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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 64| Part 1| January 2008| Page o230
https://doi.org/10.1107/S1600536807065002

Piperazinediium bis­­(2-carb­oxy­pyridine-3-carboxyl­ate)

Hossein Aghabozorg,a* Faranak Manteghia and Mohammad Ghadermazib

aFaculty of Chemistry, Teacher Training University, 49 Mofateh Avenue 15614, Tehran, Iran, and bDepartment of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran
*Correspondence e-mail: haghabozorg@yahoo.com

(Received 31 October 2007; accepted 2 December 2007; online 12 December 2007)

The asymmetric unit of the title salt, C4H12N22+·2C7H4NO4− or pipzH22+·2(py-2,3-dcH−), prepared by a reaction between pyridine-2,3-dicarboxylic acid (py-2,3-dcH2) and piperazine (pipz), contains a monoanion and half of a centrosymmetric dication. The anionic fragment individually has two intra­molecular hydrogen bonds, an almost linear O—H⋯O bond between two carboxyl­ate groups and a C—H⋯O bond between the aromatic ring and carboxyl­ate group. Other O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds are responsible for three-dimensional expansion of the structure.

Related literature

For related literature, see: Aghabozorg et al. (2006[Aghabozorg, H., Ghadermazi, M., Manteghi, F. & Nakhjavan, B. (2006). Z. Anorg. Allg. Chem. 632, 2058-2064.]); Aghabozorg, Daneshvar et al. (2007[Aghabozorg, H., Daneshvar, S., Motyeian, E., Ghadermazi, M. & Attar Gharamaleki, J. (2007). Acta Cryst. E63, m2468-m2469.]); Aghabozorg, Sadr-khanlou et al. (2007[Aghabozorg, H., Sadr-khanlou, E., Soleimannejad, J. & Adams, H. (2007). Acta Cryst. E63, m1769.]); Khalil & Attia (1999[Khalil, M. M. & Attia, A. E. (1999). J. Chem. Eng. Data, 44, 180.]); Manteghi et al. (2007[Manteghi, F., Ghadermazi, M. & Aghabozorg, H. (2007). Acta Cryst. E63, o2809.]).

[Scheme 1]

Experimental

Crystal data

  • C4H12N22+·2C7H4NO4−

  • Mr = 420.38

  • Monoclinic, P 21 /c

  • a = 8.0116 (6) Å

  • b = 11.0588 (9) Å

  • c = 10.4621 (7) Å

  • β = 106.574 (2)°

  • V = 888.42 (11) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.13 mm−1

  • T = 100 (2) K

  • 0.20 × 0.15 × 0.15 mm
Data collection

  • Bruker SMART APEXII diffractometer

  • Absorption correction: none

  • 6962 measured reflections

  • 2341 independent reflections

  • 2104 reflections with I > 2σ(I)

  • Rint = 0.015
Refinement

  • R[F2 > 2σ(F2)] = 0.034

  • wR(F2) = 0.084

  • S = 1.03

  • 2341 reflections

  • 136 parameters

  • H-atom parameters constrained

  • Δρmax = 0.43 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O3—H3O⋯O1 0.85 1.57 2.4219 (11) 175
N2—H2A⋯O2i 0.90 1.94 2.7778 (12) 154
N2—H2B⋯O1 0.90 1.97 2.7571 (11) 146
C3—H3A⋯O4 0.95 2.31 2.6773 (13) 102
C8—H8A⋯O2ii 0.99 2.58 3.2982 (13) 130
C9—H9A⋯O4iii 0.99 2.39 3.3491 (14) 163
Symmetry codes: (i) [-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]; (iii) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2005[Bruker (2005). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: APEX2; data reduction: APEX2; program(s) used to solve structure: SHELXTL (Sheldrick, 1998[Sheldrick, G. M. (1998). SHELXTL. Version 5.10. Bruker AXS Inc., Madison, Wisconsin, USA.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL and Mercury (Version 1.4.2; Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536807065002/om2187sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807065002/om2187Isup2.hkl

