Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270113017423/cu3028sup1.cif | |
Rietveld powder data file (CIF format) https://doi.org/10.1107/S0108270113017423/cu30283sup2.rtv |
CCDC reference: 963384
2-Aminopyridine, (1) (see Scheme 1), is an effective supramolecular reagent that readily cocrystallizes with a number of organic compounds containing at least one carboxylic acid group (Bis & Zaworotko, 2005; Bis et al., 2006). During cocrystallization, 2-aminopyridine (pKa = 6.67) may remove the H atom from the carboxylic acid, resulting in an organic salt instead of in a cocrystal. Among these cocrystals or salts, a 2-aminopyridine–carboxylic acid supramolecular heterosynthon (see Scheme 1) is frequently observed (Shan et al., 2002). A search of the Cambridge Structural Database (CSD, Version 5.34; Allen, 2002) for organic compounds including only the elements C, H, O and N was conducted, and revealed 39 crystal structures containing both 2-aminopyridine and carboxylic acid, with such a supramolecular heterosynthon observed in all of them. Among the 48 [39 in previous sentence? Please clarify] crystal structures, the carboxylic acids form salts with 2-aminopyridine, with the exception of 4-nitrophthalic acid (Karmakar et al., 2008). In the case of cocrystallization of 2-aminopyridine with fumaric acid, (2) (see Scheme 1, pKa = 3.02), the organic salt (form I) bis(2-aminopyridinium) fumarate–fumaric acid (1/1), (3), was reported (Ballabh et al., 2002; Büyükgüngör et al., 2004). This organic salt crystallizes in the space group P21/c, with one 2-aminopyridinium cation, half of the fumaric acid molecule and half of the fumarate dianion in the asymmetric unit.
Fumaric acid in neutral and/or ionic forms is frequently observed when it cocrystallizes with other small organic compounds. A search of the CSD for fumaric acid in neutral or ionized forms, including only the elements C, N, O and H, revealed a total of 152 crystal structures, of which four contain fumaric acid in both neutral and monoanionic forms and 16 contain fumaric acid in both the neutral and dianionic forms. In the remaining 132 structures, the neutral form occurs in 58, the monoanionic form in 43 and the dianionic form in 31 structures. A further investigation of the crystal structures containing fumaric acid in the dianionic form showed that the fumarate dianions lie on a centre of inversion, with four exceptions [CSD refcodes COCPEQ (Reference?), HUSTIY (Reference?), VEVSAR (Reference?) and XELJED (Reference?)]. In the present work, a new polymorph of (3), viz. form II, was obtained and its crystal structure determined by powder X-ray diffraction.
Form II of (3) was obtained by dissolving 2-aminopyridine (0.470 g, 5.00 mmol) and fumaric acid (0.580 g, 5.00 mmol) in methanol (50 ml) and heating at 353 K for 10 min. A white crystalline powder was obtained after cooling and crystallization over a period of 5 h at ambient temperature.
The ionic form of the title solvated salt, due to proton transfer from fumaric acid to the aromatic N atom of the 2-aminopyrdine molecule, was confirmed by FT–IR characterization. Two reasonably strong bands at 1634 and 1576 cm-1 were assigned to the asymmetric stretching of the –COO- anionic group. The strongest band at 1671 cm-1 is consistent with C═O stretching of the free –COOH group involved in unsaturated hydrogen bonding.
For measurement of the powder X-ray diffraction pattern, the sample was finely ground and loaded into a borosilicate capillary (0.7 mm diameter). It was spun during data collection to improve powder averaging. The powder X-ray diffraction pattern was recorded at ambient temperature in transmission mode on a Rigaku SmartLab diffractometer (9 kW rotating anode, Cu Kα1, Ge monochromated; D/teX Ultra one-dimensional detector; counting rate 0.2° min-1; 2θ range 5–70°; collection time 6 h).
