Piperazinediium dioxamate

Murugavel, S.; Selvakumar, R.; Govindarajan, S.; Kannan, P.S.; SubbiahPandi, A.

doi:10.1107/S1600536809012513

organic compounds

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ISSN: 2056-9890

Volume 65| Part 5| May 2009| Page o1004

doi:10.1107/S1600536809012513

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Piperazinediium dioxamate

S. Murugavel,^a R. Selvakumar,^b S. Govindarajan,^b P. S. Kannan ^c and A. SubbiahPandi ^d ^*

^aDepartment of Physics, Thanthai Periyar Government Institute of Technology, Vellore 632 002, India, ^bDepartment of Chemistry, Bharathiar University, Coimbatore 641 046, India, ^cDepartment of Physics, S.M.K. Fomra Institute of Technology, Thaiyur, Chennai 603 103, India, and ^dDepartment of Physics, Presidency College (Autonomous), Chennai 600 005, India
^*Correspondence e-mail: a_spandian@yahoo.com

(Received 16 March 2009; accepted 2 April 2009; online 8 April 2009)

The title compound, C₄H₁₂N₂²⁺·2C₂H₂NO₃⁻, contains a network of doubly protanated piperazinium cations (lying about centres of inversion) and dioxamate anions. The piperazinium dication adopts a typical chair conformation. The crystal structure is stabilized by cation–to–anion N—H⋯O and anion–to–anion N—H⋯O hydrogen bonds.

Related literature

For related structures, see: Büyükgüngör & Odabaşoğlu (2008 ); Wilkinson & Harrison (2007 ). For biological applications of piperazines, see: Berkheij et al. (2005 ); Humle & Cherrier (1999 ). For the synthesis of a ligand with two piperazine arms, see: Bharathi et al. (2006 ). For the use of piperazine derivatives as buffers, see: Good et al. (1966 ). For the piperazine nucleus and its ability to bind to multiple receptors, see: Dinsmore & Beshore (2002 ).

Experimental

Crystal data

C₄H₁₂N₂²⁺·2C₂H₂NO₃⁻
M_r = 264.25
Monoclinic, P 2₁ /c
a = 6.4323 (4) Å
b = 6.7681 (4) Å
c = 13.0032 (7) Å
β = 94.488 (2)°
V = 564.35 (6) Å³
Z = 2
Mo Kα radiation
μ = 0.13 mm⁻¹
T = 293 K
0.24 × 0.22 × 0.16 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.969, T_max = 0.979
9313 measured reflections
2606 independent reflections
2197 reflections with I > 2σ(I)
R_int = 0.021

Refinement

R[F² > 2σ(F²)] = 0.041
wR(F²) = 0.119
S = 1.09
2606 reflections
82 parameters
3 restraints
H-atom parameters constrained
Δρ_max = 0.36 e Å⁻³
Δρ_min = −0.34 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O1ⁱ	0.86	2.24	3.0232 (9)	152
N1—H1B⋯O3ⁱⁱ	0.86	2.07	2.8622 (8)	153
N2—H2A⋯O1ⁱⁱⁱ	0.90	2.37	3.0589 (8)	133
N2—H2A⋯O2ⁱⁱⁱ	0.90	1.94	2.7475 (9)	149
N2—H2B⋯O1^iv	0.90	1.87	2.7509 (9)	164
Symmetry codes: (i) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) -x+1, -y, -z; (iii) x, y+1, z; (iv) $[-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2004 ); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT and XPREP (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia (1997 ) and PLATON (Spek, 2009 ); software used to prepare material for publication: SHELXL97 and PLATON.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809012513/lx2097sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809012513/lx2097Isup2.hkl

checkCIF report

Comment top

Piperazines are among the most important building blocks in today's drug discovery. The piperazine nucleus is capable of binding to multiple receptors with high affinity and therefore piperazine has been classified as a privileged structure (Dinsmore et al., 2002). They are found in biologically active compounds across a number of different therapeutic areas (Berkheij et al., 2005) such as antifungal, antibacterial, antimalarial, antipsychotic, antidepressant and antitumour activity against colon, prostate, breast, lung and leukemia tumors (Humle & Cherrier, 1999). Also Piperazine derivatives are widely used as buffers (Good et al., 1966), and can act as complexing reagents with metal ions (Bharathi et al., 2006). Encouraged by the above information, we report the crystal structure of the title compound, piperazinium bis (dioxamate) (I) (Fig. 1).

