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ISSN: 2414-3146

7-Bromo-2,3-bis­­[(prop-2-yn-1-yl)sulfan­yl]pyrido[2,3-b]pyrazine

CROSSMARK_Color_square_no_text.svg

aLaboratoire de Chimie Organique Appliquée, Université Sidi Mohamed Ben Abdallah, Faculté des Sciences et Techniques, Route d'Imouzzer, BP 2202, Fez, Morocco, bDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, and cLaboratoire de Chimie Organique Hétérocyclique URAC 21, Pôle de Compétence Pharmacochimie, Av. Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
*Correspondence e-mail: sikine.meriem@gmail.com

Edited by J. Simpson, University of Otago, New Zealand (Received 15 November 2016; accepted 23 November 2016; online 29 November 2016)

In the title compound, C13H8BrN3S2, one propynyl substituent lies approximately in the plane of the pyrido­pyrazine ring system, while the other is twisted away from this plane. In the crystal, offset ππ stacking inter­actions between the pyridine and pyrazine rings with a centroid–centroid distance of 3.740 (1) Å stack the mol­ecules along the a-axis direction. At the conclusion of the initial refinement, a significant residual peak remained in the difference map. This suggested an alternate location for the Br atom but at a very low occupancy. Further refinement with Br disordered over two sites yielded a population ratio for the two Br sites of 97:3. As the refined location of the minor Br site leads to unequal C—C—Br angles, we feel that the results indicate a `whole mol­ecule' disorder rather than the presence of a minor amount of an isomer. Unfortunately, the very low amount of the second component of the disorder prevented the location of any of its other atoms.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Pyrido-pyrazine heterocyclic compounds are important in organic chemistry and are also known to be important biologically (Richter et al., 2006[Richter, H. G. F., Adams, D. R., Benardeau, A., Bickerdike, M. J., Bentley, J. M., Blench, T. J., Cliffe, I. A., Dourish, C., Hebeisen, P., Kennett, G. A., Knight, A. R., Malcolm, C. S., Mattei, P., Misra, A., Mizrahi, J., Monck, N. J. T., Plancher, J.-M., Roever, S., Roffey, J. R. A., Taylor, S. & Vickers, S. P. (2006). Bioorg. Med. Chem. Lett. 16, 1207-1211.]). Their uses include as anti­malarial agents (Shekhar et al., 2014[Shekhar, A. C., Rao, P. S., Narsaiah, B., Allanki, A. D. & Sijwali, P. S. (2014). Med. Chem. 77, 280-287.]), anti-cancer drugs (Gong et al., 2011[Gong, Y. D., Dong, M. S., Lee, S. B., Kim, N., Bae, M. S. & Kang, N. S. (2011). Bioorg. Med. Chem. 19, 5639-5647.]), as anti-inflammatories (Hodgetts et al., 2010[Hodgetts, K. J., Blum, C. A., Caldwell, T., Bakthavatchalam, R., Zheng, X., Capitosti, S., Krause, J. E., Cortright, D., Crandall, M., Murphy, B. A., Boyce, S., Jones, A. B. & Chenard, B. L. (2010). Bioorg. Med. Chem. Lett. 20, 4359-4363.]) and as HIV-1 integrase inhibitors (Wai et al., 2007[Wai, J. S., Kim, B., Fisher, T. E., Zhuang, L., Embrey, M. W., Williams, P. D., Staas, D. D., Culberson, C., Lyle, T. A., Vacca, J. P., Hazuda, D. J., Felock, P. J., Schleif, W. A., Gabryelski, L. J., Jin, L., Chen, I. W., Ellis, J. D., Mallai, R. & Young, S. D. (2007). Bioorg. Med. Chem. Lett. 17, 5595-5599.]). They are also used as inhibitors of anaplastic lymphoma kinase (Milkiewicz et al., 2010[Milkiewicz, K. L., Weinberg, L. R., Albom, M. S., Angeles, T. S., Cheng, M., Ghose, A. K., Roemmele, R. C., Theroff, J. P., Underiner, T. L., Zificsak, C. A. & Dorsey, B. D. (2010). Bioorg. Med. Chem. 18, 4351-4362.]). As a continuation of our research in the field of substituted pyrido[2,3-b]pyrazine deriv­atives (Hjouji et al., 2014[Hjouji, M. Y., Kandri Rodi, Y., Misbahi, K., Chahdi, O., Akhazzane, F. M. & Essassi, E. M. (2014). J. Mar. Chim. Hétérocycl. 13, 65-71.]), we report here the synthesis of a new product by the reaction of propargyl bromide with an excess of pyrido[2,3-b]pyrazine­(1H,4H)-2,3-di­thiol in dimethyl formamide in the presence of potassium carbonate and a catalytic qu­antity of tetra-n-butyl­ammonium bromide. The structure of another pyrido [2,3-b]pyrazine derivative has been reported previously (Fun et al., 2011[Fun, H.-K., Hemamalini, M., Hazra, A. & Goswami, S. (2011). Acta Cryst. E67, o3120.]).