The powder pattern was indexed using the program X-CELL (Neumann, 2003), giving a unit cell with triclinic symmetry [a = 13.36, b = 9.60 and c = 3.82 Å; α = 91.71, β = 91.74 and γ = 94.30°; FOM = 3.79 × 103). This unit cell was transformed to the following unit cell in the standard setting: a = 3.82, b = 9.60 and c = 13.36 Å; α = 94.30, β = 91.74 and γ = 91.71°. A good quality Le Bail fit (Le Bail et al., 1988), using the GSAS program package (Larson & Von Dreele, 2004) interfaced by EXPGUI (Toby, 2001), was obtained using this unit cell, thus confirming the correctness of the unit cell. Density considerations suggest that there are two 2-aminopyridine molecules and two fumaric acid molecules in the unit cell. An initial attempt at structure solution using the simulated annealing method implemented in Materials Studio software (Accelrys, 2011) with the space group P1 (one 2-aminopyridine and one fumaric acid molecule in the asymmetric unit) was not successful. The structure solution was then carried out in the space group P1 (two 2-aminopyridine molecules and two fumaric acid molecules in the asymmetric unit), leading to a reasonable crystal structure with no short contacts except for hydrogen bonds. However, a close inspection of the obtained crystal structure in the space group P1 suggested two adjacent 2-aminopyridine molecules are approximately related by an inversion centre. Therefore, the structure solution was finally carried out in the space group P1 with one 2-aminopyridine molecule and two halves of a fumaric acid molecule in the asymmetric unit. The 2-aminopyridine molecule and the two halves of the fumaric acid molecule were treated as motion groups without internal torsional degrees of freedom. The positions and orientations of the motion groups were varied and therefore a total of 18 variables were optimized during the structure search.
A reasonable crystal structure solution (Rwp = 5.22% and Rp = 3.58%) was obtained after two cycles of 150000 simulated annealing steps and this was taken as the initial structural model for Rietveld refinement using GSAS. In the Rietveld refinement, standard restraints were applied to bond lengths and angles, and planar restraints were applied to the 2-aminopyridine and fumaric acid molecules. These restraints were gradually released towards the end of the Rietveld refinement. Isotropic displacement parameters were refined independently for each molecule. In the final stage of the Rietveld refinement, H atoms were introduced from geometric arguments (C—H = 0.95 Å, O—H = 0.90 Å and N—H = 0.90 Å) using the CRYSTALS program package (Betteridge et al., 2003), with a fixed isotropic displacement parameter (0.05 Å2). The fumaric acid molecule, which forms an approximately intermolecular planar hydrogen-bonded trimer with two neighbouring 2-aminopyridine molecules via dimeric N—H···O hydrogen bonds, was deprotonated and therefore the dianion model was employed for the Rietveld refinement. The other fumaric acid molecule, linking adjacent hydrogen-bonded trimers via a single N—H···O hydrogen bond, was treated as a free fumaric acid molecule for the Rietveld refinement. The following parameters were refined: scale factor, lattice parameters, 2θ zero error, peak profile parameters, atomic coordinates and isotropic displacement parameters. The standard uncertainties of the atomic coordinates were corrected using the procedure described by Scott (1983). The final Rietveld refinement leads to a good quality of fit (Fig. 6). The discrepancies between the experimental and calculated powder X-ray diffraction pattern in the final Rietveld refinement are comparable with those of the Le Bail fit, confirming the completeness of the structure refinement.
A view of form II of (3) with the atom-labelling scheme is shown in Fig. 1. In the crystal structure, both the fumaric acid molecule and the fumarate dianion lie on inversion centres. The fumarate dianion is involved in dimeric hydrogen-bonding interactions with two neighbouring 2-aminopyridinium cations via independent N1—H6···O1 and N2—H8···O2 hydrogen bonding, resulting in an approximately intermolecular planar hydrogen-bonded trimer, outlined by a rectangle in Fig. 2. The interlinking between adjacent hydrogen-bonded trimers is achieved through inversion-related dimeric N2—H6···O2 hydrogen-bonding interactions. The extension of these two types of dimeric N—H···O hydrogen-bonding interaction link the 2-aminopyrdium cations and fumarate dianions into a ribbon-like packing motif. These motifs are parallel to each other and present shifted π–π stacking interactions, with an interplanar distance of 3.434 (3) Å along the c axis. The free fumaric acid molecule provides a further hydrogen-bonding interaction (O3—H10···O1) to link the ribbon-like packing motifs into the three-dimensional crystal structure of form II, shown in Fig. 3.
