Piperazine-1,4-diium bis­(4-nitro­benzoate) dihydrate

Rajkumar, R.; Kumar, P.P.; Gunasekaran, B.

doi:10.1107/S2414314617012913

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 2| Part 9| September 2017| x171291

https://doi.org/10.1107/S2414314617012913

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Piperazine-1,4-diium bis(4-nitrobenzoate) dihydrate

R. Rajkumar,^a P. Praveen Kumar ^a ^* and B. Gunasekaran ^b ^*

^aDepartment of Physics, Presidency College, Chennai 600 005, Tamil Nadu, India, and ^bDepartment of Physics & Nano Technology, SRM University, SRM Nagar, Kattankulathur, Kancheepuram Dist, Chennai 603 203, Tamil Nadu, India
^*Correspondence e-mail: ppkpresidency@gmail.com, phdguna@gmail.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 4 September 2017; accepted 10 September 2017; online 12 September 2017)

The asymmetric unit of the title molecular salt, C₄H₁₂N₂²⁺·2C₇H₄NO₄⁻ ·2H₂O, is composed of half a protonated piperazine dication, located about an inversion center, a benzoate anion and a water molecule of crystallization. In the crystal, the various units are linked by N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds, forming a supramolecular three-dimensional framework.

Keywords: crystal structure; piperazine; nitro benzoic acid; piperazine-1,4-diium; molecular salt; hydrogen bonding.

CCDC reference: 1573567

Structure description

Piperazine derivatives are found in a number of biologically active compounds, including several marketed drugs, and the piperazine ring is considered to be a privileged structure in drug discovery (Suzuki et al., 1997 ). Piperazines are frequently used as building blocks for pharmaceuticals (Kaloustian et al., 1976 ), and exhibit a substantial degree of selective RNA binding (Dega-Szafran et al., 2002 ).

The asymmetric unit of the title molecular salt comprises half a protonated piperazine dication, a benzoate anion and a water molecule of crystallization (Fig. 1). The piperazine dication is located about an inversion center and the ring has a chair conformation. The geometric parameters agree well with those reported for a similar compound, piperazine-1,4-diium bis(4-aminobenzenesulfonate) (Kumar et al., 2015 ).

Figure 1
The molecular structure of the title compound, with atom labelling and 30% probability displacement ellipsoids. The unlabelled atoms of the piperazine-1,4-diium dication are related to the labelled atoms by inversion symmetry (symmetry operation: −x + 1, −y + 1, −z + 2).

In the crystal, the various units are linked by N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds, forming a supramolecular three-dimensional framework (Table 1 and Fig. 2).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2A⋯O3	0.94 (2)	1.82 (2)	2.747 (2)	169 (2)
N2—H2B⋯O5ⁱ	0.92 (2)	1.85 (2)	2.751 (2)	162 (2)
O5—H5A⋯O4	0.89 (2)	1.85 (2)	2.733 (2)	168 (2)
O5—H5B⋯O3ⁱⁱ	0.91 (2)	1.88 (2)	2.761 (2)	164 (2)
C8—H8A⋯O2ⁱⁱⁱ	0.97	2.51	3.326 (3)	141
C9—H9B⋯O5	0.97	2.52	3.312 (2)	139
Symmetry codes: (i) -x+2, -y+2, -z+2; (ii) x+1, y, z; (iii) -x, -y+1, -z+1.

Figure 2
A view along the a axis of the crystal packing of the title compound. Hydrogen bonds (Table 1

) are shown as dashed lines, and H atoms not involved in these interactions have been omitted for clarity.