In the title compound (Fig. 1[link]), one propynyl substituent lies approximately in the plane of the pyrido­pyrazine ring system while the other is twisted away from this plane as shown by the C6—S1—C8—C9 [175.29 (17)°] and C7—S2—C11—C12 [76.78 (19)°] torsion angles. In the crystal, the mol­ecules form stacks along the a-axis direction (Fig. 2[link]) through offset ππ-stacking inter­actions between the pyridine and pyrazine rings (Fig. 3[link]) with a centroid–centroid distance of 3.740 (1) Å and an inter­planar separation of 3.440 (1) Å.

[Figure 1]
Figure 1
The title mol­ecule with the labeling scheme and 50% probability displacement ellipsoids. Only the major disorder component is shown.
[Figure 2]
Figure 2
Packing of the title compound projected onto (100).
[Figure 3]
Figure 3
Details of the offset-ππ stacking. [Symmetry codes: (i) −1 + x, y, z; (ii) 1 + x, y, z.]

Synthesis and crystallization

Propargyl bromide (0.16 ml, 1.82 mmol) was added to a solution of 7-bromo­pyrido[2,3-b]pyrazine-2,3-di­thiol (0.2 g, 0.73 mmol), K2CO3 (0.3 g, 2.19 mmol), tetra-n-butyl ammonium bromide (0.03 g, 0.1 mmol) in DMF (10 ml). The mixture was then stirred for 6 h at room temperature. The solvent was evaporated under reduced pressure and the product isolated by chromatography on a silica gel column with ethyl acetate/hexane (1/3) as eluent. The compound forms pale yellow columnar crystals in 20% yield and was recrystallized from a solvent mixture (di­chloro­methane–hexa­ne: 1/2).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1[link]. At the conclusion of the initial refinement, a significant residual peak remained in the difference map at ca 1.85 Å from C4. This suggested an alternate location for Br1 but at a very low occupancy. Further refinement with Br1 disordered over two sites yielded a population ratio for the two Br sites of 97:3. As the refined location of the minor Br site leads to unequal C—C—Br angles, we feel that the results indicate a `whole mol­ecule' disorder rather than the presence of a minor amount of an isomer. Unfortunately, the very low amount of the second component of the disorder prevented the location of any of its other atoms.

Table 1
Experimental details

Crystal data
Chemical formula C13H8BrN3S2
Mr 350.25
Crystal system, space group Monoclinic, P21/c
Temperature (K) 150
a, b, c (Å) 4.2159 (1), 16.7730 (5), 19.4656 (5)
β (°) 91.149 (1)
V3) 1376.20 (6)
Z 4
Radiation type Cu Kα
μ (mm−1) 6.81
Crystal size (mm) 0.20 × 0.08 × 0.04
 
Data collection
Diffractometer Bruker D8 VENTURE PHOTON 100 CMOS
Absorption correction Multi-scan (SADABS; Bruker, 2016[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.46, 0.77
No. of measured, independent and observed [I > 2σ(I)] reflections 21387, 2726, 2513
Rint 0.035
(sin θ/λ)max−1) 0.618
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.086, 1.05
No. of reflections 2726
No. of parameters 176
No. of restraints 1
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.50, −0.57
Computer programs: APEX3 and SAINT (Bruker, 2016[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), DIAMOND (Brandenburg & Putz, 2012[Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.]) and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Structural data


Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

7-Bromo-2,3-bis[(prop-2-yn-1-yl)sulfanyl]pyrido[2,3-b]pyrazine top
Crystal data top
C13H8BrN3S2F(000) = 696
Mr = 350.25Dx = 1.690 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54178 Å
a = 4.2159 (1) ÅCell parameters from 9904 reflections
b = 16.7730 (5) Åθ = 3.5–72.4°
c = 19.4656 (5) ŵ = 6.81 mm1
β = 91.149 (1)°T = 150 K
V = 1376.20 (6) Å3Column, pale yellow
Z = 40.20 × 0.08 × 0.04 mm
Data collection top
Bruker D8 VENTURE PHOTON 100 CMOS
diffractometer
2726 independent reflections
Radiation source: INCOATEC IµS micro-focus source2513 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.035
Detector resolution: 10.4167 pixels mm-1θmax = 72.4°, θmin = 3.5°
ω scansh = 55
Absorption correction: multi-scan
(SADABS; Bruker, 2016)
k = 2020
Tmin = 0.46, Tmax = 0.77l = 2424
21387 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.033Hydrogen site location: mixed
wR(F2) = 0.086H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0425P)2 + 1.2838P]
where P = (Fo2 + 2Fc2)/3
2726 reflections(Δ/σ)max = 0.001
176 parametersΔρmax = 0.50 e Å3
1 restraintΔρmin = 0.57 e Å3
Special details top

