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

Sikine, M.; Mague, J.T.; Kandri Rodi, Y.; Essassi, E.M.; Ouzidan, Y.

doi:10.1107/S2414314616018812

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 11| November 2016| x161881

https://doi.org/10.1107/S2414314616018812

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

Meriem Sikine,^a ^* Joel T. Mague,^b Youssef Kandri Rodi,^a El Mokhtar Essassi ^c and Younes Ouzidan ^a

^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 π–π 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.

Keywords: crystal structure; pyridopyrazine; offset π-stacking.

CCDC reference: 1518915

Structure description

Pyrido-pyrazine heterocyclic compounds are important in organic chemistry and are also known to be important biologically (Richter et al., 2006 ). Their uses include as antimalarial agents (Shekhar et al., 2014 ), anti-cancer drugs (Gong et al., 2011 ), as anti-inflammatories (Hodgetts et al., 2010 ) and as HIV-1 integrase inhibitors (Wai et al., 2007 ). They are also used as inhibitors of anaplastic lymphoma kinase (Milkiewicz et al., 2010 ). As a continuation of our research in the field of substituted pyrido[2,3-b]pyrazine derivatives (Hjouji et al., 2014 ), 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 ).

In the title compound (Fig. 1), 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) through offset π–π-stacking interactions between the pyridine and pyrazine rings (Fig. 3) with a centroid–centroid distance of 3.740 (1) Å and an interplanar separation of 3.440 (1) Å.

Figure 1
The title molecule with the labeling scheme and 50% probability displacement ellipsoids. Only the major disorder component is shown.

Figure 2
Packing of the title compound projected onto (100).

Figure 3
Details of the offset-π–π 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. 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
M_r	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)
V (Å³)	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 )
T_min, T_max	0.46, 0.77
No. of measured, independent and observed [I > 2σ(I)] reflections	21387, 2726, 2513
R_int	0.035
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.50, −0.57
Computer programs: APEX3 and SAINT (Bruker, 2016), SHELXT (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ), DIAMOND (Brandenburg & Putz, 2012 ) and SHELXTL (Sheldrick, 2008 ).

Structural data

CCDC reference: 1518915

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314616018812/sj4070sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616018812/sj4070Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314616018812/sj4070Isup3.cml

checkCIF report

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

C₁₃H₈BrN₃S₂	F(000) = 696
M_r = 350.25	D_x = 1.690 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54178 Å
a = 4.2159 (1) Å	Cell parameters from 9904 reflections
b = 16.7730 (5) Å	θ = 3.5–72.4°
c = 19.4656 (5) Å	µ = 6.81 mm⁻¹
β = 91.149 (1)°	T = 150 K
V = 1376.20 (6) Å³	Column, pale yellow
Z = 4	0.20 × 0.08 × 0.04 mm

Data collection top

Bruker D8 VENTURE PHOTON 100 CMOS diffractometer	2726 independent reflections
Radiation source: INCOATEC IµS micro-focus source	2513 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.035
Detector resolution: 10.4167 pixels mm^-1	θ_max = 72.4°, θ_min = 3.5°
ω scans	h = −5→5
Absorption correction: multi-scan (SADABS; Bruker, 2016)	k = −20→20
T_min = 0.46, T_max = 0.77	l = −24→24
21387 measured reflections

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)] = 0.033	Hydrogen site location: mixed
wR(F²) = 0.086	H-atom parameters constrained
S = 1.05	w = 1/[σ²(F_o²) + (0.0425P)² + 1.2838P] where P = (F_o² + 2F_c²)/3
2726 reflections	(Δ/σ)_max = 0.001
176 parameters	Δρ_max = 0.50 e Å⁻³
1 restraint	Δρ_min = −0.57 e Å⁻³

