research communications
2-({[(Pyridin-1-ium-2-ylmethyl)carbamoyl]formamido}methyl)pyridin-1-ium bis(3,5-dicarboxybenzoate):
and Hirshfeld surface analysisaDepartment of Physics, Bhavan's Sheth R. A. College of Science, Ahmedabad, Gujarat 380 001, India, bDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia, and cCentre for Crystalline Materials, Faculty of Science and Technology, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
*Correspondence e-mail: edwardt@sunway.edu.my
The 14H16N4O22+·2C9H5O6−, comprises half a dication, being located about a centre of inversion, and one anion, in a general position. The central C4N2O2 group of atoms in the dication are almost planar (r.m.s. deviation = 0.009 Å), and the carbonyl groups lie in an anti disposition to enable the formation of intramolecular amide-N—H⋯O(carbonyl) hydrogen bonds. To a first approximation, the pyridinium and amide N atoms lie to the same side of the molecule [Npy—C—C—Namide torsion angle = 34.8 (2)°], and the anti pyridinium rings are approximately perpendicular to the central part of the molecule [dihedral angle = 68.21 (8)°]. In the anion, one carboxylate group is almost coplanar with the ring to which it is connected [Cben—Cben—Cq—O torsion angle = 2.0 (3)°], whereas the other carboxylate and carboxylic acid groups are twisted out of the plane [torsion angles = 16.4 (3) and 15.3 (3)°, respectively]. In the crystal, anions assemble into layers parallel to (10-4) via hydroxy-O—H⋯O(carbonyl) and charge-assisted hydroxy-O—H⋯O(carboxylate) hydrogen bonds. The dications are linked into supramolecular tapes by amide-N—H⋯O(amide) hydrogen bonds, and thread through the voids in the anionic layers, being connected by charge-assisted pyridinium-N—O(carboxylate) hydrogen bonds, so that a three-dimensional architecture ensues. An analysis of the Hirshfeld surface points to the importance of O—H⋯O hydrogen bonding in the crystal structure.
of the title salt, CKeywords: crystal structure; salt; hydrogen bonding; carboxylate; diamide; Hirshfeld surface analysis.
CCDC reference: 1447965
1. Chemical context
Of the isomeric N,N′-bis(pyridin-n-ylmethyl)ethanediamides, n = 2, 3 or 4, the molecule with n = 2 appears to have attracted the least attention in co-crystallization studies; for the chemical structure of the diprotonated form of the n = 2 isomer see Scheme 1. By contrast, the n = 3 and 4 molecules have attracted interest from the crystal engineering community in terms of their ability to form co-crystals with iodo-containing species leading to aggregates featuring N⋯I halogen bonding (Goroff et al., 2005; Jin et al., 2013) as well as carboxylic acids (Nguyen et al., 2001). It is the latter that has formed the focus of our interest in co-crystallization experiments of these molecules which has led to the characterization of both co-crystals (Arman, Kaulgud et al., 2012; Arman, Miller et al., 2012) and salts (Arman et al., 2013). It was during the course of recent studies in this area (Syed et al., 2016) that the title salt was isolated from the 1:1 co-crystallization experiment between the n = 2 isomer and trimesic acid. The crystal and molecular structures as well as a Hirshfeld surface analysis of this salt is described herein.
2. Structural commentary
The title salt, Fig. 1, was prepared from the 1:1 reaction of trimesic acid and N,N′-bis(pyridin-2-ylmethyl)ethanediamide conducted in ethanol. The harvested crystals were shown by crystallography to comprise (2-pyridinium)CH2N(H)C(=O)C(=O)CH2N(H)(2–pyridinium) dications and 3,5-dicarboxybenzoate anions in the ratio 1:2; as the dication is located about a centre of inversion, one anion is found in the The confirmation for the transfer of protons during the co-crystallization experiment is found in (i) the pattern of hydrogen-bonding interactions as discussed in Supramolecular features, and (ii) the geometric characteristics of the ions. Thus, the C—N—C angle in the pyridyl ring has expanded by over 3° cf. that found in the only neutral form of N,N′-bis(pyridin-2-ylmethyl)ethanediamide characterized crystallographically in an all-organic molecule, i.e. in a 1:2 with 2-aminobenzoic acid (Arman, Miller et al., 2012), Table 1. The observed angle is in agreement with the sole example of a diprotonated form of the molecule, i.e. in a 1:2 salt with 2,6-dinitrobenzoate (Arman et al., 2013), Table 1. Further, the experimental equivalence of the C14—O2, O3 bond lengths, i.e. 1.259 (2) and 1.250 (2) Å is consistent with deprotonation and the formation of a carboxylate group, and contrasts the great disparity in the C15—O4, O5 [1.206 (2) and 1.320 (2) Å] and C16—O6, O7 [1.229 (2) and 1.315 (2) Å] bond lengths.
In the dication, the central C4N2O2 chromophore is almost planar, having an r.m.s. deviation of 0.009 Å and, from symmetry, the carbonyl groups are anti. An intramolecular amide-N—H⋯O(carbonyl) hydrogen bond is noted, Table 2. The pyridinium-N1 and amide-N2 atoms are approximately syn as seen in the value of the N1—C1—C6—N2 torsion angle of 34.8 (2)°. This planarity does not extend to the terminal pyridinium rings which are approximately perpendicular to and lying to either side of the central chromophore, forming dihedral angles of 68.21 (8)°. The central C7—C7i bond length of 1.538 (4) Å is considered long for a C—C bond involving sp2-hybridized atoms (Spek, 2009). Geometric data for the two previously characterized molecules (Arman, Miller et al., 2012; Arman et al., 2013) related to the dication are collected in Table 1. To a first approximation, the three molecules present the same features as described above with the notable exception of the relative disposition of the pyridinium-N1 and amide-N2 atoms. Thus, in the neutral form of the molecule, these are anti, the N1—C1—C6—N2 torsion angle being 165.01 (10) Å, and almost perpendicular in the salt, with N1—C1—C6—N2 being 73.84 (15)°. These differences are highlighted in the overlay diagram shown in Fig. 2.
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In the anion, the C13—C8—C14—O2 and C9—C10—C15—O4 torsion angles of 15.3 (3) and 16.4 (3)°, respectively, indicate twisted conformations between these residues and the ring to which they are attached whereas the C11—C12—C16—O6 torsion angle of 2.0 (3)° shows this carboxylic acid group to be co-planar with the ring. The conformational flexibility in 3,5-dicarboxybenzoate anions is well illustrated in arguably the four most closely related structures in the crystallographic literature (Groom & Allen, 2014), identified from approximately 35 organic salts containing this anion. Referring to Scheme 2, the most closely related structure features the dication C_I with two protonated pyridyl N atoms (Santra et al., 2009). Here, with two crystallographically independent anions, twists are noted from the mean-plane data collated in Table 3. For one anion, all groups are twisted out of the least-squares plane through the benzene ring but, in the second anion, the carboxylate group is effectively co-planar with the ring with up to a large twist noted for one of the carboxylic acid groups. In the other example with a diprotonated cation, C_II (Singh et al., 2015), both independent anions exhibit twists of less than 8° with all three residues effectively co-planar in one of the anions. In the example with a single protonated pyridyl residue, C_III (Ferguson et al., 1998), twists are evident for one of the carboxylic acid groups and for the carboxylate but, the second carboxylic acid residue is effectively co-planar. Finally, in the mono-protonated species related to C_I, i.e. C_IV (Basu et al., 2009), twists are evident for all groups with the maximum twists observed in the series for the carboxylate residue, i.e. 25.13 (10)°, and for one of the carboxylic acid groups, i.e. 22.50 (10)°.
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3. Supramolecular features
The molecular packing may be conveniently described in terms of O—H⋯O hydrogen bonding to define an anionic network which is connected into a three-dimensional architecture by N—H⋯O hydrogen bonds; Table 2 collates geometric data for the intermolecular interactions discussed in this section. Thus, centrosymmetrically related C—O6,O7 carboxylic acid groups associate via hydroxy-O—H⋯O(carbonyl) hydrogen bonds to form a familiar eight-membered {⋯HOCO}2 synthon. These are connected by charge-assisted hydroxy-O—H⋯O(carboxylate) hydrogen bonds that form C(8) chains. The result is a network of anions lying parallel to (10) and having an undulating topology, Fig. 3a. The dications also self-associate to form supramolecular tapes via C(4) chains featuring pairs of amide-N—H⋯O(amide) hydrogen bonds and 10-membered {⋯HNC2O}2 synthons, Fig. 3b. The tapes are aligned along the a axis and, in essence, thread through the voids in the anionic layers to form a three-dimensional architecture, Fig. 3c. The links between the anionic layers and cationic tapes are hydrogen bonds of the type charge-assisted pyridinium-N—O(carboxylate). In this scheme, no apparent role for the carbonyl-O4 atom is evident. However, this atoms accepts two C—H⋯O interactions from pyridyl- and methylene-H to consolidate the molecular packing. Additional stabilization is afforded by pyridyl-C—H⋯O(carboxylate, carbonyl) interactions, Table 2.