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. H-atoms attached to carbon were placed in calculated positions (C—H = 0.95 - 0.99 Å) and included as riding contributions with isotropic displacement parameters 1.2 times those of the attached atoms. At the conclusion of the initial refinement, a significant residual peak remained the difference map at ca. 1.85 Å from C4. This suggested an alternate location for Br1 but at a very low occupancy. Further refinement with Br1 disordered over two sites yielded a population ratio for the two Br sites of 97:3. Because the refined location of the minor Br site leads to unequal C–C–Br angles, we feel that the results indicate a "whole molecule" disorder rather than the presence of a minor amount of an isomer. Unfortunately, the very low amount of the second component of the disorder prevented location of any of its other atoms.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Br11.33510 (8)0.89445 (2)0.98676 (2)0.05325 (13)0.9711 (8)
C31.0987 (6)0.87110 (17)0.90621 (13)0.0414 (6)0.9711 (8)
C40.9795 (7)0.93338 (16)0.86557 (14)0.0438 (6)0.9711 (8)
H41.03300.98640.87840.053*0.9711 (8)
Br1A1.186 (3)1.0075 (6)0.9223 (5)0.05325 (13)0.0289 (8)
C3A1.0987 (6)0.87110 (17)0.90621 (13)0.0414 (6)0.0289 (8)
H3A1.22020.88120.94830.050*0.0289 (8)
C4A0.9795 (7)0.93338 (16)0.86557 (14)0.0438 (6)0.0289 (8)
S10.21077 (15)0.74574 (3)0.64709 (3)0.03557 (15)
S20.46504 (15)0.60113 (3)0.72597 (3)0.03503 (15)
N10.5283 (5)0.83752 (11)0.73672 (10)0.0324 (4)
N20.7585 (5)0.70372 (12)0.81113 (10)0.0337 (4)
N30.7976 (6)0.92284 (12)0.81063 (11)0.0400 (5)
C10.8373 (6)0.78020 (14)0.83001 (12)0.0330 (5)
C21.0335 (6)0.79318 (16)0.88808 (13)0.0385 (5)
H21.11840.74990.91400.046*
C50.7232 (6)0.84662 (14)0.79321 (12)0.0331 (5)
C60.4557 (6)0.76449 (14)0.71894 (12)0.0313 (5)
C70.5753 (5)0.69566 (13)0.75688 (12)0.0313 (5)
C80.1351 (6)0.84778 (14)0.61874 (12)0.0355 (5)
H8A0.01530.87700.65400.043*
H8B0.33830.87590.61170.043*
C90.0480 (6)0.84493 (15)0.55455 (13)0.0378 (5)
C100.1994 (7)0.84327 (18)0.50324 (14)0.0484 (7)
H100.32170.84190.46170.058*
C110.6516 (6)0.53851 (14)0.79116 (12)0.0343 (5)
H11A0.66910.48350.77310.041*
H11B0.86910.55830.80080.041*
C120.4780 (6)0.53656 (14)0.85501 (13)0.0355 (5)
C130.3346 (7)0.53361 (17)0.90614 (15)0.0467 (6)
H130.21880.53120.94750.056*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0562 (2)0.0577 (2)0.04545 (19)0.01377 (14)0.01003 (14)0.00496 (13)
C30.0422 (14)0.0438 (14)0.0383 (13)0.0088 (11)0.0013 (11)0.0023 (11)
C40.0508 (15)0.0350 (13)0.0456 (15)0.0115 (11)0.0034 (12)0.0030 (11)
Br1A0.0562 (2)0.0577 (2)0.04545 (19)0.01377 (14)0.01003 (14)0.00496 (13)
C3A0.0422 (14)0.0438 (14)0.0383 (13)0.0088 (11)0.0013 (11)0.0023 (11)
C4A0.0508 (15)0.0350 (13)0.0456 (15)0.0115 (11)0.0034 (12)0.0030 (11)
S10.0424 (3)0.0295 (3)0.0345 (3)0.0006 (2)0.0039 (2)0.0022 (2)
S20.0422 (3)0.0260 (3)0.0367 (3)0.0005 (2)0.0040 (2)0.0007 (2)
N10.0370 (10)0.0273 (9)0.0330 (10)0.0003 (8)0.0024 (8)0.0015 (8)
N20.0363 (10)0.0287 (9)0.0360 (10)0.0014 (8)0.0004 (8)0.0038 (8)
N30.0496 (12)0.0284 (10)0.0420 (12)0.0048 (9)0.0006 (9)0.0001 (9)
