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

Cati, D.S.; Stoeckli-Evans, H.

doi:10.1107/S1600536814009519

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Volume 70| Part 7| July 2014| Pages 18-22

https://doi.org/10.1107/S1600536814009519

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Crystal structures of N-(pyridin-2-ylmethyl)pyrazine-2-carboxamide (monoclinic polymorph) and N-(pyridin-4-ylmethyl)pyrazine-2-carboxamide¹

Dilovan S. Cati ^a and Helen Stoeckli-Evans ^b ^*

^aDebiopharm International S.A., Chemin Messidor 5-7, CP 5911, CH-1002 Lausanne, Switzerland, and ^bInstitute of Physics, University of Neuchâtel, rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
^*Correspondence e-mail: helen.stoeckli-evans@unine.ch

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 25 April 2014; accepted 25 April 2014; online 23 June 2014)

The title compounds, C₁₁H₁₀N₄O (HL1) and C₁₁H₁₀N₄O (HL2), are pyridine 2-ylmethyl and 4-ylmethyl derivatives, respectively, of pyrazine-2-carboxamide. HL1 was measured at 153 K and crystallized in the monoclinic space group P2₁/c with Z = 4. There has been a report of the same structure measured at room temperature but assumed to crystallize in the triclinic space group P-1 with Z = 4 [Sasan et al. (2008 ). Monatsh. Chem. 139, 773–780]. In HL1, the pyridine ring is inclined to the pyrazine ring by 61.34 (6)°, while in HL2 this dihedral angle is 84.33 (12)°. In both molecules, there is a short N—H⋯N interaction involving the pyrazine carboxamide unit. In the crystal of HL1, molecules are linked by N—H⋯N hydrogen bonds, forming inversion dimers with an R₂²(10) ring motif. The dimers are linked via bifurcated-acceptor C—H⋯O hydrogen bonds, forming sheets lying parallel to (102). The sheets are linked via C—H⋯N hydrogen bonds, forming a three-dimensional structure. In the crystal of HL2, molecules are linked by N—H⋯N and C—H⋯N hydrogen bonds to form chains propagating along [010]. The chains are linked via C—H⋯O hydrogen bonds, forming sheets lying parallel to (100). Within the sheets there are π–π interactions involving neighbouring pyrazine rings [inter-centroid distance = 3.711 (15) Å]. Adjacent sheets are linked via parallel slipped π–π interactions involving inversion-related pyridine rings [inter-centroid distance = 3.6395 (17) Å], forming a three-dimensional structure.

Keywords: crystal structure; pyrazine; pyridine; carboxamide.

CCDC references: 1004272; 1004273

1. 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 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 ).

2. 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 P2₁/c with Z = 4. The β angle is 91.461 (11)° and the systematic absences, the R_i_nt value (0.0348) and the successful refinement {R1 [I > 2σ(I)] = 0.0319} clearly show that at 153 K the space group is monoclinic P2₁/c. The same structure measured at room temperature was reported to crystallize in the triclinic space group P $[\overline{1}]$ with Z = 4 (Sasan et al., 2008). However, the three cell angles are close 90 (2)° [α = 91.802 (6), β = 89.834 (7), γ = 91.845 (6)°] and the crystal used was a very narrow needle. The final R1 [I > 2σ(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—H⋯N interaction is shown as a dashed line (see Table 1

for details).

In the molecule of HL1 there is a short N—H⋯N hydrogen bond present in the pyrazine carboxamide unit (Table 1), and the amide group, C5(=O1)N3, is approximately coplanar with the pyrazine (N1/N2/C1–C4) ring [dihedral angle = 2.56 (14)°]. The pyrazine and pyridine (N4/C7–C10) rings are inclined to one another by 61.34 (6)°. In the triclinic structure mentioned above, the same angle in the two independent molecules is 63.31 (13) and 61.94 (13)°.

Table 1
Hydrogen-bond geometry (Å, °) for HL1

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3N⋯N1	0.901 (16)	2.332 (15)	2.7136 (15)	105.4 (11)
N3—H3N⋯N4ⁱ	0.901 (16)	2.206 (16)	2.9929 (14)	145.6 (13)
C3—H3⋯O1ⁱⁱ	0.95	2.51	3.1544 (15)	125
C4—H4⋯O1ⁱⁱ	0.95	2.56	3.1748 (15)	123
C10—H10⋯N2ⁱⁱⁱ	0.95	2.62	3.5678 (17)	174
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) $[x+1, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (iii) $[-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

The molecular structure of HL2 is illustrated in Fig. 2. Here too there is a short intramolecular N—H⋯N contact involving the pyrazine carboxamide unit (Table 2), and the amide group, C5(=O1)N3, is almost coplanar with the pyrazine (N1/N2/C1–C4) ring with a dihedral angle of 3.9 (3)°. Here the pyrazine and pyridine (N4/C7–C10) rings are almost normal to one another with a dihedral angle of 84.33 (12)°.