4. Analysis of the Hirshfeld surfaces
Crystal Explorer 3.1 (Wolff et al., 2012) was used to generate Hirshfeld surfaces (Spackman & Jayatilaka, 2009) mapped over dnorm, de and electrostatic potential for the title salt. The electrostatic potentials were calculated using TONTO (Spackman et al., 2008; Jayatilaka et al., 2005) integrated with Crystal Explorer, and mapped on the Hirshfeld surfaces using the STO-3G basis set at the Hartree–Fock level theory over the range ±0.25 au. The contact distances di and de from the Hirshfeld surface to the nearest atom inside and outside, respectively, enable the analysis of the intermolecular interactions through the mapping of dnorm. The combination of de and di in the form of two-dimensional fingerprint plots provides a summary of intermolecular contacts in the crystal (Rohl et al., 2008).
Views of the Hirshfeld surface mapped over dnorm in the title salt are given in Fig. 4. The formation of charge-assisted hydroxyl-O—H⋯O(carboxylate) and pyridinium-N—H⋯O(carboxylate) hydrogen bonds in the crystal appear as distinct dark-red spots near the respective donor and acceptor atoms. In Fig. 5, the blue and red colouration are the corresponding regions on the surface mapped over the electrostatic potential. The dark-red spots on the Hirshfeld surface of the dication corresponds to a pair of amide-N—H⋯O(amide) hydrogen bonds leading to the supramolecular tape. Intermolecular C—H⋯O and N—H⋯O interactions, representing weak hydrogen bonds over and above those discussed above in Supramolecular features, result in light-red spots near some of the carbon, nitrogen and oxygen atoms, Fig. 4. Hence, the contribution to the surface from these interactions involve not only O⋯H/H⋯O contacts but also C⋯O/O⋯C and N⋯O/O⋯N contacts, Table 4. The relative contributions of the different contacts to the Hirshfeld surfaces are collated in Table 5 for the entire structure and also delineated for the dication and anion. The linkage of ions through the formation of hydrogen bonds is illustrated in Fig. 6.
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The overall two-dimensional fingerprint plot (FP) of the salt together with those of the dication and anion, and FP's delineated into H⋯H, O⋯H/H⋯O, C⋯H/H⋯C and C⋯O/O⋯C contacts are illustrated in Fig. 7. The O⋯H/H⋯O contacts have the largest overall contribution to the Hirshfeld surface, i.e. 43.2%, and these interactions dominate in the The prominent spike with green points appearing in the lower left region in the FP for the anion at de + di ∼ 1.7 Å has a major contribution, i.e. 47.2%, from O⋯H contacts; the spike at the same de + di distance is due to a small contribution, 10.0%, from H⋯O contacts. The different contributions from O⋯H and H⋯O contacts to the Hirshfeld surface of the dication, i.e. 6.8 and 34.8%, respectively, lead to asymmetric peaks at de + di ∼ 1.8 and 2.0 Å, respectively, indicating the varying strength of these interactions. However, the overall FP of the salt delineated into O⋯H/H⋯O contacts shows a symmetric pair of spikes at de + di ∼ 1.7 Å with nearly equal contributions from O⋯H and H⋯O contacts. A smaller contribution is made by the H⋯H contacts, Table 1, and these appear as the scattered points without a distinct peak, Fig. 7. The presence of short interatomic C⋯H/H⋯C contacts, Table 4, result in a 17.3% overall contribution to the surface, although there are no C—H⋯π contacts within the acceptance distance criteria for such interactions (Spek, 2009). These are represented by a pair of symmetrical wings at de + di ∼ 2.9 Å in the FP plot, Fig. 7. The contribution from C⋯O/O⋯C contacts to the Hirshfeld surface is also evident from the presence of intermolecular C—H⋯O interactions as well as short interatomic C⋯O/O⋯C contact, Table 4. These appear as cross-over wings in the (de, di) region between 1.7 and 2.7 Å. A small but significant contribution to the Hirshfeld surface of the dication due to N⋯O/O⋯N contacts is the result of intermolecular amide-N—H⋯O(amide) interactions.
The intermolecular interactions were further analysed using a recently reported descriptor, the enrichment ratio, ER (Jelsch et al., 2014), which is based on Hirshfeld surface analysis and gives an indication of the relative likelihood of specific intermolecular interactions to form; the calculated ratios are given in Table 6. The relatively poor content of hydrogen atoms in the salt and the involvements of many hydrogen atoms in the intermolecular interactions, as discussed above, reduces the ER value of non-bonded H⋯H contacts to a value less unity, i.e. 0.8, due to a 23.7% contribution from the 54.5% available Hirshfeld surface and anticipated 29.7% random contacts. The ER value of 1.4 corresponding to O⋯H/H⋯O contacts results from a relatively high 43.2% contribution by O—H⋯O, N—H⋯O and C—H⋯O interactions. The carbon and oxygen atoms involved in the intermolecular C—H⋯O interactions and short inter C⋯O/O⋯C contacts are at distances shorter than the sum of their respective van der Waals radii, hence they also have a high formation propensity, so the ER value is > 1. The C⋯H/H⋯C contacts in the crystal are enriched due to the poor nitrogen content and the presence of short interatomic C⋯H/H⋯C contacts so the ratio is close to unity, i.e. 0.99. Finally, the ER value of 1.68 corresponding to N⋯O/O⋯N contacts for the surface of dication is the result of the charge-assisted N—H⋯O interactions consistent with their high propensity to form.
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5. Database survey
As mentioned in the Chemical context, N,N′-bis(pyridin-2-ylmethyl)ethanediamide (LH2), has not been as well studied as the n = 3 and 4 isomers. This notwithstanding, the coordination chemistry of LH2 is more advanced and diverse. Thus, co-crystals have been reported with a metal complex, i.e. [Mn(1,10-phenanthroline)3][ClO4]2·(LH2) (Liu et al., 1999). Monodentate coordination via a pyridyl-N atom was found in mononuclear HgI2(LH2)2 (Zeng et al., 2008). Bidentate, bridging via both pyridyl-N atoms has been observed in binuclear {[Me2(4-HO2CC6H4CH2)Pt(4,4′-di-t-butyl-2,2′-bipyridyl]2(LH2)}22+ (Fraser et al., 2002) and in a polymeric silver salt, {AgBF4(LH2)·H2O}n (Schauer et al., 1998). In the analogous triflate salt {Ag2(O3SCF3)2(LH2)3}n (Arman et al., 2010), one LH2 bridges as in the BF4 salt (Schauer et al., 1998) but the other two LH2 molecules bridge one Ag+ via a pyridyl-N atom and another via the second pyridyl-N atom as well as a carbonyl-O atom, i.e. are tridentate. In a variation, tetradentate, bridging coordination via all four nitrogen atoms is found in polymeric [CuL(LH2)(OH2]n (Lloret et al., 1989). Deprotonation of LH2 leads to a tetradentate ligand coordinating via all four nitrogen atoms in PdL (Reger et al., 2003). There are several examples of hexadentate-N4O2 coordination in copper(II) chemistry, as in the aforementioned [CuL(LH2)(OH2]n (Lloret et al., 1989) and, for example, in polymeric [CuL(μ2-4,4′-bipyridyl-)(OH2)]2 (Zhang et al., 2001).
6. Synthesis and crystallization
The diamide (0.25 g), prepared in accord with the literature procedure (Schauer et al., 1997), in ethanol (10 ml) was added to a ethanol solution (10 ml) of trimesic acid (Acros Organic, 0.18 g). The mixture was stirred for 2 h at room temperature. After standing for a few minutes, a white precipitate formed which was filtered off by vacuum suction. The filtrate was then left to stand under ambient conditions, yielding pale-yellow crystals after 2 weeks.
7. Refinement
Crystal data, data collection and structure . The carbon-bound H atoms were placed in calculated positions (C—H = 0.95–0.99 Å) and were included in the in the riding-model approximation, with Uiso(H) set to 1.2Ueq(C). The oxygen- and nitrogen-bound H atoms were located in a difference Fourier map but were refined with distance restraints of O—H = 0.84±0.01 Å and N—H = 0.88±0.01 Å, and with Uiso(H) set to 1.5Ueq(O) and 1.2Ueq(N).
details are summarized in Table 7
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Supporting information
CCDC reference: 1447965
10.1107/S2056989016000980/hb7560sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S2056989016000980/hb7560Isup2.hkl
Supporting information file. DOI: 10.1107/S2056989016000980/hb7560Isup3.cml
Of the isomeric N,N'-bis(pyridin-n-ylmethyl)ethanediamides, n = 2, 3 or 4, the molecule with n = 2 appears to have attracted the least attention in co-crystallization studies; for the chemical structure of the diprotonated form of the n = 2 isomer see Scheme 1. By contrast, the n = 3 and 4 molecules have attracted interest from the crystal engineering community in terms of their ability to form co-crystals with iodo-containing species leading to aggregates featuring N···I halogen bonding (Goroff et al., 2005; Jin et al., 2013) as well as carboxylic acids (Nguyen et al., 2001). It is the latter that has formed the focus of our interest in co-crystallization experiments of these molecules which has led to the characterization of both co-crystals (Arman, Kaulgud et al., 2012; Arman, Miller et al., 2012) and salts (Arman et al., 2013). It was during the course of recent studies in this area (Syed et al., 2016) that the title salt was isolated from the 1:1 co-crystallization experiment between the n = 2 isomer and trimesic acid. The crystal and molecular structures as well as a Hirshfeld surface analysis of this salt is described herein.
