2,6-Diamino­pyridinium pyridinium-2,6-dicarboxylate: a redetermination

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.

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

---

S1. Comment

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 π–π stacking between parallel planes of (pydaH)⁺ fragments, with an interplanar distance of about 3.3 Å.

S2. Experimental

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.

S3. Refinement

H atoms attached to N atoms were located in a difference Fourier map and refined in the riding model with U_iso(H) = 1.5U_eq(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 U_iso(H) = 1.2U_eq(C).

Computing details

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

	Fig. 1. The structure of the title compound, showing the atom-numbering scheme and with displacement ellipsoids at the 50% probability level.
	Fig. 2. The crystal packing of the title compound; hydrogen bonds are indicated by dashed lines.

2,6-Diaminopyridinium pyridinium-2,6-dicarboxylate

Crystal data

C5H8N3^+·C7H4NO4^−	F(000) = 576
Mr = 276.26	Dx = 1.468 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
a = 10.282 (2) Å	Cell parameters from 24 reflections
b = 10.417 (2) Å	θ = 11–12°
c = 11.765 (2) Å	µ = 0.11 mm^−1
β = 97.42 (3)°	T = 293 K
V = 1249.6 (4) Å^3	Prism, yellow
Z = 4	0.4 × 0.3 × 0.2 mm

Data collection

Enraf–Nonius CAD-4 diffractometer	Rint = 0.059
Radiation source: normal-focus sealed tube	θmax = 27.0°, θmin = 2.0°
Graphite monochromator	h = 0→13
θ/5/3θ scans	k = −1→13
2919 measured reflections	l = −15→14
2692 independent reflections	2 standard reflections every 100 reflections
1596 reflections with I > 2σ(I)	intensity decay: 3%

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.052	Hydrogen site location: difference Fourier map
wR(F^2) = 0.167	H-atom parameters constrained
S = 1.05	w = 1/[σ^2(Fo^2) + (0.09P)^2 + 0.2P] where P = (Fo^2 + 2Fc^2)/3
2692 reflections	(Δ/σ)max = 0.004
181 parameters	Δρmax = 0.20 e Å^−3
0 restraints	Δρmin = −0.23 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
N1	0.12688 (17)	0.06344 (18)	0.42642 (15)	0.0373 (4)
N2	0.0211 (2)	0.0173 (2)	0.24775 (17)	0.0520 (6)
N3	0.2509 (2)	0.0921 (2)	0.60029 (17)	0.0522 (6)
C1	0.0269 (2)	0.0893 (2)	0.34275 (19)	0.0405 (5)
C2	−0.0581 (2)	0.1879 (3)	0.3599 (2)	0.0512 (6)
C3	−0.0394 (3)	0.2537 (3)	0.4616 (3)	0.0560 (7)
C4	0.0620 (3)	0.2249 (2)	0.5456 (2)	0.0518 (6)
C5	0.1486 (2)	0.1279 (2)	0.52765 (19)	0.0408 (5)
H1N	0.1810	0.0054	0.4145	0.056*
H2NA	0.0699	−0.0534	0.2471	0.078*
H2NB	−0.0519	0.0109	0.2033	0.078*
H3NA	0.2993	0.0188	0.5868	0.078*
H3NB	0.2539	0.1233	0.6689	0.078*
H2	−0.1270	0.2089	0.3038	0.062*
H3	−0.0971	0.3192	0.4742	0.068*
H4	0.0729	0.2709	0.6140	0.062*
O1	0.7057 (2)	−0.3494 (2)	0.66109 (14)	0.0643 (6)
O2	0.79479 (18)	−0.51829 (19)	0.58186 (16)	0.0618 (6)
O3	0.3745 (2)	−0.1361 (2)	0.52513 (15)	0.0745 (7)
O4	0.27391 (16)	−0.13365 (18)	0.34582 (14)	0.0513 (5)
N4	0.54035 (17)	−0.31074 (19)	0.47899 (14)	0.0381 (5)
C6	0.6323 (2)	−0.3983 (2)	0.47129 (18)	0.0391 (5)
C7	0.6374 (3)	−0.4566 (3)	0.3668 (2)	0.0519 (7)
C8	0.5471 (3)	−0.4194 (3)	0.2749 (2)	0.0590 (7)
C9	0.4532 (2)	−0.3290 (3)	0.28847 (19)	0.0491 (6)
C10	0.4508 (2)	−0.2736 (2)	0.39340 (17)	0.0384 (5)
C11	0.7226 (2)	−0.4260 (2)	0.5829 (2)	0.0453 (6)
C12	0.3560 (2)	−0.1724 (2)	0.42312 (19)	0.0443 (6)
H4N	0.5462	−0.2631	0.5451	0.057*
H7	0.6994	−0.5196	0.3583	0.062*
H8	0.5506	−0.4555	0.2034	0.072*
H9	0.3914	−0.3062	0.2271	0.059*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0379 (10)	0.0376 (10)	0.0366 (10)	0.0042 (8)	0.0058 (7)	−0.0002 (8)
N2	0.0524 (12)	0.0604 (14)	0.0401 (11)	0.0018 (10)	−0.0062 (9)	−0.0037 (10)
N3	0.0615 (13)	0.0584 (14)	0.0346 (10)	0.0035 (11)	−0.0013 (9)	−0.0088 (9)
C1	0.0405 (12)	0.0411 (13)	0.0392 (12)	−0.0032 (10)	0.0029 (9)	0.0061 (10)
C2	0.0435 (14)	0.0472 (15)	0.0618 (16)	0.0084 (12)	0.0029 (11)	0.0079 (12)
C3	0.0536 (16)	0.0453 (15)	0.0708 (19)	0.0084 (12)	0.0152 (13)	−0.0007 (13)
C4	0.0636 (16)	0.0441 (14)	0.0499 (15)	−0.0019 (12)	0.0158 (12)	−0.0088 (11)
C5	0.0485 (13)	0.0388 (12)	0.0356 (11)	−0.0076 (10)	0.0077 (9)	−0.0004 (10)
O1	0.0830 (14)	0.0721 (14)	0.0337 (9)	0.0184 (10)	−0.0081 (8)	−0.0008 (9)
O2	0.0602 (12)	0.0622 (12)	0.0578 (11)	0.0218 (10)	−0.0117 (9)	0.0041 (9)
O3	0.0908 (15)	0.0913 (16)	0.0392 (10)	0.0425 (12)	−0.0003 (9)	−0.0117 (10)
O4	0.0480 (10)	0.0608 (12)	0.0436 (9)	0.0165 (8)	0.0005 (7)	0.0069 (8)
N4	0.0423 (11)	0.0436 (11)	0.0276 (9)	0.0035 (8)	0.0021 (7)	0.0014 (8)
C6	0.0366 (11)	0.0455 (13)	0.0347 (11)	0.0041 (10)	0.0031 (9)	0.0052 (10)
C7	0.0508 (14)	0.0595 (16)	0.0445 (13)	0.0168 (12)	0.0027 (11)	−0.0055 (12)
C8	0.0627 (16)	0.0746 (19)	0.0377 (13)	0.0190 (14)	−0.0006 (11)	−0.0138 (13)
C9	0.0506 (14)	0.0636 (16)	0.0308 (11)	0.0110 (12)	−0.0031 (10)	−0.0021 (11)
C10	0.0364 (12)	0.0456 (13)	0.0325 (11)	0.0029 (10)	0.0021 (9)	0.0050 (9)
C11	0.0479 (13)	0.0489 (15)	0.0378 (13)	0.0070 (12)	−0.0002 (10)	0.0071 (11)
C12	0.0493 (14)	0.0472 (14)	0.0368 (12)	0.0061 (11)	0.0074 (10)	0.0021 (10)

