research communications
trans-2,5-Dimethylpiperazine-1,4-diium bis(perchlorate) dihydrate: and Hirshfeld surface analysis
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
The 6H16N22+·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.
of the title hydrated molecular salt, CKeywords: 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 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 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).
of (I)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 Ow—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⋯Ow 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.
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 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) and Spackman & Jayatilaka (2009).
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 . 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) with Uiso(H) = 1.5Ueq(O).
details are summarized in Table 2
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Supporting information
CCDC reference: 1470800
https://doi.org/10.1107/S205698901600520X/hb7574sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S205698901600520X/hb7574Isup2.hkl
Data collection: APEX2 (Bruker, 2014); cell
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).C6H16N22+·2ClO4−·2H2O | F(000) = 736 |
Mr = 351.14 | Dx = 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 |
D8 VENTURE Bruker AXS diffractometer | 1557 independent reflections |
Radiation source: Incoatec microfocus sealed tube | 1457 reflections with I > 2σ(I) |
Multilayer monochromator | Rint = 0.023 |
rotation images scans | θmax = 27.5°, θmin = 3.1° |
Absorption correction: multi-scan (SADABS; Bruker, 2014) | h = −21→21 |
Tmin = 0.775, Tmax = 0.878 | k = −9→9 |
7760 measured reflections | l = −18→15 |
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(Fo2) + (0.0308P)2 + 1.9533P] where P = (Fo2 + 2Fc2)/3 |
1557 reflections | (Δ/σ)max = 0.001 |
100 parameters | Δρmax = 0.34 e Å−3 |
3 restraints | Δρmin = −0.41 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. |
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. |
x | y | z | Uiso*/Ueq | ||
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* |
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) |
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. |
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···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+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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