Table 2
Hydrogen-bond geometry (Å, °) for HL2

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3N⋯N1	0.83 (3)	2.27 (3)	2.713 (3)	114 (2)
N3—H3N⋯N2ⁱ	0.83 (3)	2.52 (3)	3.214 (3)	142 (2)
C2—H2⋯N1ⁱⁱ	0.93	2.47	3.315 (3)	151
C8—H8⋯O1ⁱⁱⁱ	0.93	2.55	3.373 (3)	148
Symmetry codes: (i) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

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—H⋯N interaction is shown as a dashed line (see Table 2

for details).

3. Supramolecular features

In the crystal of HL1, molecules are linked by N—H⋯N hydrogen bonds, forming inversion dimers with an R₂²(10) ring motif. The dimers are linked via bifurcated-acceptor C—H⋯O hydrogen bonds, forming sheets lying parallel to (102) (see Table 1 and Fig. 3). The sheets are linked via C—H⋯N hydrogen bonds, forming a three-dimensional structure (Table 1 and Fig. 4).

Figure 3
A partial view along the a axis of the crystal packing of compound HL1. The N—H⋯N, C—H⋯O and C-H⋯N hydrogen bonds are shown as dashed lines (see Table 1

for details).

Figure 4
The crystal packing of compound HL1 viewed along the b axis. The N—H⋯N, C—H⋯O and C—H⋯N hydrogen bonds are shown as dashed lines (see Table 1

for details).

In the crystal of HL2, molecules are linked by N—H⋯N and C—H⋯N hydrogen bonds to form chains propagating along [010], as shown in Table 2 and Fig. 5. The chains are linked via C—H⋯O hydrogen bonds, forming sheets lying parallel to (100). Within the sheets there are π–π interactions involving neighbouring pyrazine rings [Cg1⋯Cg1ⁱ = 3.7113 (15) Å; Cg1 is the centroid of the pyrazine ring N1/N2/C1–C4; symmetry code: (i) = x, −y + $[{1\over 2}]$ , z − $[{1\over 2}]$ ]. The sheets are linked via slipped parallel π–π interactions involving inversion-related pyridine rings [Cg2⋯Cg2ⁱⁱ = 3.6395 (11) Å, normal distance = 3.4164 (11), slippage = 1.255 Å; Cg2 is the centroid of pyridine ring N4/C7–C11; symmetry code: (ii) −x, −y, −z], forming a three-dimensional structure (Table 2 and Fig. 6).

Figure 5
A partial view along the c axis of the crystal packing of compound HL2. The N—H⋯N, and C—H⋯N hydrogen bonds are shown as dashed lines (see Table 2

for details).

Figure 6
The crystal packing of compound HL2 viewed along the c axis. The N—H⋯N, C—H⋯O and C—H⋯N hydrogen bonds are shown as dashed lines (see Table 2

for details).

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) (Khavasi et al., 2010 ) 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.

5. 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 two-necked 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 CH₂Cl₂. The organic extract was dried over Na₂SO₄. The resulting yellow product was purified by recrystallization from hexane, or by column chromatography on silica gel using CH₂Cl₂ 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 CH₂Cl₂ as eluant (r = 2 cm, l = 8 cm). A yellow band of 2-(aminomethyl)pyridine remained on the column. After evaporation, the ligand could be recrystallized from diethyl ether, acetonitrile or ethyl acetate. HL1 is very soluble in MeOH and in CH₂Cl₂. Recrystallization from diethyl ether gave colourless blocks of HL1 (yield 91%; m.p. 388 K). Analysis for C₁₁H₁₀N₄O (M_r = 214.46 g/mol) Calculated (%) C: 61.67 H: 4.71 N: 26.15; Found (%) C: 61.80 H: 4.76 N: 26.45. Spectroscopic data are available in the supporting information.

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). Anal. for C₁₁H₁₀N₄O (M_r = 214.46 g/mol) Calculated (%) C: 61.67 H: 4.71 N: 26.15 Found (%) C: 61.57 H: 4.75 N: 26.20. Spectroscopic data are available in the supporting information.

6. 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).