Synthesis and crystallization

4.3 g (0.057 mol) of piperazine and 8.4 g (0.029 mol) of 4-nitrobenzoic acid were dissolved in 50 ml of double-distilled water and stirred at room temperature for 5 h to obtain an homogeneous solution. The solution was filtered and allowed to evaporate in a dust-free atmosphere. After a few days, yellow block-like crystals were obtained (yield 94%, m.p. 370 K).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	0.5C₄H₁₂N₂²⁺·C₇H₄NO₄⁻·H₂O
M_r	228.21
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	296
a, b, c (Å)	6.5793 (5), 6.8094 (5), 12.3767 (9)
α, β, γ (°)	92.085 (4), 99.427 (3), 109.301 (4)
V (Å³)	513.81 (7)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	0.12
Crystal size (mm)	0.20 × 0.20 × 0.15

Data collection
Diffractometer	Bruker Kappa APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2008 )
T_min, T_max	0.976, 0.982
No. of measured, independent and observed [I > 2σ(I)] reflections	10658, 2019, 1369
R_int	0.043
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.106, 0.97
No. of reflections	2019
No. of parameters	162
No. of restraints	6
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.17
Computer programs: APEX2 and SAINT (Bruker, 2008), SHELXS97 and SHELXL97 (Sheldrick, 2008 ), PLATON (Spek, 2009 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 1573567

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314617012913/su4164sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314617012913/su4164Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314617012913/su4164Isup3.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Piperazine-1,4-diium bis(4-nitrobenzoate) dihydrate top

Crystal data top

0.5C₄H₁₂N₂²⁺·C₇H₄NO₄⁻·H₂O	Z = 2
M_r = 228.21	F(000) = 240
Triclinic, P1	D_x = 1.475 Mg m⁻³
a = 6.5793 (5) Å	Mo Kα radiation, λ = 0.71073 Å
b = 6.8094 (5) Å	Cell parameters from 2927 reflections
c = 12.3767 (9) Å	θ = 6.2–30.1°
α = 92.085 (4)°	µ = 0.12 mm⁻¹
β = 99.427 (3)°	T = 296 K
γ = 109.301 (4)°	Block, yellow
V = 513.81 (7) Å³	0.20 × 0.20 × 0.15 mm

Data collection top

Bruker Kappa APEXII CCD diffractometer	2019 independent reflections
Radiation source: fine-focus sealed tube	1369 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.043
Detector resolution: 0 pixels mm^-1	θ_max = 26.0°, θ_min = 3.2°
ω and φ scans	h = −8→8
Absorption correction: multi-scan (SADABS; Bruker, 2008)	k = −8→8
T_min = 0.976, T_max = 0.982	l = −15→15
10658 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.039	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.106	w = 1/[σ²(F_o²) + (0.045P)² + 0.1764P] where P = (F_o² + 2F_c²)/3
S = 0.97	(Δ/σ)_max < 0.001
2019 reflections	Δρ_max = 0.16 e Å⁻³
162 parameters	Δρ_min = −0.17 e Å⁻³
6 restraints	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.069 (7)