In form I, both the fumaric acid molecule and the fumarate dianion lie on inversion centres. As shown in Fig. 4, the fumarate dianion is linked to two neighbouring 2-aminopyridinium cations via dimeric N—H···O hydrogen bonding to form an approximately planar intermolecular hydrogen-bonded trimer, which is similar to that in form II. Two adjacent hydrogen-bonded trimers are linked through single N—H···O hydrogen bonding. The extension of the dimeric N—H···O hydrogen bonding and single N—H···O hydrogen bonding links the hydrogen-bonded trimers into a staircase-like packing motif. There are no significant π–π stacking interactions between adjacent hydrogen-bonded trimers, as a consequence of the large offset. The free fumaric acid molecule in form I provides a further hydrogen-bonding interaction, linking the motifs into the three-dimensional crystal structure of form I, shown in Fig. 5.
Data collection: SmartLab software (Rigaku, 2013); cell refinement: GSAS (Larson & Von Dreele, 2004); data reduction: GSAS (Larson & Von Dreele, 2004); program(s) used to solve structure: Reflex implemented in Materials Studio (Accelrys, 2011); program(s) used to refine structure: GSAS (Larson & Von Dreele, 2004); molecular graphics: ORTEP-3 (Farrugia, 2012), DIAMOND (Brandenburg, 1999) and Mercury (Macrae et al., 2008); software used to prepare material for publication: publCIF (Westrip, 2010).
2C5H7N2+·C4H2O42−·C4H4O4 | Z = 1 |
Mr = 420.38 | F(000) = 220 |
Triclinic, P1 | triclinic |
Hall symbol: -P 1 | Dx = 1.432 Mg m−3 |
a = 3.81686 (7) Å | Melting point: 463 K |
b = 9.6064 (3) Å | Cu Kα1 radiation, λ = 1.54056 Å |
c = 13.3605 (4) Å | µ = 0.98 mm−1 |
α = 94.2974 (15)° | T = 298 K |
β = 91.7433 (14)° | Particle morphology: powder |
γ = 91.7169 (14)° | white |
V = 488.02 (3) Å3 | cylinder, 10 × 0.7 mm |
Rigaku SmartLab diffractometer | Data collection mode: transmission |
Radiation source: rotating-anode X-ray tube | Scan method: continuous |
Ge 220 monochromator | 2θmin = 5.0°, 2θmax = 70.0°, 2θstep = 0.02° |
Specimen mounting: borosilicate caplillary |
Refinement on Inet | 56 parameters |
Least-squares matrix: full | 77 restraints |
Rp = 0.035 | 0 constraints |
Rwp = 0.046 | Hydrogen site location: inferred from neighbouring sites |
Rexp = 0.032 | H-atom parameters not refined |
R(F2) = 0.1101 | Weighting scheme based on measured s.u.'s |
χ2 = 2.103 | (Δ/σ)max = 0.05 |
3251 data points | Background function: fixed background by interpolation |
Excluded region(s): none | Preferred orientation correction: none |
Profile function: Thompson–Cox–Hastings pseudo-Voigt |
2C5H7N2+·C4H2O42−·C4H4O4 | γ = 91.7169 (14)° |
Mr = 420.38 | V = 488.02 (3) Å3 |
Triclinic, P1 | Z = 1 |
