Crystal structure of 2-amino-1,3-di-bromo-6-oxo-5,6-di-hydro-pyrido[1,2-a]quinoxalin-11-ium bromide monohydrate.

In the title hydrated salt, C12H8Br2N3O(+)·Br(-)·H2O, which was synthesized by the reaction of the pyridine derivative Schiff base N (1),N (4)-bis-(pyridine-2-yl-methyl-ene)benzene-1,4-di-amine with bromine, the asymmetric unit contains a 2-amino-1,3-di-bromo-6-oxo-5,6-di-hydro-pyrido[1,2-a]quinoxalin-11-ium cation, with a protonated pyridine moiety, a bromide anion and a water mol-ecule of solvation. The cation is non-planar with the di-bromo-substituted benzene ring, forming dihedral angles of 24.3 (4) and 11.5 (4)° with the fused pyridine and pyrazine ring moieties, respectively. In the crystal, the cations are linked through a centrosymmetric hydrogen-bonded cyclic R 4 (2)(8) Br2(H2O)2 unit by N-H⋯Br, N-H⋯O and O-H⋯Br hydrogen bonds, forming one-dimensional ribbons extending along b, with the planes of the cations lying parallel to (100).

Chemical context

Quinoxaline and its derivatives are an important class of benzo-heterocycles (Kurasawa et al., 1988 ▸; Cheeseman & Werstiuk, 1978 ▸), displaying a broad spectrum of biological activities (Seitz et al., 2002 ▸; Toshima et al., 2002 ▸) which have made them important structures in combinatorial drug-discovery literature (Wu & Ede, 2001 ▸; Lee et al., 1997 ▸). These compounds have also found applications as dyes (Zaragoza et al., 1999 ▸; Sonawane & Rangnekar, 2002 ▸) and building blocks in the synthesis of organic semiconductors (Katoh et al., 2000 ▸; Dailey et al., 2001 ▸) and they also serve as useful rigid subunits in macrocyclic receptors for mol­ecular recognition (Mizuno et al., 2002 ▸) and chemically controllable switches (Elwahy, 2000 ▸). The present work is a part of an ongoing structural study of Schiff bases and their utilization in the synthesis of new organic and polynuclear coordination compounds (Faizi & Sen, 2014 ▸; Moroz et al., 2012 ▸). We report here the synthesis and crystal structure of 2-amino-1,3-di­bromo-6-oxo-5,6-di­hydro­pyrido[1,2-a]quinoxalin-11-ium bromide monohydrate (refcode ADOQBM). Previously, we have reported new methods for the preparation of substituted quinoxaline derivatives together with their crystallographic characterization. However, there are very few reported structures of compounds similar to the title compound, one being the doubly protonated dibromide salt 2-aza­niumyl-3-bromo-6-oxo-5,6-di­hydro­pyrido[1,2-a]quinoxalin-11-ium dibromide (Faizi et al., 2015 ▸).

The title singly protonated monobromide monohydrate salt, C12H8Br2N3O+·Br−·H2O, was synthesized from the reaction the pyridine derivative Schiff base N1,N4–bis­(pyridine-2-yl­methyl­ene)benzene-1,4-di­amine (BPYBD) with mol­ecular bromine. The cyclization occurs by oxidation of BPYBD, reduction of mol­ecular bromine and finally hydrolysis of the imine bond which creates the charge at the pyridine nitro­gen atom in the quinoxaline ring system. The structure is reported herein.

Structural commentary

The asymmetric unit of the title compound contains a discrete 2-amino-1,3-di­bromo-6-oxo-5,6-di­hydro­pyrido[1,2-a]quinoxalin-11-ium cation with a protonated pyridine moiety, and a bromide counter-anion and a water mol­ecule of solvation (Fig. 1 ▸). The cation is non-planar compared to the previously reported structure (Faizi et al., 2015 ▸). The mean plane of the pyridine ring forms a dihedral angle of 24.2 (4)° with the benzene ring and 14.6 (4)° with the pyrazine ring of the fused system while the dihedral angle between the pyrazine and the benzene ring is 11.5 (4)°. A shorter C10—N3 distance of 1.367 (9) Å, compared to the usual aromatic C—Namine single bond distance of 1.43 (3) Å, might be due to the electron-withdrawing effect of the positively charged pyridine N atom, and the ortho-substituted bromine atom which decreases the C—Namine bond order. Other C—C and C—N bond distances are well within the limits expected for aromatic rings (Koner & Ray, 2008 ▸; Kanderal et al., 2005 ▸; Fritsky et al., 2006 ▸). Present also in the cations are intra­molecular N3—H⋯Br1 and N3—H⋯Br2 inter­actions [3.048 (7), 3.006 (7) Å, respectively, Table 1 ▸].

