Crystal structures of N-(pyridin-2-ylmethyl)pyrazine-2-carboxamide (monoclinic polymorph) and N-(pyridin-4-ylmethyl)pyrazine-2-carboxamide

The title molecules, HL1 and HL2, differ in their conformation with the pyridine ring being inclined to the pyrazine ring by 61.34 (6) and 84.33 (12)°, respectively. The crystal packing is also slightly different, with molecules of HL1 linked by pairs of N—H⋯N hydrogen bonds, forming inversion dimers, while for HL2 molecules are linked by N—H⋯N and C—H⋯N hydrogen bonds, forming chains along [010].


Chemical context
The title compounds form part of a series of ligands synthesized in order to study their coordination chemistry with 3d transition metals (Cati, 2002).
They have been used to construct coordination polymers and multi-nuclear compounds, and to study their magnetic ISSN 1600-5368 properties (Cati et al., 2004). Similar ligands have been synthesized by other groups who have studied, for example, the magnetic properties of some copper(II) complexes (Hausmann et al., 2003;Kingele et al., 2007).

Structural commentary
The molecular structure of ligand HL1 is illustrated in Fig. 1. HL1 was measured at 153 K and crystallized in the monoclinic space group P2 1 /c with Z = 4. The angle is 91.461 (11) and the systematic absences, the R int value (0.0348) and the successful refinement {R1 [I > 2(I)] = 0.0319} clearly show that at 153 K the space group is monoclinic P2 1 /c. The same structure measured at room temperature was reported to crystallize in the triclinic space group P1 with Z = 4 (Sasan et al., 2008). However, the three cell angles are close 90 (2) [ = 91.802 (6), = 89.834 (7), = 91.845 (6) ] and the crystal used was a very narrow needle. The final R1 [I > 2(I)] factor was rather high at 0.0699, hence it is possible that the choice of crystal system and space group are incorrect. However, this could not be confirmed when analysing the coordinates using the AddSymm routine in PLATON (Spek, 2009).

Figure 1
A view of the molecular structure of HL1, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. The short intramolecular N-HÁ Á ÁN interaction is shown as a dashed line (see Table 1 for details).

Figure 2
A view of the molecular structure of HL2, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. The short intramolecular N-HÁ Á ÁN interaction is shown as a dashed line (see Table 2 for details).

Figure 3
A partial view along the a axis of the crystal packing of compound HL1. The N-HÁ Á ÁN, C-HÁ Á ÁO and C-HÁ Á ÁN hydrogen bonds are shown as dashed lines (see Table 1 for details).
In the crystal of HL1, molecules are linked by N-HÁ Á ÁN hydrogen bonds, forming inversion dimers with an R 2 2 (10) ring motif. The dimers are linked via bifurcated-acceptor C-HÁ Á ÁO hydrogen bonds, forming sheets lying parallel to (102) (see Table 1 and Fig. 3). The sheets are linked via C-HÁ Á ÁN hydrogen bonds, forming a three-dimensional structure (Table 1 and Fig. 4).

Database survey
A search of the Cambridge Structural Database (Version 5.35, last update November 2013; Allen, 2002) indicated the presence of 282 structures containing the pyrazine-2-carboxamide unit. 81 of these concern pyrazine-2-carboxamide itself. There were 10 hits for complexes of ligand HL1. These include a cobalt(III) (Hellyer et al., 2009), a chromium(III)  and four copper(II) complexes (Mohamadou et al., 2012;Khavasi et al., 2011), all of which are mononuclear with the ligand coordinating in a tridentate manner. There are also two polymeric mercury chloride complexes (Khavasi & Sadegh, 2010), a binuclear manganese chloride complex (Khavasi et al., 2009), and a polymeric silver tetrafluoroborate complex (Hellyer et al., 2009), where the ligand coordinates in a bis-monodentate manner. Plus the report of the ligand itself as mentioned above (Sasan et al., 2008). For ligand HL2 there were no hits. The crystal packing of compound HL1 viewed along the b axis. The N-HÁ Á ÁN, C-HÁ Á ÁO and C-HÁ Á ÁN hydrogen bonds are shown as dashed lines (see Table 1 for details).

Figure 6
The crystal packing of compound HL2 viewed along the c axis. The N-HÁ Á ÁN, C-HÁ Á ÁO and C-HÁ Á ÁN hydrogen bonds are shown as dashed lines (see Table 2 for details).

Figure 5
A partial view along the c axis of the crystal packing of compound HL2. The N-HÁ Á ÁN, and C-HÁ Á ÁN hydrogen bonds are shown as dashed lines (see Table 2 for details).

Synthesis and crystallization
The precursor pyrazine-2-carboxylic acid methyl ester (2-pze) was prepared following the procedure described by Alvarez-Ibarra et al. (1994). 6.21 g (50 mmol) of pyrazine-2-carboxylic acid were added to 50 ml of absolute methanol in a twonecked flask (100 ml). The mixture was heated to 303 K and then 0.4 ml of concentrated sulfuric acid was added slowly. The mixture was heated for 23 h, at least. It was then poured over ice and made alkaline using NaOH (2 N), then extracted with CH 2 Cl 2 . The organic extract was dried over Na 2 SO 4 . The resulting yellow product was purified by recrystallization from hexane, or by column chromatography on silica gel using CH 2 Cl 2 as eluant, giving finally colourless crystals (yield 80%).
The ligand HL1 was prepared by refluxing 2-pze (1.80 g, 13 mmol) and an excess of 2-(aminomethyl)pyridine (1.84 g, 17 mmol) in 12 ml of methanol, for 6 h in a two-necked flask (50 ml). A yellowish oil remained when the methanol was evaporated off. The excess of 2-(aminomethyl)pyridine was eliminated by column chromatography on silica gel using CH 2 Cl 2 as eluant (r = 2 cm, l = 8 cm HL2 was prepared using the same procedure as for HL1. 2-pze (1.38 g, 10 mmol) with, this time, an excess of 4-(aminomethyl)pyridine (1.73 g, 16 mmol) were refluxed in 20 ml of methanol, for 20 h in a two-necked flask (50 ml). 4-(aminomethyl)pyridine (1g, 10 mmol) was then added to the red solution. After 4 h the solution was evaporated to about 8 ml. HL2 crystallized out at room temperature. About 20 ml of diethyl ether was added to filtrate the product. It was then recrystallized from a mixture of 3 ml of methanol and 40 ml of diethyl ether to give colourless blocks (yield 84%; m.p. 422 K).

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 3. The NH H atoms were located in difference Fourier maps and freely refined. The C-bound H atoms were included in calculated positions and treated as riding atoms: C-H = 0.95 Å for HL1 and = 0.93 Å for HL2, with U iso (H) = 1.2U eq (C).  (Macrae et al., 2008); software used to prepare material for publication: SHELXL2013 (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).