Rafal Popek1, Guy Crundwell1. 1. Department of Chemistry & Biochemistry, Central Connecticut State University, New Britain, CT 06053, USA.
Abstract
The crystal structures of 2,3-bis-(thio-phen-2-yl)pyrido[2,3-b]pyrazine, C15H9N3S2 (1), and 7-bromo-2,3-bis-(thio-phen-2-yl)pyrido[2,3-b]pyrazine, C15H8BrN3S2 (2), are discussed. Both mol-ecules crystallize in space group P21/c. In 1, the thienyl rings are inclined to the mean plane of the pyrido-pyrazine moiety by 6.16 (7) and 86.66 (8)°, where as in 2 the corresponding dihedral angles are 33.29 (11) and 19.84 (9)°. The pyrido-pyrazine moiety is relatively planar in 1 with the two rings being inclined to each other by 1.33 (7)°. In 2, however, the pyrido-pyrazine moiety is buckled with the corresponding dihedral angle being larger at 8.78 (10)°. In the crystal of 1, the packing creates inter-secting bilayers; the layering results from the pyrido-pyrazine moieties being engaged in offset π-stacking, where the inter-planar distance is 3.431 (9) Å with an offset 1.14 Å. In the crystal of 2, the mol-ecules pack head-to-head and are linked by a series of C-H⋯Br and C-H⋯N inter-molecular inter-actions, forming layers parallel to the ab plane.
The crystal structures of 2,3-bis-(thio-phen-2-yl)pyrido[2,3-b]pyrazine, C15H9N3S2 (1), and 7-bromo-2,3-bis-(thio-phen-2-yl)pyrido[2,3-b]pyrazine, C15H8BrN3S2 (2), are discussed. Both mol-ecules crystallize in space group P21/c. In 1, the thienyl rings are inclined to the mean plane of the pyrido-pyrazine moiety by 6.16 (7) and 86.66 (8)°, where as in 2 the corresponding dihedral angles are 33.29 (11) and 19.84 (9)°. The pyrido-pyrazine moiety is relatively planar in 1 with the two rings being inclined to each other by 1.33 (7)°. In 2, however, the pyrido-pyrazine moiety is buckled with the corresponding dihedral angle being larger at 8.78 (10)°. In the crystal of 1, the packing creates inter-secting bilayers; the layering results from the pyrido-pyrazine moieties being engaged in offset π-stacking, where the inter-planar distance is 3.431 (9) Å with an offset 1.14 Å. In the crystal of 2, the mol-ecules pack head-to-head and are linked by a series of C-H⋯Br and C-H⋯N inter-molecular inter-actions, forming layers parallel to the ab plane.
Nitrogen-containing heterocyclic aryl substituents at the 2- and 2,3- positions on quinoxalines have been shown repeatedly to engage in bidentate behavior in binding metals, utilizing the quinoxaline nitrogen atom. For example, 2-(2-pyridyl)quinoxaline has shown bidentate behavior with a variety of metals; focusing on silver, specifically, it can form 1:1 complexes assembling in one-dimensional chains (Shanmuga Sundara Raj et al., 1999 ▸) or form 2:1 mononuclear complexes (Bi et al., 2009 ▸) to cite just a few. With that bidentate behavior in mind, we aimed to test the bonding capabilities of thienyl sulfur atoms at the 2-, and 2,3- positions on mono- and di-thienylquinoxalines. Thienyl-substituted quinoxalines have been shown to form bis-complexes with silver(I) (Crundwell et al., 2014 ▸; Crundwell, 2013 ▸); however, so far we have not seen (N,S) bidentate behavior from the nitrogen on the quinoxaline and sulfur on the thienyl ring with a metal.Monothienyl and/or 2,3-dithienyl-substituted pyrido[2,3-b]pyrazines are interesting ligands related to their quinoxaline analogs since they have an additional heterocyclic nitrogen atom. This could potentially create novel silver(I) frameworks and allow insight into the preference of silver when it binds to the heterocycles in these ligands. To date, little work has been done with monothienylpyrido[2,3-b]pyrazines or 2,3-dithienylpyrido[2,3-b]pyrazines. The crystal structure of 3-(2-thienyl)pyrido[2,3-b]pyrazine has been determined (Lassagne et al., 2015 ▸). A few other 2,3-diarylpyrido[2,3-b]pyrazines and their subsequent metal complexes have been characterized through diffraction studies. The crystal structure of 2,3-di(1H-2-pyrrolyl)pyrido[2,3-b]pyrazine, which is a colormetric ion sensor, has been determined as well as a nickel(II) complex in which two ligands bind to the nickel via the outermost nitrogen atom on the pyridopyrazine moiety (Ghosh et al., 2006 ▸). Rhenium(I) complexes with the generic formula [ReBr(CO)3(L)] have been synthesized with a few 2,3-diarylpyrido[2,3-b]pyrazines (Yeo et al., 2010 ▸). These complexes are interesting because they utilize both nitrogen atoms on the same side of the pyridopyrazine moiety to bind the metal.