Figure 1

The mol­ecular conformation and atom-numbering scheme for the title compound, with non-H atoms drawn as 40% probability displacement ellipsoids.

Table 1

Hydrogen-bond geometry (, )

DHA	DH	HA	D A	DHA
N2H5Br3i	0.86	2.49	3.332(6)	166
N3H3BBr1	0.86	2.60	3.048(7)	113
N3H3BBr3ii	0.86	2.84	3.581(7)	145
N3H3AO1iii	0.86	2.17	2.977(9)	155
N3H3ABr2	0.86	2.56	3.006(7)	113
O2H11Br3iv	0.89	2.50	3.383(6)	180
O2H12Br1v	0.88	2.61	3.309(7)	137

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

Supra­molecular features

In the crystal, the cations are linked through a centrosymmetric hydrogen-bonded cyclic (8) Br2(H2O)2 unit and N—H⋯Br, N—H⋯O and O—H⋯Br hydrogen bonds (Table 1 ▸), forming broad one-dimensional ribbons extending along b (Fig. 2 ▸). The planes of the cations lie parallel to (100). Fig. 3 ▸ shows the packing in the unit cell, viewed along the b axis, in which layers of quinoxalinium cations are embedded between ionic layers of anions and vice versa, forming an alternating hydro­carbon–ionic layer structure. No inter­molecular π–π inter­ations are evident in the hydro­carbon layer in the structure.

Figure 2

The one-dimensional hydrogen-bonded ribbon structure, viewed along the a-axis direction. Inter-species inter­actions are shown as dashed lines.

Figure 3

The layering of the ribbon structures, viewed along the b axis.

Database survey

There are very few examples of similar compounds in the literature, a search of the Cambridge Structural Database (Version 5.35, May 2014 ▸; Groom & Allen, 2014) revealing the structure of 2-aza­niumyl-3-bromo-6-oxo-5,6-di­hydro­pyrido[1,2-a]quinoxalin-11-ium dibromide (Faizi et al., 2015 ▸), in which the 2-amino-1,2-dibromide ring in the title compound is replaced by a 2-aza­niumyl-3-bromo ring. Other similar structures have been reported (Faizi & Sen, 2014 ▸; Koner et al., 2008 ▸).

Synthesis and crystallization

Mol­ecular bromine (440 mg, 144.0 µL, 2.80 mmol) was added to a methano­lic solution (10 mL) of Schiff base, N1,N4-bis (pyridine-2-yl­methyl­ene)benzene-1,4-di­amine (BPYBD) (197 mg, 0.70 mmol). The color of the solution immediately changed from yellow to orange. The reaction mixture was stirred for 4 h at room temperature under a fume hood. The resulting yellow precipitate was recovered by filtration, washed several times with small portions of acetone and then with diethyl ether to give 200 mg (yield: 64%) of 2-amino-1,3-di­bromo-6-oxo-5,6-di­hydro­pyrido[1,2-a]quinoxalin-11-ium bromide monohydrate (ADOQBM). The crystal of the title compound suitable for X-ray analysis was obtained within three days by slow evaporation of a solution of the compound in methanol.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. All N-bound H atoms were located in difference-Fourier maps and their positions were then held fixed. The isotropic displacement parameters were refined for these atoms. Aromatic H atoms were placed in calculated positions and treated as riding on their parent C atoms [C—H = 0.93 Å and U iso(H) = 1.2 or 1.5U eq(C)].

Table 2

Experimental details

Crystal data
Chemical formula	C12H8Br2N3O+BrH2O
M r	467.93
Crystal system, space group	Triclinic, P
Temperature (K)	100
a, b, c ()	7.5069(7), 9.7435(10), 10.782(1)
, , ()	88.490(7), 73.798(7), 71.981(7)
V (3)	718.61(12)
Z	2
Radiation type	Mo K
(mm1)	8.42
Crystal size (mm)	0.20 0.15 0.11
Data collection
Diffractometer	Bruker SMART APEX CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2003 ▸)
T min, T max	0.259, 0.365
No. of measured, independent and observed [I > 2(I)] reflections	8077, 2187, 1681
R int	0.163
max ()	23.8
(sin /)max (1)	0.568
Refinement
R[F 2 > 2(F 2)], wR(F 2), S	0.059, 0.155, 1.00
No. of reflections	2187
No. of parameters	181
H-atom treatment	H-atom parameters constrained
max, min (e 3)	1.18, 1.16