C10.0354 (12)0.0307 (11)0.0328 (11)0.0044 (9)0.0026 (9)0.0020 (9)
C20.0388 (13)0.0399 (13)0.0366 (13)0.0049 (10)0.0018 (10)0.0063 (10)
C50.0381 (12)0.0281 (11)0.0333 (11)0.0024 (9)0.0040 (9)0.0022 (9)
C60.0330 (11)0.0302 (11)0.0310 (11)0.0008 (9)0.0037 (9)0.0024 (9)
C70.0321 (11)0.0279 (11)0.0342 (11)0.0007 (9)0.0040 (9)0.0026 (9)
C80.0418 (13)0.0316 (12)0.0332 (12)0.0028 (10)0.0010 (10)0.0029 (9)
C90.0415 (13)0.0353 (12)0.0367 (13)0.0063 (10)0.0043 (10)0.0035 (10)
C100.0532 (16)0.0515 (16)0.0401 (14)0.0140 (13)0.0056 (12)0.0024 (12)
C110.0376 (12)0.0255 (10)0.0397 (12)0.0013 (9)0.0025 (10)0.0013 (9)
C120.0365 (12)0.0272 (11)0.0424 (13)0.0034 (9)0.0080 (10)0.0009 (10)
C130.0525 (16)0.0452 (15)0.0423 (15)0.0083 (12)0.0004 (12)0.0001 (12)
Geometric parameters (Å, º) top
Br1—C31.882 (3)N2—C11.373 (3)
C3—C21.380 (4)N3—C51.358 (3)
C3—C41.398 (4)C1—C21.404 (3)
C4—N31.315 (4)C1—C51.404 (3)
C4—H40.9500C2—H20.9500
Br1A—C4A1.866 (4)C6—C71.455 (3)
C3A—C21.380 (4)C8—C91.456 (3)
C3A—C4A1.398 (4)C8—H8A0.9900
C3A—H3A0.9729C8—H8B0.9900
C4A—N31.315 (4)C9—C101.175 (4)
S1—C61.750 (2)C10—H100.9500
S1—C81.824 (2)C11—C121.455 (4)
S2—C71.755 (2)C11—H11A0.9900
S2—C111.814 (2)C11—H11B0.9900
N1—C61.307 (3)C12—C131.176 (4)
N1—C51.368 (3)C13—H130.9500
N2—C71.303 (3)
C2—C3—C4119.7 (2)N3—C5—N1116.0 (2)
C2—C3—Br1120.6 (2)N3—C5—C1123.0 (2)
C4—C3—Br1119.6 (2)N1—C5—C1121.0 (2)
N3—C4—C3123.8 (2)N1—C6—C7122.2 (2)
N3—C4—H4118.1N1—C6—S1120.73 (18)
C3—C4—H4118.1C7—C6—S1117.11 (17)
C2—C3A—C4A119.7 (2)N2—C7—C6121.5 (2)
C2—C3A—H3A118.6N2—C7—S2121.34 (18)
C4A—C3A—H3A121.6C6—C7—S2117.14 (17)
N3—C4A—C3A123.8 (2)C9—C8—S1108.37 (17)
N3—C4A—Br1A145.9 (4)C9—C8—H8A110.0
C3A—C4A—Br1A90.3 (4)S1—C8—H8A110.0
C6—S1—C899.78 (11)C9—C8—H8B110.0
C7—S2—C11100.09 (11)S1—C8—H8B110.0
C6—N1—C5116.8 (2)H8A—C8—H8B108.4
C7—N2—C1116.8 (2)C10—C9—C8179.0 (3)
C4A—N3—C5117.2 (2)C9—C10—H10180.0
C4—N3—C5117.2 (2)C12—C11—S2113.08 (17)
N2—C1—C2119.7 (2)C12—C11—H11A109.0
N2—C1—C5121.7 (2)S2—C11—H11A109.0
C2—C1—C5118.5 (2)C12—C11—H11B109.0
C3A—C2—C1117.6 (2)S2—C11—H11B109.0
C3—C2—C1117.6 (2)H11A—C11—H11B107.8
C3—C2—H2121.2C13—C12—C11178.6 (3)
C1—C2—H2121.2C12—C13—H13180.0
C2—C3—C4—N31.9 (4)C4—N3—C5—C11.5 (4)
Br1—C3—C4—N3176.1 (2)C6—N1—C5—N3179.6 (2)
C2—C3A—C4A—N31.9 (4)C6—N1—C5—C10.2 (3)
Br1A—C3A—C4A—N3179.5 (5)N2—C1—C5—N3179.9 (2)
C2—C3A—C4A—Br1A177.6 (4)C2—C1—C5—N31.0 (4)
C3A—Br1A—C4A—N3179.2 (7)N2—C1—C5—N10.1 (4)
C3A—C4A—N3—C50.1 (4)C2—C1—C5—N1179.2 (2)
Br1A—C4A—N3—C5179.2 (7)C5—N1—C6—C70.1 (3)
C3—C4—N3—C50.1 (4)C5—N1—C6—S1179.46 (17)
C7—N2—C1—C2179.9 (2)C8—S1—C6—N10.2 (2)
C7—N2—C1—C50.7 (3)C8—S1—C6—C7179.20 (18)
C4A—C3A—C2—C12.3 (4)C1—N2—C7—C61.0 (3)
C4—C3—C2—C12.3 (4)C1—N2—C7—S2178.35 (17)
Br1—C3—C2—C1175.62 (18)N1—C6—C7—N20.8 (4)
N2—C1—C2—C3A178.1 (2)S1—C6—C7—N2179.84 (18)
C5—C1—C2—C3A1.0 (4)N1—C6—C7—S2178.63 (18)
N2—C1—C2—C3178.1 (2)S1—C6—C7—S20.7 (2)
C5—C1—C2—C31.0 (4)C11—S2—C7—N23.2 (2)
C4A—N3—C5—N1178.7 (2)C11—S2—C7—C6177.38 (18)
C4—N3—C5—N1178.7 (2)C6—S1—C8—C9175.29 (17)
C4A—N3—C5—C11.5 (4)C7—S2—C11—C1276.78 (19)
 

Acknowledgements

The support of NSF–MRI grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged.

References

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