Special details top

Refinement. The NH₂ and water H atoms were located in difference-Fourier maps and refined with distance restraints: N—H = O—H = 0.90 (2) Å and H···H = 1.48 (2) Å. The C-bound H atoms were fixed geometrically and allowed to ride on their parent atoms: C—H = 0.93 - 0.97 Å with U_iso(H) = 1.2U_eq(C).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.3881 (3)	0.7745 (2)	0.62147 (14)	0.0307 (4)
C2	0.1832 (3)	0.7949 (3)	0.60281 (15)	0.0380 (5)
H2	0.1225	0.8221	0.6620	0.046*
C3	0.0685 (3)	0.7751 (3)	0.49680 (15)	0.0397 (5)
H3	−0.0688	0.7898	0.4840	0.048*
C4	0.1595 (3)	0.7335 (3)	0.41069 (14)	0.0344 (4)
C5	0.3615 (3)	0.7113 (3)	0.42579 (15)	0.0413 (5)
H5	0.4204	0.6824	0.3663	0.050*
C6	0.4745 (3)	0.7332 (3)	0.53230 (15)	0.0392 (5)
H6	0.6125	0.7199	0.5444	0.047*
C7	0.5200 (3)	0.7940 (3)	0.73631 (15)	0.0380 (5)
C8	0.5409 (3)	0.3454 (3)	0.93267 (14)	0.0353 (4)
H8A	0.4891	0.3739	0.8590	0.042*
H8B	0.5943	0.2294	0.9265	0.042*
C9	0.7243 (3)	0.5354 (3)	0.99088 (15)	0.0354 (4)
H9A	0.7843	0.5032	1.0622	0.042*
H9B	0.8405	0.5752	0.9483	0.042*
N1	0.0338 (3)	0.7086 (3)	0.29788 (13)	0.0487 (5)
N2	0.6427 (2)	0.7116 (2)	1.00540 (12)	0.0334 (4)
O1	0.1169 (3)	0.6756 (3)	0.22173 (13)	0.0826 (6)
O2	−0.1475 (3)	0.7239 (3)	0.28617 (13)	0.0698 (5)
O3	0.4310 (2)	0.8115 (2)	0.81642 (10)	0.0483 (4)
O4	0.7073 (2)	0.7872 (3)	0.74364 (12)	0.0700 (5)
O5	1.0952 (2)	0.9029 (2)	0.88996 (11)	0.0438 (4)
H2A	0.588 (3)	0.752 (3)	0.9379 (12)	0.052 (6)*
H2B	0.753 (3)	0.828 (3)	1.0429 (14)	0.055 (6)*
H5B	1.187 (3)	0.863 (4)	0.8539 (17)	0.071 (8)*
H5A	0.971 (3)	0.884 (4)	0.8424 (17)	0.082 (8)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0281 (9)	0.0282 (9)	0.0337 (10)	0.0086 (7)	0.0028 (7)	0.0026 (7)
C2	0.0356 (10)	0.0517 (12)	0.0316 (10)	0.0195 (9)	0.0099 (8)	0.0041 (8)
C3	0.0273 (10)	0.0534 (12)	0.0394 (11)	0.0165 (9)	0.0026 (8)	0.0067 (9)
C4	0.0359 (10)	0.0337 (10)	0.0284 (10)	0.0080 (8)	−0.0003 (8)	0.0027 (7)
C5	0.0449 (12)	0.0483 (11)	0.0352 (11)	0.0200 (9)	0.0121 (9)	0.0002 (8)
C6	0.0304 (10)	0.0464 (11)	0.0448 (12)	0.0188 (9)	0.0063 (8)	0.0031 (9)
C7	0.0368 (11)	0.0379 (10)	0.0374 (11)	0.0154 (9)	−0.0028 (8)	−0.0002 (8)
C8	0.0370 (10)	0.0389 (10)	0.0308 (10)	0.0148 (8)	0.0053 (8)	−0.0005 (8)
C9	0.0282 (9)	0.0434 (10)	0.0352 (10)	0.0138 (8)	0.0042 (7)	0.0044 (8)
N1	0.0537 (11)	0.0490 (10)	0.0354 (10)	0.0133 (9)	−0.0041 (8)	0.0025 (8)
N2	0.0303 (8)	0.0332 (8)	0.0308 (9)	0.0059 (7)	0.0001 (7)	0.0011 (7)
O1	0.0929 (14)	0.1240 (16)	0.0322 (9)	0.0438 (12)	0.0045 (9)	−0.0088 (9)
O2	0.0550 (10)	0.0952 (13)	0.0524 (10)	0.0289 (9)	−0.0153 (8)	0.0047 (9)
O3	0.0507 (9)	0.0685 (10)	0.0309 (7)	0.0293 (7)	0.0029 (6)	0.0072 (6)
O4	0.0425 (9)	0.1151 (14)	0.0537 (10)	0.0404 (9)	−0.0115 (7)	−0.0104 (9)
O5	0.0361 (8)	0.0481 (8)	0.0389 (8)	0.0074 (7)	0.0006 (6)	−0.0047 (6)

Geometric parameters (Å, º) top

C1—C6	1.382 (2)	C8—N2ⁱ	1.487 (2)
C1—C2	1.384 (2)	C8—C9	1.505 (3)
C1—C7	1.516 (2)	C8—H8A	0.9700
C2—C3	1.380 (3)	C8—H8B	0.9700
C2—H2	0.9300	C9—N2	1.484 (2)
C3—C4	1.369 (2)	C9—H9A	0.9700
C3—H3	0.9300	C9—H9B	0.9700
C4—C5	1.370 (3)	N1—O1	1.213 (2)
C4—N1	1.474 (2)	N1—O2	1.217 (2)
C5—C6	1.380 (3)	N2—C8ⁱ	1.487 (2)
C5—H5	0.9300	N2—H2A	0.940 (14)
C6—H6	0.9300	N2—H2B	0.922 (15)
C7—O4	1.237 (2)	O5—H5B	0.908 (15)
C7—O3	1.252 (2)	O5—H5A	0.892 (16)