Structural details
The molecular structure of compound 1 is shown in Fig. 1 ▸. One of the two thienyl rings (C8–C11/S1) is nearly coplanar with the pyridopyrazine ring [the dihedral angle being 6.16 (7)°], therefore making most of the molecule appear flat. The r.m.s. deviation for all non-hydrogen atoms in the pyridopyrazine moiety and the nearly coplanar thiophene ring (C8–C11/S1) is only 0.0123 (16) Å. The mean plane of the other thienyl ring (C12–C15/S2) is nearly perpendicular to the plane created by the rest of the molecule, forming an angle of 86.67 (4)°. Finally, although unsubstituted thienyl ring-flip disorders are common on unsubstituted 2- or 3-thienyl rings (Crundwell et al., 2003 ▸), there was not enough evidence of such a disorder to include it in the refinement model for 1.
Figure 1
A view of the molecular structure of compound 1, with the atom labeling and displacement ellipsoids drawn at the 50% probability level.
The molecular structure of compound 2 is shown in Fig. 2 ▸. This bromo derivative is less planar than the un<span class="Chemical">brominated compound 1. The r.m.s. atomic displacement for the non-hydrogen atoms in the pyridopyrazine ring is 0.104 (2) Å. The mean planes of the thienyl rings (C8–C11/S1 and C12–C15/S2) form angles of 33.29 (11) and 19.84 (9)°, respectively, with the mean plane of the pyridopyrazine moiety. The later is buckled with the pyrazine and pyridine rings being inclined to each other by 8.78 (10)°, compared to only 1.33 (7) ° in 1.
Figure 2
A view of the molecular structure of compound 2, with the atom labeling and displacement ellipsoids drawn at the 50% probability level.
All bond lengths and angles in both compounds 1 and 2 are within expected values and close to those reported for similar compounds (see Database survey).
Supramolecular Features
In the crystal of 1, the packing can be described as a series of bilayers (Fig. 3 ▸). Using Mercury software (Macrae et al., 2008 ▸) for the analysis, in can be seen that the molecules lie in planes with an offset π-stacking distance of 3.431 (9) Å, measured between the planar thienyl ring in one molecule and a portion of the pyridopyrazine ring system of a neighboring molecule. There are two other types of very weak intermolecular interactions in the crystal. The thienyl-ring sulfur atom S1 points directly at a neighboring inversion-related co-planar thienyl-ring sulfur atom at a distance of 3.570 (8) Å, roughly comparable to the sum of the van der Waals radii (3.8 Å). In addition, the pyridopyrazinehydrogen atom H3 is in a position to interact with the sp
2 carbon atom C15i on the tilted thienyl ring (C12–C15/S2) at (i) x + 1, −y + , z − , at a distance of 2.870 (8) Å and forming an angle C3—H3⋯C15i of 152.37 (8)°. These interactions are shown as colored dotted lines in Fig. 4 ▸.