The title salt, Fig. 1, was prepared from the 1:1 reaction of trimesic acid and N,N'-bis(pyridin-2-ylmethyl)ethanediamide conducted in ethanol. The harvested crystals were shown by crystallography to comprise (2-pyridinium)CH2N(H)C(═O)C(═O)CH2N(H)(2–pyridinium) dications and 3,5-dicarboxybenzoate anions in the ratio 1:2; as the dication is located about a centre of inversion, one anion is found in the The confirmation for the transfer of protons during the co-crystallization experiment is found in i) the pattern of hydrogen-bonding interactions as discussed in Supramolecular features, and ii) the geometric characteristics of the ions. Thus, the C—N—C angle in the pyridyl ring has expanded by over 3° cf. that found in the only neutral form of N,N'-bis(pyridin-2-ylmethyl)ethanediamide characterized crystallographically in an all-organic molecule, i.e. in a 1:2 with 2-aminobenzoic acid (Arman, Miller et al., 2012), Table 1. The observed angle is in agreement with the sole example of a diprotonated form of the molecule, i.e. in a 1:2 salt with 2,6-dinitrobenzoate (Arman et al., 2013), Table 1. Further, the experimental equivalence of the C14—O2, O3 bond lengths, i.e. 1.259 (2) and 1.250 (2) Å is consistent with deprotonation and the formation of a carboxylate group, and contrasts the great disparity in the C15—O4, O5 [1.206 (2) and 1.320 (2) Å] and C16—O6, O7 [1.229 (2) and 1.315 (2) Å] bond lengths.
In the dication, the central C4N2O2 chromophore is almost planar, having an r.m.s. deviation of 0.009 Å and, from symmetry, the carbonyl groups are anti. An intramolecular amide-N—H···O(carbonyl) hydrogen bond is noted, Table 2. The pyridinium-N1 and amide-N2 atoms are approximately syn as seen in the value of the N1—C1—C6—N2 torsion angle of 34.8 (2)°. This planarity does not extend to the terminal pyridinium rings which are approximately perpendicular to and lying to either side of the central chromophore, forming dihedral angles of 68.21 (8)°. The central C7—C7i bond length of 1.538 (4) Å is considered long for a C—C bond involving sp2-hybridized atoms (Spek, 2009). Geometric data for the two previously characterized molecules (Arman, Miller et al., 2012; Arman et al., 2013) related to the dication are collected in Table 1. To a first approximation, the three molecules present the same features as described above with the notable exception of the relative disposition of the pyridinium-N1 and amide-N2 atoms. Thus, in the neutral form of the molecule, these are anti, the N1—C1—C6—N2 torsion angle being 165.01 (10) Å, and almost perpendicular in the salt, with N1—C1—C6—N2 being 73.84 (15)°. These differences are highlighted in the overlay diagram shown in Fig. 2.
In the anion, the C13—C8—C14—O2 and C9—C10—C15—O4 torsion angles of 15.3 (3) and 16.4 (3)°, respectively, indicate twisted conformations between these residues and the ring to which they are attached whereas the C11—C12—C16—O6 torsion angle of 2.0 (3)° shows this carboxylic acid group to be co-planar with the ring. The conformational flexibility in 3,5-dicarboxybenzoate anions is well illustrated in arguably the four most closely related structures in the crystallographic literature (Groom & Allen, 2014), identified from approximately 35 organic salts containing this anion. Referring to Scheme 2, the most closely related structure features the dication C_I with two protonated pyridyl N atoms (Santra et al., 2009). Here, with two crystallographically independent anions, twists are noted from the mean-plane data collated in Table 2. For one anion, all groups are twisted out of the least-squares plane through the benzene ring but, in the second anion, the carboxylate group is effectively co-planar with the ring with up to a large twist noted for one of the carboxylic acid groups. In the other example with a diprotonated cation, C_II (Singh et al., 2015), both independent anions exhibit twists of less than 8° with all three residues effectively co-planar in one of the anions. In the example with a single protonated pyridyl residue, C_III (Ferguson et al., 1998), twists are evident for one of the carboxylic acid groups and for the carboxylate but, the second carboxylic acid residue is effectively co-planar. Finally, in the mono-protonated species related to C_I, i.e. C_IV (Basu et al., 2009), twists are evident for all groups with the maximum twists observed in the series for the carboxylate residue, i.e. 25.13 (10)°, and for one of the carboxylic acid groups, i.e. 22.50 (10)°.
The molecular packing may be conveniently described in terms of O—H···O hydrogen bonding to define an anionic network which is connected into a three-dimensional architecture by N—H···O hydrogen bonds; Table 3 collates geometric data for the intermolecular interactions discussed in this section. Thus, centrosymmetrically related C—O6,O7 carboxylic acid groups associate via hydroxy-O—H···O(carbonyl) hydrogen bonds to form a familiar eight-membered {···HOCO}2 synthon. These are connected by charge-assisted hydroxy-O—H···O(carboxylate) hydrogen bonds that form C(8) chains. The result is a network of anions lying parallel to (104) and having an undulating topology, Fig. 3a. The dications also self-associate but, to form supramolecular tapes via C(4) chains featuring pairs of amide-N—H···O(amide) hydrogen bonds and 10-membered {···HNC2O}2 synthons, Fig. 3b. The tapes are aligned along the a axis and, in essence, thread through the voids in the anionic layers to form a three-dimensional architecture, Fig. 3c. The links between the anionic layers and cationic tapes are hydrogen bonds of the type charge-assisted pyridinium-N—O(carboxylate). In this scheme, no apparent role for the carbonyl-O4 atom is evident. However, this atoms accepts two C—H···O interactions from pyridyl- and methylene-H to consolidate the molecular packing. Additional stabilization is afforded by pyridyl-C—H···O(carboxylate, carbonyl) interactions, Table 3.
Crystal Explorer 3.1 (Wolff et al., 2012) was used to generate Hirshfeld surfaces (Spackman & Jayatilaka, 2009) mapped over dnorm, de and electrostatic potential for the title salt. The electrostatic potentials were calculated using TONTO (Spackman et al., 2008; Jayatilaka et al., 2005) integrated with Crystal Explorer, and mapped on the Hirshfeld surfaces using the STO-3G basis set at the Hartree–Fock level theory over the range ±0.25 au. The contact distances di and de from the Hirshfeld surface to the nearest atom inside and outside, respectively, enable the analysis of the intermolecular interactions through the mapping of dnorm. The combination of de and di in the form of two-dimensional fingerprint plots provides a summary of intermolecular contacts in the crystal (Rohl et al., 2008).
Views of the Hirshfeld surface mapped over dnorm in the title salt are given in Fig. 4. The formation of charge-assisted hydroxyl-O—H···O(carboxylate) and pyridinium-N—H···O(carboxylate) hydrogen bonds in the crystal appear as distinct dark-red spots near the respective donor and acceptor atoms. In Fig. 5, the blue and red colouration are the corresponding regions on the surface mapped over the electrostatic potential. The dark-red spots on the Hirshfeld surface of the dication corresponds to a pair of amide-N—H···O(amide) hydrogen bonds leading to the supramolecular tape. Intermolecular C—H···O and N—H···O interactions, representing weak hydrogen bonds over and above those discussed above in Supramolecular features, result in light-red spots near some of the carbon, nitrogen and oxygen atoms, Fig. 4. Hence, the contribution to the surface from these interactions involve not only O···H/H···O contacts but also C···O/O···C and N···O/O···N contacts, Table 4. The relative contributions of the different contacts to the Hirshfeld surfaces are collated in Table 5 for the entire structure and also delineated for the dication and anion. The linkage of ions through the formation of hydrogen bonds is illustrated in Fig. 6.
The overall two-dimensional fingerprint plot (FP) of the salt together with those of the dication and anion, and FP's delineated into H···H, O···H/H···O, C···H/H···C and C···O/O···C contacts are illustrated in Fig. 7. The O···H/H···O contacts have the largest overall contribution to the Hirshfeld surface, i.e. 43.2%, and these interactions dominate in the π contacts within the acceptance distance criteria for such interactions (Spek, 2009). These are represented by a pair of symmetrical wings at de + di ~ 2.9 Å in the FP plot, Fig. 7. The contribution from C···O/O···C contacts to the Hirshfeld surface is also evident from the presence of intermolecular C—H···O interactions as well as short interatomic C···O/O···C contact, Table 5. These appear as cross-over wings in the de, di region between 1.7 and 2.7 Å. A small but significant contribution to the Hirshfeld surface of the dication due to N···O/O···N contacts is the result of intermolecular amide-N—H···O(amide) interactions.