Table 3
Experimental details

	HL1	HL2
Crystal data
Chemical formula	C₁₁H₁₀N₄O	C₁₁H₁₀N₄O
M_r	214.23	214.23
Crystal system, space group	Monoclinic, P2₁/c	Monoclinic, P2₁/c
Temperature (K)	153	293
a, b, c (Å)	4.1527 (4), 20.4629 (18), 12.0106 (11)	13.8564 (14), 11.1841 (11), 6.9122 (10)
β (°)	91.461 (11)	104.356 (14)
V (Å³)	1020.28 (16)	1037.7 (2)
Z	4	4
Radiation type	Mo Kα	Mo Kα
μ (mm⁻¹)	0.10	0.09
Crystal size (mm)	0.50 × 0.40 × 0.35	0.38 × 0.30 × 0.19

Data collection
Diffractometer	Stoe IPDS 1	Stoe AED2 four-circle
No. of measured, independent and observed [I > 2σ(I)] reflections	7822, 1958, 1548	4132, 1937, 1198
R_int	0.035	0.032
(sin θ/λ)_max (Å⁻¹)	0.615	0.605

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.088, 1.03	0.054, 0.127, 1.10
No. of reflections	1958	1937
No. of parameters	149	150
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.17, −0.17	0.17, −0.16
Computer programs: EXPOSE, CELL and INTEGRATE in IPDSI, STADI4 and X-RED (Stoe & Cie, 1997 ), SHELXS97 and SHELXL2013 (Sheldrick, 2008 ), Mercury (Macrae et al., 2008 ), PLATON (Spek, 2009) and publCIF (Westrip, 2010 ).

Supporting information

CCDC references: 1004272; 1004273

Crystal structure: contains datablocks HL1, HL2, global. DOI: https://doi.org/10.1107/S1600536814009519/hb0007sup1.cif

Structure factors: contains datablock HL1. DOI: https://doi.org/10.1107/S1600536814009519/hb0007HL1sup2.hkl

Structure factors: contains datablock HL2. DOI: https://doi.org/10.1107/S1600536814009519/hb0007HL2sup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536814009519/hb0007HL1sup4.cml

Supporting information file. DOI: https://doi.org/10.1107/S1600536814009519/hb0007HL2sup5.cml

checkCIF report

Computing details top

Data collection: EXPOSE in IPDSI (Stoe & Cie, 1997) for HL1; STADI4 (Stoe & Cie, 1997) for HL2. Cell refinement: CELL in IPDSI (Stoe & Cie, 1997) for HL1; STADI4 (Stoe & Cie, 1997) for HL2. Data reduction: INTEGRATE in IPDSI (Stoe & Cie, 1997) for HL1; X-RED (Stoe & Cie, 1997) for HL2. For both compounds, program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2013 (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

(HL1) N-(Pyridin-2-ylmethyl)pyrazine-2-carboxamide top

Crystal data top

C₁₁H₁₀N₄O	F(000) = 448
M_r = 214.23	D_x = 1.395 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 4.1527 (4) Å	Cell parameters from 6532 reflections
b = 20.4629 (18) Å	θ = 2.0–25.9°
c = 12.0106 (11) Å	µ = 0.10 mm⁻¹
β = 91.461 (11)°	T = 153 K
V = 1020.28 (16) Å³	Block, colourless
Z = 4	0.50 × 0.40 × 0.35 mm

Data collection top

Stoe IPDS 1 diffractometer	1548 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.035
Plane graphite monochromator	θ_max = 25.9°, θ_min = 2.0°
φ rotation scans	h = −5→5
7822 measured reflections	k = −25→25
1958 independent reflections	l = −14→14

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.032	Hydrogen site location: mixed
wR(F²) = 0.088	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ²(F_o²) + (0.0539P)² + 0.0704P] where P = (F_o² + 2F_c²)/3
1958 reflections	(Δ/σ)_max < 0.001
149 parameters	Δρ_max = 0.17 e Å⁻³
0 restraints	Δρ_min = −0.17 e Å⁻³

