research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

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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 Ow—H⋯O (w = water) hydrogen bonds. These chains are cross-linked by the dications via N—H⋯Ow 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.

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[Brockunier, L. L., He, J., Colwell, L. F. Jr, Habulihaz, B., He, H., Leiting, B., Lyons, K. A., Marsilio, F., Patel, R. A., Teffera, Y., Wu, J. K., Thornberry, N. A., Weber, A. E. & Parmee, E. R. (2004). Bioorg. Med. Chem. Lett. 14, 4763-4766.]; Bogatcheva et al., 2006[Bogatcheva, E., Hanrahan, C., Nikonenko, B., Samala, R., Chen, P., Gearhart, J., Barbosa, F., Einck, L., Nacy, C. A. & Protopopova, M. (2006). J. Med. Chem. 49, 3045-3048.]).

[Scheme 1]

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)[link].

2. Structural commentary

The asymmetric unit of (I)[link] is composed of a half of a trans-2,5-dimethylpipeazine-1,4-dium dication, one perchlorate anion and one water mol­ecule (Fig. 1[link]). 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[Gatfaoui, S., Roisnel, T., Dhaouadi, H. & Marouani, H. (2014). Acta Cryst. E70, o725.]). Otherwise, the bond lengths and angle in the dication are normal (Rother et al., 1997[Rother, G., Worzala, H. & Bentrup, U. (1997). Z. Kristallogr. New Cryst. Struct. 212, 199.]; Gatfaoui et al., 2014[Gatfaoui, S., Roisnel, T., Dhaouadi, H. & Marouani, H. (2014). Acta Cryst. E70, o725.]; Essid et al., 2015[Essid, M., Roisnel, T., Rzaigui, M. & Marouani, H. (2015). Monatsh. Chem. DOI 10.1007/s00706-015-1485-9]).

[Figure 1]
Figure 1
An ORTEP view of (I)[link] 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[Toumi Akriche, S., Rzaigui, M., Al-Hokbany, N. & Mahfouz, R. M. (2010). Acta Cryst. E66, o300.]; Berrah et al., 2012[Berrah, F., Bouacida, S., Anana, H. & Roisnel, T. (2012). Acta Cryst. E64, o1601-o1602.]).

3. Supra­molecular features

In the extended structure, the anions are connected to the water mol­ecules through Ow—H⋯O hydrogen bonds (Table 1[link]), generating a corrugated C22(5) chain running along the [010] direction (Fig. 2[link]). These chains are linked via the trans-2,5-dimethlpiperazine-1,4-diium cations through N—H⋯O, N—H⋯Ow and weak C—H⋯O hydrogen bonds, forming a three-dimensional supra­molecular network (Fig. 3[link]). 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 DA 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⋯O3iv 0.90 2.42 3.0293 (15) 125
N1—H1N⋯OWv 0.90 2.55 3.1994 (16) 130
N1—H2N⋯OWi 0.90 1.91 2.8019 (15) 172
C1—H1B⋯O3iv 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]
Figure 2
Hydrogen-bonded supra­molecular chains involving anions and water mol­ecules of compound (I)[link], represented through the ab plane.
[Figure 3]
Figure 3
Projection of (I)[link] 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)[link] were prepared using CrystalExplorer (Wolff et al., 2012[Wolff, S. K., Grimwood, D. J., McKinnon, J. J., Turner, M. J., Jayatilaka, D. & Spackman, M. A. (2012). CrystalExplorer. University of Western Australia.]) and are shown in Figs. 4[link] and 5[link], respectively. The inter­action between N—H and oxygen atoms can be seen in the Hirshfeld surface as the bright-red area in Fig. 4[link] (labeled a). The light-red spots are due to Ow—H⋯O inter­actions (labeled b). For the salt, O⋯H/H⋯O contacts, which are attributed to N—H⋯Ow and Ow—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[Spackman, M. A. & McKinnon, J. J. (2002). CrystEngComm, 4, 378-392.]) and Spackman & Jayatilaka (2009[Spackman, M. A. & Jayatilaka, D. (2009). CrystEngComm, 11, 19-32.]).

[Figure 4]
Figure 4
Hirshfeld surface around the constituents of (I)[link] coloured according to dnorm. The surfaces are shown as transparent to allow visualization of the orientation and conformation of the functional groups.
[Figure 5]
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[link]. 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 Uiso(H) = 1.2Ueq(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[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) with Uiso(H) = 1.5Ueq(O).

Table 2
Experimental details

Crystal data
Chemical formula C6H16N22+·2ClO4·2H2O
Mr 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)
V3) 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[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.775, 0.878
No. of measured, independent and observed [I > 2σ(I)] reflections 7760, 1557, 1457
Rint 0.023
(sin θ/λ)max−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
Δρmax, Δρmin (e Å−3) 0.34, −0.41
Computer programs: APEX2 and SAINT (Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]), SHELXL2014/7 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), ORTEP-3 for Windows and WinGX publication routines (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]).