The prominent spike with green points appearing in the lower left region in the FP for the anion at de + di ~ 1.7 Å has a major contribution, i.e. 47.2%, from O···H contacts; the spike at the same de + di distance is due to a small contribution, 10.0%, from H···O contacts. The different contributions from O···H and H···O contacts to the Hirshfeld surface of the dication, i.e. 6.8 and 34.8 %, respectively, lead to asymmetric peaks at de + di ~ 1.8 and 2.0 Å, respectively, indicating the varying strength of these interactions. However, the overall FP of the salt delineated into O···H/H···O contacts shows a symmetric pair of spikes at de + di ~ 1.7 Å with nearly equal contributions from O···H and H···O contacts. A smaller contribution is made by the H···H contacts, Table 1, and these appear as the scattered points without a distinct peak, Fig. 7. The presence of short interatomic C···H/H···C contacts, Table 5, result in a 17.3% overall contribution to the surface, although there are no C—H···The intermolecular interactions were further analysed using a recently reported descriptor, the enrichment ratio, ER (Jelsch et al., 2014), which is based on Hirshfeld surface analysis and gives an indication of the relative likelihoods of specific intermolecular interactions to form; the calculated ratios are given in Table 6. The relatively poor content of hydrogen atoms in the salt and the involvements of many hydrogen atoms in the intermolecular interactions, as discussed above, reduces ER value of non-bonded H···H contacts to a value less unity, i.e. 0.8, due to a 23.7% contribution from the 54.5% available Hirshfeld surface and anticipated 29.7% random contacts. The ER value of 1.4 corresponding to O···H/H···O contacts results from a relatively high 43.2% contribution by O—H···O, N—H···O and C—H···O interactions. The carbon and oxygen atoms involved in the intermolecular C—H···O interactions and short inter C···O/O···C contacts are at distances shorter than the sum of their respective van der Waals radii, hence they also have a high formation propensity, so the ER value is > 1. The C···H/H···C contacts in the crystal are enriched due to the poor nitrogen content and the presence of short interatomic C···H/H···C contacts so the ratio is close to unity, i.e. 0.99. Finally, the ER value of 1.68 corresponding to N···O/O···N contacts for the surface of dication is the result of the charge-assisted N—H···O interactions consistent with their high propensity to form.
\ As mentioned in the Chemical context, N,N'-bis(pyridin-2-ylmethyl)ethanediamide (LH2), has not been as well studied as the n = 3 and 4 isomers. This notwithstanding, the coordination chemistry of LH2 is more advanced and diverse. Thus, co-crystals have been reported with a metal complex, i.e. [Mn(1,10-phenanthroline)3][ClO4]2.(LH2) (Liu et al., 1999). Monodentate coordination via a pyridyl-N atom was found in mononuclear HgI2(LH2)2 (Zeng et al., 2008). Bidentate, bridging via both pyridyl-N atoms has been observed in binuclear {[Me2(4-HO2CC6H4CH2)Pt(4,4'-di-t-butyl-2,2'-bipyridyl]\ 2(LH2)}22+ (Fraser et al., 2002) and in a polymeric silver salt, {AgBF4(LH2)·H2O}n (Schauer et al., 1998). In the analogous triflate salt {Ag2(O3SCF3)2(LH2)3}n (Arman et al., 2010), one LH2 bridges as in the BF4 salt (Schauer et al., 1998) but the other two LH2 molecules bridge one Ag+ via a pyridyl-N atom and another via the second pyridyl-N atom as well as a carbonyl-O atom, i.e. are tridentate. In a variation, tetradentate, bridging coordination via all four nitrogen atoms is found in polymeric [CuL(LH2)(OH2]n (Lloret et al., 1989). Deprotonation of LH2 leads to a tetradentate ligand coordinating via all four nitrogen atoms in PdL (Reger et al., 2003). There are several examples of hexadentate-N4O2 coordination in copper(II) chemistry, as in the aforementioned [CuL(LH2)(OH2]n (Lloret et al., 1989) and, for example, in polymeric [CuL(µ2-4,4'-bipyridyl-)(OH2)]2 (Zhang et al., 2001).
The diamide (0.25 g), prepared in accord with the literature procedure (Schauer et al., 1997), in ethanol (10 ml) was added to a ethanol solution (10 ml) of trimesic acid (Acros Organic, 0.18 g). The mixture was stirred for 2 h at room temperature. After standing for a few minutes, a white precipitate formed which was filtered off by vacuum suction. The filtrate was then left to stand under ambient conditions, yielding pale-yellow crystals after 2 weeks.
Crystal data, data collection and structure
details are summarized in Table 7. The carbon-bound H atoms were placed in calculated positions (C—H = 0.95–0.99 Å) and were included in the in the riding-model approximation, with Uiso(H) set to 1.2Ueq(C). The oxygen- and nitrogen-bound H atoms were located in a difference Fourier map but were refined with distance restraints of O—H = 0.84±0.01 Å and N—H = 0.88±0.01 Å, and with Uiso(H) set to 1.5Ueq(O) and 1.2Ueq(N).Of the isomeric N,N'-bis(pyridin-n-ylmethyl)ethanediamides, n = 2, 3 or 4, the molecule with n = 2 appears to have attracted the least attention in co-crystallization studies; for the chemical structure of the diprotonated form of the n = 2 isomer see Scheme 1. By contrast, the n = 3 and 4 molecules have attracted interest from the crystal engineering community in terms of their ability to form co-crystals with iodo-containing species leading to aggregates featuring N···I halogen bonding (Goroff et al., 2005; Jin et al., 2013) as well as carboxylic acids (Nguyen et al., 2001). It is the latter that has formed the focus of our interest in co-crystallization experiments of these molecules which has led to the characterization of both co-crystals (Arman, Kaulgud et al., 2012; Arman, Miller et al., 2012) and salts (Arman et al., 2013). It was during the course of recent studies in this area (Syed et al., 2016) that the title salt was isolated from the 1:1 co-crystallization experiment between the n = 2 isomer and trimesic acid. The crystal and molecular structures as well as a Hirshfeld surface analysis of this salt is described herein.
The title salt, Fig. 1, was prepared from the 1:1 reaction of trimesic acid and N,N'-bis(pyridin-2-ylmethyl)ethanediamide conducted in ethanol. The harvested crystals were shown by crystallography to comprise (2-pyridinium)CH2N(H)C(═O)C(═O)CH2N(H)(2–pyridinium) dications and 3,5-dicarboxybenzoate anions in the ratio 1:2; as the dication is located about a centre of inversion, one anion is found in the The confirmation for the transfer of protons during the co-crystallization experiment is found in i) the pattern of hydrogen-bonding interactions as discussed in Supramolecular features, and ii) the geometric characteristics of the ions. Thus, the C—N—C angle in the pyridyl ring has expanded by over 3° cf. that found in the only neutral form of N,N'-bis(pyridin-2-ylmethyl)ethanediamide characterized crystallographically in an all-organic molecule, i.e. in a 1:2 with 2-aminobenzoic acid (Arman, Miller et al., 2012), Table 1. The observed angle is in agreement with the sole example of a diprotonated form of the molecule, i.e. in a 1:2 salt with 2,6-dinitrobenzoate (Arman et al., 2013), Table 1. Further, the experimental equivalence of the C14—O2, O3 bond lengths, i.e. 1.259 (2) and 1.250 (2) Å is consistent with deprotonation and the formation of a carboxylate group, and contrasts the great disparity in the C15—O4, O5 [1.206 (2) and 1.320 (2) Å] and C16—O6, O7 [1.229 (2) and 1.315 (2) Å] bond lengths.
In the dication, the central C4N2O2 chromophore is almost planar, having an r.m.s. deviation of 0.009 Å and, from symmetry, the carbonyl groups are anti. An intramolecular amide-N—H···O(carbonyl) hydrogen bond is noted, Table 2. The pyridinium-N1 and amide-N2 atoms are approximately syn as seen in the value of the N1—C1—C6—N2 torsion angle of 34.8 (2)°. This planarity does not extend to the terminal pyridinium rings which are approximately perpendicular to and lying to either side of the central chromophore, forming dihedral angles of 68.21 (8)°. The central C7—C7i bond length of 1.538 (4) Å is considered long for a C—C bond involving sp2-hybridized atoms (Spek, 2009). Geometric data for the two previously characterized molecules (Arman, Miller et al., 2012; Arman et al., 2013) related to the dication are collected in Table 1. To a first approximation, the three molecules present the same features as described above with the notable exception of the relative disposition of the pyridinium-N1 and amide-N2 atoms. Thus, in the neutral form of the molecule, these are anti, the N1—C1—C6—N2 torsion angle being 165.01 (10) Å, and almost perpendicular in the salt, with N1—C1—C6—N2 being 73.84 (15)°. These differences are highlighted in the overlay diagram shown in Fig. 2.