C6—C1—C2	118.80 (16)	N2ⁱ—C8—H8A	109.6
C6—C1—C7	118.92 (15)	C9—C8—H8A	109.6
C2—C1—C7	122.28 (16)	N2ⁱ—C8—H8B	109.6
C3—C2—C1	120.31 (17)	C9—C8—H8B	109.6
C3—C2—H2	119.8	H8A—C8—H8B	108.1
C1—C2—H2	119.8	N2—C9—C8	110.25 (14)
C4—C3—C2	119.09 (17)	N2—C9—H9A	109.6
C4—C3—H3	120.5	C8—C9—H9A	109.6
C2—C3—H3	120.5	N2—C9—H9B	109.6
C3—C4—C5	122.35 (16)	C8—C9—H9B	109.6
C3—C4—N1	118.67 (16)	H9A—C9—H9B	108.1
C5—C4—N1	118.97 (17)	O1—N1—O2	123.50 (18)
C4—C5—C6	117.74 (17)	O1—N1—C4	118.42 (18)
C4—C5—H5	121.1	O2—N1—C4	118.08 (18)
C6—C5—H5	121.1	C9—N2—C8ⁱ	111.36 (14)
C5—C6—C1	121.70 (17)	C9—N2—H2A	112.4 (11)
C5—C6—H6	119.1	C8ⁱ—N2—H2A	106.2 (12)
C1—C6—H6	119.1	C9—N2—H2B	111.1 (13)
O4—C7—O3	124.85 (17)	C8ⁱ—N2—H2B	108.3 (12)
O4—C7—C1	117.09 (17)	H2A—N2—H2B	107.3 (15)
O3—C7—C1	118.05 (16)	H5B—O5—H5A	108.0 (17)
N2ⁱ—C8—C9	110.14 (14)

C6—C1—C2—C3	−0.3 (3)	C6—C1—C7—O4	5.3 (3)
C7—C1—C2—C3	−179.75 (17)	C2—C1—C7—O4	−175.23 (18)
C1—C2—C3—C4	0.5 (3)	C6—C1—C7—O3	−173.33 (17)
C2—C3—C4—C5	−0.2 (3)	C2—C1—C7—O3	6.2 (3)
C2—C3—C4—N1	178.82 (17)	N2ⁱ—C8—C9—N2	−56.7 (2)
C3—C4—C5—C6	−0.3 (3)	C3—C4—N1—O1	178.66 (19)
N1—C4—C5—C6	−179.32 (17)	C5—C4—N1—O1	−2.3 (3)
C4—C5—C6—C1	0.5 (3)	C3—C4—N1—O2	−0.8 (3)
C2—C1—C6—C5	−0.3 (3)	C5—C4—N1—O2	178.29 (18)
C7—C1—C6—C5	179.25 (17)	C8—C9—N2—C8ⁱ	57.4 (2)

Symmetry code: (i) −x+1, −y+1, −z+2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···O3	0.94 (2)	1.82 (2)	2.747 (2)	169 (2)
N2—H2B···O5ⁱⁱ	0.92 (2)	1.85 (2)	2.751 (2)	162 (2)
O5—H5A···O4	0.89 (2)	1.85 (2)	2.733 (2)	168 (2)
O5—H5B···O3ⁱⁱⁱ	0.91 (2)	1.88 (2)	2.761 (2)	164 (2)
C8—H8A···O2^iv	0.97	2.51	3.326 (3)	141
C9—H9B···O5	0.97	2.52	3.312 (2)	139

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

Acknowledgements

The authors acknowledge the SAIF, IIT Madras, Chennai, for the data collection.

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