Special details top

Experimental. Spectrosopic data for HL1: ¹H NMR (400 MHz, DMSO-d6; code Hh/NH, Hl/C3, Hn/C1, Hm/C2, Hb/C11, Hd/C9, He/C8, Hc/C10, Hg/C6): 9.50 (t, 1H, Jhg = 6.0, Hh); 9.23 (d, 1H, Jlm = 1.5, Hl); 8.91 (d, 1H, Jnm = 2.5, Hn); 8.78 (dd, 1H, Jmn = 2.5, Jml = 1.5, Hm); 8.53 (ddd, 1H, Jbc = 4.8, Jbd = 1.8, Jbe = 0.8, Hb); 7.76 (td, 1H, Jdc = 7.7, Jdb = 1.8, Hd); 7.35 (d, 1H, Jed = 7.9, He); 7.28 (dd, 1H, Jcd = 7.7, Jcb = 4.8, Hc); 4.64 (d, 2H, Jgh = 6.0, He). ¹³C NMR (400 MHz, DMSO-d6): 163.9, 158.6, 149.7, 148.6, 145.5, 144.4, 144.3, 137.6, 123.1, 121.9, 45.0. IR (KBr pellet, cm^-1): 3248 (m), 3066 (w), 3018 (w), 2949 (w), 1669 (versus), 1593 (m), 1570 (m), 1517 (versus), 1478 (m), 1462 (s), 1440 (s), 1423 (s), 1389 (s), 1350 (m), 1320 (m), 1287 (s), 1250 (m), 1221 (m), 1168 (s), 1148 (m), 1103 (m), 1055 (m), 1021 (s), 1000 (m), 975 (m), 870 (m), 840 (w), 776 (m), 753 (s), 707 (m), 634 (m), 611 (m), 528 (m), 444 (m).

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.7345 (3)	0.30055 (5)	0.42625 (8)	0.0260 (2)
N2	0.7780 (3)	0.16917 (5)	0.49125 (9)	0.0343 (3)
N3	0.4290 (2)	0.38859 (5)	0.55546 (8)	0.0224 (2)
H3N	0.514 (4)	0.3982 (7)	0.4892 (13)	0.037 (4)*
N4	0.5222 (3)	0.53951 (5)	0.66045 (8)	0.0293 (3)
O1	0.3074 (2)	0.30857 (4)	0.67870 (7)	0.0344 (2)
C1	0.6100 (3)	0.27903 (5)	0.52119 (9)	0.0215 (3)
C2	0.6318 (3)	0.21416 (6)	0.55317 (10)	0.0287 (3)
H2	0.5401	0.2011	0.6213	0.034*
C3	0.9010 (3)	0.19099 (6)	0.39702 (10)	0.0305 (3)
H3	1.0071	0.1609	0.3501	0.037*
C4	0.8800 (3)	0.25567 (6)	0.36486 (10)	0.0290 (3)
H4	0.9724	0.2686	0.2967	0.035*
C5	0.4355 (3)	0.32697 (6)	0.59277 (9)	0.0229 (3)
C6	0.2435 (3)	0.43932 (6)	0.60984 (10)	0.0263 (3)
H6A	0.0627	0.4186	0.6488	0.032*
H6B	0.1503	0.4688	0.5522	0.032*
C7	0.4391 (3)	0.47934 (5)	0.69249 (9)	0.0219 (3)
C8	0.5266 (3)	0.45428 (6)	0.79615 (10)	0.0271 (3)
H8	0.4640	0.4113	0.8163	0.033*
C9	0.7051 (3)	0.49220 (6)	0.86977 (10)	0.0312 (3)
H9	0.7682	0.4757	0.9410	0.037*
C10	0.7906 (4)	0.55455 (6)	0.83801 (11)	0.0350 (3)
H10	0.9115	0.5822	0.8870	0.042*
C11	0.6957 (4)	0.57556 (6)	0.73353 (11)	0.0376 (3)
H11	0.7569	0.6183	0.7117	0.045*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0305 (6)	0.0246 (5)	0.0231 (5)	−0.0011 (4)	0.0045 (4)	−0.0005 (4)
N2	0.0434 (7)	0.0239 (5)	0.0356 (6)	0.0046 (5)	0.0043 (5)	−0.0006 (4)
N3	0.0263 (5)	0.0207 (5)	0.0201 (5)	0.0007 (4)	0.0020 (4)	−0.0008 (4)
N4	0.0412 (7)	0.0219 (5)	0.0249 (5)	0.0016 (4)	0.0022 (4)	0.0007 (4)
O1	0.0454 (6)	0.0295 (5)	0.0288 (5)	0.0000 (4)	0.0154 (4)	0.0036 (4)
C1	0.0219 (6)	0.0217 (6)	0.0208 (5)	−0.0024 (5)	−0.0014 (4)	−0.0008 (4)
C2	0.0369 (8)	0.0247 (6)	0.0246 (6)	0.0006 (5)	0.0032 (5)	0.0016 (5)
C3	0.0327 (7)	0.0275 (6)	0.0313 (7)	0.0029 (5)	0.0039 (5)	−0.0067 (5)
C4	0.0321 (7)	0.0305 (6)	0.0246 (6)	−0.0012 (5)	0.0056 (5)	−0.0028 (5)
C5	0.0233 (6)	0.0242 (6)	0.0211 (6)	−0.0021 (5)	−0.0003 (5)	−0.0001 (4)
C6	0.0244 (7)	0.0248 (6)	0.0296 (6)	0.0062 (5)	−0.0010 (5)	−0.0021 (5)
C7	0.0210 (6)	0.0213 (6)	0.0235 (6)	0.0055 (5)	0.0057 (4)	−0.0011 (4)
C8	0.0275 (7)	0.0258 (6)	0.0281 (6)	0.0005 (5)	0.0024 (5)	0.0046 (5)
C9	0.0333 (7)	0.0374 (7)	0.0228 (6)	0.0044 (6)	−0.0001 (5)	0.0010 (5)
C10	0.0420 (8)	0.0310 (7)	0.0317 (7)	−0.0002 (6)	−0.0034 (6)	−0.0093 (5)
C11	0.0554 (9)	0.0207 (6)	0.0366 (7)	−0.0046 (6)	−0.0022 (6)	−0.0006 (5)