In the crystal structure of (I), the piperazinium dication lies on a centre of inversion and adopts a typical chair conformation. The bond lengths in (I) are normal and comparable with the corresponding values observed in the related structure (Wilkinson & Harrison, 2007). The dihedral angle between the piperazinium dication and oxamate anion is 9.54 (3)°. The crystal structure (Fig. 2) is stabilized by cation–to–anion N—H···O hydrogen bonds between the N—H atoms of the piperazinium ring and the O atoms of the oxamate (Fig. 2 and Table 1; symmetry code as in Fig. 2). The crystal packing is further stabilized by anion–to–anion N—H···O hydrogen bonds between the N—H atoms and the O atoms from the neighbouring oxamate anions (Fig. 2 and Table 1; symmetry code as in Fig. 2). Thus, the symmetry–related molecules are cross linked by these hydrogen bonds to generate a three–dimensional network.

Related literature top

For related structures, see: Büyükgüngör & Odabaşoğlu (2008); Wilkinson & Harrison (2007). For biological applications, see: Berkheij et al. (2005); Humle & Cherrier (1999). For the synthesis of a ligand with two piperazine arms, see: Bharathi et al. (2006). For the use of piperazine derivatives as a buffer, see: Good et al. (1966). For the piperazine nucleus and its ability to bind to multiple receptors, see: Dinsmore & Beshore (2002).

Experimental top

Piperazinium bis(dioxamate) was prepared by adding aqueous solution (15ml) of piperazine (0.194g; 0.001mol) to the solution (15ml) of oxamic acid (0.089g; 0.001mol). The resulting clear solution was concentrated over water-bath to half the volume and kept for crystallization at room temperature. The transparent single crystals suitable for x-ray diffraction obtained after two days were filtered off, washed with ethanol and air dried.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT and XPREP (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia (1997) and PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are presented as a small cycles of arbitrary radius.
	Fig. 2. N—H···O hydrogen bonds (dotted lines) in the title compound.[Symmetry code: (i) -x+1, y-1/2, -z+1/2 ; (ii) -x+1, -y, -z; (iii) x, y+1, z; (iv)-x, y+1/2, -z+1/2 (v) -x+1, y+1/2, -z+1/2; (vi) -x, y-1/2, -z+1/2; (vii) x, y-1, z.]

Piperazinediium dioxamate top

Crystal data top

C₄H₁₂N₂²⁺·2C₂H₂NO₃⁻	F(000) = 280
M_r = 264.25	D_x = 1.555 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2743 reflections
a = 6.4323 (4) Å	θ = 3.1–36.3°
b = 6.7681 (4) Å	µ = 0.13 mm⁻¹
c = 13.0032 (7) Å	T = 293 K
β = 94.488 (2)°	Block, colourless
V = 564.35 (6) Å³	0.24 × 0.22 × 0.16 mm
Z = 2

Data collection top

Bruker APEXII CCD diffractometer	2606 independent reflections
Radiation source: fine-focus sealed tube	2197 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.021
Detector resolution: 10.0 pixels mm^-1	θ_max = 36.3°, θ_min = 3.1°
ω scans	h = −10→10
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	k = −11→10
T_min = 0.969, T_max = 0.979	l = −20→9
9313 measured reflections

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)] = 0.041	Hydrogen site location: difference Fourier map
wR(F²) = 0.119	H-atom parameters constrained
S = 1.09	w = 1/[σ²(F_o²) + (0.0667P)² + 0.0606P] where P = (F_o² + 2F_c²)/3
2606 reflections	(Δ/σ)_max < 0.001
82 parameters	Δρ_max = 0.36 e Å⁻³
3 restraints	Δρ_min = −0.34 e Å⁻³