checkCIF report


Comment top

Pyridinedicarboxylic acids are of great interest in medicinal chemistry because of the wide variety of their physiological properties displayed by natural as well as synthetic acids. These acids are present in many natural products, such as alkaloids, vitamins and coenzymes. Pyridinedicarboxylic acid metal complexes are therefore, especially interesting model systems (Khalil & Attia, 1999). Pyridine-2,3-dicarboxylic acid (py-2,3-dcH2) and piperazine (pipz) with other acids and bases are found in many ion pairs, such as (pipzH2)2(pydc) (Aghabozorg et al., 2006) and (pnH2)(py-2,3-dc).H2O (Manteghi et al., 2007). Moreover, a polymeric complex {(pipzH2)[Zn(py-2,3-dc)2].4H2O}n including fragments of the title zwitterion has been synthesized (Aghabozorg, Daneshvar et al., 2007). In all mentioned compounds, piperazine is biprotonated and pyridine-2,3-dicarboxylic acid is doubly deprotonated. But in the title ion pair and a complex formulated as [Zn(py-2,3-dcH)2(H2O)2] (Aghabozorg, Sadr-khanlou et al., 2007), pyridine-2,3-dicarboxylic acid is singly deprotonated. Fig. 1 shows the monoanion and the dication and the strong intramolecular hydrogen bond (see table of hydrogen-bond geometry). Fig. 2 illustrates the hydrogen bonded layers parallel to bc plane. The title ion pair has three C—H···O hydrogen bonds amongst them the C3—H3A···O4 has a short distance (H···O, 2.31 Å) compared with common C—H···O bonds, although its angle is far from linearity. Additionally, as shown in Fig. 3, the ion pair has a π-π stacking at the distance of 3.6623 (7) Å between the π-rings (symmetry code: 1 - x, -y, 1 - z).

Related literature top

For related literature, see: Aghabozorg et al. (2006); Aghabozorg, Daneshvar et al. (2007); Aghabozorg, Sadr-khanlou et al. (2007); Khalil & Attia (1999); Manteghi et al. (2007).

Experimental top

The title compound was synthesized via reaction of 1.67 g (10 mmol) of pyridine-2,3-dicarboxylic acid with 0.86 g (20 mmol) piperazine in a teterahydrofuran (THF) solution (50 ml). After a while, the obtained white precipitate was filtered out and dissolved in water to recrystallize. Colorless crystals of the title compound were obtained after 1 week.

Refinement top

The H(N) and H(O) atoms were found from difference Fourier map. The H(C) atom positions were calculated. All the hydrogen atoms were refined in isotropic approximatiom within riding model with the Uiso(H) parameters equal to 1.2Ueq(Ci), 1.2Ueq(Nj) and 1.5Ueq(O) where U(Ci), U(Cj) and U(O) are the equivalent thermal parameters of the carbon, nitrogen and oxygen atoms correspondingly to which corresponding H atoms are bonded.

Structure description top

Pyridinedicarboxylic acids are of great interest in medicinal chemistry because of the wide variety of their physiological properties displayed by natural as well as synthetic acids. These acids are present in many natural products, such as alkaloids, vitamins and coenzymes. Pyridinedicarboxylic acid metal complexes are therefore, especially interesting model systems (Khalil & Attia, 1999). Pyridine-2,3-dicarboxylic acid (py-2,3-dcH2) and piperazine (pipz) with other acids and bases are found in many ion pairs, such as (pipzH2)2(pydc) (Aghabozorg et al., 2006) and (pnH2)(py-2,3-dc).H2O (Manteghi et al., 2007). Moreover, a polymeric complex {(pipzH2)[Zn(py-2,3-dc)2].4H2O}n including fragments of the title zwitterion has been synthesized (Aghabozorg, Daneshvar et al., 2007). In all mentioned compounds, piperazine is biprotonated and pyridine-2,3-dicarboxylic acid is doubly deprotonated. But in the title ion pair and a complex formulated as [Zn(py-2,3-dcH)2(H2O)2] (Aghabozorg, Sadr-khanlou et al., 2007), pyridine-2,3-dicarboxylic acid is singly deprotonated. Fig. 1 shows the monoanion and the dication and the strong intramolecular hydrogen bond (see table of hydrogen-bond geometry). Fig. 2 illustrates the hydrogen bonded layers parallel to bc plane. The title ion pair has three C—H···O hydrogen bonds amongst them the C3—H3A···O4 has a short distance (H···O, 2.31 Å) compared with common C—H···O bonds, although its angle is far from linearity. Additionally, as shown in Fig. 3, the ion pair has a π-π stacking at the distance of 3.6623 (7) Å between the π-rings (symmetry code: 1 - x, -y, 1 - z).

