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

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ISSN: 2056-9890

3-Carb­oxy­pyrazino[2,3-f][1,10]phenanthrolin-9-ium-2-carboxyl­ate

aDepartment of Chemistry and Chemical Engineering, Shaanxi Key Laboratory of Chemical Reaction Engineering, Yan'an University, Yan'an, Shaanxi 716000, People's Republic of China, and bCollege of Mechanical & Material Engineering, Functional Materials Research Institute, China Three Gorges University, Yichang 443002, People's Republic of China
*Correspondence e-mail: chemfufeng@126.com

(Received 15 November 2009; accepted 26 February 2010; online 3 March 2010)

In the title zwitterionic compound, C16H8N4O4, the dihedral angle between the carboxyl and carboxyl­ate groups is 72.14 (2)°. In the crystal, mol­ecules are linked by strong inter­molecular O—H⋯O and N+—H⋯O hydrogen bonds into double chains extended along [001]. These chains are additionally stabilized by ππ stacking inter­actions between the pyridine and benzene rings [centroid–centroid distance = 3.5542 (8) Å].

Related literature

For coordination compounds of the title ligand, see: Weng et al. (2009[Weng, Z.-H., Liu, D.-C., Chen, Z.-L., Zou, H.-H., Qin, S.-N. & Liang, F.-P. (2009). Cryst. Growth Des. 9, 4163-4170.]).

[Scheme 1]

Experimental

Crystal data
  • C16H8N4O4

  • Mr = 320.26

  • Triclinic, [P \overline 1]

  • a = 7.302 (2) Å

  • b = 9.662 (3) Å

  • c = 10.726 (3) Å

  • α = 63.564 (3)°

  • β = 71.386 (3)°

  • γ = 78.283 (4)°

  • V = 640.5 (3) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.12 mm−1

  • T = 293 K

  • 0.32 × 0.21 × 0.15 mm

Data collection
  • Bruker SMART CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.969, Tmax = 0.982

  • 4652 measured reflections

  • 2243 independent reflections

  • 1268 reflections with I > 2σ(I)

  • Rint = 0.037

Refinement
  • R[F2 > 2σ(F2)] = 0.062

  • wR(F2) = 0.177

  • S = 1.05

  • 2243 reflections

  • 221 parameters

  • 1 restraint

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.38 e Å−3

  • Δρmin = −0.31 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O3—H3⋯O1i 0.82 1.82 2.638 (4) 171
N2—H2⋯O2ii 0.81 (2) 1.87 (3) 2.638 (4) 159 (5)
Symmetry codes: (i) -x, -y, -z+1; (ii) x, y, z+1.

Data collection: SMART (Bruker, 1997[Bruker (1997). SMART and SAINT. Bruker AXS Inc., Madison,Wisconsin, USA.]); cell refinement: SAINT (Bruker, 1997[Bruker (1997). SMART and SAINT. Bruker AXS Inc., Madison,Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

[2,3-f]Pyrazino[1,10]phenanthroline-2,3-dicarboxylic acid (H2ppdb) is a multidentate O/N-donor ligand, which was rarely used up to date (Weng et al., 2009). Owing to the presence of two carboxylic groups and a large conjugated π system, H2ppdb hoards the recognition information for the formation of interesting supramolecular structures. We attempted to synthesize a TmIII complex with the H2ppdb ligand in hydrothermal synthesis conditions however we were unsuccessful. Instead of crystals of the complex, single crystals of the H2ppdb were isolated and the structure of H2ppdb is reported here.

The molecular structure of title compound is shown in Fig. 1. One of the carboxyl groups is deprotonated and the proton is transferred to the phenantroline fragment. Intermolecular hydrogen-bonding and π-π stacking interactions are the most important features of the title compound. O—H···O and N—H···O hydrogen bonds (Table 1), and π-π stacking interactions between the pyridine rings and phenyl rings from the neighboring H2ppdb molecules [centroid–centroid distances = 3.5542 (8) Å] link the molecules into a double chain extending along the c axis. The double chains are further connected by weak C—H···O hydrogen bonds involving the carboxyl oxygen and the C—H groups adjacent to the pyridine rings and π-π stacking interactions as indicated by a center-to-center distance of 3.7402 (7) Å, forming a three-dimensional supramolecular network (Fig.2).