Figure 3
A view along the a axis of the crystal packing of compound 1. Extra molecules were added to illustrate the stacking that occurs in planes.
Figure 4
Intermolecular interactions in the crystal of 1. The S⋯S interactions are shown as dotted yellow lines. The C—H⋯π (thienyl ring) interactions are shown in white.
In the crystal of the brominated derivative 2, molecules pack through a number of intermolecular interactions (Fig. 5 ▸, Table 1 ▸). Several interactions between the bromine atoms and neighboring hydrogens create a head-to-head, sheet-like structure (Fig. 6 ▸). Bromine atoms form C—H⋯Br contacts at distances of 3.005 and 3.049 Å with the hydrogen atoms on C5 and C3, respectively. Within the same plane there are also interactions between the pyridopyrazine nitrogen atom, N1, and adjacent thienyl-ring hydrogen atoms on C15 at 2.645 Å. Finally, two types of interactions that connect molecules between planes are also present. A thienyl-ring hydrogen (on C11) is in contact with an sp
2 carbon (C14) in another layer at 2.775 Å and the π-system of the C12–C15/S2 thienyl ring is stacked over a neighboring pyridopyrazine moiety at 3.394 (9) Å. These interactions are shown as colored dotted lines in Fig. 6 ▸.
Figure 5
A view along the a axis of the crystal packing of compound 2. Extra molecules were added to illustrate the stacking that occurs in planes.
Table 1
Hydrogen-bond geometry (Å, °) for 2
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
C3—H3⋯Br1i
0.93
3.01
3.836 (1)
150
C5—H5⋯Br1ii
0.93
3.05
3.851 (1)
145
C15—H15⋯N1iii
0.93
2.65
3.572 (1)
175
C11—H11⋯C14iv
0.93
2.78
3.637 (1)
155
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .
Figure 6
Intermolecular interactions in the crystal of 2, highlighting the two-dimensional network of C—H⋯Br (brown dotted lines) and C—H⋯N (blue dotted lines) interactions that lie in the same plane. The dangling contacts on the thienyl rings, indicating C—H⋯π (thienyl ring) and C—H⋯π (pyridopyrazine) interactions, are shown with white dotted lines.
Database Survey
A search of the CSD (Version 5.39, August 2018 update; Groom et al., 2016 ▸) revealed the crystal structures of two other arylpyrido[2,3-b]pyrazines, in addition to those already mentioned in the Chemical context section. In 7-<span class="Chemical">bromo-3-[4-(piperidin-1-yl)phenyl]pyrido[2,3-b]pyrazine, the brominated pyridopyrazine ring remains coplanar with its aryl substituent (CSD refcode MUPVOK; Kekesi et al., 2014 ▸). The same result is not found for 2,3-bis(5-bromo-1H-indol-3-yl)-7-chloropyrido[2,3-b]pyrazine acetone monosolvate (JUGCOF; Manivannan et al., 2015 ▸), whose conformation resembles that of compound 2, with both substituents being inclined to the mean plane of the pyridopyrazine ring.
Pyrido[2,3-b]pyrazines without halogenated pyridopyrazine rings are prevalent in the literature. Examples include: 2-(4-fluorophenyl)-3-(pyridin-4-yl)pyrido[2,3-b]pyrazine (BUDYAB; Koch et al., 2009a
▸), 4-[3-(4-fluorophenyl)pyrido[2,3-b]pyrazin-2-yl]-N- isopropylpyridin-2-amine (BUFBAG; Koch et al., 2009c
▸), 3-(4-fluorophenyl)-2-(pyridin-4-yl)pyrido[2,3-b]pyrazine (PUFNUA; Koch et al., 2009b
▸), 4,4′-pyrido[2,3-b]pyrazine-2,3-diylbis(N,N-diphenylaniline) (WUDQAO, WUDQAO01; Xu et al., 2015 ▸) and 4′,4′′-(pyrido[2,3-b]pyrazine-2,3-diyl)bis[(1,1′-biphenyl)-4-carbonitrile]chloroform monosolvate (YEMQUF; Gupta et al., 2018 ▸). In all of these structures, both substituents are inclined to the mean plane of the pyridopyrazine ring, similar to the situation in compound 2.