For related literature, see: Aghabozorg et al. (2006); Aghabozorg, Daneshvar et al. (2007); Aghabozorg, Sadr-khanlou et al. (2007); Khalil & Attia (1999); Manteghi et al. (2007).

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: APEX2 (Bruker, 2005); data reduction: APEX2 (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 1998); program(s) used to refine structure: SHELXTL (Sheldrick, 1998); molecular graphics: SHELXTL (Sheldrick, 1998) and Mercury (Version 1.4.2; Macrae et al., 2006); software used to prepare material for publication: SHELXTL (Sheldrick, 1998).

Figures top
[Figure 1] Fig. 1. A view of the ion pair drawn at 50% probability level. Symmetry related atoms are labeled "i" and are generated by 2 - x, 1 - y, 1 - z. Some of the hydrogen bonds are shown and are depicted by dashed lines.
[Figure 2] Fig. 2. Hydrogen bonded layers parallel to bc plane. Hydrogen atoms are omitted for clarity except those involved in hydrogen bonding.
[Figure 3] Fig. 3. The π-π stacking at the distance of 3.6623 (7) Å (symmetry code: 1 - x, -y, 1 - z).
Piperazinediium bis(2-carboxypyridine-3-carboxylate) top
Crystal data top
C4H12N22+·2C7H4NO4−F(000) = 440
Mr = 420.38Dx = 1.571 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2095 reflections
a = 8.0116 (6) Åθ = 2.7–28.6°
b = 11.0588 (9) ŵ = 0.13 mm−1
c = 10.4621 (7) ÅT = 100 K
β = 106.574 (2)°Prism, colourless
V = 888.42 (11) Å30.20 × 0.15 × 0.15 mm
Z = 2
Data collection top
Bruker SMART APEXII
diffractometer		2104 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.015
Graphite monochromatorθmax = 29.0°, θmin = 2.7°
φ and ω scansh = −10→10
6962 measured reflectionsk = −15→15
2341 independent reflectionsl = −14→12
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)] = 0.034Hydrogen site location: mixed
wR(F2) = 0.084H-atom parameters constrained
S = 1.03 w = 1/[σ2(Fo2) + (0.035P)2 + 0.450P]
where P = (Fo2 + 2Fc2)/3
2341 reflections(Δ/σ)max < 0.001
136 parametersΔρmax = 0.43 e Å−3
0 restraintsΔρmin = −0.22 e Å−3
Crystal data top
C4H12N22+·2C7H4NO4−V = 888.42 (11) Å3
Mr = 420.38Z = 2
Monoclinic, P21/cMo Kα radiation
a = 8.0116 (6) ŵ = 0.13 mm−1
b = 11.0588 (9) ÅT = 100 K
c = 10.4621 (7) Å0.20 × 0.15 × 0.15 mm
β = 106.574 (2)°
Data collection top
Bruker SMART APEXII
diffractometer		2104 reflections with I > 2σ(I)
6962 measured reflectionsRint = 0.015
2341 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0340 restraints
wR(F2) = 0.084H-atom parameters constrained
S = 1.03Δρmax = 0.43 e Å−3
2341 reflectionsΔρmin = −0.22 e Å−3
136 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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 > σ(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
O10.88615 (11)0.17340 (7)0.51531 (8)0.02036 (18)
O20.98274 (10)0.08122 (7)0.70930 (8)0.02041 (18)
O30.72179 (11)0.13267 (7)0.28657 (8)0.02033 (18)
H3O0.78420.14670.36570.030*
O40.54664 (10)−0.00934 (8)0.17740 (8)0.02126 (18)
N10.77161 (11)−0.10247 (8)0.63974 (9)0.01409 (18)
N20.98062 (11)0.40793 (8)0.59237 (8)0.01352 (17)
H2A1.00470.44410.67260.016*
H2B0.95550.33000.60360.016*
C10.76624 (12)−0.02324 (8)0.54104 (10)0.01174 (18)
C20.65530 (12)−0.04141 (9)0.41030 (10)0.01209 (19)
C30.54476 (13)−0.14260 (9)0.39063 (10)0.0147 (2)
H3A0.4655−0.15650.30520.018*
C40.54919 (13)−0.22223 (9)0.49329 (11)0.0161 (2)
H4A0.4736−0.29020.48020.019*
C50.66802 (14)−0.19939 (9)0.61616 (10)0.0160 (2)
H5A0.6760−0.25520.68670.019*
C60.88903 (13)0.08412 (9)0.59330 (10)0.01317 (19)
C70.63871 (13)0.03075 (9)0.28268 (10)0.01448 (19)
C81.13286 (13)0.40868 (9)0.53727 (10)0.0146 (2)
H8A1.10670.35800.45600.018*
H8B1.23530.37360.60360.018*
C90.82508 (13)0.46401 (9)0.49653 (10)0.0147 (2)