In the anion, the C13—C8—C14—O2 and C9—C10—C15—O4 torsion angles of 15.3 (3) and 16.4 (3)°, respectively, indicate twisted conformations between these residues and the ring to which they are attached whereas the C11—C12—C16—O6 torsion angle of 2.0 (3)° shows this carboxylic acid group to be co-planar with the ring. The conformational flexibility in 3,5-dicarboxybenzoate anions is well illustrated in arguably the four most closely related structures in the crystallographic literature (Groom & Allen, 2014), identified from approximately 35 organic salts containing this anion. Referring to Scheme 2, the most closely related structure features the dication C_I with two protonated pyridyl N atoms (Santra et al., 2009). Here, with two crystallographically independent anions, twists are noted from the mean-plane data collated in Table 2. For one anion, all groups are twisted out of the least-squares plane through the benzene ring but, in the second anion, the carboxylate group is effectively co-planar with the ring with up to a large twist noted for one of the carboxylic acid groups. In the other example with a diprotonated cation, C_II (Singh et al., 2015), both independent anions exhibit twists of less than 8° with all three residues effectively co-planar in one of the anions. In the example with a single protonated pyridyl residue, C_III (Ferguson et al., 1998), twists are evident for one of the carboxylic acid groups and for the carboxylate but, the second carboxylic acid residue is effectively co-planar. Finally, in the mono-protonated species related to C_I, i.e. C_IV (Basu et al., 2009), twists are evident for all groups with the maximum twists observed in the series for the carboxylate residue, i.e. 25.13 (10)°, and for one of the carboxylic acid groups, i.e. 22.50 (10)°.
The molecular packing may be conveniently described in terms of O—H···O hydrogen bonding to define an anionic network which is connected into a three-dimensional architecture by N—H···O hydrogen bonds; Table 3 collates geometric data for the intermolecular interactions discussed in this section. Thus, centrosymmetrically related C—O6,O7 carboxylic acid groups associate via hydroxy-O—H···O(carbonyl) hydrogen bonds to form a familiar eight-membered {···HOCO}2 synthon. These are connected by charge-assisted hydroxy-O—H···O(carboxylate) hydrogen bonds that form C(8) chains. The result is a network of anions lying parallel to (104) and having an undulating topology, Fig. 3a. The dications also self-associate but, to form supramolecular tapes via C(4) chains featuring pairs of amide-N—H···O(amide) hydrogen bonds and 10-membered {···HNC2O}2 synthons, Fig. 3b. The tapes are aligned along the a axis and, in essence, thread through the voids in the anionic layers to form a three-dimensional architecture, Fig. 3c. The links between the anionic layers and cationic tapes are hydrogen bonds of the type charge-assisted pyridinium-N—O(carboxylate). In this scheme, no apparent role for the carbonyl-O4 atom is evident. However, this atoms accepts two C—H···O interactions from pyridyl- and methylene-H to consolidate the molecular packing. Additional stabilization is afforded by pyridyl-C—H···O(carboxylate, carbonyl) interactions, Table 3.
Crystal Explorer 3.1 (Wolff et al., 2012) was used to generate Hirshfeld surfaces (Spackman & Jayatilaka, 2009) mapped over dnorm, de and electrostatic potential for the title salt. The electrostatic potentials were calculated using TONTO (Spackman et al., 2008; Jayatilaka et al., 2005) integrated with Crystal Explorer, and mapped on the Hirshfeld surfaces using the STO-3G basis set at the Hartree–Fock level theory over the range ±0.25 au. The contact distances di and de from the Hirshfeld surface to the nearest atom inside and outside, respectively, enable the analysis of the intermolecular interactions through the mapping of dnorm. The combination of de and di in the form of two-dimensional fingerprint plots provides a summary of intermolecular contacts in the crystal (Rohl et al., 2008).
Views of the Hirshfeld surface mapped over dnorm in the title salt are given in Fig. 4. The formation of charge-assisted hydroxyl-O—H···O(carboxylate) and pyridinium-N—H···O(carboxylate) hydrogen bonds in the crystal appear as distinct dark-red spots near the respective donor and acceptor atoms. In Fig. 5, the blue and red colouration are the corresponding regions on the surface mapped over the electrostatic potential. The dark-red spots on the Hirshfeld surface of the dication corresponds to a pair of amide-N—H···O(amide) hydrogen bonds leading to the supramolecular tape. Intermolecular C—H···O and N—H···O interactions, representing weak hydrogen bonds over and above those discussed above in Supramolecular features, result in light-red spots near some of the carbon, nitrogen and oxygen atoms, Fig. 4. Hence, the contribution to the surface from these interactions involve not only O···H/H···O contacts but also C···O/O···C and N···O/O···N contacts, Table 4. The relative contributions of the different contacts to the Hirshfeld surfaces are collated in Table 5 for the entire structure and also delineated for the dication and anion. The linkage of ions through the formation of hydrogen bonds is illustrated in Fig. 6.
The overall two-dimensional fingerprint plot (FP) of the salt together with those of the dication and anion, and FP's delineated into H···H, O···H/H···O, C···H/H···C and C···O/O···C contacts are illustrated in Fig. 7. The O···H/H···O contacts have the largest overall contribution to the Hirshfeld surface, i.e. 43.2%, and these interactions dominate in the π contacts within the acceptance distance criteria for such interactions (Spek, 2009). These are represented by a pair of symmetrical wings at de + di ~ 2.9 Å in the FP plot, Fig. 7. The contribution from C···O/O···C contacts to the Hirshfeld surface is also evident from the presence of intermolecular C—H···O interactions as well as short interatomic C···O/O···C contact, Table 5. These appear as cross-over wings in the de, di region between 1.7 and 2.7 Å. A small but significant contribution to the Hirshfeld surface of the dication due to N···O/O···N contacts is the result of intermolecular amide-N—H···O(amide) interactions.
The prominent spike with green points appearing in the lower left region in the FP for the anion at de + di ~ 1.7 Å has a major contribution, i.e. 47.2%, from O···H contacts; the spike at the same de + di distance is due to a small contribution, 10.0%, from H···O contacts. The different contributions from O···H and H···O contacts to the Hirshfeld surface of the dication, i.e. 6.8 and 34.8 %, respectively, lead to asymmetric peaks at de + di ~ 1.8 and 2.0 Å, respectively, indicating the varying strength of these interactions. However, the overall FP of the salt delineated into O···H/H···O contacts shows a symmetric pair of spikes at de + di ~ 1.7 Å with nearly equal contributions from O···H and H···O contacts. A smaller contribution is made by the H···H contacts, Table 1, and these appear as the scattered points without a distinct peak, Fig. 7. The presence of short interatomic C···H/H···C contacts, Table 5, result in a 17.3% overall contribution to the surface, although there are no C—H···The intermolecular interactions were further analysed using a recently reported descriptor, the enrichment ratio, ER (Jelsch et al., 2014), which is based on Hirshfeld surface analysis and gives an indication of the relative likelihoods of specific intermolecular interactions to form; the calculated ratios are given in Table 6. The relatively poor content of hydrogen atoms in the salt and the involvements of many hydrogen atoms in the intermolecular interactions, as discussed above, reduces ER value of non-bonded H···H contacts to a value less unity, i.e. 0.8, due to a 23.7% contribution from the 54.5% available Hirshfeld surface and anticipated 29.7% random contacts. The ER value of 1.4 corresponding to O···H/H···O contacts results from a relatively high 43.2% contribution by O—H···O, N—H···O and C—H···O interactions. The carbon and oxygen atoms involved in the intermolecular C—H···O interactions and short inter C···O/O···C contacts are at distances shorter than the sum of their respective van der Waals radii, hence they also have a high formation propensity, so the ER value is > 1. The C···H/H···C contacts in the crystal are enriched due to the poor nitrogen content and the presence of short interatomic C···H/H···C contacts so the ratio is close to unity, i.e. 0.99. Finally, the ER value of 1.68 corresponding to N···O/O···N contacts for the surface of dication is the result of the charge-assisted N—H···O interactions consistent with their high propensity to form.
\ As mentioned in the Chemical context, N,N'-bis(pyridin-2-ylmethyl)ethanediamide (LH2), has not been as well studied as the n = 3 and 4 isomers. This notwithstanding, the coordination chemistry of LH2 is more advanced and diverse. Thus, co-crystals have been reported with a metal complex, i.e. [Mn(1,10-phenanthroline)3][ClO4]2.(LH2) (Liu et al., 1999). Monodentate coordination via a pyridyl-N atom was found in mononuclear HgI2(LH2)2 (Zeng et al., 2008). Bidentate, bridging via both pyridyl-N atoms has been observed in binuclear {[Me2(4-HO2CC6H4CH2)Pt(4,4'-di-t-butyl-2,2'-bipyridyl]\ 2(LH2)}22+ (Fraser et al., 2002) and in a polymeric silver salt, {AgBF4(LH2)·H2O}n (Schauer et al., 1998). In the analogous triflate salt {Ag2(O3SCF3)2(LH2)3}n (Arman et al., 2010), one LH2 bridges as in the BF4 salt (Schauer et al., 1998) but the other two LH2 molecules bridge one Ag+ via a pyridyl-N atom and another via the second pyridyl-N atom as well as a carbonyl-O atom, i.e. are tridentate. In a variation, tetradentate, bridging coordination via all four nitrogen atoms is found in polymeric [CuL(LH2)(OH2]n (Lloret et al., 1989). Deprotonation of LH2 leads to a tetradentate ligand coordinating via all four nitrogen atoms in PdL (Reger et al., 2003). There are several examples of hexadentate-N4O2 coordination in copper(II) chemistry, as in the aforementioned [CuL(LH2)(OH2]n (Lloret et al., 1989) and, for example, in polymeric [CuL(µ2-4,4'-bipyridyl-)(OH2)]2 (Zhang et al., 2001).
