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The crystal structure of the title compound, C5H8N3+·C7H4NO4 or (pydaH)+(pydcH) (pyda is 2,6-diamino­pyridine and pydcH2 is pyridine-2,6-dicarboxylic acid), shows both intra- and inter­molecular proton transfers from carboxyl groups to the ring N atoms of (pydc)2− and pyda. This determination corrects a previous report which formulated this compound as (pydaH2)2+(pydc)2− [Moghimi, Ranjbar, Aghabozorg, Jalali, Shamsipur, Yap & Rahbarnoohi (2002), J. Mol. Struct. 605, 133–149]. Ion-pairing, hydrogen-bonding and π–π stacking inter­actions link the fragments to form a self-associated system.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805027431/wn6355sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536805027431/wn6355Isup2.hkl
Contains datablock I

CCDC reference: 217572

Key indicators

  • Single-crystal X-ray study
  • T = 293 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.052
  • wR factor = 0.167
  • Data-to-parameter ratio = 14.9

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ .... ? PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given ....... ? PLAT199_ALERT_1_C Check the Reported _cell_measurement_temperature 293 K PLAT200_ALERT_1_C Check the Reported _diffrn_ambient_temperature . 293 K PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.04 PLAT369_ALERT_2_C Long C(sp2)-C(sp2) Bond C6 - C11 ... 1.53 Ang. PLAT711_ALERT_1_C BOND Unknown or Inconsistent Label .......... H2A C2 H2A PLAT711_ALERT_1_C BOND Unknown or Inconsistent Label .......... H3A C3 H3A PLAT711_ALERT_1_C BOND Unknown or Inconsistent Label .......... H4A C4 H4A PLAT711_ALERT_1_C BOND Unknown or Inconsistent Label .......... H7A C7 H7A PLAT711_ALERT_1_C BOND Unknown or Inconsistent Label .......... H8A C8 H8A PLAT711_ALERT_1_C BOND Unknown or Inconsistent Label .......... H9A C9 H9A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H2A C3 C2 H2A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H2A C1 C2 H2A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H3A C2 C3 H3A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H3A C4 C3 H3A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H4A C3 C4 H4A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H4A C5 C4 H4A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H7A C6 C7 H7A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H7A C8 C7 H7A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H8A C9 C8 H8A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H8A C7 C8 H8A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H9A C10 C9 H9A PLAT712_ALERT_1_C ANGLE Unknown or Inconsistent Label .......... H9A C8 C9 H9A PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........ 4 PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd. # 1 C7 H4 N O4
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 26 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 21 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 3 ALERT type 4 Improvement, methodology, query or suggestion

Comment top

Hydrogen-bonding interactions between carboxylic acids and 2-aminopyridine units have been investigated in a recent publication (Bensemann et al., 2003). We have previously reported some self-associated proton-transfer systems, using pyridine-2,6-dicarboxylic acid (pydcH2) and 4-hydroxypyridine-2,6-dicarboxylic acid (hypydcH2) as proton donors. The proton acceptors in these studies were creatinine (creat) and guanidine (G), which formed the proton-transfer compounds (creatH)(pydcH)·H2O, (GH)2(pydc) and (GH)(hypydcH) (Moghimi, Sharif & Aghabozorg, 2004; Moghimi, Sheshmani et al., 2004; Moghimi et al., 2005). Hydrogen-bonding and ion-pairing interactions are observed in all of these compounds.

Here, we report the structure of a self-associated system, (pydaH)+(pydcH), (I). This determination corrects a previous report which formulated this compound as (pydaH2)2+(pydc)2−, (II) (Moghimi, Ranjbar, Aghabozorg, Jalali, Shamsipur, Yap & Rahbarnoohi, 2002). In (II), the protons were assigned to the amino groups of the cation, whereas in (I), they are assigned to the ring N atoms of both cation and anion. In (II), there was a short N···O contact [2.770 (5) Å] between the ring N atom of the cation and a carboxyl O atom; this interaction corresponds to the hydrogen bond N1—H1N···O4 [D···A = 2.788 (3) Å; Table 2] in (I).

Several metal complexes contain the (pydaH)+ counterion, in which the proton is connected to the ring N atom (Aghabozorg et al., 2005; Moghimi, Shokrollahi et al., 2004; Ranjbar et al., 2003a,b; Moghimi, Ranjbar, Aghabozorg, Jalali, Shamsipur & Chadha, 2002a,b; Ranjbar, Moghimi et al., 2002; Ranjbar, Taghavipur et al., 2002; Ranjbar et al., 2001). Another ionic compound, (pydaH)+(NO3), also has the proton linked to the ring N atom (Aghabozorg et al., 2005). Furthermore, the anionic fragment (pydcH) has been reported as the predominant form of dipicolinic acid at pH 3.5 (Peral & Gallego, 2000). These findings support our contention that the structure reported here is correct and that the structure of (II) is incorrect.