Geometric parameters (Å, º)

N1—C1	1.354 (3)	O1—C11	1.247 (3)
N1—C5	1.361 (3)	O2—C11	1.215 (3)
N1—H1N	0.8452	O3—C12	1.250 (3)
N2—C1	1.343 (3)	O4—C12	1.226 (3)
N2—H2NA	0.8889	N4—C6	1.326 (3)
N2—H2NB	0.8594	N4—C10	1.331 (3)
N3—C5	1.320 (3)	N4—H4N	0.9185
N3—H3NA	0.9361	C6—C7	1.376 (3)
N3—H3NB	0.8674	C6—C11	1.536 (3)
C1—C2	1.381 (3)	C7—C8	1.385 (4)
C2—C3	1.370 (4)	C7—H7A	0.9300
C2—H2A	0.9300	C8—C9	1.372 (4)
C3—C4	1.375 (4)	C8—H8A	0.9300
C3—H3A	0.9300	C9—C10	1.364 (3)
C4—C5	1.380 (4)	C9—H9A	0.9300
C4—H4A	0.9300	C10—C12	1.508 (3)
C1—N1—C5	124.2 (2)	C6—N4—C10	125.27 (19)
C1—N1—H1N	118.4	C6—N4—H4N	117.4
C5—N1—H1N	117.4	C10—N4—H4N	116.6
C1—N2—H2NA	120.2	N4—C6—C7	118.3 (2)
C1—N2—H2NB	119.3	N4—C6—C11	115.35 (19)
H2NA—N2—H2NB	112.6	C7—C6—C11	126.3 (2)
C5—N3—H3NA	121.2	C6—C7—C8	118.2 (2)
C5—N3—H3NB	115.2	C6—C7—H7A	120.9
H3NA—N3—H3NB	120.6	C8—C7—H7A	120.9
N2—C1—N1	116.3 (2)	C9—C8—C7	120.9 (2)
N2—C1—C2	125.3 (2)	C9—C8—H8A	119.6
N1—C1—C2	118.5 (2)	C7—C8—H8A	119.6
C3—C2—C1	118.6 (2)	C10—C9—C8	119.3 (2)
C3—C2—H2A	120.7	C10—C9—H9A	120.3
C1—C2—H2A	120.7	C8—C9—H9A	120.3
C2—C3—C4	121.9 (2)	N4—C10—C9	118.0 (2)
C2—C3—H3A	119.1	N4—C10—C12	115.60 (19)
C4—C3—H3A	119.1	C9—C10—C12	126.4 (2)
C3—C4—C5	119.5 (2)	O2—C11—O1	131.1 (2)
C3—C4—H4A	120.2	O2—C11—C6	116.2 (2)
C5—C4—H4A	120.2	O1—C11—C6	112.6 (2)
N3—C5—N1	117.0 (2)	O4—C12—O3	128.2 (2)
N3—C5—C4	125.7 (2)	O4—C12—C10	117.4 (2)
N1—C5—C4	117.3 (2)	O3—C12—C10	114.3 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O4	0.85	1.97	2.788 (3)	164
N3—H3NA···O3	0.94	1.97	2.888 (3)	167
N3—H3NB···O1^i	0.87	2.01	2.851 (3)	163
N4—H4N···O1	0.92	2.19	2.589 (3)	106
N4—H4N···O3	0.92	2.20	2.598 (3)	106
N2—H2NA···O4	0.89	2.41	3.128 (3)	138
N2—H2NB···O2^ii	0.86	1.99	2.838 (3)	170

Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) x−1, −y−1/2, z−1/2.