Related literature top

For coordination compounds of the title ligand, see: Weng et al. (2009).

Experimental top

All chemicals were of analytical reagent grade, commercially available and used without further purification. A mixture of H2ppdb (0.1 mmol, 0.0320 g), Tm2O3(0.05 mmol, 0.0193 g) was adjusted to pH 1.5 with HNO3 (0.2 mol/L). It was then sealed in a 25 ml Teflon-lined stainless steel reactor together with water (10 ml), heated at 140 °C for 4 days, and then cooled slowly to room temperature, to furnish yellow crystals.

Refinement top

The H atom attached to N atom was located in a difference Fourier map and refined with the N—H distance restrained to 0.82 (2) Å and Uiso(H) = 1.5Ueq(N). The other H atoms were placed in idealized positions, with C-H = 0.93 and O-H = 0.82 Å, and constrained to ride on their parent atoms with Uiso(H) = 1.2Ueq(C) or Uiso(H) = 1.5Ueq(O).

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT (Bruker, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The structure of the title compound with the atom-numbering scheme showing displacement ellipsoids at the 50% probability level.
[Figure 2] Fig. 2. Tthree-dimensional supramolecular network formed by hydrogen bonds and π-π stacking interactions.
3-Carboxypyrazino[2,3-f][1,10]phenanthrolin-9-ium-2-carboxylate top
Crystal data top
C16H8N4O4Z = 2
Mr = 320.26F(000) = 328
Triclinic, P1Dx = 1.661 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.302 (2) ÅCell parameters from 1426 reflections
b = 9.662 (3) Åθ = 2.5–25.0°
c = 10.726 (3) ŵ = 0.12 mm1
α = 63.564 (3)°T = 293 K
β = 71.386 (3)°Prism, colorless
γ = 78.283 (4)°0.32 × 0.21 × 0.15 mm
V = 640.5 (3) Å3
Data collection top
Bruker SMART CCD
diffractometer
2243 independent reflections
Radiation source: fine-focus sealed tube1268 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.037
phi and ω scansθmax = 25.0°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 88
Tmin = 0.969, Tmax = 0.982k = 1111
4652 measured reflectionsl = 1212
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)] = 0.062Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.177H atoms treated by a mixture of independent and constrained refinement
S = 1.05 w = 1/[σ2(Fo2) + (0.0802P)2 + 0.2P]
where P = (Fo2 + 2Fc2)/3
2243 reflections(Δ/σ)max < 0.001
221 parametersΔρmax = 0.38 e Å3
1 restraintΔρmin = 0.31 e Å3
Crystal data top
C16H8N4O4γ = 78.283 (4)°
Mr = 320.26V = 640.5 (3) Å3
Triclinic, P1Z = 2
a = 7.302 (2) ÅMo Kα radiation
b = 9.662 (3) ŵ = 0.12 mm1
c = 10.726 (3) ÅT = 293 K
α = 63.564 (3)°0.32 × 0.21 × 0.15 mm
β = 71.386 (3)°
Data collection top
Bruker SMART CCD
diffractometer
2243 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
1268 reflections with I > 2σ(I)
Tmin = 0.969, Tmax = 0.982Rint = 0.037
4652 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0621 restraint
wR(F2) = 0.177H atoms treated by a mixture of independent and constrained refinement