The structure of (I) shows both intra- and intermolecular proton transfers. Ion-pairing and hydrogen-bonding interactions link the components of the system. A number of N—H···O hydrogen bonds with D···A distances ranging from 2.598 (3) to 3.128 (3) Å (Table 2) are observed in the crystal structure, producing a three-dimensional network (Fig. 2) There is evidence of ππ stacking between parallel planes of (pydaH)+ fragments, with an interplanar distance of about 3.3 Å.

Experimental top

The title compound was prepared by the reaction of 2,6-diaminopyridine and pyridine-2,6-dicarboxylic acid in a 1:1 molar ratio in water. Light-yellow crystals of (I) were obtained by slow concentration of the solution at room temperature.

Refinement top

H atoms attached to N atoms were located in a difference Fourier map and refined in the riding model with Uiso(H) = 1.5Ueq(N). All other H atoms were positioned geometrically and constrained to ride on their parent C atoms, with C—H distances of 0.93 Å and with Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1984); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms, 1996); program(s) used to solve structure: SHELXTL-Plus (Sheldrick, 1998); program(s) used to refine structure: SHELXTL-Plus; molecular graphics: SHELXTL-Plus; software used to prepare material for publication: SHELXTL-Plus.

Figures top
[Figure 1] Fig. 1. The structure of the title compound, showing the atom-numbering scheme and with displacement ellipsoids at the 50% probability level.
[Figure 2] Fig. 2. The crystal packing of the title compound; hydrogen bonds are indicated by dashed lines.
2,6-Diaminopyridinium pyridinium-2,6-dicarboxylate top
Crystal data top
C5H8N3+·C7H4NO4F(000) = 576
Mr = 276.26Dx = 1.468 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 10.282 (2) ÅCell parameters from 24 reflections
b = 10.417 (2) Åθ = 11–12°
c = 11.765 (2) ŵ = 0.11 mm1
β = 97.42 (3)°T = 293 K
V = 1249.6 (4) Å3Prism, yellow
Z = 40.4 × 0.3 × 0.2 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.059
Radiation source: normal-focus sealed tubeθmax = 27.0°, θmin = 2.0°
Graphite monochromatorh = 013
θ/5/3θ scansk = 113
2919 measured reflectionsl = 1514
2692 independent reflections2 standard reflections every 100 reflections
1596 reflections with I > 2σ(I) intensity decay: 3%
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)] = 0.052Hydrogen site location: difference Fourier map
wR(F2) = 0.167H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.09P)2 + 0.2P]
where P = (Fo2 + 2Fc2)/3
2692 reflections(Δ/σ)max = 0.004
181 parametersΔρmax = 0.20 e Å3
0 restraintsΔρmin = 0.23 e Å3
Crystal data top
C5H8N3+·C7H4NO4V = 1249.6 (4) Å3
Mr = 276.26Z = 4
Monoclinic, P21/cMo Kα radiation
a = 10.282 (2) ŵ = 0.11 mm1
b = 10.417 (2) ÅT = 293 K
c = 11.765 (2) Å0.4 × 0.3 × 0.2 mm
β = 97.42 (3)°
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.059
2919 measured reflections2 standard reflections every 100 reflections
2692 independent reflections intensity decay: 3%
1596 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0520 restraints
wR(F2) = 0.167H-atom parameters constrained
S = 1.05Δρmax = 0.20 e Å3
2692 reflectionsΔρmin = 0.23 e Å3
181 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
N10.12688 (17)0.06344 (18)0.42642 (15)0.0373 (4)
N20.0211 (2)0.0173 (2)0.24775 (17)0.0520 (6)
N30.2509 (2)0.0921 (2)0.60029 (17)0.0522 (6)
C10.0269 (2)0.0893 (2)0.34275 (19)0.0405 (5)
C20.0581 (2)0.1879 (3)0.3599 (2)0.0512 (6)
C30.0394 (3)0.2537 (3)0.4616 (3)0.0560 (7)
C40.0620 (3)0.2249 (2)0.5456 (2)0.0518 (6)
C50.1486 (2)0.1279 (2)0.52765 (19)0.0408 (5)
H1N0.18100.00540.41450.056*
H2NA0.06990.05340.24710.078*
H2NB0.05190.01090.20330.078*
H3NA0.29930.01880.58680.078*
H3NB0.25390.12330.66890.078*
H20.12700.20890.30380.062*
H30.09710.31920.47420.068*
H40.07290.27090.61400.062*
O10.7057 (2)0.3494 (2)0.66109 (14)0.0643 (6)
O20.79479 (18)0.51829 (19)0.58186 (16)0.0618 (6)
O30.3745 (2)0.1361 (2)0.52513 (15)0.0745 (7)
O40.27391 (16)0.13365 (18)0.34582 (14)0.0513 (5)