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

	x	y	z	U_iso*/U_eq	Occ. (<1)
Br1	1.33510 (8)	0.89445 (2)	0.98676 (2)	0.05325 (13)	0.9711 (8)
C3	1.0987 (6)	0.87110 (17)	0.90621 (13)	0.0414 (6)	0.9711 (8)
C4	0.9795 (7)	0.93338 (16)	0.86557 (14)	0.0438 (6)	0.9711 (8)
H4	1.0330	0.9864	0.8784	0.053*	0.9711 (8)
Br1A	1.186 (3)	1.0075 (6)	0.9223 (5)	0.05325 (13)	0.0289 (8)
C3A	1.0987 (6)	0.87110 (17)	0.90621 (13)	0.0414 (6)	0.0289 (8)
H3A	1.2202	0.8812	0.9483	0.050*	0.0289 (8)
C4A	0.9795 (7)	0.93338 (16)	0.86557 (14)	0.0438 (6)	0.0289 (8)
S1	0.21077 (15)	0.74574 (3)	0.64709 (3)	0.03557 (15)
S2	0.46504 (15)	0.60113 (3)	0.72597 (3)	0.03503 (15)
N1	0.5283 (5)	0.83752 (11)	0.73672 (10)	0.0324 (4)
N2	0.7585 (5)	0.70372 (12)	0.81113 (10)	0.0337 (4)
N3	0.7976 (6)	0.92284 (12)	0.81063 (11)	0.0400 (5)
C1	0.8373 (6)	0.78020 (14)	0.83001 (12)	0.0330 (5)
C2	1.0335 (6)	0.79318 (16)	0.88808 (13)	0.0385 (5)
H2	1.1184	0.7499	0.9140	0.046*
C5	0.7232 (6)	0.84662 (14)	0.79321 (12)	0.0331 (5)
C6	0.4557 (6)	0.76449 (14)	0.71894 (12)	0.0313 (5)
C7	0.5753 (5)	0.69566 (13)	0.75688 (12)	0.0313 (5)
C8	0.1351 (6)	0.84778 (14)	0.61874 (12)	0.0355 (5)
H8A	0.0153	0.8770	0.6540	0.043*
H8B	0.3383	0.8759	0.6117	0.043*
C9	−0.0480 (6)	0.84493 (15)	0.55455 (13)	0.0378 (5)
C10	−0.1994 (7)	0.84327 (18)	0.50324 (14)	0.0484 (7)
H10	−0.3217	0.8419	0.4617	0.058*
C11	0.6516 (6)	0.53851 (14)	0.79116 (12)	0.0343 (5)
H11A	0.6691	0.4835	0.7731	0.041*
H11B	0.8691	0.5583	0.8008	0.041*
C12	0.4780 (6)	0.53656 (14)	0.85501 (13)	0.0355 (5)
C13	0.3346 (7)	0.53361 (17)	0.90614 (15)	0.0467 (6)
H13	0.2188	0.5312	0.9475	0.056*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br1	0.0562 (2)	0.0577 (2)	0.04545 (19)	−0.01377 (14)	−0.01003 (14)	−0.00496 (13)
C3	0.0422 (14)	0.0438 (14)	0.0383 (13)	−0.0088 (11)	0.0013 (11)	−0.0023 (11)
C4	0.0508 (15)	0.0350 (13)	0.0456 (15)	−0.0115 (11)	0.0034 (12)	−0.0030 (11)
Br1A	0.0562 (2)	0.0577 (2)	0.04545 (19)	−0.01377 (14)	−0.01003 (14)	−0.00496 (13)
C3A	0.0422 (14)	0.0438 (14)	0.0383 (13)	−0.0088 (11)	0.0013 (11)	−0.0023 (11)
C4A	0.0508 (15)	0.0350 (13)	0.0456 (15)	−0.0115 (11)	0.0034 (12)	−0.0030 (11)
S1	0.0424 (3)	0.0295 (3)	0.0345 (3)	0.0006 (2)	−0.0039 (2)	0.0022 (2)
S2	0.0422 (3)	0.0260 (3)	0.0367 (3)	−0.0005 (2)	−0.0040 (2)	0.0007 (2)
N1	0.0370 (10)	0.0273 (9)	0.0330 (10)	0.0003 (8)	0.0024 (8)	0.0015 (8)
N2	0.0363 (10)	0.0287 (9)	0.0360 (10)	−0.0014 (8)	0.0004 (8)	0.0038 (8)
N3	0.0496 (12)	0.0284 (10)	0.0420 (12)	−0.0048 (9)	0.0006 (9)	0.0001 (9)
C1	0.0354 (12)	0.0307 (11)	0.0328 (11)	−0.0044 (9)	0.0026 (9)	0.0020 (9)
C2	0.0388 (13)	0.0399 (13)	0.0366 (13)	−0.0049 (10)	−0.0018 (10)	0.0063 (10)
C5	0.0381 (12)	0.0281 (11)	0.0333 (11)	−0.0024 (9)	0.0040 (9)	0.0022 (9)
C6	0.0330 (11)	0.0302 (11)	0.0310 (11)	0.0008 (9)	0.0037 (9)	0.0024 (9)
C7	0.0321 (11)	0.0279 (11)	0.0342 (11)	0.0007 (9)	0.0040 (9)	0.0026 (9)
C8	0.0418 (13)	0.0316 (12)	0.0332 (12)	0.0028 (10)	0.0010 (10)	0.0029 (9)
C9	0.0415 (13)	0.0353 (12)	0.0367 (13)	0.0063 (10)	0.0043 (10)	0.0035 (10)
C10	0.0532 (16)	0.0515 (16)	0.0401 (14)	0.0140 (13)	−0.0056 (12)	−0.0024 (12)
C11	0.0376 (12)	0.0255 (10)	0.0397 (12)	0.0013 (9)	−0.0025 (10)	0.0013 (9)
C12	0.0365 (12)	0.0272 (11)	0.0424 (13)	−0.0034 (9)	−0.0080 (10)	0.0009 (10)
C13	0.0525 (16)	0.0452 (15)	0.0423 (15)	−0.0083 (12)	0.0004 (12)	−0.0001 (12)