Crystal data top

C₄H₁₂N₂²⁺·2C₂H₂NO₃⁻	V = 564.35 (6) Å³
M_r = 264.25	Z = 2
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.4323 (4) Å	µ = 0.13 mm⁻¹
b = 6.7681 (4) Å	T = 293 K
c = 13.0032 (7) Å	0.24 × 0.22 × 0.16 mm
β = 94.488 (2)°

Data collection top

Bruker APEXII CCD diffractometer	2606 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	2197 reflections with I > 2σ(I)
T_min = 0.969, T_max = 0.979	R_int = 0.021
9313 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.041	3 restraints
wR(F²) = 0.119	H-atom parameters constrained
S = 1.09	Δρ_max = 0.36 e Å⁻³
2606 reflections	Δρ_min = −0.34 e Å⁻³
82 parameters

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
N2	0.08666 (10)	0.95960 (10)	0.40409 (4)	0.02372 (13)
H2A	0.1752	0.9900	0.3562	0.028*
H2B	0.0161	0.8502	0.3830	0.028*
C3	−0.06294 (12)	1.12524 (12)	0.41301 (5)	0.02590 (15)
H3A	−0.1436	1.1441	0.3475	0.031*
H3B	0.0132	1.2462	0.4297	0.031*
C4	0.20790 (11)	0.91851 (12)	0.50401 (6)	0.02572 (15)
H4A	0.2938	1.0320	0.5240	0.031*
H4B	0.2992	0.8064	0.4962	0.031*
O1	0.13426 (8)	0.15896 (9)	0.19612 (4)	0.02683 (13)
O2	0.44704 (10)	−0.03929 (12)	0.30376 (4)	0.03431 (16)
O3	0.28309 (12)	0.09059 (12)	0.05073 (4)	0.03678 (17)
N1	0.61883 (11)	−0.06196 (13)	0.15969 (5)	0.03142 (17)
H1A	0.7247	−0.1186	0.1917	0.038*
H1B	0.6182	−0.0387	0.0946	0.038*
C1	0.27471 (10)	0.08954 (10)	0.14582 (4)	0.02114 (13)
C2	0.45721 (11)	−0.01070 (11)	0.21043 (5)	0.02200 (14)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N2	0.0244 (3)	0.0285 (3)	0.0190 (2)	−0.0053 (2)	0.00670 (19)	−0.0034 (2)
C3	0.0285 (3)	0.0280 (3)	0.0214 (3)	−0.0015 (3)	0.0027 (2)	0.0021 (2)
C4	0.0208 (3)	0.0312 (4)	0.0254 (3)	0.0001 (2)	0.0034 (2)	−0.0022 (2)
O1	0.0230 (2)	0.0337 (3)	0.0242 (2)	0.0066 (2)	0.00426 (18)	0.00091 (19)
O2	0.0304 (3)	0.0553 (4)	0.0179 (2)	0.0129 (3)	0.0059 (2)	0.0084 (2)
O3	0.0432 (4)	0.0502 (4)	0.0168 (2)	0.0188 (3)	0.0017 (2)	0.0017 (2)
N1	0.0291 (3)	0.0460 (4)	0.0200 (2)	0.0156 (3)	0.0067 (2)	0.0051 (2)
C1	0.0232 (3)	0.0222 (3)	0.0181 (2)	0.0024 (2)	0.0014 (2)	0.0006 (2)
C2	0.0225 (3)	0.0261 (3)	0.0178 (3)	0.0038 (2)	0.0039 (2)	0.0019 (2)

Geometric parameters (Å, º) top

N2—C3	1.4879 (11)	C4—H4B	0.9700
N2—C4	1.4883 (10)	O1—C1	1.2478 (5)
N2—H2A	0.9000	O2—C2	1.2357 (8)
N2—H2B	0.9000	O3—C1	1.2419 (5)
C3—C4ⁱ	1.5095 (10)	N1—C2	1.3205 (9)
C3—H3A	0.9700	N1—H1A	0.8600
C3—H3B	0.9700	N1—H1B	0.8600
C4—C3ⁱ	1.5095 (10)	C1—O3	1.2419 (5)
C4—H4A	0.9700	C1—C2	1.5459 (10)