N40.54035 (17)0.31074 (19)0.47899 (14)0.0381 (5)
C60.6323 (2)0.3983 (2)0.47129 (18)0.0391 (5)
C70.6374 (3)0.4566 (3)0.3668 (2)0.0519 (7)
C80.5471 (3)0.4194 (3)0.2749 (2)0.0590 (7)
C90.4532 (2)0.3290 (3)0.28847 (19)0.0491 (6)
C100.4508 (2)0.2736 (2)0.39340 (17)0.0384 (5)
C110.7226 (2)0.4260 (2)0.5829 (2)0.0453 (6)
C120.3560 (2)0.1724 (2)0.42312 (19)0.0443 (6)
H4N0.54620.26310.54510.057*
H70.69940.51960.35830.062*
H80.55060.45550.20340.072*
H90.39140.30620.22710.059*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0379 (10)0.0376 (10)0.0366 (10)0.0042 (8)0.0058 (7)0.0002 (8)
N20.0524 (12)0.0604 (14)0.0401 (11)0.0018 (10)0.0062 (9)0.0037 (10)
N30.0615 (13)0.0584 (14)0.0346 (10)0.0035 (11)0.0013 (9)0.0088 (9)
C10.0405 (12)0.0411 (13)0.0392 (12)0.0032 (10)0.0029 (9)0.0061 (10)
C20.0435 (14)0.0472 (15)0.0618 (16)0.0084 (12)0.0029 (11)0.0079 (12)
C30.0536 (16)0.0453 (15)0.0708 (19)0.0084 (12)0.0152 (13)0.0007 (13)
C40.0636 (16)0.0441 (14)0.0499 (15)0.0019 (12)0.0158 (12)0.0088 (11)
C50.0485 (13)0.0388 (12)0.0356 (11)0.0076 (10)0.0077 (9)0.0004 (10)
O10.0830 (14)0.0721 (14)0.0337 (9)0.0184 (10)0.0081 (8)0.0008 (9)
O20.0602 (12)0.0622 (12)0.0578 (11)0.0218 (10)0.0117 (9)0.0041 (9)
O30.0908 (15)0.0913 (16)0.0392 (10)0.0425 (12)0.0003 (9)0.0117 (10)
O40.0480 (10)0.0608 (12)0.0436 (9)0.0165 (8)0.0005 (7)0.0069 (8)
N40.0423 (11)0.0436 (11)0.0276 (9)0.0035 (8)0.0021 (7)0.0014 (8)
C60.0366 (11)0.0455 (13)0.0347 (11)0.0041 (10)0.0031 (9)0.0052 (10)
C70.0508 (14)0.0595 (16)0.0445 (13)0.0168 (12)0.0027 (11)0.0055 (12)
C80.0627 (16)0.0746 (19)0.0377 (13)0.0190 (14)0.0006 (11)0.0138 (13)
C90.0506 (14)0.0636 (16)0.0308 (11)0.0110 (12)0.0031 (10)0.0021 (11)
C100.0364 (12)0.0456 (13)0.0325 (11)0.0029 (10)0.0021 (9)0.0050 (9)
C110.0479 (13)0.0489 (15)0.0378 (13)0.0070 (12)0.0002 (10)0.0071 (11)
C120.0493 (14)0.0472 (14)0.0368 (12)0.0061 (11)0.0074 (10)0.0021 (10)
Geometric parameters (Å, º) top
N1—C11.354 (3)O1—C111.247 (3)
N1—C51.361 (3)O2—C111.215 (3)
N1—H1N0.8452O3—C121.250 (3)
N2—C11.343 (3)O4—C121.226 (3)
N2—H2NA0.8889N4—C61.326 (3)
N2—H2NB0.8594N4—C101.331 (3)
N3—C51.320 (3)N4—H4N0.9185
N3—H3NA0.9361C6—C71.376 (3)
N3—H3NB0.8674C6—C111.536 (3)
C1—C21.381 (3)C7—C81.385 (4)
C2—C31.370 (4)C7—H7A0.9300
C2—H2A0.9300C8—C91.372 (4)
C3—C41.375 (4)C8—H8A0.9300
C3—H3A0.9300C9—C101.364 (3)
C4—C51.380 (4)C9—H9A0.9300
C4—H4A0.9300C10—C121.508 (3)
C1—N1—C5124.2 (2)C6—N4—C10125.27 (19)
C1—N1—H1N118.4C6—N4—H4N117.4
C5—N1—H1N117.4C10—N4—H4N116.6
C1—N2—H2NA120.2N4—C6—C7118.3 (2)
C1—N2—H2NB119.3N4—C6—C11115.35 (19)
H2NA—N2—H2NB112.6C7—C6—C11126.3 (2)
C5—N3—H3NA121.2C6—C7—C8118.2 (2)
C5—N3—H3NB115.2C6—C7—H7A120.9
H3NA—N3—H3NB120.6C8—C7—H7A120.9
N2—C1—N1116.3 (2)C9—C8—C7120.9 (2)
N2—C1—C2125.3 (2)C9—C8—H8A119.6
N1—C1—C2118.5 (2)C7—C8—H8A119.6
C3—C2—C1118.6 (2)C10—C9—C8119.3 (2)
C3—C2—H2A120.7C10—C9—H9A120.3
C1—C2—H2A120.7C8—C9—H9A120.3
C2—C3—C4121.9 (2)N4—C10—C9118.0 (2)
C2—C3—H3A119.1N4—C10—C12115.60 (19)
C4—C3—H3A119.1C9—C10—C12126.4 (2)
C3—C4—C5119.5 (2)O2—C11—O1131.1 (2)
C3—C4—H4A120.2O2—C11—C6116.2 (2)
C5—C4—H4A120.2O1—C11—C6112.6 (2)
N3—C5—N1117.0 (2)O4—C12—O3128.2 (2)
N3—C5—C4125.7 (2)O4—C12—C10117.4 (2)
N1—C5—C4117.3 (2)O3—C12—C10114.3 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···O40.851.972.788 (3)164
N3—H3NA···O30.941.972.888 (3)167
N3—H3NB···O1i0.872.012.851 (3)163
N4—H4N···O10.922.192.589 (3)106
N4—H4N···O30.922.202.598 (3)106
N2—H2NA···O40.892.413.128 (3)138
N2—H2NB···O2ii0.861.992.838 (3)170
Symmetry codes: (i) x+1, y+1/2, z+3/2; (ii) x1, y1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC5H8N3+·C7H4NO4
Mr276.26
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)10.282 (2), 10.417 (2), 11.765 (2)
β (°) 97.42 (3)
V3)1249.6 (4)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.4 × 0.3 × 0.2
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
2919, 2692, 1596
Rint0.059
(sin θ/λ)max1)0.640
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.167, 1.05
No. of reflections2692
No. of parameters181
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.20, 0.23

