (I).

2. Structural commentary

The asymmetric unit of (I) is composed of a half of a trans-2,5-dimethylpipeazine-1,4-dium dication, one perchlorate anion and one water molecule (Fig. 1). The complete dication is generated by crystallographic inversion symmetry, leading to a typical chair conformation, with the methyl groups occupying equatorial positions [puckering parameters: Q = 0.7341 Å, θ = 90 and φ = −16 °], which is similar the conformation of the same species in its nitrate salt (Gatfaoui et al., 2014 ). Otherwise, the bond lengths and angle in the dication are normal (Rother et al., 1997 ; Gatfaoui et al., 2014; Essid et al., 2015 ).

Figure 1
An ORTEP view of (I)

with displacement ellipsoids drawn at the 30% probability level. Symmetry code: (i) −x + $[{1\over 2}]$ , −y + $[{1\over 2}]$ , −z.

The perchlorate anion displays its expected tetrahedral geometry around the chlorine atom. Interatomic bond lengths and angles of the perchlorate anion lie respectively within the ranges [1.4327 (10)–1.4452 (11) Å] and [109.01 (7)- 110.28 (7) °]. Similar geometrical features have also been noticed in other crystal structures (Toumi Akriche et al., 2010 ; Berrah et al., 2012 ).

3. Supramolecular features

In the extended structure, the anions are connected to the water molecules through O_w—H⋯O hydrogen bonds (Table 1), generating a corrugated C₂²(5) chain running along the [010] direction (Fig. 2). These chains are linked via the trans-2,5-dimethlpiperazine-1,4-diium cations through N—H⋯O, N—H⋯O_w and weak C—H⋯O hydrogen bonds, forming a three-dimensional supramolecular network (Fig. 3). These data show that each organic cation is connected to six inorganic chains.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
OW—H1W⋯O1ⁱ	0.85 (1)	2.03 (1)	2.8637 (16)	167 (2)
OW—H2W⋯O2ⁱⁱ	0.85 (1)	2.23 (1)	2.9932 (16)	150 (2)
N1—H1N⋯O4ⁱⁱⁱ	0.90	2.18	2.9067 (15)	137
N1—H1N⋯O3^iv	0.90	2.42	3.0293 (15)	125
N1—H1N⋯OW^v	0.90	2.55	3.1994 (16)	130
N1—H2N⋯OWⁱ	0.90	1.91	2.8019 (15)	172
C1—H1B⋯O3^iv	0.97	2.56	3.1007 (17)	116
Symmetry codes: (i) $[-x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (ii) $[-x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ ; (iii) $[x, -y+1, z+{\script{1\over 2}}]$ ; (iv) $[-x, y+1, -z+{\script{1\over 2}}]$ ; (v) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ .

Figure 2
Hydrogen-bonded supramolecular chains involving anions and water molecules of compound (I)

, represented through the ab plane.

Figure 3
Projection of (I)

along the b axis. The H-atoms not involved in hydrogen bonding are omitted.

4. Hirshfeld surface analysis

The three-dimensional Hirshfeld surfaces and two-dimensional fingerprint plots of (I) were prepared using CrystalExplorer (Wolff et al., 2012 ) and are shown in Figs. 4 and 5, respectively. The interaction between N—H and oxygen atoms can be seen in the Hirshfeld surface as the bright-red area in Fig. 4 (labeled a). The light-red spots are due to O_w—H⋯O interactions (labeled b). For the salt, O⋯H/H⋯O contacts, which are attributed to N—H⋯O_w and O_w—H⋯O hydrogen-bonding interactions, appear as two sharp symmetric spikes in the two-dimensional fingerprint maps. They have the most significant contribution to the total Hirshfeld surfaces. The H⋯H contacts appear in the middle of the scattered points in the two-dimensional fingerprint maps. For further information on Hirshfeld surfaces, see: Spackman & McKinnon (2002 ) and Spackman & Jayatilaka (2009 ).

Figure 4
Hirshfeld surface around the constituents of (I)

coloured according to d_norm. The surfaces are shown as transparent to allow visualization of the orientation and conformation of the functional groups.

Figure 5
Fingerprint plots of the major contacts: (a) H⋯O and (b) H⋯H.