For related literature, see:
The diamide (0.25 g), prepared in accord with the literature procedure (Schauer et al., 1997), in ethanol (10 ml) was added to a ethanol solution (10 ml) of trimesic acid (Acros Organic, 0.18 g). The mixture was stirred for 2 h at room temperature. After standing for a few minutes, a white precipitate formed which was filtered off by vacuum suction. The filtrate was then left to stand under ambient conditions, yielding pale-yellow crystals after 2 weeks.
detailsCrystal data, data collection and structure
details are summarized in Table 7. The carbon-bound H atoms were placed in calculated positions (C—H = 0.95–0.99 Å) and were included in the in the riding-model approximation, with Uiso(H) set to 1.2Ueq(C). The oxygen- and nitrogen-bound H atoms were located in a difference Fourier map but were refined with distance restraints of O—H = 0.84±0.01 Å and N—H = 0.88±0.01 Å, and with Uiso(H) set to 1.5Ueq(O) and 1.2Ueq(N).Data collection: CrysAlis PRO (Agilent, 2014); cell
CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis PRO (Agilent, 2014); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012), QMol (Gans & Shalloway, 2001) and DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).Fig. 1. The molecular structures of the ions comprising the title salt, showing the atom-labelling scheme and displacement ellipsoids at the 50% probability level: (a) 2-({[(pyridin-1-ium-2-ylmethyl)carbamoyl]formamido}methyl)pyridin-1-ium, and (b) 3,5-dicarboxybenzoate; unlabelled atoms are related by the symmetry operation -x, 1 - y, 1 - z. | |
Fig. 2. Overlay diagram of the dication in the title compound (red image), the neutral molecule in its co-crystal (green), and dication in the literature salt (blue). The molecules have been overlapped so that the O═C—C═O residues are coincident. The ring N atoms are indicated by an asterisk. | |
Fig. 3. Molecular packing in the title salt: (a) supramolecular layers mediated by O—H···O hydrogen bonds, (b) supramolecular tapes mediated by N—H···O hydrogen bonds, and (c) a view of the unit-cell contents shown in projection down the a axis, whereby the supramolecular layers, illustrated in Fig. 3(a), are linked by charge-assisted N—H···O(carboxylate) hydrogen bonds to consolidate a three-dimensional architecture. The O—H···O and N—H···O hydrogen bonds are shown as orange and blue dashed lines, respectively. | |
Fig. 4. Views of the Hirshfeld surface mapped over dnorm in the title salt: (a) dication, (b) and (c) anion. | |
Fig. 5. View of the Hirshfeld surface mapped over the calculated electrostatic potential the tri-ion aggregate in the title salt. | |
Fig. 6. Views of the Hirshfeld surfaces mapped over the calculated electrostatic potential in the title salt emphasizing the interactions between the: (a) dianions, and (b) the environment about the anion. | |
Fig. 7. The two-dimensional fingerprint plots for the title salt: (a) dication, (b) anion, and (c) full structure, showing contributions from different contacts, i.e. H···H, O···H/H···O, C···H/H···C, and (e) C···O/O···C. |
C14H16N4O22+·2C9H5O6− | F(000) = 716 |
Mr = 690.56 | Dx = 1.543 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 5.0436 (3) Å | Cell parameters from 6152 reflections |
b = 18.4232 (10) Å | θ = 3.4–29.2° |
c = 16.0796 (9) Å | µ = 0.12 mm−1 |
β = 95.878 (5)° | T = 100 K |
V = 1486.25 (15) Å3 | Prism, pale-yellow |
Z = 2 | 0.30 × 0.10 × 0.05 mm |
Agilent SuperNova Dual diffractometer with an Atlas detector | 3410 independent reflections |
Radiation source: SuperNova (Mo) X-ray Source | 2656 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.069 |
Detector resolution: 10.4041 pixels mm-1 | θmax = 27.5°, θmin = 3.4° |
ω scan | h = −6→6 |
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2014) | k = −23→23 |
Tmin = 0.580, Tmax = 1.000 | l = −20→20 |
17686 measured reflections |
Refinement on F2 | 4 restraints |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.051 | w = 1/[σ2(Fo2) + (0.0563P)2 + 0.8519P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.134 | (Δ/σ)max < 0.001 |
S = 1.07 | Δρmax = 0.46 e Å−3 |
3410 reflections | Δρmin = −0.26 e Å−3 |
238 parameters |
C14H16N4O22+·2C9H5O6− | V = 1486.25 (15) Å3 |
Mr = 690.56 | Z = 2 |
Monoclinic, P21/c | Mo Kα radiation |
a = 5.0436 (3) Å | µ = 0.12 mm−1 |
b = 18.4232 (10) Å | T = 100 K |
c = 16.0796 (9) Å | 0.30 × 0.10 × 0.05 mm |
β = 95.878 (5)° |
Agilent SuperNova Dual diffractometer with an Atlas detector | 3410 independent reflections |
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2014) | 2656 reflections with I > 2σ(I) |
Tmin = 0.580, Tmax = 1.000 | Rint = 0.069 |
17686 measured reflections |
R[F2 > 2σ(F2)] = 0.051 | 238 parameters |
wR(F2) = 0.134 | 4 restraints |
S = 1.07 | Δρmax = 0.46 e Å−3 |
3410 reflections | Δρmin = −0.26 e Å−3 |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.2441 (3) | 0.56058 (7) | 0.47153 (9) | 0.0231 (3) | |
N1 | −0.3956 (3) | 0.69095 (9) | 0.53385 (11) | 0.0198 (4) | |
H1N | −0.285 (4) | 0.6629 (11) | 0.5665 (12) | 0.024* | |
N2 | −0.2089 (3) | 0.56875 (9) | 0.45086 (11) | 0.0194 (4) | |
H2N | −0.364 (3) | 0.5516 (12) | 0.4615 (14) | 0.023* | |
C1 | −0.3894 (4) | 0.69266 (10) | 0.45027 (12) | 0.0187 (4) | |
C2 | −0.5582 (4) | 0.73355 (11) | 0.57322 (13) | 0.0226 (4) | |
H2 | −0.5589 | 0.7300 | 0.6321 | 0.027* | |
C3 | −0.7242 (4) | 0.78235 (11) | 0.52887 (13) | 0.0241 (4) | |
H3 | −0.8446 | 0.8113 | 0.5562 | 0.029* | |
C4 | −0.7117 (4) | 0.78821 (11) | 0.44357 (13) | 0.0234 (4) | |
H4 | −0.8184 | 0.8231 | 0.4122 | 0.028* | |
C5 | −0.5438 (4) | 0.74330 (10) | 0.40389 (13) | 0.0209 (4) | |
H5 | −0.5349 | 0.7472 | 0.3453 | 0.025* | |
C6 | −0.2190 (4) | 0.63885 (10) | 0.40966 (13) | 0.0208 (4) | |
H6A | −0.2906 | 0.6325 | 0.3504 | 0.025* | |
