Crystal structure of 2-aza­niumyl-3-bromo-6-oxo-5,6-di­hydro­pyrido[1,2-a]quinoxalin-11-ium dibromide

The title salt, C₁₂H₁₀BrN₃O²⁺·2Br⁻, was synthesized from the reaction of N¹,N⁴-bis­(pyridin-2-yl­methyl­idene)benzene-1,4-di­amine and bromine in a methanol solution. All non-H atoms of the 2-aza­niumyl-3-bromo-6-oxo-5,6-di­hydro­pyrido[1,2-a]quinoxalin-11-ium cation are nearly coplanar, the maximum deviation being 0.114 (4) Å. In the crystal, the cations and anions are linked through N—H...Br hydrogen bonds and weak C—H...Br inter­actions, forming a three-dimensional supra­molecular architecture. A short Br...Br contact [3.3088 (9) Å] is observed in the crystal.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.009 Å
• R factor = 0.047
• wR factor = 0.130
• Data-to-parameter ratio = 14.0

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT341_ALERT_3_C Low Bond Precision on  C-C Bonds ...............     0.0091 Ang.
PLAT410_ALERT_2_C Short Intra H...H Contact  H1     ..  H11     ..       1.97 Ang.
PLAT434_ALERT_2_C Short Inter HL..HL Contact  Br1    ..  Br3     .       3.31 Ang.

Alert level G
PLAT005_ALERT_5_G No _iucr_refine_instructions_details  in the CIF     Please Do !
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          4 Report
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          3 Note
PLAT899_ALERT_4_G SHELXL97   is Deprecated and Succeeded by SHELXL       2014 Note
PLAT909_ALERT_3_G Percentage of Observed Data at Theta(Max) still          51 %

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   3 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   5 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   2 ALERT type 5 Informative message, check

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S1. Comment

Quinoxalines are an important class of heterocyclic compounds, some of which are found to be useful as fluorophores, dyes, and antibiotics (Duffy et al., 2002; Gazit et al., 1996). Many drug candidates bearing quinoxaline core structures are in clinical trials in antiviral, anticancer and CNS (central nervous system) therapeutic areas (Harmenberg et al., 1991; Naylor et al., 1993). The present work is a part of an ongoing structural study of Schiff bases and their utilization in the synthesis of previously unknown organic and polynuclear coordination compounds (Faizi & Sen, 2014; Faizi et al., 2014; Moroz et al., 2012), and we report here synthesis and structure of 2-azaniumyl-3-bromo-6-oxo-5,6-dihydropyrido[1,2-a]quinoxalin-11-ium bromide (ABODQ). There are very few examples similar to title compound have been reported in the literature (Eiden & Peter, 1966).

The title compound was synthesized from the reaction of two equimolar amounts of molecular bromine and pyridine derivative Schiff base N1,N4-bis(pyridine-2-ylmethylene) benzene-1,4-diamine (BPYBD). The cyclization occurs by oxidation of BPYBD, reduction of molecular bromine and finally hydrolysis of the imine bond which creates the dication at two of the nitrogen atoms in the quinoxaline ring system.

In the structure of the title bromide salt, the dication is essentially planar with a longer C10—N3 distance of 1.45 (3) Å, compared to the usual C_aro—N_amine single bond distance of 1.43 (3) Å. This might be due to the electron withdrawing effect of positively charged pyridine, which increased the C-N_amine 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).

The asymmetric unit contains a discrete 2-azaniumyl-3-bromo-6-oxo-5,6-dihydropyrido[1,2-a]quinoxalin-11-ium cation, with a protonated amine, pyridine group, and two bromide anion (Fig 1). In title compound, the ions are connected into a three dimensional hydrogen-bonded network via N—H···Br and C—H···Br hydrogen bonds (Table 1). All H_ammonium atoms and H_pyrazine N—H group are involved in hydrogen bonds with two different bromide ions, and each anion accepts hydrogen bonds from three different cations. No intermolecular π–π interations are evident in the hydrocarbon layer in title compound.