5. Synthesis and crystallization

The title compound was prepared from an alcoholic solution containing trans-2,5-dimethylpiparazine (0.1 g, 1 mmol, purity 99%, Aldrich) dissolved in ethanol (20 ml) and perchloric acid HClO₄ (0.2 g, 2 mmol, purity 96%, Aldrich) with a molar ratio of 1:2. This mixture was stirred for 1 h. After a week of evaporation at room temperature, colorless single crystals of suitable dimensions for crystallographic study were formed, and were isolated by filtration and washed with a small amount of distilled water. The crystals can be stable for months under normal conditions of temperature and humidity.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were located in a difference map but were placed geometrically and refined using a riding model, with C—H = 0.96 Å (methyl), or 0.98 Å (methine), N—H = 0.90 Å (NH₂) with U_iso(H) = 1.2U_eq(C or N). The H atoms of the water molecule were refined with a distance restraint of O—H = 0.85 (1) Å using DFIX and DANG commands (Sheldrick, 2015 ) with U_iso(H) = 1.5U_eq(O).

Table 2
Experimental details

Crystal data
Chemical formula	C₆H₁₆N₂²⁺·2ClO₄⁻·2H₂O
M_r	351.14
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	150
a, b, c (Å)	16.8603 (8), 7.2655 (3), 14.4534 (6)
β (°)	128.751 (1)
V (Å³)	1380.78 (10)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.52
Crystal size (mm)	0.44 × 0.29 × 0.25

Data collection
Diffractometer	Bruker D8 VENTURE
Absorption correction	Multi-scan (SADABS; Bruker, 2014 )
T_min, T_max	0.775, 0.878
No. of measured, independent and observed [I > 2σ(I)] reflections	7760, 1557, 1457
R_int	0.023
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.028, 0.074, 1.13
No. of reflections	1557
No. of parameters	100
No. of restraints	3
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.34, −0.41
Computer programs: APEX2 and SAINT (Bruker, 2014), SIR97 (Altomare et al., 1999 ), SHELXL2014/7 (Sheldrick, 2015), ORTEP-3 for Windows and WinGX publication routines (Farrugia, 2012 ).

Supporting information

CCDC reference: 1470800

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S205698901600520X/hb7574sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S205698901600520X/hb7574Isup2.hkl

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL2014/7 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX publication routines (Farrugia, 2012).

trans-2,5-Dimethylpiperazine-1,4-diium bis(perchlorate) dihydrate top

Crystal data top

C₆H₁₆N₂²⁺·2ClO₄⁻·2H₂O	F(000) = 736
M_r = 351.14	D_x = 1.689 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 16.8603 (8) Å	Cell parameters from 7552 reflections
b = 7.2655 (3) Å	θ = 3.1–27.5°
c = 14.4534 (6) Å	µ = 0.52 mm⁻¹
β = 128.751 (1)°	T = 150 K
V = 1380.78 (10) Å³	Prism, colourless
Z = 4	0.44 × 0.29 × 0.25 mm

Data collection top

D8 VENTURE Bruker AXS diffractometer	1557 independent reflections
Radiation source: Incoatec microfocus sealed tube	1457 reflections with I > 2σ(I)
Multilayer monochromator	R_int = 0.023
rotation images scans	θ_max = 27.5°, θ_min = 3.1°
Absorption correction: multi-scan (SADABS; Bruker, 2014)	h = −21→21
T_min = 0.775, T_max = 0.878	k = −9→9
7760 measured reflections	l = −18→15

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.028	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.074	H atoms treated by a mixture of independent and constrained refinement
S = 1.13	w = 1/[σ²(F_o²) + (0.0308P)² + 1.9533P] where P = (F_o² + 2F_c²)/3
1557 reflections	(Δ/σ)_max = 0.001
100 parameters	Δρ_max = 0.34 e Å⁻³
3 restraints	Δρ_min = −0.41 e Å⁻³

Special details top

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.

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 > 2sigma(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 (Å²) top