Computer programs: SMART and SAINT (Bruker, 2003 ▸), SIR97 (Altomare et al., 1999 ▸), SHELXL97 (Sheldrick, 2008 ▸) and DIAMOND (Brandenberg Putz, 2006 ▸).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015018253/zs2343sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015018253/zs2343Isup2.hkl

CCDC reference: 1428593

Additional supporting information: crystallographic information; 3D view; checkCIF report

C12H8Br2N3O+·Br−·H2O	Z = 2
Mr = 467.93	F(000) = 448
Triclinic, P1	Dx = 2.163 Mg m−3
a = 7.5069 (7) Å	Mo Kα radiation, λ = 0.71073 Å
b = 9.7435 (10) Å	Cell parameters from 1023 reflections
c = 10.782 (1) Å	θ = 1.5–23.5°
α = 88.490 (7)°	µ = 8.42 mm−1
β = 73.798 (7)°	T = 100 K
γ = 71.981 (7)°	Block, yellow
V = 718.61 (12) Å3	0.20 × 0.15 × 0.11 mm

Bruker SMART APEX CCD diffractometer	2187 independent reflections
Radiation source: fine-focus sealed tube	1681 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.163
/w–scans	θmax = 23.8°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2003)	h = −8→8
Tmin = 0.259, Tmax = 0.365	k = −11→10
8077 measured reflections	l = −12→12

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)] = 0.059	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.155	H-atom parameters constrained
S = 1.00	w = 1/[σ2(Fo2) + (0.0902P)2] where P = (Fo2 + 2Fc2)/3
2187 reflections	(Δ/σ)max < 0.001
181 parameters	Δρmax = 1.18 e Å−3
0 restraints	Δρmin = −1.16 e Å−3

Experimental. The OH H-atom was located in difference Fourier map and refined with with Uiso(H) = 1.2Ueq(O). The N- and C-bound H-atoms were positioned geometrically and refined using a riding model: N—H = 0.86 Å and C—H = 0.93 Å with Uiso(H) = 1.2Ueq(parent atom).

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.

	x	y	z	Uiso*/Ueq
Br3	0.26076 (12)	0.03614 (8)	0.73364 (8)	0.0441 (3)
Br2	0.27561 (13)	0.36785 (8)	0.22264 (8)	0.0446 (3)
Br1	0.30008 (13)	0.45076 (9)	−0.29950 (8)	0.0480 (3)
C3	0.1893 (12)	0.8452 (10)	0.4590 (8)	0.048 (2)
H3	0.2041	0.8791	0.5342	0.058*
C1	0.1158 (12)	0.6740 (8)	0.3479 (7)	0.0388 (19)
H1	0.0617	0.5998	0.3495	0.047*
N1	0.1941 (9)	0.7217 (6)	0.2309 (6)	0.0316 (14)
C2	0.1146 (14)	0.7316 (9)	0.4612 (8)	0.048 (2)
H2	0.0644	0.6953	0.5393	0.057*
C4	0.2417 (12)	0.9077 (9)	0.3430 (8)	0.046 (2)
H4	0.2805	0.9898	0.3414	0.055*
C12	0.2134 (10)	0.6506 (7)	0.1102 (7)	0.0306 (17)
N2	0.2314 (10)	0.8738 (6)	0.0112 (6)	0.0377 (16)
H5	0.2190	0.9269	−0.0528	0.045*
C7	0.2241 (11)	0.7334 (7)	0.0019 (7)	0.0327 (18)
C11	0.2384 (11)	0.5009 (7)	0.0921 (7)	0.0318 (18)
C9	0.2558 (11)	0.5314 (8)	−0.1296 (8)	0.0362 (19)
C10	0.2586 (10)	0.4390 (7)	−0.0288 (7)	0.0324 (18)
C8	0.2379 (11)	0.6744 (7)	−0.1175 (8)	0.0349 (18)
H6	0.2351	0.7313	−0.1879	0.042*
C5	0.2364 (11)	0.8482 (8)	0.2307 (8)	0.0353 (18)
C6	0.2565 (12)	0.9308 (8)	0.1142 (8)	0.042 (2)
O1	0.2841 (12)	1.0476 (6)	0.1172 (7)	0.071 (2)
N3	0.2950 (11)	0.2940 (7)	−0.0508 (7)	0.0457 (18)
H3A	0.3064	0.2371	0.0109	0.055*
H3B	0.3066	0.2597	−0.1263	0.055*
O2	0.3545 (11)	0.2190 (7)	0.4635 (6)	0.072 (2)
H12	0.3415	0.2338	0.5459	0.108*
H11	0.4550	0.1520	0.4120	0.108*