S = 1.05Δρmax = 0.38 e Å3
2243 reflectionsΔρmin = 0.31 e Å3
221 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
O10.1681 (4)0.2077 (3)0.4832 (3)0.0468 (8)
O20.2929 (4)0.0009 (3)0.2840 (3)0.0473 (8)
O30.0845 (4)0.3107 (4)0.2623 (3)0.0529 (8)
H30.00100.27420.33810.079*
O40.4003 (5)0.3285 (4)0.1966 (3)0.0551 (9)
N10.2349 (4)0.0766 (4)0.6468 (3)0.0324 (8)
N30.2887 (5)0.2420 (4)0.5116 (3)0.0374 (8)
N20.2403 (5)0.0825 (4)1.0943 (3)0.0317 (8)
N40.3104 (4)0.2237 (4)0.9626 (3)0.0336 (8)
C40.2334 (5)0.0835 (4)0.8748 (4)0.0285 (9)
C90.2928 (5)0.1575 (4)0.8803 (4)0.0285 (9)
C140.2812 (5)0.1585 (4)0.6532 (4)0.0291 (9)
C150.2689 (5)0.1654 (5)0.4411 (4)0.0348 (10)
C60.1733 (5)0.3119 (4)1.0965 (4)0.0352 (10)
H60.14400.41501.14770.042*
C80.2571 (5)0.0055 (4)0.9502 (4)0.0275 (9)
C10.2339 (5)0.0776 (5)0.4193 (4)0.0359 (10)
C30.2491 (5)0.0009 (4)0.7207 (4)0.0284 (9)
C130.3009 (5)0.2401 (4)0.7332 (4)0.0302 (9)
C120.3264 (6)0.3985 (5)0.6710 (4)0.0364 (10)
H120.33010.45740.57420.044*
C70.2011 (5)0.2294 (5)1.1653 (4)0.0357 (10)
H70.19200.27831.26370.043*
C100.3366 (6)0.3728 (5)0.8992 (4)0.0392 (10)
H100.34990.41940.95500.047*
C50.1900 (5)0.2382 (4)0.9509 (4)0.0343 (9)
H50.17220.29200.90270.041*
C20.2468 (5)0.0059 (5)0.5071 (4)0.0319 (9)
C110.3458 (6)0.4662 (5)0.7535 (4)0.0419 (11)
H110.36470.57120.71410.050*
C160.2599 (7)0.2711 (5)0.2886 (5)0.0442 (11)
H20.250 (7)0.035 (5)1.138 (4)0.066*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.062 (2)0.0476 (19)0.0407 (17)0.0151 (16)0.0143 (14)0.0215 (15)
O20.063 (2)0.062 (2)0.0262 (16)0.0189 (16)0.0099 (14)0.0215 (14)
O30.052 (2)0.057 (2)0.0469 (18)0.0093 (16)0.0152 (15)0.0159 (16)
O40.066 (2)0.066 (2)0.0367 (17)0.0204 (18)0.0114 (16)0.0185 (16)
N10.0352 (19)0.040 (2)0.0284 (18)0.0048 (15)0.0108 (14)0.0173 (15)
N30.051 (2)0.040 (2)0.0215 (17)0.0109 (16)0.0091 (15)0.0102 (15)
N20.039 (2)0.038 (2)0.0243 (18)0.0015 (16)0.0131 (15)0.0153 (15)
N40.042 (2)0.036 (2)0.0307 (17)0.0063 (15)0.0120 (15)0.0178 (16)
C40.028 (2)0.036 (2)0.0259 (19)0.0023 (17)0.0081 (16)0.0156 (17)
C90.032 (2)0.032 (2)0.026 (2)0.0039 (17)0.0074 (16)0.0151 (17)
C140.031 (2)0.038 (2)0.0234 (19)0.0035 (17)0.0099 (16)0.0140 (17)
C150.043 (2)0.043 (3)0.025 (2)0.006 (2)0.0110 (18)0.0165 (19)
C60.041 (2)0.030 (2)0.031 (2)0.0048 (18)0.0075 (18)0.0106 (18)
C80.028 (2)0.035 (2)0.0211 (19)0.0038 (17)0.0079 (15)0.0110 (17)
C10.036 (2)0.044 (3)0.033 (2)0.002 (2)0.0114 (19)0.019 (2)
C30.028 (2)0.036 (2)0.028 (2)0.0012 (17)0.0086 (16)0.0179 (18)
C130.030 (2)0.036 (2)0.027 (2)0.0042 (17)0.0063 (16)0.0151 (18)
C120.044 (2)0.043 (3)0.024 (2)0.012 (2)0.0076 (17)0.0122 (19)
C70.042 (2)0.034 (2)0.026 (2)0.0012 (19)0.0110 (18)0.0072 (18)
C100.050 (3)0.040 (3)0.039 (2)0.006 (2)0.017 (2)0.021 (2)
C50.038 (2)0.038 (2)0.033 (2)0.0047 (18)0.0085 (18)0.0193 (19)
C20.030 (2)0.046 (3)0.026 (2)0.0032 (18)0.0076 (17)0.0194 (19)
C110.056 (3)0.038 (2)0.036 (2)0.014 (2)0.012 (2)0.014 (2)
