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Acta Crystallogr Sect E Struct Rep Online. 2009 May 1; 65(Pt 5): o1004.
Published online 2009 April 8. doi:  10.1107/S1600536809012513
PMCID: PMC2977693

Piperazinediium dioxamate

Abstract

The title compound, C4H12N2 2+·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 [triangle]); Wilkinson & Harrison (2007 [triangle]). For biological applications of piperazines, see: Berkheij et al. (2005 [triangle]); Humle & Cherrier (1999 [triangle]). For the synthesis of a ligand with two piperazine arms, see: Bharathi et al. (2006 [triangle]). For the use of piperazine derivatives as buffers, see: Good et al. (1966 [triangle]). For the piperazine nucleus and its ability to bind to multiple receptors, see: Dinsmore & Beshore (2002 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1004-scheme1.jpg

Experimental

Crystal data

  • C4H12N2 2+·2C2H2NO3
  • M r = 264.25
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1004-efi9.jpg
  • 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 [triangle]) 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[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.119
  • S = 1.09
  • 2606 reflections
  • 82 parameters
  • 3 restraints
  • H-atom parameters constrained
  • Δρmax = 0.36 e Å−3
  • Δρmin = −0.34 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

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

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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

supplementary crystallographic information

Comment

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.

Experimental

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.

Refinement

H atoms were positioned geometrically and allowed to ride on their parent atoms, with N—H = 0.86–0.90 Å and C—H = 0.97 Å with Uiso(H)= 1.2Ueq.

Figures

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, ...

Crystal data

C4H12N22+·2C2H2NO3F(000) = 280
Mr = 264.25Dx = 1.555 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2743 reflections
a = 6.4323 (4) Åθ = 3.1–36.3°
b = 6.7681 (4) ŵ = 0.13 mm1
c = 13.0032 (7) ÅT = 293 K
β = 94.488 (2)°Block, colourless
V = 564.35 (6) Å30.24 × 0.22 × 0.16 mm
Z = 2

Data collection

Bruker APEXII CCD diffractometer2606 independent reflections
Radiation source: fine-focus sealed tube2197 reflections with I > 2σ(I)
graphiteRint = 0.021
Detector resolution: 10.0 pixels mm-1θmax = 36.3°, θmin = 3.1°
ω scansh = −10→10
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)k = −11→10
Tmin = 0.969, Tmax = 0.979l = −20→9
9313 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: difference Fourier map
wR(F2) = 0.119H-atom parameters constrained
S = 1.09w = 1/[σ2(Fo2) + (0.0667P)2 + 0.0606P] where P = (Fo2 + 2Fc2)/3
2606 reflections(Δ/σ)max < 0.001
82 parametersΔρmax = 0.36 e Å3
3 restraintsΔρmin = −0.34 e Å3

Special details

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)