Geometric parameters (Å, º) top

N1—C4	1.3323 (16)	C3—H3	0.9500
N1—C1	1.3386 (15)	C4—H4	0.9500
N2—C3	1.3307 (17)	C6—C7	1.5082 (16)
N2—C2	1.3387 (16)	C6—H6A	0.9900
N3—C5	1.3382 (15)	C6—H6B	0.9900
N3—C6	1.4570 (15)	C7—C8	1.3865 (17)
N3—H3N	0.901 (16)	C8—C9	1.3784 (18)
N4—C7	1.3379 (15)	C8—H8	0.9500
N4—C11	1.3422 (17)	C9—C10	1.3806 (18)
O1—C5	1.2319 (14)	C9—H9	0.9500
C1—C2	1.3842 (16)	C10—C11	1.3745 (19)
C1—C5	1.5028 (16)	C10—H10	0.9500
C2—H2	0.9500	C11—H11	0.9500
C3—C4	1.3808 (18)

C4—N1—C1	115.80 (10)	N3—C6—C7	113.57 (9)
C3—N2—C2	115.53 (11)	N3—C6—H6A	108.9
C5—N3—C6	121.84 (10)	C7—C6—H6A	108.9
C5—N3—H3N	119.7 (9)	N3—C6—H6B	108.9
C6—N3—H3N	117.7 (9)	C7—C6—H6B	108.9
C7—N4—C11	117.12 (10)	H6A—C6—H6B	107.7
N1—C1—C2	121.86 (11)	N4—C7—C8	122.34 (11)
N1—C1—C5	118.36 (10)	N4—C7—C6	116.69 (10)
C2—C1—C5	119.76 (10)	C8—C7—C6	120.97 (11)
N2—C2—C1	122.19 (11)	C9—C8—C7	119.49 (11)
N2—C2—H2	118.9	C9—C8—H8	120.3
C1—C2—H2	118.9	C7—C8—H8	120.3
N2—C3—C4	122.47 (11)	C8—C9—C10	118.73 (11)
N2—C3—H3	118.8	C8—C9—H9	120.6
C4—C3—H3	118.8	C10—C9—H9	120.6
N1—C4—C3	122.14 (11)	C11—C10—C9	118.14 (12)
N1—C4—H4	118.9	C11—C10—H10	120.9
C3—C4—H4	118.9	C9—C10—H10	120.9
O1—C5—N3	124.27 (11)	N4—C11—C10	124.17 (12)
O1—C5—C1	120.30 (10)	N4—C11—H11	117.9
N3—C5—C1	115.43 (10)	C10—C11—H11	117.9