	x	y	z	U_iso*/U_eq
Cl1	0.09748 (2)	0.13197 (4)	0.16201 (3)	0.01195 (12)
O1	0.14991 (10)	0.26958 (16)	0.25415 (10)	0.0307 (3)
O2	0.16959 (8)	−0.00473 (16)	0.18348 (11)	0.0254 (3)
O3	0.02214 (9)	0.04530 (16)	0.16384 (10)	0.0239 (3)
O4	0.05035 (9)	0.21898 (16)	0.04934 (9)	0.0236 (3)
OW	0.40676 (9)	0.84994 (14)	0.78311 (9)	0.0203 (2)
H1W	0.3881 (18)	0.9600 (15)	0.780 (2)	0.046 (7)*
H2W	0.3837 (15)	0.780 (2)	0.8086 (18)	0.034 (6)*
N1	0.14181 (8)	0.75580 (15)	0.43347 (10)	0.0111 (2)
H2N	0.1201	0.7208	0.3612	0.013*
H1N	0.0867	0.7774	0.4286	0.013*
C1	0.20218 (10)	0.92935 (18)	0.46870 (12)	0.0119 (3)
H1A	0.2220	0.9720	0.5442	0.014*
H1B	0.1605	1.0239	0.4099	0.014*
C2	0.20319 (10)	0.60230 (18)	0.52072 (11)	0.0114 (3)
H2	0.2243	0.6396	0.5984	0.014*
C3	0.13915 (11)	0.42938 (19)	0.48147 (13)	0.0186 (3)
H3A	0.0801	0.4542	0.4754	0.028*
H3B	0.1785	0.3334	0.5385	0.028*
H3C	0.1183	0.3911	0.4056	0.028*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.01181 (18)	0.01242 (18)	0.01379 (18)	−0.00022 (10)	0.00907 (14)	0.00166 (10)
O1	0.0321 (6)	0.0200 (6)	0.0225 (6)	−0.0075 (5)	0.0085 (5)	−0.0069 (5)
O2	0.0215 (6)	0.0256 (6)	0.0347 (6)	0.0119 (5)	0.0203 (5)	0.0101 (5)
O3	0.0246 (6)	0.0246 (6)	0.0358 (6)	−0.0064 (4)	0.0253 (5)	−0.0012 (5)
O4	0.0269 (6)	0.0308 (6)	0.0190 (5)	0.0105 (5)	0.0171 (5)	0.0119 (4)
OW	0.0272 (6)	0.0152 (5)	0.0174 (5)	−0.0013 (4)	0.0135 (5)	0.0000 (4)
N1	0.0077 (5)	0.0131 (5)	0.0124 (5)	0.0006 (4)	0.0062 (4)	0.0008 (4)
C1	0.0120 (6)	0.0101 (6)	0.0142 (6)	0.0011 (5)	0.0084 (5)	0.0006 (5)
C2	0.0110 (6)	0.0113 (6)	0.0122 (6)	0.0008 (5)	0.0074 (5)	0.0020 (5)
C3	0.0163 (6)	0.0139 (6)	0.0230 (7)	−0.0034 (5)	0.0111 (6)	0.0008 (5)

Geometric parameters (Å, º) top

Cl1—O3	1.4327 (10)	C1—C2ⁱ	1.5218 (17)
Cl1—O4	1.4363 (10)	C1—H1A	0.9700
Cl1—O1	1.4425 (11)	C1—H1B	0.9700
Cl1—O2	1.4452 (11)	C2—C3	1.5163 (18)
OW—H1W	0.850 (9)	C2—C1ⁱ	1.5218 (17)
OW—H2W	0.850 (9)	C2—H2	0.9800
N1—C1	1.4955 (16)	C3—H3A	0.9600
N1—C2	1.5071 (16)	C3—H3B	0.9600
N1—H2N	0.9000	C3—H3C	0.9600
N1—H1N	0.9000

O3—Cl1—O4	110.28 (7)	N1—C1—H1B	109.5
O3—Cl1—O1	109.01 (7)	C2ⁱ—C1—H1B	109.5
O4—Cl1—O1	109.03 (7)	H1A—C1—H1B	108.1
O3—Cl1—O2	109.29 (7)	N1—C2—C3	110.17 (10)
O4—Cl1—O2	109.87 (7)	N1—C2—C1ⁱ	108.88 (10)
O1—Cl1—O2	109.34 (7)	C3—C2—C1ⁱ	111.63 (11)
H1W—OW—H2W	109.1 (17)	N1—C2—H2	108.7
C1—N1—C2	111.99 (10)	C3—C2—H2	108.7
C1—N1—H2N	109.2	C1ⁱ—C2—H2	108.7
C2—N1—H2N	109.2	C2—C3—H3A	109.5
C1—N1—H1N	109.2	C2—C3—H3B	109.5
C2—N1—H1N	109.2	H3A—C3—H3B	109.5
H2N—N1—H1N	107.9	C2—C3—H3C	109.5
N1—C1—C2ⁱ	110.74 (10)	H3A—C3—H3C	109.5
N1—C1—H1A	109.5	H3B—C3—H3C	109.5
C2ⁱ—C1—H1A	109.5

Symmetry code: (i) −x+1/2, −y+3/2, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
OW—H1W···O1ⁱ	0.85 (1)	2.03 (1)	2.8637 (16)	167 (2)
OW—H2W···O2ⁱⁱ	0.85 (1)	2.23 (1)	2.9932 (16)	150 (2)
N1—H1N···O4ⁱⁱⁱ	0.90	2.18	2.9067 (15)	137
N1—H1N···O3^iv	0.90	2.42	3.0293 (15)	125
N1—H1N···OW^v	0.90	2.55	3.1994 (16)	130
N1—H2N···OWⁱ	0.90	1.91	2.8019 (15)	172
C1—H1B···O3^iv	0.97	2.56	3.1007 (17)	116

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

Acknowledgements

This work was supported by the Tunisian Ministry of Higher Education Scientific Research.

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