C160.046 (3)0.057 (3)0.035 (2)0.016 (2)0.010 (2)0.020 (2)
Geometric parameters (Å, º) top
O1—C11.244 (4)C9—C81.449 (5)
O2—C11.270 (4)C14—C31.398 (5)
O3—C161.341 (5)C14—C131.450 (5)
O3—H30.8200C15—C21.400 (5)
O4—C161.196 (5)C15—C161.510 (5)
N1—C21.330 (4)C6—C51.373 (5)
N1—C31.346 (4)C6—C71.380 (5)
N3—C151.323 (5)C6—H60.9300
N3—C141.354 (4)C1—C21.520 (5)
N2—C71.319 (5)C13—C121.397 (5)
N2—C81.360 (4)C12—C111.365 (5)
N2—H20.808 (19)C12—H120.9300
N4—C101.316 (5)C7—H70.9300
N4—C91.347 (4)C10—C111.402 (5)
C4—C51.393 (5)C10—H100.9300
C4—C81.392 (5)C5—H50.9300
C4—C31.458 (5)C11—H110.9300
C9—C131.404 (5)
C16—O3—H3109.5N1—C3—C14121.7 (3)
C2—N1—C3116.5 (3)N1—C3—C4118.7 (3)
C15—N3—C14116.4 (3)C14—C3—C4119.6 (3)
C7—N2—C8121.8 (3)C12—C13—C9117.8 (3)
C7—N2—H2120 (3)C12—C13—C14123.1 (3)
C8—N2—H2118 (3)C9—C13—C14119.1 (3)
C10—N4—C9117.1 (3)C11—C12—C13119.4 (4)
C5—C4—C8118.4 (3)C11—C12—H12120.3
C5—C4—C3122.8 (3)C13—C12—H12120.3
C8—C4—C3118.8 (3)N2—C7—C6121.3 (4)
N4—C9—C13123.0 (3)N2—C7—H7119.3
N4—C9—C8117.6 (3)C6—C7—H7119.3
C13—C9—C8119.4 (3)N4—C10—C11124.5 (4)
N3—C14—C3121.2 (3)N4—C10—H10117.7
N3—C14—C13117.5 (3)C11—C10—H10117.7
C3—C14—C13121.3 (3)C6—C5—C4120.6 (3)
N3—C15—C2122.3 (3)C6—C5—H5119.7
N3—C15—C16112.3 (3)C4—C5—H5119.7
C2—C15—C16125.2 (3)N1—C2—C15121.7 (3)
C5—C6—C7118.5 (4)N1—C2—C1118.1 (3)
C5—C6—H6120.8C15—C2—C1120.1 (3)
C7—C6—H6120.8C12—C11—C10118.1 (4)
N2—C8—C4119.4 (3)C12—C11—H11121.0
N2—C8—C9118.8 (3)C10—C11—H11121.0
C4—C8—C9121.8 (3)O4—C16—O3120.5 (4)
O1—C1—O2127.5 (4)O4—C16—C15121.8 (4)
O1—C1—C2119.1 (3)O3—C16—C15117.4 (4)
O2—C1—C2113.4 (4)
C10—N4—C9—C130.1 (5)C8—C9—C13—C142.5 (5)
C10—N4—C9—C8177.9 (3)N3—C14—C13—C120.1 (5)
C15—N3—C14—C31.6 (5)C3—C14—C13—C12177.7 (3)
C15—N3—C14—C13179.5 (3)N3—C14—C13—C9179.6 (3)
C14—N3—C15—C21.7 (6)C3—C14—C13—C91.8 (5)
C14—N3—C15—C16174.5 (3)C9—C13—C12—C111.2 (6)
C7—N2—C8—C40.4 (5)C14—C13—C12—C11179.3 (3)
C7—N2—C8—C9177.6 (3)C8—N2—C7—C60.6 (6)
C5—C4—C8—N21.0 (5)C5—C6—C7—N20.9 (6)
C3—C4—C8—N2179.2 (3)C9—N4—C10—C110.5 (6)
C5—C4—C8—C9176.9 (3)C7—C6—C5—C40.2 (6)
C3—C4—C8—C91.3 (5)C8—C4—C5—C60.7 (5)
N4—C9—C8—N21.0 (5)C3—C4—C5—C6178.8 (3)
C13—C9—C8—N2176.9 (3)C3—N1—C2—C151.2 (5)
N4—C9—C8—C4178.8 (3)C3—N1—C2—C1179.3 (3)
C13—C9—C8—C41.0 (5)N3—C15—C2—N13.3 (6)
C2—N1—C3—C142.1 (5)C16—C15—C2—N1172.4 (4)
C2—N1—C3—C4178.9 (3)N3—C15—C2—C1177.2 (3)
N3—C14—C3—N13.7 (6)C16—C15—C2—C17.1 (6)
C13—C14—C3—N1178.5 (3)O1—C1—C2—N116.9 (5)
N3—C14—C3—C4177.3 (3)O2—C1—C2—N1163.8 (3)
C13—C14—C3—C40.5 (5)O1—C1—C2—C15162.6 (4)
C5—C4—C3—N14.9 (5)O2—C1—C2—C1516.8 (5)
C8—C4—C3—N1177.0 (3)C13—C12—C11—C100.9 (6)
C5—C4—C3—C14176.1 (3)N4—C10—C11—C120.0 (6)
C8—C4—C3—C142.0 (5)N3—C15—C16—O473.0 (5)
N4—C9—C13—C120.7 (6)C2—C15—C16—O4110.9 (5)
C8—C9—C13—C12177.0 (3)N3—C15—C16—O3100.7 (4)
N4—C9—C13—C14179.8 (3)C2—C15—C16—O375.3 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3···O1i0.821.822.638 (4)171
N2—H2···O2ii0.81 (2)1.87 (3)2.638 (4)159 (5)
Symmetry codes: (i) x, y, z+1; (ii) x, y, z+1.