a = 3.81686 (7) Å | Cu Kα1 radiation, λ = 1.54056 Å |
b = 9.6064 (3) Å | µ = 0.98 mm−1 |
c = 13.3605 (4) Å | T = 298 K |
α = 94.2974 (15)° | cylinder, 10 × 0.7 mm |
β = 91.7433 (14)° |
Rigaku SmartLab diffractometer | Scan method: continuous |
Specimen mounting: borosilicate caplillary | 2θmin = 5.0°, 2θmax = 70.0°, 2θstep = 0.02° |
Data collection mode: transmission |
Rp = 0.035 | 3251 data points |
Rwp = 0.046 | 56 parameters |
Rexp = 0.032 | 77 restraints |
R(F2) = 0.1101 | H-atom parameters not refined |
χ2 = 2.103 |
x | y | z | Uiso*/Ueq | ||
C1 | 0.4140 (9) | −0.0637 (3) | 0.3110 (2) | 0.0574 (17)* | |
C2 | 0.5022 (12) | −0.1952 (3) | 0.2710 (3) | 0.0574 (17)* | |
C3 | 0.6521 (10) | −0.2062 (3) | 0.1775 (2) | 0.0574 (17)* | |
C4 | 0.7108 (13) | −0.0868 (3) | 0.1264 (3) | 0.0574 (17)* | |
C5 | 0.6188 (9) | 0.0404 (3) | 0.1718 (2) | 0.0574 (17)* | |
N1 | 0.4726 (8) | 0.0531 (3) | 0.2622 (2) | 0.0574 (17)* | |
N2 | 0.2559 (11) | −0.0328 (3) | 0.4011 (2) | 0.0574 (17)* | |
C6 | 0.0550 (12) | 0.4783 (3) | 0.4548 (2) | 0.0573 (18)* | |
C7 | 0.1394 (12) | 0.3332 (4) | 0.4281 (3) | 0.0573 (18)* | |
O1 | 0.2607 (13) | 0.3020 (5) | 0.3440 (3) | 0.0573 (18)* | |
O2 | 0.1002 (14) | 0.2366 (5) | 0.4878 (4) | 0.0573 (18)* | |
C8 | 0.0728 (12) | 0.5194 (3) | 0.0445 (2) | 0.0446 (15)* | |
C9 | 0.1499 (11) | 0.4202 (4) | 0.1185 (2) | 0.0446 (15)* | |
O3 | 0.2628 (11) | 0.4739 (3) | 0.2093 (3) | 0.0446 (15)* | |
O4 | 0.1169 (14) | 0.2934 (5) | 0.1027 (3) | 0.0446 (15)* | |
H1 | 0.09385 | 0.54597 | 0.40786 | 0.05* | |
H2 | 0.45982 | −0.2753 | 0.3065 | 0.05* | |
H3 | 0.71397 | −0.29491 | 0.14842 | 0.05* | |
H4 | 0.81353 | −0.09242 | 0.06245 | 0.05* | |
H5 | 0.65775 | 0.12202 | 0.13712 | 0.05* | |
H6 | 0.41278 | 0.13712 | 0.28949 | 0.05* | |
H7 | 0.20681 | −0.10125 | 0.44133 | 0.05* | |
H8 | 0.21241 | 0.05613 | 0.42116 | 0.05* | |
H9 | 0.10018 | 0.61646 | 0.06349 | 0.05* | |
H10 | 0.30717 | 0.40402 | 0.24851 | 0.05* |
C1—C2 | 1.389 (3) | N2—H7 | 0.8988 |
C1—N1 | 1.355 (3) | N2—H8 | 0.8980 |
C1—N2 | 1.380 (3) | C6—C6i | 1.332 (6) |
C2—C3 | 1.387 (3) | C6—C7 | 1.461 (3) |
C2—H2 | 0.9466 | C6—H1 | 0.9481 |
C3—C4 | 1.394 (3) | O1—C7 | 1.247 (4) |
C3—H3 | 0.9489 | O2—C7 | 1.277 (4) |
C4—C5 | 1.383 (3) | C8—C8ii | 1.321 (6) |
C4—H4 | 0.9491 | C8—C9 | 1.452 (3) |
C5—H5 | 0.9503 | C8—H9 | 0.9500 |
N1—C1 | 1.355 (3) | O3—C9 | 1.336 (3) |
N1—C5 | 1.346 (3) | O3—H10 | 0.8986 |
N1—H6 | 0.8991 | O4—C9 | 1.223 (4) |
C2—C1—N1 | 122.2 (2) | C5—N1—H6 | 120.73 |
C2—C1—N2 | 126.6 (2) | C1—N2—H7 | 119.95 |
N1—C1—N2 | 111.1 (2) | C1—N2—H8 | 120.11 |
C1—C2—C3 | 118.4 (2) | H7—N2—H8 | 119.87 |
C1—C2—H2 | 120.74 | C6i—C6—C7 | 122.6 (3) |
C3—C2—H2 | 120.86 | C6i—C6—H1 | 118.1 |
C2—C3—C4 | 119.8 (2) | C7—C6—H1 | 119.18 |