H9A0.72700.46590.53650.018*
H9B0.78920.41490.41410.018*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0283 (4)0.0139 (3)0.0167 (4)−0.0056 (3)0.0029 (3)0.0024 (3)
O20.0234 (4)0.0200 (4)0.0146 (4)−0.0074 (3)0.0003 (3)0.0013 (3)
O30.0268 (4)0.0184 (4)0.0135 (3)−0.0025 (3)0.0021 (3)0.0034 (3)
O40.0197 (4)0.0294 (4)0.0129 (4)−0.0027 (3)0.0019 (3)0.0005 (3)
N10.0165 (4)0.0130 (4)0.0133 (4)0.0001 (3)0.0051 (3)0.0006 (3)
N20.0147 (4)0.0136 (4)0.0120 (4)−0.0018 (3)0.0033 (3)0.0006 (3)
C10.0120 (4)0.0110 (4)0.0129 (4)0.0007 (3)0.0047 (3)−0.0008 (3)
C20.0119 (4)0.0128 (4)0.0123 (4)0.0023 (3)0.0047 (3)−0.0005 (3)
C30.0124 (4)0.0162 (4)0.0158 (5)0.0002 (3)0.0044 (4)−0.0040 (4)
C40.0160 (4)0.0131 (4)0.0209 (5)−0.0022 (3)0.0082 (4)−0.0034 (4)
C50.0202 (5)0.0125 (4)0.0171 (5)−0.0004 (4)0.0084 (4)0.0011 (4)
C60.0136 (4)0.0123 (4)0.0145 (4)−0.0005 (3)0.0054 (3)−0.0009 (3)
C70.0130 (4)0.0181 (5)0.0128 (4)0.0035 (3)0.0044 (3)0.0017 (4)
C80.0143 (4)0.0156 (4)0.0143 (4)0.0032 (3)0.0046 (4)0.0000 (3)
C90.0113 (4)0.0181 (5)0.0138 (4)−0.0013 (3)0.0023 (3)0.0003 (4)
Geometric parameters (Å, º) top
O1—C61.2769 (12)C2—C31.4053 (14)
O2—C61.2319 (12)C2—C71.5284 (14)
O3—C71.3036 (13)C3—C41.3815 (15)
O3—H3O0.8501C3—H3A0.9500
O4—C71.2209 (13)C4—C51.3872 (15)
N1—C51.3348 (13)C4—H4A0.9500
N1—C11.3456 (12)C5—H5A0.9500
N2—C81.4903 (13)C8—C9i1.5129 (14)
N2—C91.4933 (13)C8—H8A0.9900
N2—H2A0.9000C8—H8B0.9900
N2—H2B0.9000C9—C8i1.5129 (14)
C1—C21.4169 (13)C9—H9A0.9900
C1—C61.5394 (13)C9—H9B0.9900
C7—O3—H3O110.0N1—C5—H5A118.5
C5—N1—C1119.93 (9)C4—C5—H5A118.5
C8—N2—C9110.87 (7)O2—C6—O1122.99 (9)
C8—N2—H2A112.1O2—C6—C1118.55 (9)
C9—N2—H2A110.9O1—C6—C1118.44 (9)
C8—N2—H2B107.1O4—C7—O3120.92 (9)
C9—N2—H2B108.1O4—C7—C2118.56 (9)
H2A—N2—H2B107.5O3—C7—C2120.51 (9)
N1—C1—C2121.50 (9)N2—C8—C9i110.92 (8)
N1—C1—C6110.63 (8)N2—C8—H8A109.5
C2—C1—C6127.85 (9)C9i—C8—H8A109.5
C3—C2—C1116.74 (9)N2—C8—H8B109.5
C3—C2—C7113.19 (8)C9i—C8—H8B109.5
C1—C2—C7130.06 (9)H8A—C8—H8B108.0
C4—C3—C2121.22 (9)N2—C9—C8i110.15 (8)
C4—C3—H3A119.4N2—C9—H9A109.6
C2—C3—H3A119.4C8i—C9—H9A109.6
C3—C4—C5117.58 (9)N2—C9—H9B109.6
C3—C4—H4A121.2C8i—C9—H9B109.6
C5—C4—H4A121.2H9A—C9—H9B108.1
N1—C5—C4122.94 (9)
C5—N1—C1—C2−1.52 (14)N1—C1—C6—O25.34 (13)
C5—N1—C1—C6176.91 (9)C2—C1—C6—O2−176.36 (10)
N1—C1—C2—C33.28 (14)N1—C1—C6—O1−173.07 (9)
C6—C1—C2—C3−174.85 (9)C2—C1—C6—O15.23 (15)
N1—C1—C2—C7−174.82 (9)C3—C2—C7—O4−6.01 (13)
C6—C1—C2—C77.04 (16)C1—C2—C7—O4172.15 (10)
C1—C2—C3—C4−2.13 (14)C3—C2—C7—O3174.22 (9)
C7—C2—C3—C4176.30 (9)C1—C2—C7—O3−7.62 (16)
C2—C3—C4—C5−0.66 (15)C9—N2—C8—C9i57.28 (11)
C1—N1—C5—C4−1.56 (15)C8—N2—C9—C8i−56.84 (11)
C3—C4—C5—N12.64 (15)
Symmetry code: (i) −x+2, −y+1, −z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3O···O10.851.572.4219 (11)175
N2—H2A···O2ii0.901.942.7778 (12)154
N2—H2B···O10.901.972.7571 (11)146
C3—H3A···O40.952.312.6773 (13)102
C8—H8A···O2iii0.992.583.2982 (13)130
C9—H9A···O4iv0.992.393.3491 (14)163
Symmetry codes: (ii) −x+2, y+1/2, −z+3/2; (iii) x, −y+1/2, z−1/2; (iv) x, −y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC4H12N22+·2C7H4NO4−
Mr420.38
Crystal system, space groupMonoclinic, P21/c
Temperature (K)100
a, b, c (Å)8.0116 (6), 11.0588 (9), 10.4621 (7)
β (°) 106.574 (2)
V (Å3)888.42 (11)
Z2
Radiation typeMo Kα
µ (mm−1)0.13
Crystal size (mm)0.20 × 0.15 × 0.15
Data collection
DiffractometerBruker SMART APEXII
Absorption correction–
No. of measured, independent and
observed [I > 2σ(I)] reflections		6962, 2341, 2104
Rint0.015
(sin θ/λ)max (Å−1)0.682
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.034, 0.084, 1.03
No. of reflections2341
No. of parameters136
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.43, −0.22