Experimental details

Crystal data
Chemical formulaC16H8N4O4
Mr320.26
Crystal system, space groupTriclinic, P1
Temperature (K)293
a, b, c (Å)7.302 (2), 9.662 (3), 10.726 (3)
α, β, γ (°)63.564 (3), 71.386 (3), 78.283 (4)
V3)640.5 (3)
Z2
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.32 × 0.21 × 0.15
Data collection
DiffractometerBruker SMART CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.969, 0.982
No. of measured, independent and
observed [I > 2σ(I)] reflections
4652, 2243, 1268
Rint0.037
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.062, 0.177, 1.05
No. of reflections2243
No. of parameters221
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.38, 0.31

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3···O1i0.821.822.638 (4)171
N2—H2···O2ii0.808 (19)1.87 (3)2.638 (4)159 (5)
Symmetry codes: (i) x, y, z+1; (ii) x, y, z+1.
 

Acknowledgements

This work was supported financially by the National Natural Science Foundation of China (grant No. 20773104), the Program for New Century Excellent Talents in Universities (NCET-06–0891), the Natural Science Foundation of Hubei Provinces of China (2008CDB030) and the Important Project of Hubei Provincial Education Office (Z20091301).

References

First citationBruker (1997). SMART and SAINT. Bruker AXS Inc., Madison,Wisconsin, USA.  Google Scholar
First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWeng, Z.-H., Liu, D.-C., Chen, Z.-L., Zou, H.-H., Qin, S.-N. & Liang, F.-P. (2009). Cryst. Growth Des. 9, 4163–4170.  Web of Science CSD CrossRef CAS Google Scholar

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