Geometric parameters (Å, º) top

Br1—C3	1.882 (3)	N2—C1	1.373 (3)
C3—C2	1.380 (4)	N3—C5	1.358 (3)
C3—C4	1.398 (4)	C1—C2	1.404 (3)
C4—N3	1.315 (4)	C1—C5	1.404 (3)
C4—H4	0.9500	C2—H2	0.9500
Br1A—C4A	1.866 (4)	C6—C7	1.455 (3)
C3A—C2	1.380 (4)	C8—C9	1.456 (3)
C3A—C4A	1.398 (4)	C8—H8A	0.9900
C3A—H3A	0.9729	C8—H8B	0.9900
C4A—N3	1.315 (4)	C9—C10	1.175 (4)
S1—C6	1.750 (2)	C10—H10	0.9500
S1—C8	1.824 (2)	C11—C12	1.455 (4)
S2—C7	1.755 (2)	C11—H11A	0.9900
S2—C11	1.814 (2)	C11—H11B	0.9900
N1—C6	1.307 (3)	C12—C13	1.176 (4)
N1—C5	1.368 (3)	C13—H13	0.9500
N2—C7	1.303 (3)

C2—C3—C4	119.7 (2)	N3—C5—N1	116.0 (2)
C2—C3—Br1	120.6 (2)	N3—C5—C1	123.0 (2)
C4—C3—Br1	119.6 (2)	N1—C5—C1	121.0 (2)
N3—C4—C3	123.8 (2)	N1—C6—C7	122.2 (2)
N3—C4—H4	118.1	N1—C6—S1	120.73 (18)
C3—C4—H4	118.1	C7—C6—S1	117.11 (17)
C2—C3A—C4A	119.7 (2)	N2—C7—C6	121.5 (2)
C2—C3A—H3A	118.6	N2—C7—S2	121.34 (18)
C4A—C3A—H3A	121.6	C6—C7—S2	117.14 (17)
N3—C4A—C3A	123.8 (2)	C9—C8—S1	108.37 (17)
N3—C4A—Br1A	145.9 (4)	C9—C8—H8A	110.0
C3A—C4A—Br1A	90.3 (4)	S1—C8—H8A	110.0
C6—S1—C8	99.78 (11)	C9—C8—H8B	110.0
C7—S2—C11	100.09 (11)	S1—C8—H8B	110.0
C6—N1—C5	116.8 (2)	H8A—C8—H8B	108.4
C7—N2—C1	116.8 (2)	C10—C9—C8	179.0 (3)
C4A—N3—C5	117.2 (2)	C9—C10—H10	180.0
C4—N3—C5	117.2 (2)	C12—C11—S2	113.08 (17)
N2—C1—C2	119.7 (2)	C12—C11—H11A	109.0
N2—C1—C5	121.7 (2)	S2—C11—H11A	109.0
C2—C1—C5	118.5 (2)	C12—C11—H11B	109.0
C3A—C2—C1	117.6 (2)	S2—C11—H11B	109.0
C3—C2—C1	117.6 (2)	H11A—C11—H11B	107.8
C3—C2—H2	121.2	C13—C12—C11	178.6 (3)
C1—C2—H2	121.2	C12—C13—H13	180.0

C2—C3—C4—N3	1.9 (4)	C4—N3—C5—C1	−1.5 (4)
Br1—C3—C4—N3	−176.1 (2)	C6—N1—C5—N3	179.6 (2)
C2—C3A—C4A—N3	1.9 (4)	C6—N1—C5—C1	−0.2 (3)
Br1A—C3A—C4A—N3	179.5 (5)	N2—C1—C5—N3	−179.9 (2)
C2—C3A—C4A—Br1A	−177.6 (4)	C2—C1—C5—N3	1.0 (4)
C3A—Br1A—C4A—N3	−179.2 (7)	N2—C1—C5—N1	−0.1 (4)
C3A—C4A—N3—C5	0.1 (4)	C2—C1—C5—N1	−179.2 (2)
Br1A—C4A—N3—C5	179.2 (7)	C5—N1—C6—C7	−0.1 (3)
C3—C4—N3—C5	0.1 (4)	C5—N1—C6—S1	−179.46 (17)
C7—N2—C1—C2	179.9 (2)	C8—S1—C6—N1	0.2 (2)
C7—N2—C1—C5	0.7 (3)	C8—S1—C6—C7	−179.20 (18)
C4A—C3A—C2—C1	−2.3 (4)	C1—N2—C7—C6	−1.0 (3)
C4—C3—C2—C1	−2.3 (4)	C1—N2—C7—S2	178.35 (17)
Br1—C3—C2—C1	175.62 (18)	N1—C6—C7—N2	0.8 (4)
N2—C1—C2—C3A	−178.1 (2)	S1—C6—C7—N2	−179.84 (18)
C5—C1—C2—C3A	1.0 (4)	N1—C6—C7—S2	−178.63 (18)
N2—C1—C2—C3	−178.1 (2)	S1—C6—C7—S2	0.7 (2)
C5—C1—C2—C3	1.0 (4)	C11—S2—C7—N2	3.2 (2)
C4A—N3—C5—N1	178.7 (2)	C11—S2—C7—C6	−177.38 (18)
C4—N3—C5—N1	178.7 (2)	C6—S1—C8—C9	175.29 (17)
C4A—N3—C5—C1	−1.5 (4)	C7—S2—C11—C12	76.78 (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.

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