C4—N1—C1—C2	0.03 (17)	C2—C1—C5—N3	179.54 (11)
C4—N1—C1—C5	−178.51 (11)	C5—N3—C6—C7	95.48 (13)
C3—N2—C2—C1	0.06 (19)	C11—N4—C7—C8	−0.18 (18)
N1—C1—C2—N2	−0.1 (2)	C11—N4—C7—C6	179.86 (11)
C5—C1—C2—N2	178.43 (11)	N3—C6—C7—N4	104.41 (12)
C2—N2—C3—C4	0.03 (19)	N3—C6—C7—C8	−75.55 (14)
C1—N1—C4—C3	0.05 (18)	N4—C7—C8—C9	0.12 (18)
N2—C3—C4—N1	−0.1 (2)	C6—C7—C8—C9	−179.92 (11)
C6—N3—C5—O1	−5.16 (19)	C7—C8—C9—C10	0.33 (19)
C6—N3—C5—C1	174.05 (10)	C8—C9—C10—C11	−0.7 (2)
N1—C1—C5—O1	177.36 (11)	C7—N4—C11—C10	−0.2 (2)
C2—C1—C5—O1	−1.21 (18)	C9—C10—C11—N4	0.6 (2)
N1—C1—C5—N3	−1.88 (16)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···N1	0.901 (16)	2.332 (15)	2.7136 (15)	105.4 (11)
N3—H3N···N4ⁱ	0.901 (16)	2.206 (16)	2.9929 (14)	145.6 (13)
C3—H3···O1ⁱⁱ	0.95	2.51	3.1544 (15)	125
C4—H4···O1ⁱⁱ	0.95	2.56	3.1748 (15)	123
C10—H10···N2ⁱⁱⁱ	0.95	2.62	3.5678 (17)	174

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

(HL2) N-(Pyridin-4-ylmethyl)pyrazine-2-carboxamide top

Crystal data top

C₁₁H₁₀N₄O	F(000) = 448
M_r = 214.23	D_x = 1.371 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 13.8564 (14) Å	Cell parameters from 20 reflections
b = 11.1841 (11) Å	θ = 10.4–17.6°
c = 6.9122 (10) Å	µ = 0.09 mm⁻¹
β = 104.356 (14)°	T = 293 K
V = 1037.7 (2) Å³	Block, colourless
Z = 4	0.38 × 0.30 × 0.19 mm

Data collection top

Stoe AED2 four-circle diffractometer	R_int = 0.032
Radiation source: fine-focus sealed tube	θ_max = 25.5°, θ_min = 2.4°
Plane graphite monochromator	h = −16→16
2θ/ω scans	k = −13→0
4132 measured reflections	l = −8→8
1937 independent reflections	2 standard reflections every 60 min
1198 reflections with I > 2σ(I)	intensity decay: 2%

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.054	w = 1/[σ²(F_o²) + (0.0426P)² + 0.1904P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.127	(Δ/σ)_max < 0.001
S = 1.10	Δρ_max = 0.17 e Å⁻³
1937 reflections	Δρ_min = −0.16 e Å⁻³
150 parameters	Extinction correction: SHELXL2013 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.014 (2)