H6B | −0.0358 | 0.6584 | 0.4107 | 0.025* | |
C7 | 0.0204 (4) | 0.53666 (11) | 0.47870 (12) | 0.0197 (4) | |
O2 | 0.8690 (3) | 0.32072 (7) | 0.27064 (9) | 0.0253 (3) | |
O3 | 1.1233 (3) | 0.39299 (8) | 0.35861 (9) | 0.0298 (4) | |
O4 | 1.2729 (3) | 0.64690 (8) | 0.25738 (10) | 0.0260 (3) | |
O5 | 0.9119 (3) | 0.69980 (7) | 0.19086 (9) | 0.0243 (3) | |
H5O | 0.994 (5) | 0.7391 (9) | 0.2034 (16) | 0.036* | |
O6 | 0.2374 (3) | 0.55161 (7) | 0.03570 (9) | 0.0220 (3) | |
O7 | 0.1837 (3) | 0.43588 (7) | 0.07250 (9) | 0.0217 (3) | |
H7O | 0.049 (3) | 0.4407 (14) | 0.0370 (13) | 0.033* | |
C8 | 0.8550 (4) | 0.44714 (10) | 0.24689 (12) | 0.0183 (4) | |
C9 | 0.9905 (4) | 0.51294 (10) | 0.25715 (12) | 0.0178 (4) | |
H9 | 1.1439 | 0.5167 | 0.2964 | 0.021* | |
C10 | 0.9018 (4) | 0.57340 (10) | 0.20997 (12) | 0.0171 (4) | |
C11 | 0.6784 (4) | 0.56752 (10) | 0.15260 (12) | 0.0180 (4) | |
H11 | 0.6170 | 0.6086 | 0.1205 | 0.022* | |
C12 | 0.5438 (4) | 0.50196 (10) | 0.14184 (12) | 0.0178 (4) | |
C13 | 0.6305 (4) | 0.44181 (10) | 0.18970 (12) | 0.0180 (4) | |
H13 | 0.5360 | 0.3972 | 0.1832 | 0.022* | |
C14 | 0.9579 (4) | 0.38131 (10) | 0.29671 (12) | 0.0197 (4) | |
C15 | 1.0500 (4) | 0.64353 (10) | 0.22231 (12) | 0.0191 (4) | |
C16 | 0.3081 (4) | 0.49865 (10) | 0.07891 (12) | 0.0184 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0151 (7) | 0.0200 (7) | 0.0337 (8) | −0.0005 (5) | −0.0001 (6) | 0.0019 (6) |
N1 | 0.0211 (9) | 0.0166 (8) | 0.0204 (9) | −0.0001 (6) | −0.0033 (7) | 0.0019 (7) |
N2 | 0.0166 (8) | 0.0145 (8) | 0.0264 (9) | 0.0000 (6) | −0.0006 (7) | 0.0020 (7) |
C1 | 0.0193 (9) | 0.0160 (9) | 0.0197 (10) | −0.0030 (7) | −0.0031 (7) | 0.0000 (8) |
C2 | 0.0266 (11) | 0.0206 (10) | 0.0197 (10) | −0.0036 (8) | −0.0014 (8) | −0.0006 (8) |
C3 | 0.0276 (11) | 0.0176 (10) | 0.0272 (11) | −0.0007 (8) | 0.0027 (8) | −0.0034 (8) |
C4 | 0.0274 (11) | 0.0145 (9) | 0.0270 (11) | 0.0008 (8) | −0.0032 (8) | 0.0008 (8) |
C5 | 0.0252 (10) | 0.0166 (9) | 0.0201 (10) | −0.0018 (8) | −0.0024 (8) | 0.0006 (8) |
C6 | 0.0221 (10) | 0.0176 (10) | 0.0221 (10) | −0.0002 (7) | −0.0006 (8) | 0.0021 (8) |
C7 | 0.0188 (9) | 0.0191 (10) | 0.0207 (10) | −0.0003 (7) | −0.0002 (7) | −0.0034 (8) |
O2 | 0.0290 (8) | 0.0153 (7) | 0.0298 (8) | 0.0007 (6) | −0.0060 (6) | 0.0020 (6) |
O3 | 0.0359 (9) | 0.0218 (8) | 0.0281 (8) | 0.0010 (6) | −0.0140 (7) | 0.0031 (6) |
O4 | 0.0214 (7) | 0.0204 (7) | 0.0341 (9) | −0.0014 (6) | −0.0071 (6) | −0.0030 (6) |
O5 | 0.0260 (8) | 0.0135 (7) | 0.0313 (8) | −0.0026 (6) | −0.0074 (6) | 0.0017 (6) |
O6 | 0.0220 (7) | 0.0185 (7) | 0.0234 (7) | −0.0015 (5) | −0.0072 (6) | 0.0036 (6) |
O7 | 0.0210 (7) | 0.0163 (7) | 0.0256 (8) | −0.0035 (5) | −0.0084 (6) | 0.0020 (6) |
C8 | 0.0220 (10) | 0.0154 (9) | 0.0171 (9) | 0.0028 (7) | 0.0009 (7) | 0.0000 (7) |
C9 | 0.0186 (9) | 0.0192 (9) | 0.0149 (9) | 0.0011 (7) | −0.0012 (7) | −0.0019 (7) |
C10 | 0.0178 (9) | 0.0148 (9) | 0.0185 (9) | −0.0003 (7) | 0.0016 (7) | −0.0013 (7) |
C11 | 0.0204 (10) | 0.0146 (9) | 0.0185 (10) | 0.0037 (7) | −0.0004 (8) | 0.0013 (7) |
C12 | 0.0175 (9) | 0.0169 (9) | 0.0184 (10) | 0.0010 (7) | −0.0001 (7) | 0.0001 (7) |
C13 | 0.0194 (9) | 0.0150 (9) | 0.0196 (10) | 0.0000 (7) | 0.0013 (7) | −0.0018 (7) |
C14 | 0.0206 (9) | 0.0164 (9) | 0.0214 (10) | 0.0021 (7) | −0.0010 (8) | 0.0016 (8) |
C15 | 0.0226 (10) | 0.0166 (9) | 0.0176 (9) | −0.0001 (7) | 0.0000 (8) | −0.0015 (7) |
C16 | 0.0199 (10) | 0.0162 (9) | 0.0186 (10) | −0.0001 (7) | −0.0001 (8) | 0.0002 (7) |
O1—C7 | 1.227 (2) | O3—C14 | 1.250 (2) |
N1—C2 | 1.340 (3) | O4—C15 | 1.206 (2) |
N1—C1 | 1.348 (3) | O5—C15 | 1.320 (2) |
N1—H1N | 0.892 (10) | O5—H5O | 0.848 (10) |
N2—C7 | 1.335 (3) | O6—C16 | 1.229 (2) |
N2—C6 | 1.450 (2) | O7—C16 | 1.315 (2) |
N2—H2N | 0.878 (10) | O7—H7O | 0.847 (10) |
C1—C5 | 1.384 (3) | C8—C13 | 1.387 (3) |
C1—C6 | 1.504 (3) | C8—C9 | 1.393 (3) |
C2—C3 | 1.377 (3) | C8—C14 | 1.516 (3) |
C2—H2 | 0.9500 | C9—C10 | 1.395 (3) |
C3—C4 | 1.384 (3) | C9—H9 | 0.9500 |
C3—H3 | 0.9500 | C10—C11 | 1.385 (3) |
C4—C5 | 1.385 (3) | C10—C15 | 1.496 (3) |
C4—H4 | 0.9500 | C11—C12 | 1.388 (3) |
C5—H5 | 0.9500 | C11—H11 | 0.9500 |
C6—H6A | 0.9900 | C12—C13 | 1.394 (3) |
C6—H6B | 0.9900 | C12—C16 | 1.481 (3) |
C7—C7i | 1.538 (4) | C13—H13 | 0.9500 |
O2—C14 | 1.259 (2) | ||
C2—N1—C1 | 122.36 (17) | C15—O5—H5O | 110.7 (18) |
C2—N1—H1N | 116.1 (15) | C16—O7—H7O | 107.8 (17) |
C1—N1—H1N | 121.5 (15) | C13—C8—C9 | 119.82 (17) |
C7—N2—C6 | 122.43 (17) | C13—C8—C14 | 120.39 (17) |
C7—N2—H2N | 122.4 (15) | C9—C8—C14 | 119.77 (17) |
C6—N2—H2N | 114.8 (15) | C8—C9—C10 | 120.28 (17) |
N1—C1—C5 | 118.93 (18) | C8—C9—H9 | 119.9 |
N1—C1—C6 | 119.35 (17) | C10—C9—H9 | 119.9 |
C5—C1—C6 | 121.71 (18) | C11—C10—C9 | 119.56 (17) |
N1—C2—C3 | 120.45 (19) | C11—C10—C15 | 121.15 (17) |
N1—C2—H2 | 119.8 | C9—C10—C15 | 119.29 (17) |
C3—C2—H2 | 119.8 | C10—C11—C12 | 120.34 (17) |
C2—C3—C4 | 118.52 (19) | C10—C11—H11 | 119.8 |
C2—C3—H3 | 120.7 | C12—C11—H11 | 119.8 |
C4—C3—H3 | 120.7 | C11—C12—C13 | 120.10 (17) |
C3—C4—C5 | 120.13 (19) | C11—C12—C16 | 117.97 (16) |
C3—C4—H4 | 119.9 | C13—C12—C16 | 121.92 (17) |
C5—C4—H4 | 119.9 | C8—C13—C12 | 119.89 (17) |
C1—C5—C4 | 119.44 (19) | C8—C13—H13 | 120.1 |
C1—C5—H5 | 120.3 | C12—C13—H13 | 120.1 |
C4—C5—H5 | 120.3 | O3—C14—O2 | 127.13 (18) |
N2—C6—C1 | 112.55 (17) | O3—C14—C8 | 116.59 (17) |
N2—C6—H6A | 109.1 | O2—C14—C8 | 116.27 (17) |
C1—C6—H6A | 109.1 | O4—C15—O5 | 124.63 (17) |
N2—C6—H6B | 109.1 | O4—C15—C10 | 122.39 (17) |
C1—C6—H6B | 109.1 | O5—C15—C10 | 112.98 (16) |
H6A—C6—H6B | 107.8 | O6—C16—O7 | 123.05 (17) |
O1—C7—N2 | 125.63 (19) | O6—C16—C12 | 121.29 (17) |
O1—C7—C7i | 121.6 (2) | O7—C16—C12 | 115.66 (16) |
N2—C7—C7i | 112.8 (2) | ||
C2—N1—C1—C5 | 4.2 (3) | C10—C11—C12—C13 | 1.0 (3) |