xyzUiso*/Ueq
N20.08666 (10)0.95960 (10)0.40409 (4)0.02372 (13)
H2A0.17520.99000.35620.028*
H2B0.01610.85020.38300.028*
C3−0.06294 (12)1.12524 (12)0.41301 (5)0.02590 (15)
H3A−0.14361.14410.34750.031*
H3B0.01321.24620.42970.031*
C40.20790 (11)0.91851 (12)0.50401 (6)0.02572 (15)
H4A0.29381.03200.52400.031*
H4B0.29920.80640.49620.031*
O10.13426 (8)0.15896 (9)0.19612 (4)0.02683 (13)
O20.44704 (10)−0.03929 (12)0.30376 (4)0.03431 (16)
O30.28309 (12)0.09059 (12)0.05073 (4)0.03678 (17)
N10.61883 (11)−0.06196 (13)0.15969 (5)0.03142 (17)
H1A0.7247−0.11860.19170.038*
H1B0.6182−0.03870.09460.038*
C10.27471 (10)0.08954 (10)0.14582 (4)0.02114 (13)
C20.45721 (11)−0.01070 (11)0.21043 (5)0.02200 (14)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N20.0244 (3)0.0285 (3)0.0190 (2)−0.0053 (2)0.00670 (19)−0.0034 (2)
C30.0285 (3)0.0280 (3)0.0214 (3)−0.0015 (3)0.0027 (2)0.0021 (2)
C40.0208 (3)0.0312 (4)0.0254 (3)0.0001 (2)0.0034 (2)−0.0022 (2)
O10.0230 (2)0.0337 (3)0.0242 (2)0.0066 (2)0.00426 (18)0.00091 (19)
O20.0304 (3)0.0553 (4)0.0179 (2)0.0129 (3)0.0059 (2)0.0084 (2)
O30.0432 (4)0.0502 (4)0.0168 (2)0.0188 (3)0.0017 (2)0.0017 (2)
N10.0291 (3)0.0460 (4)0.0200 (2)0.0156 (3)0.0067 (2)0.0051 (2)
C10.0232 (3)0.0222 (3)0.0181 (2)0.0024 (2)0.0014 (2)0.0006 (2)
C20.0225 (3)0.0261 (3)0.0178 (3)0.0038 (2)0.0039 (2)0.0019 (2)

Geometric parameters (Å, °)

N2—C31.4879 (11)C4—H4B0.9700
N2—C41.4883 (10)O1—C11.2478 (5)
N2—H2A0.9000O2—C21.2357 (8)
N2—H2B0.9000O3—C11.2419 (5)
C3—C4i1.5095 (10)N1—C21.3205 (9)
C3—H3A0.9700N1—H1A0.8600
C3—H3B0.9700N1—H1B0.8600
C4—C3i1.5095 (10)C1—O31.2419 (5)
C4—H4A0.9700C1—C21.5459 (10)
C3—N2—C4111.75 (6)N2—C4—H4B109.6
C3—N2—H2A109.3C3i—C4—H4B109.6
C4—N2—H2A109.3H4A—C4—H4B108.1
C3—N2—H2B109.3C2—N1—H1A120.0
C4—N2—H2B109.3C2—N1—H1B120.0
H2A—N2—H2B107.9H1A—N1—H1B120.0
N2—C3—C4i110.33 (6)O3—C1—O1127.54 (7)
N2—C3—H3A109.6O3—C1—O1127.54 (7)
C4i—C3—H3A109.6O3—C1—C2116.96 (6)
N2—C3—H3B109.6O3—C1—C2116.96 (6)
C4i—C3—H3B109.6O1—C1—C2115.50 (5)
H3A—C3—H3B108.1O2—C2—N1123.63 (7)
N2—C4—C3i110.48 (6)O2—C2—C1120.41 (6)
N2—C4—H4A109.6N1—C2—C1115.96 (5)
C3i—C4—H4A109.6
C4—N2—C3—C4i−56.67 (9)O3—C1—C2—O2−170.89 (8)
C3—N2—C4—C3i56.75 (9)O1—C1—C2—O28.52 (11)
O3—O3—C1—O10.00 (4)O3—C1—C2—N18.95 (11)
O3—O3—C1—C20.00 (4)O3—C1—C2—N18.95 (11)
O3—C1—C2—O2−170.89 (8)O1—C1—C2—N1−171.64 (7)

Symmetry codes: (i) −x, −y+2, −z+1.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1A···O1ii0.862.243.0232 (9)152
N1—H1B···O3iii0.862.072.8622 (8)153
N2—H2A···O1iv0.902.373.0589 (8)133
N2—H2A···O2iv0.901.942.7475 (9)149
N2—H2B···O1v0.901.872.7509 (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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LX2097).

References

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  • Bharathi, K. S., Rahiman, A. K., Rajesh, K., Sreedaran, S., Aravindan, P. G., Velmurugan, D. & Narayanan, V. (2006). Polyhedron, 25, 2859-2868.
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