Special details top

Experimental. Spectroscopic data for HL2: ¹H NMR (400 MHz, DMSO-d6; code Hh/NH, Hl/C3, Hn/C1, Hm/C2, Hb/C11, Hd/C9, Ha/C11/, He/C8, Hg/C6): 9.63 (t, 1H, Jhg = 6.3, Hh); 9.21 (d, 1H, Jlm = 1.5, Hl); 8.90 (d, 1H, Jnm = 2.5, Hn); 8.77 (dd, 1H, Jmn = 2.5, Jml = 1.5, Hm); 8.49 (dd, 2H, Jba = 4.4, Jbe = 1.6, Hb = Hd); 7.31 (dd, 2H, Jab = 4.4, Jad = 1.6, Ha = He); 4.54 (d, 2H, Jgh = 6.3, Hg). ¹³C NMR (400 MHz, DMSO-d6): 164.2, 150.4, 149.0, 148.5, 145.4, 144.5, 144.3, 123.0, 42.4. IR (KBr pellet, cm^-1): 3366 (versus), 3089 (s), 3050 (m), 3031 (s), 2967 (m), 2935 (s), 1966 (w), 1924 (w), 1834 (w), 1674 (versus), 1634 (s), 1602 (versus), 1585 (s), 1564 (s) 1526 (versus), 1467 (versus), 1429 (versus), 1415 (versus), 1399 (versus), 1359 (s), 1329 (s), 1288 (versus), 1240 (m), 1216 (versus), 1167 (s), 1155 (s), 1059 (versus), 1025 (versus), 1020 (versus), 993 (s), 981 (s), 968 (s), 887 (m), 870 (s), 842 (s), 832 (s), 804 (versus), 775 (s), 731 (m), 652 (versus), 608 (s), 517 (s), 479 (m), 445 (versus), 411 (m).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.32038 (14)	0.28041 (15)	0.2248 (3)	0.0618 (6)
N1	0.52051 (15)	0.08089 (17)	0.2297 (3)	0.0456 (6)
N2	0.61838 (17)	0.29856 (19)	0.2153 (3)	0.0530 (6)
N3	0.32823 (16)	0.0787 (2)	0.2548 (3)	0.0495 (6)
H3N	0.367 (2)	0.022 (2)	0.251 (4)	0.057 (9)*
N4	0.04496 (18)	−0.1046 (2)	−0.2659 (4)	0.0677 (7)
C1	0.47371 (18)	0.1855 (2)	0.2255 (3)	0.0389 (6)
C2	0.5226 (2)	0.2927 (2)	0.2174 (4)	0.0477 (7)
H2	0.4870	0.3635	0.2132	0.057*
C3	0.6641 (2)	0.1935 (2)	0.2189 (4)	0.0531 (7)
H3	0.7309	0.1925	0.2166	0.064*
C4	0.61612 (19)	0.0861 (2)	0.2258 (4)	0.0510 (7)
H4	0.6515	0.0153	0.2279	0.061*
C5	0.36661 (19)	0.1863 (2)	0.2342 (4)	0.0442 (6)
C6	0.22661 (19)	0.0590 (2)	0.2660 (4)	0.0548 (7)
H6A	0.1972	0.1350	0.2877	0.066*
H6B	0.2267	0.0080	0.3795	0.066*
C7	0.16399 (17)	0.0020 (2)	0.0798 (4)	0.0431 (6)
C8	0.1571 (2)	0.0498 (2)	−0.1071 (4)	0.0534 (7)
H8	0.1922	0.1187	−0.1216	0.064*
C9	0.0979 (2)	−0.0052 (3)	−0.2711 (5)	0.0652 (8)
H9	0.0943	0.0291	−0.3953	0.078*
C10	0.0528 (2)	−0.1497 (2)	−0.0853 (5)	0.0627 (8)
H10	0.0171	−0.2188	−0.0752	0.075*
C11	0.11055 (19)	−0.1010 (2)	0.0887 (4)	0.0517 (7)
H11	0.1134	−0.1374	0.2110	0.062*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0615 (13)	0.0417 (11)	0.0868 (15)	0.0116 (10)	0.0272 (11)	−0.0013 (10)
N1	0.0459 (13)	0.0334 (12)	0.0586 (14)	0.0012 (10)	0.0149 (10)	−0.0024 (10)
N2	0.0553 (15)	0.0427 (14)	0.0610 (15)	−0.0100 (11)	0.0144 (11)	−0.0006 (11)
N3	0.0421 (14)	0.0421 (14)	0.0663 (16)	−0.0008 (11)	0.0170 (11)	−0.0043 (11)
N4	0.0590 (16)	0.0684 (18)	0.0749 (19)	0.0011 (13)	0.0148 (14)	−0.0111 (15)
C1	0.0441 (14)	0.0323 (13)	0.0399 (14)	−0.0006 (11)	0.0101 (11)	−0.0028 (11)
C2	0.0560 (18)	0.0325 (15)	0.0531 (17)	0.0008 (12)	0.0109 (13)	−0.0023 (12)
C3	0.0488 (17)	0.0505 (16)	0.0607 (17)	−0.0050 (14)	0.0149 (13)	0.0007 (14)
C4	0.0496 (16)	0.0406 (15)	0.0646 (18)	0.0044 (13)	0.0174 (13)	−0.0019 (13)
C5	0.0501 (16)	0.0376 (14)	0.0447 (15)	0.0009 (13)	0.0117 (12)	−0.0045 (12)
C6	0.0471 (16)	0.0585 (18)	0.0625 (19)	−0.0012 (13)	0.0206 (14)	−0.0040 (14)
C7	0.0321 (13)	0.0416 (14)	0.0582 (18)	0.0048 (11)	0.0162 (12)	0.0016 (12)
C8	0.0442 (15)	0.0551 (17)	0.0646 (19)	−0.0022 (13)	0.0204 (14)	0.0059 (15)
C9	0.0589 (19)	0.084 (2)	0.056 (2)	0.0091 (17)	0.0214 (16)	0.0066 (17)
C10	0.0530 (18)	0.0444 (16)	0.092 (3)	−0.0008 (14)	0.0204 (17)	−0.0063 (17)
C11	0.0457 (15)	0.0439 (15)	0.0674 (19)	0.0043 (13)	0.0179 (13)	0.0087 (14)