Synthesis and crystallization
All reagents were purchased from Sigma Aldrich and used without purification. Both molecules were synthesized by reacting equimolar amounts of the corresponding 2,3-diaminopyridines with 2,2′-thenil in refluxing glacial acetic acid.2,3-Bis(thiophen-2-yl)pyrido[2,3-
]pyrazine (1): To a 250 ml round-bottom flask equipped with a magnetic stir bar were added 0.570 g of 2,3-diaminopyridine (5.23 mmol), 1.160 g of 2,2′-thenil (5.23 mmol), and 150 ml of glacial acetic acid. The solution was stirred, heated to boiling, and refluxed for 3 h. The resulting yellowish-brown solution was poured into a 250 ml beaker filled with ice, neutralized with sodium hydroxide, and isolated using vacuum filtration. A rough yield of the yellow–brown solid was 1.332 g (77%). The product was purified via column chromatography (SiO2, 80% EtOAc/20% hexane, R
f = 0.75) to yield 1.010 g of compound 1 (m.p. 451 K). ATR–IR (cm−1) 3101, 1541, 1453, 1409, 1359, 1257, 1092; 1H NMR (300 MHz, CDCl3): δ 9.50 (d, 1H), 8.79 (d, 1H), 7.90 (dd, 1H), 7.59 (m, 2H), 7.38 (dd, 2H), 7.10 (m, 2H); 13C NMR (300 MHz, CDCl3): δ 154.28, 149.68, 149.31, 147.68, 141.17, 140.56, 137.63, 135.62, 130.60, 130.46, 129.96, 129.45, 127.70, 127.64, 125.12. Yellow plate-like crystals of 1 were obtained by slow evaporation of a solution in an equal volume mixture of toluene and ethanol.7-Bromo-2,3-bis(thiophen-2-yl)pyrido[2,3-
]pyrazine (2): The above method was used for the brominated derivative by using 5-bromo-2,3-diaminopryidine as the starting diamine (m.p. 445 K); ATR–IR (cm−1) 3099, 1539, 1427, 1410, 1331, 1311, 1237, 1172, 1072; 1H NMR (300 MHz, CDCl3): δ 9.10 (d, 1H), 8.58 (d, 1H), 7.59 (m, 2H), 7.46 (m, 2H), 7.10 (m, 2H); 13C NMR (300 MHz, CDCl3): δ 155.14, 149.73, 148.44, 148.03, 140.83, 140.36, 138.89, 135.82, 130.88, 130.66, 130.33, 130.07, 127.78, 127.72, 120.81. Yellow plate-like crystals of 2 were obtained by slow evaporation of a solution in an equal volume mixture of toluene and ethanol. 1H, FTIR, and COSY NMR spectra for 2 are given in the supporting information.
Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. All the hydrogen atoms were constrained at ideal positions and refined using a riding model: C—H = 0.93Å with U
iso(H) = 1.2U
eq(C). In both compounds, some reflections were omitted because they were either partially obstructed by the beam stop or they had an Error/e.s.d. ratio higher than 5.00 where Error = Σ(D)(wD
2/
Table 2
Experimental details
1
2
Crystal data
Chemical formula
C15H9N3S2
C15H8BrN3S2
Mr
295.37
374.27
Crystal system, space group
Monoclinic, P21/c
Monoclinic, P21/c
Temperature (K)
293
293
a, b, c (Å)
5.25147 (12), 14.1093 (3), 17.7690 (3)
5.8336 (2), 29.4731 (10), 8.3160 (3)
β (°)
92.0296 (18)
95.466 (3)
V (Å3)
1315.76 (4)
1423.30 (9)
Z
4
4
Radiation type
Mo Kα
Mo Kα
μ (mm−1)
0.40
3.18
Crystal size (mm)
0.43 × 0.33 × 0.21
0.33 × 0.24 × 0.22
Data collection
Diffractometer
Rigaku Xcalibur Sapphire3
Rigaku Xcalibur Sapphire3
Absorption correction
Multi-scan (CrysAlis PRO; Rigaku OD, 2018 ▸)
Multi-scan (CrysAlis PRO; Rigaku OD, 2018 ▸)
Tmin, Tmax
0.948, 1.000
0.455, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections
19251, 4763, 3491
34519, 5255, 4166
Rint
0.021
0.034
(sin θ/λ)max (Å−1)
0.773
0.785
Refinement
R[F2 > 2σ(F2)], wR(F2), S
0.048, 0.148, 1.01
0.043, 0.110, 1.08
No. of reflections
4763
5255
No. of parameters
181
190
H-atom treatment
H-atom parameters constrained
H-atom parameters constrained
Δρmax, Δρmin (e Å−3)
0.44, −0.40
0.63, −0.67
Computer programs: CrysAlis PRO (Rigaku OD, 2018 ▸), SHELXS97 and SHELXL97 (Sheldrick, 2008 ▸), ORTEP-3 for Windows (Farrugia, 2012 ▸), Mercury (Macrae et al., 2008 ▸) and OLEX2 (Dolomanov et al., 2009 ▸).
Crystal structure: contains datablock(s) 1, Global, 2. DOI: 10.1107/S2056989018016882/xi2011sup1.cifStructure factors: contains datablock(s) 1. DOI: 10.1107/S2056989018016882/xi20111sup2.hklClick here for additional data file.Supporting information file. DOI: 10.1107/S2056989018016882/xi20111sup4.cmlStructure factors: contains datablock(s) 2. DOI: 10.1107/S2056989018016882/xi20112sup3.hklClick here for additional data file.Supporting information file. DOI: 10.1107/S2056989018016882/xi20112sup5.cmlNMRs and FTIRs of 1 and 2. DOI: 10.1107/S2056989018016882/xi2011sup6.pdfCCDC references: 1881685, 1881684Additional supporting information: crystallographic information; 3D view; checkCIF report
w = 1/[σ2(Fo2) + (0.0773P)2 + 0.306P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.148
(Δ/σ)max < 0.001
S = 1.01
Δρmax = 0.44 e Å−3
4763 reflections
Δρmin = −0.40 e Å−3
181 parameters
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.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and
goodness of fit S are based on F2, conventional R-factors R are based
on F, with F set to zero for negative F2. The threshold expression of
F2 > 2sigma(F2) is used only for calculating R-factors(gt) etc. and is
not relevant to the choice of reflections for refinement. R-factors based
on F2 are statistically about twice as large as those based on F, and R-
factors based on ALL data will be even larger.
Primary atom site location: structure-invariant direct methods
Least-squares matrix: full
Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.043
Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.110
H-atom parameters constrained
S = 1.08
w = 1/[σ2(Fo2) + (0.0474P)2 + 0.940P] where P = (Fo2 + 2Fc2)/3
5255 reflections
(Δ/σ)max < 0.001
190 parameters
Δρmax = 0.63 e Å−3
0 restraints
Δρmin = −0.67 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.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and
goodness of fit S are based on F2, conventional R-factors R are based
on F, with F set to zero for negative F2. The threshold expression of
F2 > 2sigma(F2) is used only for calculating R-factors(gt) etc. and is
not relevant to the choice of reflections for refinement. R-factors based
on F2 are statistically about twice as large as those based on F, and R-
factors based on ALL data will be even larger.