Computer programs: APEX2 (Bruker, 2005), SHELXTL (Sheldrick, 1998) and Mercury (Version 1.4.2; Macrae et al., 2006).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3O···O10.851.572.4219 (11)175
N2—H2A···O2i0.901.942.7778 (12)154
N2—H2B···O10.901.972.7571 (11)146
C3—H3A···O40.952.312.6773 (13)102
C8—H8A···O2ii0.992.583.2982 (13)130
C9—H9A···O4iii0.992.393.3491 (14)163
Symmetry codes: (i) −x+2, y+1/2, −z+3/2; (ii) x, −y+1/2, z−1/2; (iii) x, −y+1/2, z+1/2.
 

References

First citationAghabozorg, H., Daneshvar, S., Motyeian, E., Ghadermazi, M. & Attar Gharamaleki, J. (2007). Acta Cryst. E63, m2468–m2469.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationAghabozorg, H., Ghadermazi, M., Manteghi, F. & Nakhjavan, B. (2006). Z. Anorg. Allg. Chem. 632, 2058–2064.  Web of Science CSD CrossRef CAS Google Scholar
 First citationAghabozorg, H., Sadr-khanlou, E., Soleimannejad, J. & Adams, H. (2007). Acta Cryst. E63, m1769.  Web of Science CSD CrossRef IUCr Journals Google Scholar
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ISSN: 2056-9890
Volume 64| Part 1| January 2008| Page o230
https://doi.org/10.1107/S1600536807065002
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