Geometric parameters (Å, º) top

O1—C5	1.225 (3)	C3—H3	0.9300
N1—C4	1.333 (3)	C4—H4	0.9300
N1—C1	1.334 (3)	C6—C7	1.504 (3)
N2—C3	1.332 (3)	C6—H6A	0.9700
N2—C2	1.333 (3)	C6—H6B	0.9700
N3—C5	1.338 (3)	C7—C11	1.379 (3)
N3—C6	1.446 (3)	C7—C8	1.379 (4)
N3—H3N	0.83 (3)	C8—C9	1.369 (4)
N4—C10	1.325 (4)	C8—H8	0.9300
N4—C9	1.337 (4)	C9—H9	0.9300
C1—C2	1.385 (3)	C10—C11	1.381 (4)
C1—C5	1.500 (3)	C10—H10	0.9300
C2—H2	0.9300	C11—H11	0.9300
C3—C4	1.379 (3)

C4—N1—C1	116.2 (2)	N3—C6—C7	112.4 (2)
C3—N2—C2	115.2 (2)	N3—C6—H6A	109.1
C5—N3—C6	124.1 (2)	C7—C6—H6A	109.1
C5—N3—H3N	113.8 (19)	N3—C6—H6B	109.1
C6—N3—H3N	121.9 (19)	C7—C6—H6B	109.1
C10—N4—C9	115.1 (3)	H6A—C6—H6B	107.9
N1—C1—C2	121.3 (2)	C11—C7—C8	116.9 (3)
N1—C1—C5	119.0 (2)	C11—C7—C6	121.2 (2)
C2—C1—C5	119.6 (2)	C8—C7—C6	121.9 (2)
N2—C2—C1	122.8 (2)	C9—C8—C7	119.3 (3)
N2—C2—H2	118.6	C9—C8—H8	120.3
C1—C2—H2	118.6	C7—C8—H8	120.3
N2—C3—C4	122.5 (3)	N4—C9—C8	124.8 (3)
N2—C3—H3	118.7	N4—C9—H9	117.6
C4—C3—H3	118.7	C8—C9—H9	117.6
N1—C4—C3	121.9 (2)	N4—C10—C11	124.4 (3)
N1—C4—H4	119.0	N4—C10—H10	117.8
C3—C4—H4	119.0	C11—C10—H10	117.8
O1—C5—N3	124.2 (2)	C7—C11—C10	119.5 (3)
O1—C5—C1	120.9 (2)	C7—C11—H11	120.3
N3—C5—C1	114.9 (2)	C10—C11—H11	120.3

C4—N1—C1—C2	0.1 (3)	C2—C1—C5—N3	−175.8 (2)
C4—N1—C1—C5	−178.6 (2)	C5—N3—C6—C7	108.0 (3)
C3—N2—C2—C1	0.9 (4)	N3—C6—C7—C11	126.7 (3)
N1—C1—C2—N2	−0.7 (4)	N3—C6—C7—C8	−53.3 (3)
C5—C1—C2—N2	178.0 (2)	C11—C7—C8—C9	0.8 (4)
C2—N2—C3—C4	−0.5 (4)	C6—C7—C8—C9	−179.2 (2)
C1—N1—C4—C3	0.3 (4)	C10—N4—C9—C8	0.0 (4)
N2—C3—C4—N1	−0.1 (4)	C7—C8—C9—N4	−0.3 (4)
C6—N3—C5—O1	0.9 (4)	C9—N4—C10—C11	−0.1 (4)
C6—N3—C5—C1	−179.9 (2)	C8—C7—C11—C10	−0.9 (4)
N1—C1—C5—O1	−177.8 (2)	C6—C7—C11—C10	179.1 (2)
C2—C1—C5—O1	3.4 (4)	N4—C10—C11—C7	0.6 (4)
N1—C1—C5—N3	2.9 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···N1	0.83 (3)	2.27 (3)	2.713 (3)	114 (2)
N3—H3N···N2ⁱ	0.83 (3)	2.52 (3)	3.214 (3)	142 (2)
C2—H2···N1ⁱⁱ	0.93	2.47	3.315 (3)	151
C8—H8···O1ⁱⁱⁱ	0.93	2.55	3.373 (3)	148

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

Footnotes

¹This work forms part of the PhD thesis (Neuchâtel, 2002) of DSC.

Acknowledgements

This work was supported by the Swiss National Science Foundation and the University of Neuchâtel.

References

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Crystal structures of N-(pyridin-2-ylmeth­yl)pyrazine-2-carboxamide (monoclinic polymorph) and N-(pyridin-4-ylmeth­yl)pyrazine-2-carboxamide1

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

6. Refinement

Supporting information

Footnotes

Acknowledgements

References

research communications

Crystal structures of N-(pyridin-2-ylmethyl)pyrazine-2-carboxamide (monoclinic polymorph) and N-(pyridin-4-ylmethyl)pyrazine-2-carboxamide¹

3. Supramolecular features