Supporting information


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+·2ClO4·2H2OF(000) = 736
Mr = 351.14Dx = 1.689 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
a = 16.8603 (8) ÅCell parameters from 7552 reflections
b = 7.2655 (3) Åθ = 3.1–27.5°
c = 14.4534 (6) ŵ = 0.52 mm1
β = 128.751 (1)°T = 150 K
V = 1380.78 (10) Å3Prism, colourless
Z = 40.44 × 0.29 × 0.25 mm
Data collection top
D8 VENTURE Bruker AXS
diffractometer
1557 independent reflections
Radiation source: Incoatec microfocus sealed tube1457 reflections with I > 2σ(I)
Multilayer monochromatorRint = 0.023
rotation images scansθmax = 27.5°, θmin = 3.1°
Absorption correction: multi-scan
(SADABS; Bruker, 2014)
h = 2121
Tmin = 0.775, Tmax = 0.878k = 99
7760 measured reflectionsl = 1815
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.028Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.074H atoms treated by a mixture of independent and constrained refinement
S = 1.13 w = 1/[σ2(Fo2) + (0.0308P)2 + 1.9533P]
where P = (Fo2 + 2Fc2)/3
1557 reflections(Δ/σ)max = 0.001
100 parametersΔρmax = 0.34 e Å3
3 restraintsΔρmin = 0.41 e Å3
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
xyzUiso*/Ueq
Cl10.09748 (2)0.13197 (4)0.16201 (3)0.01195 (12)
O10.14991 (10)0.26958 (16)0.25415 (10)0.0307 (3)
O20.16959 (8)0.00473 (16)0.18348 (11)0.0254 (3)
O30.02214 (9)0.04530 (16)0.16384 (10)0.0239 (3)
O40.05035 (9)0.21898 (16)0.04934 (9)0.0236 (3)
OW0.40676 (9)0.84994 (14)0.78311 (9)0.0203 (2)
H1W0.3881 (18)0.9600 (15)0.780 (2)0.046 (7)*
H2W0.3837 (15)0.780 (2)0.8086 (18)0.034 (6)*
N10.14181 (8)0.75580 (15)0.43347 (10)0.0111 (2)
H2N0.12010.72080.36120.013*
H1N0.08670.77740.42860.013*
C10.20218 (10)0.92935 (18)0.46870 (12)0.0119 (3)
H1A0.22200.97200.54420.014*
H1B0.16051.02390.40990.014*
C20.20319 (10)0.60230 (18)0.52072 (11)0.0114 (3)
H20.22430.63960.59840.014*
C30.13915 (11)0.42938 (19)0.48147 (13)0.0186 (3)
H3A0.08010.45420.47540.028*
H3B0.17850.33340.53850.028*
H3C0.11830.39110.40560.028*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.01181 (18)0.01242 (18)0.01379 (18)0.00022 (10)0.00907 (14)0.00166 (10)
O10.0321 (6)0.0200 (6)0.0225 (6)0.0075 (5)0.0085 (5)0.0069 (5)
O20.0215 (6)0.0256 (6)0.0347 (6)0.0119 (5)0.0203 (5)0.0101 (5)
O30.0246 (6)0.0246 (6)0.0358 (6)0.0064 (4)0.0253 (5)0.0012 (5)
O40.0269 (6)0.0308 (6)0.0190 (5)0.0105 (5)0.0171 (5)0.0119 (4)
OW0.0272 (6)0.0152 (5)0.0174 (5)0.0013 (4)0.0135 (5)0.0000 (4)
N10.0077 (5)0.0131 (5)0.0124 (5)0.0006 (4)0.0062 (4)0.0008 (4)
C10.0120 (6)0.0101 (6)0.0142 (6)0.0011 (5)0.0084 (5)0.0006 (5)
C20.0110 (6)0.0113 (6)0.0122 (6)0.0008 (5)0.0074 (5)0.0020 (5)
C30.0163 (6)0.0139 (6)0.0230 (7)0.0034 (5)0.0111 (6)0.0008 (5)
Geometric parameters (Å, º) top
Cl1—O31.4327 (10)C1—C2i1.5218 (17)
Cl1—O41.4363 (10)C1—H1A0.9700
Cl1—O11.4425 (11)C1—H1B0.9700
Cl1—O21.4452 (11)C2—C31.5163 (18)
OW—H1W0.850 (9)C2—C1i1.5218 (17)
OW—H2W0.850 (9)C2—H20.9800
N1—C11.4955 (16)C3—H3A0.9600
N1—C21.5071 (16)C3—H3B0.9600
N1—H2N0.9000C3—H3C0.9600
N1—H1N0.9000
O3—Cl1—O4110.28 (7)N1—C1—H1B109.5
O3—Cl1—O1109.01 (7)C2i—C1—H1B109.5
O4—Cl1—O1109.03 (7)H1A—C1—H1B108.1
O3—Cl1—O2109.29 (7)N1—C2—C3110.17 (10)
O4—Cl1—O2109.87 (7)N1—C2—C1i108.88 (10)
O1—Cl1—O2109.34 (7)C3—C2—C1i111.63 (11)
H1W—OW—H2W109.1 (17)N1—C2—H2108.7
C1—N1—C2111.99 (10)C3—C2—H2108.7
C1—N1—H2N109.2C1i—C2—H2108.7
C2—N1—H2N109.2C2—C3—H3A109.5
C1—N1—H1N109.2C2—C3—H3B109.5
C2—N1—H1N109.2H3A—C3—H3B109.5
H2N—N1—H1N107.9C2—C3—H3C109.5
N1—C1—C2i110.74 (10)H3A—C3—H3C109.5
N1—C1—H1A109.5H3B—C3—H3C109.5
C2i—C1—H1A109.5
Symmetry code: (i) x+1/2, y+3/2, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
OW—H1W···O1i0.85 (1)2.03 (1)2.8637 (16)167 (2)
OW—H2W···O2ii0.85 (1)2.23 (1)2.9932 (16)150 (2)
N1—H1N···O4iii0.902.182.9067 (15)137
N1—H1N···O3iv0.902.423.0293 (15)125
N1—H1N···OWv0.902.553.1994 (16)130
N1—H2N···OWi0.901.912.8019 (15)172
C1—H1B···O3iv0.972.563.1007 (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) x1/2, y+3/2, z1/2.
 

Acknowledgements

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

References

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