C2—N1—C1—C6 | −174.80 (18) | C10—C11—C12—C16 | −179.31 (17) |
C1—N1—C2—C3 | −1.2 (3) | C9—C8—C13—C12 | 1.0 (3) |
N1—C2—C3—C4 | −2.4 (3) | C14—C8—C13—C12 | −177.46 (18) |
C2—C3—C4—C5 | 2.9 (3) | C11—C12—C13—C8 | −1.4 (3) |
N1—C1—C5—C4 | −3.5 (3) | C16—C12—C13—C8 | 178.90 (18) |
C6—C1—C5—C4 | 175.42 (18) | C13—C8—C14—O3 | −165.39 (18) |
C3—C4—C5—C1 | 0.0 (3) | C9—C8—C14—O3 | 16.1 (3) |
C7—N2—C6—C1 | −125.7 (2) | C13—C8—C14—O2 | 15.3 (3) |
N1—C1—C6—N2 | 34.8 (2) | C9—C8—C14—O2 | −163.19 (18) |
C5—C1—C6—N2 | −144.13 (19) | C11—C10—C15—O4 | −163.64 (19) |
C6—N2—C7—O1 | −1.8 (3) | C9—C10—C15—O4 | 16.4 (3) |
C6—N2—C7—C7i | 179.1 (2) | C11—C10—C15—O5 | 16.2 (3) |
C13—C8—C9—C10 | −0.2 (3) | C9—C10—C15—O5 | −163.84 (17) |
C14—C8—C9—C10 | 178.26 (17) | C11—C12—C16—O6 | 2.0 (3) |
C8—C9—C10—C11 | −0.2 (3) | C13—C12—C16—O6 | −178.26 (18) |
C8—C9—C10—C15 | 179.80 (17) | C11—C12—C16—O7 | −178.40 (17) |
C9—C10—C11—C12 | −0.2 (3) | C13—C12—C16—O7 | 1.3 (3) |
C15—C10—C11—C12 | 179.82 (18) |
Symmetry code: (i) −x, −y+1, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···O1i | 0.88 (2) | 2.38 (2) | 2.704 (2) | 102 (1) |
O7—H7O···O6ii | 0.85 (2) | 1.77 (2) | 2.614 (2) | 178 (2) |
O5—H5O···O2iii | 0.85 (2) | 1.69 (2) | 2.5352 (19) | 175 (2) |
N2—H2N···O1iv | 0.88 (2) | 2.01 (2) | 2.816 (2) | 153 (2) |
N1—H1N···O3v | 0.89 (2) | 1.73 (2) | 2.604 (2) | 169 (2) |
C5—H5···O4vi | 0.95 | 2.46 | 3.019 (3) | 117 |
C6—H6A···O4vi | 0.99 | 2.55 | 3.362 (3) | 140 |
C2—H2···O2i | 0.95 | 2.50 | 3.251 (3) | 136 |
C3—H3···O6vii | 0.95 | 2.59 | 3.068 (2) | 112 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x, −y+1, −z; (iii) −x+2, y+1/2, −z+1/2; (iv) x−1, y, z; (v) −x+1, −y+1, −z+1; (vi) x−2, y, z; (vii) x−1, −y+3/2, z+1/2. |
Coformer | C—Npy—C | C4N2O2/N-ring | C(═O)—C(═O) | Npy—C—C—Namide | Refcodeb | Ref. |
2-NH2C6H4CO2Hc | 119.01 (11) | 69.63 (6) | 1.54119 (16) | 165.01 (10) | DIDZEX | Arman, Miller et al. (2012) |
2,6-(NO2)2C6H3CO2-d | 123.00 (12) | 72.92 (5) | 1.5339 (18) | 73.84 (15) | TIPHEH | Arman et al. (2013) |
3,5-(CO2H)2C6H3CO2- | 122.36 (18) | 68.21 (8) | 1.538 (3) | 34.8 (2) | – | this work |
Notes: (a) All diamide molecules/dianions are centrosymmetric; (b) Groom & Allen (2014); (c) 1:2 co-crystal with 2-aminobenzoic acid; (d) 1:2 salt with 2,6-dinitrobenzoate in which both pyridyl-N atoms are protonated. |
Cation | C6/CO2 | C6/CO2H | C6/CO2H | CSD Refcodeb | Ref. |
C_Ic | 8.6 (2) | 4.96 (19) | 12.82 (16) | QUFYIA | Santra et al. (2009) |
1.6 (2) | 8.9 (2) | 19.13 (15) | |||
C_IIc | 4.5 (3) | 7.5 (4) | 3.43 (18) | LUBJAV | Singh et al. (2015) |
2.1 (4) | 2.0 (4) | 2.6 (3) | |||
C_III | 5.92 (11) | 1.69 (14) | 10.38 (10) | NIFGOY | Ferguson et al. (1998) |
C_IV | 25.13 (10) | 22.50 (10) | 11.60 (7) | CUMQUX | Basu et al. (2009) |
dication | 15.70 (13) | 16.34 (12) | 1.99 (10) | – | this work |
Notes: (a) Refer to Scheme 2 for chemical structures; (b) Groom & Allen (2014); (c) Two independent anions. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···O1i | 0.877 (17) | 2.38 (2) | 2.704 (2) | 102.2 (14) |
O7—H7O···O6ii | 0.846 (18) | 1.768 (18) | 2.614 (2) | 178 (2) |
O5—H5O···O2iii | 0.85 (2) | 1.689 (19) | 2.5352 (19) | 175 (2) |
N2—H2N···O1iv | 0.877 (17) | 2.006 (15) | 2.816 (2) | 153 (2) |
N1—H1N···O3v | 0.89 (2) | 1.73 (2) | 2.604 (2) | 168.7 (19) |
C5—H5···O4vi | 0.95 | 2.46 | 3.019 (3) | 117 |
C6—H6A···O4vi | 0.99 | 2.55 | 3.362 (3) | 140 |
C2—H2···O2i | 0.95 | 2.50 | 3.251 (3) | 136 |
C3—H3···O6vii | 0.95 | 2.59 | 3.068 (2) | 112 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x, −y+1, −z; (iii) −x+2, y+1/2, −z+1/2; (iv) x−1, y, z; (v) −x+1, −y+1, −z+1; (vi) x−2, y, z; (vii) x−1, −y+3/2, z+1/2. |
Contact | Distance | Symmetry operation |
C1···O1 | 3.096 (2) | -1 + x, y, z |
C7···O3 | 3.072 (3) | 1 - x, 1 - y, 1 - z |
C11···O4 | 3.141 (3) | -1 + x, y, z |
C14···H1N | 2.74 (2) | 1 - x, 1 - y, 1 - z |
C10···H6A | 2.77 | 1+x, y, z |
C14···H5O | 2.631 (17) | -x, -1/2 + y, 1/2 - z |
C16···H7O | 2.70 (2) | -x, 1 - y, -z |
Contact | Dication | Anion | Salt |
O···H/H···O | 41.6 | 47.2 | 43.2 |
H···H | 25.1 | 16.7 | 23.7 |
C···H/H···C | 20.2 | 17.4 | 17.3 |
C···O/O···C | 6.6 | 12.8 | 10.2 |
N···H/H···N | 2.3 | 0.3 | 1.1 |
C···C | 0.2 | 3.0 | 2.2 |
O···O | 1.2 | 2.0 | 1.0 |
N···O/O···N | 2.3 | 0.1 | 1.2 |
N···C/C···N | 0.5 | 0.5 | 0.1 |
Contact | Dication | Anion | Salt |
O···H/H···O | 1.37 | 1.50 | 1.40 |
H···H | 0.77 | 0.69 | 0.80 |
C···H/H···C | 1.27 | 0.96 | 0.99 |
C···O/O···C | 0.90 | 1.09 | 1.13 |
N···H/H···N | 0.77 | 0.68 | 0.88 |
N···O/O···N | 1.68 | – | – |
Experimental details
Crystal data | |
Chemical formula | C14H16N4O22+·2C9H5O6− |
Mr | 690.56 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 5.0436 (3), 18.4232 (10), 16.0796 (9) |
β (°) | 95.878 (5) |
V (Å3) | 1486.25 (15) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.30 × 0.10 × 0.05 |
Data collection | |
Diffractometer | Agilent SuperNova Dual diffractometer with an Atlas detector |
Absorption correction | Multi-scan (CrysAlis PRO; Agilent, 2014) |
Tmin, Tmax | 0.580, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 17686, 3410, 2656 |
Rint | 0.069 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.051, 0.134, 1.07 |
No. of reflections | 3410 |
No. of parameters | 238 |
No. of restraints | 4 |
Δρmax, Δρmin (e Å−3) | 0.46, −0.26 |
Computer programs: CrysAlis PRO (Agilent, 2014), SHELXS97 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015), ORTEP-3 for Windows (Farrugia, 2012), QMol (Gans & Shalloway, 2001) and DIAMOND (Brandenburg, 2006), publCIF (Westrip, 2010).
Footnotes
‡Additional correspondence author, e-mail: mmjotani@rediffmail.com.
Acknowledgements
The authors thank the Exploratory Research Grant Scheme (ER008-2013A) for support.
References
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