Related literature

For applications of quinoxalines, see: Duffy et al. (2002); Gazit et al. (1996); Harmenberg et al. (1991); Naylor et al. (1993). For types of quinoxalines and a structure similar to title compound, see: Eiden & Peter (1966); Koner & Ray (2008); Fritsky et al. (2006); Kanderal et al. (2005); Moroz et al. (2012). For background to and applications of related compounds, see: Faizi & Sen (2014); Faizi et al. (2014).

S2. Experimental

Molecular bromine (220 mg, 72.0 mL, 1.40 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 was immediately changed from yellow to orange. The reaction mixture was stirred for 4 h at room temperature under hood. The resulting yellow precipitate was recovered by filtration, washed several times with a small portions of acetone and then with diethyl ether to give 200 mg (64%) of 2-azaniumyl-3-bromo-6-oxo-5,6-dihydropyrido [1,2-a]quinoxalin-11-ium bromide (ABODQ). The crystal of the title compound suitable for X-ray analysis was obtained within 3 days by slow evaporation of the methanol solvent.

S3. Refinement

H atoms were placed in calculated positions and treated as riding on their parent atoms with C—H = 0.95 Å, N—H = 0.88 or 0.91 Å. U_iso(H) = 1.5U_eq(N) for the amino-H atoms and 1.2U_eq(C,N) for the others.

Computing details

Data collection: SMART (Bruker, 2003); cell refinement: SAINT (Bruker, 2003); data reduction: SAINT (Bruker, 2003); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenberg & Putz, 2006); software used to prepare material for publication: DIAMOND (Brandenberg & Putz, 2006).

Figures

Fig. 1. The molecular conformation and atom-numbering scheme for the title compound, with non-H atoms drawn as 40% probability displacement ellipsoids.

2-Azaniumyl-3-bromo-6-oxo-5,6-dihydropyrido[1,2-a]quinoxalin-11-ium dibromide

Crystal data

C12H10BrN3O^2+·2Br^−	F(000) = 864
Mr = 451.96	Dx = 2.179 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 999 reflections
a = 5.6782 (2) Å	θ = 2.6–28.6°
b = 11.9822 (4) Å	µ = 8.78 mm^−1
c = 20.2528 (7) Å	T = 100 K
β = 90.891 (2)°	Block, yellow
V = 1377.78 (8) Å^3	0.30 × 0.25 × 0.20 mm
Z = 4

Data collection

Bruker SMART APEX CCD diffractometer	2424 independent reflections
Radiation source: fine-focus sealed tube	1804 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.106
ω scans	θmax = 25.0°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −6→6
Tmin = 0.178, Tmax = 0.273	k = −14→14
14369 measured reflections	l = −23→24

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.130	H-atom parameters constrained
S = 0.97	w = 1/[σ^2(Fo^2) + (0.0801P)^2] where P = (Fo^2 + 2Fc^2)/3
2424 reflections	(Δ/σ)max < 0.001
173 parameters	Δρmax = 1.23 e Å^−3
0 restraints	Δρmin = −0.88 e Å^−3