Computer programs: CAD-4 Software (Enraf–Nonius, 1984), CAD-4 Software, XCAD4 (Harms, 1996), SHELXTL-Plus (Sheldrick, 1998), SHELXTL-Plus.

Selected geometric parameters (Å, º) top
N1—C11.354 (3)O3—C121.250 (3)
N1—C51.361 (3)O4—C121.226 (3)
N2—C11.343 (3)N4—C61.326 (3)
N3—C51.320 (3)N4—C101.331 (3)
O1—C111.247 (3)C6—C111.536 (3)
O2—C111.215 (3)C10—C121.508 (3)
C1—N1—C5124.2 (2)O2—C11—O1131.1 (2)
N2—C1—N1116.3 (2)O2—C11—C6116.2 (2)
N3—C5—N1117.0 (2)O1—C11—C6112.6 (2)
C6—N4—C10125.27 (19)O4—C12—O3128.2 (2)
N4—C6—C11115.35 (19)O4—C12—C10117.4 (2)
N4—C10—C12115.60 (19)O3—C12—C10114.3 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···O40.851.972.788 (3)164
N3—H3NA···O30.941.972.888 (3)167
N3—H3NB···O1i0.872.012.851 (3)163
N4—H4N···O10.922.192.589 (3)106
N4—H4N···O30.922.202.598 (3)106
N2—H2NA···O40.892.413.128 (3)138
N2—H2NB···O2ii0.861.992.838 (3)170
Symmetry codes: (i) x+1, y+1/2, z+3/2; (ii) x1, y1/2, z1/2.
 

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