C3—N2—C4	111.75 (6)	N2—C4—H4B	109.6
C3—N2—H2A	109.3	C3ⁱ—C4—H4B	109.6
C4—N2—H2A	109.3	H4A—C4—H4B	108.1
C3—N2—H2B	109.3	C2—N1—H1A	120.0
C4—N2—H2B	109.3	C2—N1—H1B	120.0
H2A—N2—H2B	107.9	H1A—N1—H1B	120.0
N2—C3—C4ⁱ	110.33 (6)	O3—C1—O1	127.54 (7)
N2—C3—H3A	109.6	O3—C1—O1	127.54 (7)
C4ⁱ—C3—H3A	109.6	O3—C1—C2	116.96 (6)
N2—C3—H3B	109.6	O3—C1—C2	116.96 (6)
C4ⁱ—C3—H3B	109.6	O1—C1—C2	115.50 (5)
H3A—C3—H3B	108.1	O2—C2—N1	123.63 (7)
N2—C4—C3ⁱ	110.48 (6)	O2—C2—C1	120.41 (6)
N2—C4—H4A	109.6	N1—C2—C1	115.96 (5)
C3ⁱ—C4—H4A	109.6

C4—N2—C3—C4ⁱ	−56.67 (9)	O3—C1—C2—O2	−170.89 (8)
C3—N2—C4—C3ⁱ	56.75 (9)	O1—C1—C2—O2	8.52 (11)
O3—O3—C1—O1	0.00 (4)	O3—C1—C2—N1	8.95 (11)
O3—O3—C1—C2	0.00 (4)	O3—C1—C2—N1	8.95 (11)
O3—C1—C2—O2	−170.89 (8)	O1—C1—C2—N1	−171.64 (7)

Symmetry code: (i) −x, −y+2, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1ⁱⁱ	0.86	2.24	3.0232 (9)	152
N1—H1B···O3ⁱⁱⁱ	0.86	2.07	2.8622 (8)	153
N2—H2A···O1^iv	0.90	2.37	3.0589 (8)	133
N2—H2A···O2^iv	0.90	1.94	2.7475 (9)	149
N2—H2B···O1^v	0.90	1.87	2.7509 (9)	164

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

Experimental details

Crystal data
Chemical formula	C₄H₁₂N₂²⁺·2C₂H₂NO₃⁻
M_r	264.25
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	6.4323 (4), 6.7681 (4), 13.0032 (7)
β (°)	94.488 (2)
V (Å³)	564.35 (6)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.13
Crystal size (mm)	0.24 × 0.22 × 0.16

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.969, 0.979
No. of measured, independent and observed [I > 2σ(I)] reflections	9313, 2606, 2197
R_int	0.021
(sin θ/λ)_max (Å⁻¹)	0.834

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.119, 1.09
No. of reflections	2606
No. of parameters	82
No. of restraints	3
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.36, −0.34

Computer programs: APEX2 (Bruker, 2004), APEX2 and SAINT (Bruker, 2004), SAINT and XPREP (Bruker, 2004), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia (1997) and PLATON (Spek, 2009), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1ⁱ	0.86	2.24	3.0232 (9)	151.7
N1—H1B···O3ⁱⁱ	0.86	2.07	2.8622 (8)	152.7
N2—H2A···O1ⁱⁱⁱ	0.90	2.37	3.0589 (8)	133.2
N2—H2A···O2ⁱⁱⁱ	0.90	1.94	2.7475 (9)	149.1
N2—H2B···O1^iv	0.90	1.87	2.7509 (9)	164.1

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

Acknowledgements

SM and ASP thank Dr Babu Vargheese, SAIF, IIT, Madras, India, for his help with the data collection.

References

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