	U11	U22	U33	U12	U13	U23
Br3	0.0499 (5)	0.0360 (5)	0.0489 (5)	−0.0143 (4)	−0.0173 (4)	0.0057 (4)
Br2	0.0516 (6)	0.0273 (5)	0.0573 (6)	−0.0140 (4)	−0.0184 (4)	0.0127 (4)
Br1	0.0565 (6)	0.0389 (5)	0.0510 (6)	−0.0130 (4)	−0.0206 (4)	−0.0041 (4)
C3	0.044 (5)	0.051 (6)	0.051 (5)	−0.013 (4)	−0.017 (4)	−0.003 (4)
C1	0.046 (5)	0.029 (4)	0.043 (5)	−0.014 (4)	−0.012 (4)	0.004 (4)
N1	0.033 (3)	0.022 (3)	0.045 (4)	−0.012 (3)	−0.016 (3)	0.007 (3)
C2	0.061 (6)	0.042 (5)	0.040 (5)	−0.016 (5)	−0.017 (4)	0.012 (4)
C4	0.052 (5)	0.033 (4)	0.060 (6)	−0.018 (4)	−0.021 (4)	−0.006 (4)
C12	0.032 (4)	0.022 (4)	0.040 (4)	−0.011 (3)	−0.010 (3)	0.000 (3)
N2	0.052 (4)	0.018 (3)	0.044 (4)	−0.010 (3)	−0.016 (3)	0.006 (3)
C7	0.036 (4)	0.016 (4)	0.047 (5)	−0.007 (3)	−0.015 (4)	0.006 (3)
C11	0.033 (4)	0.017 (4)	0.051 (5)	−0.014 (3)	−0.014 (3)	0.009 (3)
C9	0.037 (4)	0.030 (4)	0.048 (5)	−0.013 (4)	−0.018 (4)	−0.004 (4)
C10	0.029 (4)	0.016 (4)	0.053 (5)	−0.005 (3)	−0.017 (4)	0.004 (4)
C8	0.038 (4)	0.020 (4)	0.045 (5)	−0.008 (3)	−0.009 (4)	0.002 (3)
C5	0.036 (4)	0.018 (4)	0.049 (5)	−0.002 (3)	−0.014 (4)	−0.004 (3)
C6	0.053 (5)	0.017 (4)	0.057 (5)	−0.013 (4)	−0.016 (4)	0.002 (4)
O1	0.115 (6)	0.030 (3)	0.086 (5)	−0.041 (4)	−0.038 (4)	0.007 (3)
N3	0.069 (5)	0.022 (3)	0.052 (4)	−0.019 (3)	−0.022 (4)	0.003 (3)
O2	0.077 (5)	0.063 (4)	0.064 (4)	−0.005 (4)	−0.020 (4)	0.015 (4)