C2—C3—H3 | 120.04 | C6—C7—O1 | 118.9 (3) |
C4—C3—H3 | 120.12 | C6—C7—O2 | 122.9 (3) |
C3—C4—C5 | 118.2 (2) | O1—C7—O2 | 118.2 (3) |
C3—C4—H4 | 120.98 | C8ii—C8—C9 | 122.4 (3) |
C5—C4—H4 | 120.80 | C8ii—C8—H9 | 118.1 |
C4—C5—N1 | 122.8 (2) | C9—C8—H9 | 119.01 |
C4—C5—H5 | 118.52 | C8—C9—O3 | 116.6 (2) |
N1—C5—H5 | 118.71 | C8—C9—O4 | 124.4 (3) |
C1—N1—C5 | 118.6 (2) | O3—C9—O4 | 119.1 (3) |
C1—N1—H6 | 120.71 | C9—O3—H10 | 109.29 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x, −y+1, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H6···O1 | 0.90 | 1.812 | 2.710 (5) | 176.0 |
N2—H8···O2 | 0.90 | 1.954 | 2.842 (5) | 170.0 |
N2—H7···O2iii | 0.90 | 2.030 | 2.877 (6) | 156.7 |
O3—H10···O1 | 0.90 | 1.676 | 2.532 (5) | 157.9 |
Symmetry code: (iii) −x, −y, −z+1. |
Experimental details
Crystal data | |
Chemical formula | 2C5H7N2+·C4H2O42−·C4H4O4 |
Mr | 420.38 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 298 |
a, b, c (Å) | 3.81686 (7), 9.6064 (3), 13.3605 (4) |
α, β, γ (°) | 94.2974 (15), 91.7433 (14), 91.7169 (14) |
V (Å3) | 488.02 (3) |
Z | 1 |
Radiation type | Cu Kα1, λ = 1.54056 Å |
µ (mm−1) | 0.98 |
Specimen shape, size (mm) | Cylinder, 10 × 0.7 |
Data collection | |
Diffractometer | Rigaku SmartLab diffractometer |
Specimen mounting | Borosilicate caplillary |
Data collection mode | Transmission |
Scan method | Continuous |
2θ values (°) | 2θmin = 5.0 2θmax = 70.0 2θstep = 0.02 |
Refinement | |
R factors and goodness of fit | Rp = 0.035, Rwp = 0.046, Rexp = 0.032, R(F2) = 0.1101, χ2 = 2.103 |
No. of data points | 3251 |
No. of parameters | 56 |
No. of restraints | 77 |
H-atom treatment | H-atom parameters not refined |
Computer programs: SmartLab software (Rigaku, 2013), GSAS (Larson & Von Dreele, 2004), Reflex implemented in Materials Studio (Accelrys, 2011), ORTEP-3 (Farrugia, 2012), DIAMOND (Brandenburg, 1999) and Mercury (Macrae et al., 2008), publCIF (Westrip, 2010).
C1—C2 | 1.389 (3) | C6—C6i | 1.332 (6) |
C1—N2 | 1.380 (3) | O1—C7 | 1.247 (4) |
C3—C4 | 1.394 (3) | C8—C8ii | 1.321 (6) |
C4—C5 | 1.383 (3) | O3—C9 | 1.336 (3) |
N1—C1 | 1.355 (3) | O4—C9 | 1.223 (4) |
C2—C1—N1 | 122.2 (2) | C1—N1—C5 | 118.6 (2) |
C2—C1—N2 | 126.6 (2) | C6i—C6—C7 | 122.6 (3) |
C1—C2—C3 | 118.4 (2) | O1—C7—O2 | 118.2 (3) |
C2—C3—C4 | 119.8 (2) | C8—C9—O4 | 124.4 (3) |
C4—C5—N1 | 122.8 (2) | O3—C9—O4 | 119.1 (3) |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x, −y+1, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H6···O1 | 0.90 | 1.812 | 2.710 (5) | 176.0 |
N2—H8···O2 | 0.90 | 1.954 | 2.842 (5) | 170.0 |
N2—H7···O2iii | 0.90 | 2.030 | 2.877 (6) | 156.7 |
O3—H10···O1 | 0.90 | 1.676 | 2.532 (5) | 157.9 |
Symmetry code: (iii) −x, −y, −z+1. |