Br2—C11	1.907 (7)	N2—C6	1.338 (10)
Br1—C9	1.912 (8)	N2—C7	1.393 (9)
C3—C2	1.384 (12)	N2—H5	0.8600
C3—C4	1.387 (12)	C7—C8	1.388 (11)
C3—H3	0.9300	C11—C10	1.400 (11)
C1—C2	1.355 (11)	C9—C8	1.364 (10)
C1—N1	1.370 (10)	C9—C10	1.394 (11)
C1—H1	0.9300	C10—N3	1.367 (9)
N1—C5	1.364 (9)	C8—H6	0.9300
N1—C12	1.440 (9)	C5—C6	1.471 (11)
C2—H2	0.9300	C6—O1	1.222 (9)
C4—C5	1.373 (11)	N3—H3A	0.8600
C4—H4	0.9300	N3—H3B	0.8600
C12—C7	1.399 (10)	O2—H12	0.8769
C12—C11	1.423 (9)	O2—H11	0.8900
C2—C3—C4	119.0 (8)	C12—C7—N2	120.3 (7)
C2—C3—H3	120.5	C10—C11—C12	121.3 (7)
C4—C3—H3	120.5	C10—C11—Br2	115.3 (5)
C2—C1—N1	122.1 (8)	C12—C11—Br2	123.0 (6)
C2—C1—H1	119.0	C8—C9—C10	124.3 (7)
N1—C1—H1	119.0	C8—C9—Br1	117.2 (6)
C5—N1—C1	118.1 (6)	C10—C9—Br1	118.3 (5)
C5—N1—C12	119.7 (6)	N3—C10—C11	122.5 (7)
C1—N1—C12	121.9 (6)	N3—C10—C9	121.0 (7)
C1—C2—C3	118.9 (8)	C11—C10—C9	116.3 (6)
C1—C2—H2	120.5	C9—C8—C7	118.8 (7)
C3—C2—H2	120.5	C9—C8—H6	120.6
C5—C4—C3	119.9 (8)	C7—C8—H6	120.6
C5—C4—H4	120.1	N1—C5—C4	120.2 (7)
C3—C4—H4	120.1	N1—C5—C6	120.8 (7)
C7—C12—C11	118.4 (7)	C4—C5—C6	118.7 (7)
C7—C12—N1	116.8 (6)	O1—C6—N2	123.8 (8)
C11—C12—N1	124.6 (6)	O1—C6—C5	120.2 (8)
C6—N2—C7	123.7 (6)	N2—C6—C5	115.9 (7)
C6—N2—H5	118.2	C10—N3—H3A	120.0
C7—N2—H5	118.2	C10—N3—H3B	120.0
C8—C7—C12	120.5 (7)	H3A—N3—H3B	120.0
C8—C7—N2	119.1 (7)	H12—O2—H11	123.0
C2—C1—N1—C5	−13.0 (11)	Br2—C11—C10—C9	−172.4 (6)
C2—C1—N1—C12	173.4 (7)	C8—C9—C10—N3	−173.9 (8)
N1—C1—C2—C3	2.1 (12)	Br1—C9—C10—N3	1.0 (10)
C4—C3—C2—C1	7.5 (12)	C8—C9—C10—C11	1.0 (12)
C2—C3—C4—C5	−6.1 (13)	Br1—C9—C10—C11	175.9 (5)
C5—N1—C12—C7	−16.6 (10)	C10—C9—C8—C7	0.9 (12)
C1—N1—C12—C7	156.8 (7)	Br1—C9—C8—C7	−174.0 (6)
C5—N1—C12—C11	157.9 (7)	C12—C7—C8—C9	−4.9 (11)
C1—N1—C12—C11	−28.7 (11)	N2—C7—C8—C9	171.8 (7)
C11—C12—C7—C8	6.7 (11)	C1—N1—C5—C4	14.3 (10)
N1—C12—C7—C8	−178.4 (7)	C12—N1—C5—C4	−172.0 (7)
C11—C12—C7—N2	−169.9 (7)	C1—N1—C5—C6	−159.2 (7)
N1—C12—C7—N2	5.0 (11)	C12—N1—C5—C6	14.4 (10)
C6—N2—C7—C8	−166.8 (7)	C3—C4—C5—N1	−5.0 (12)
C6—N2—C7—C12	9.8 (12)	C3—C4—C5—C6	168.7 (8)
C7—C12—C11—C10	−4.7 (11)	C7—N2—C6—O1	171.7 (9)
N1—C12—C11—C10	−179.2 (7)	C7—N2—C6—C5	−12.2 (11)
C7—C12—C11—Br2	168.1 (6)	N1—C5—C6—O1	176.1 (8)
N1—C12—C11—Br2	−6.4 (11)	C4—C5—C6—O1	2.5 (12)
C12—C11—C10—N3	175.8 (7)	N1—C5—C6—N2	−0.1 (11)
Br2—C11—C10—N3	2.4 (10)	C4—C5—C6—N2	−173.8 (7)
C12—C11—C10—C9	0.9 (11)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H5···Br3i	0.86	2.49	3.332 (6)	166
N3—H3B···Br1	0.86	2.60	3.048 (7)	113
N3—H3B···Br3ii	0.86	2.84	3.581 (7)	145
N3—H3A···O1iii	0.86	2.17	2.977 (9)	155
N3—H3A···Br2	0.86	2.56	3.006 (7)	113
O2—H11···Br3iv	0.89	2.50	3.383 (6)	180
O2—H12···Br1v	0.88	2.61	3.309 (7)	137
O2—H12···Br3	0.88	2.83	3.393 (6)	123