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	1.1684 (11)	0.3466 (5)	0.6250 (3)	0.0348 (16)
H1	1.1805	0.3779	0.5821	0.042*
C2	1.3279 (12)	0.3771 (5)	0.6724 (3)	0.0404 (17)
H2	1.4479	0.4297	0.6628	0.049*
C3	1.3135 (12)	0.3313 (6)	0.7341 (3)	0.0432 (18)
H3	1.4246	0.3511	0.7676	0.052*
C4	1.1375 (12)	0.2564 (6)	0.7472 (3)	0.0408 (17)
H4	1.1293	0.2230	0.7896	0.049*
C5	0.9719 (11)	0.2291 (5)	0.6989 (3)	0.0308 (15)
C6	0.7750 (11)	0.1557 (5)	0.7166 (3)	0.0327 (15)
C7	0.6487 (11)	0.1672 (5)	0.6019 (3)	0.0284 (14)
C8	0.4824 (11)	0.1344 (5)	0.5543 (3)	0.0297 (14)
H8	0.3582	0.0851	0.5655	0.036*
C9	0.5012 (11)	0.1750 (5)	0.4905 (3)	0.0287 (14)
C10	0.6803 (11)	0.2482 (5)	0.4745 (3)	0.0272 (14)
C11	0.8407 (11)	0.2812 (5)	0.5212 (3)	0.0294 (14)
H11	0.9619	0.3323	0.5104	0.035*
C12	0.8249 (11)	0.2387 (5)	0.5857 (3)	0.0252 (14)
N1	0.9939 (8)	0.2736 (4)	0.6368 (2)	0.0262 (11)
N2	0.6287 (9)	0.1254 (4)	0.6658 (2)	0.0319 (12)
H2A	0.5160	0.0770	0.6737	0.038*
N3	0.6987 (9)	0.2912 (4)	0.4080 (2)	0.0343 (13)
H1N3	0.8278	0.3360	0.4054	0.052*
H2N3	0.5673	0.3314	0.3976	0.052*
H3N3	0.7126	0.2334	0.3792	0.052*
O1	0.7430 (8)	0.1251 (4)	0.7735 (2)	0.0428 (12)
Br1	0.82448 (12)	0.04974 (5)	0.33038 (3)	0.0399 (2)
Br2	0.21399 (13)	0.05913 (6)	0.91141 (4)	0.0478 (3)
Br3	0.26693 (12)	0.12868 (6)	0.42784 (3)	0.0388 (2)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.035 (4)	0.036 (4)	0.033 (4)	−0.004 (3)	0.000 (3)	0.003 (3)
C2	0.038 (4)	0.036 (4)	0.047 (4)	−0.002 (3)	−0.002 (3)	−0.002 (3)
C3	0.038 (5)	0.053 (5)	0.038 (4)	0.003 (4)	−0.005 (3)	−0.015 (4)
C4	0.039 (4)	0.053 (4)	0.030 (4)	0.001 (3)	−0.002 (3)	−0.007 (3)
C5	0.031 (4)	0.040 (4)	0.021 (3)	0.004 (3)	0.002 (3)	−0.005 (3)
C6	0.030 (4)	0.040 (4)	0.028 (4)	0.006 (3)	−0.002 (3)	−0.008 (3)
C7	0.036 (4)	0.031 (4)	0.018 (3)	0.002 (3)	0.002 (3)	−0.001 (3)
C8	0.026 (4)	0.031 (3)	0.032 (4)	0.001 (3)	0.004 (3)	0.000 (3)
C9	0.029 (4)	0.033 (3)	0.024 (3)	0.004 (3)	−0.008 (3)	−0.005 (3)
C10	0.030 (4)	0.035 (4)	0.016 (3)	0.005 (3)	0.006 (2)	−0.002 (3)
C11	0.023 (4)	0.035 (4)	0.030 (3)	−0.002 (3)	0.007 (3)	−0.002 (3)
C12	0.026 (4)	0.027 (3)	0.022 (3)	0.000 (3)	0.003 (3)	−0.002 (3)
N1	0.026 (3)	0.030 (3)	0.023 (3)	0.001 (2)	0.001 (2)	−0.002 (2)
N2	0.033 (3)	0.037 (3)	0.026 (3)	−0.002 (2)	0.005 (2)	0.002 (2)
N3	0.041 (4)	0.043 (3)	0.020 (3)	0.005 (2)	0.004 (2)	0.002 (2)
O1	0.050 (3)	0.062 (3)	0.016 (2)	−0.007 (2)	0.008 (2)	0.004 (2)
Br1	0.0317 (5)	0.0464 (5)	0.0415 (4)	−0.0044 (3)	0.0032 (3)	−0.0017 (3)
Br2	0.0423 (5)	0.0435 (5)	0.0579 (5)	−0.0028 (3)	0.0115 (4)	−0.0072 (3)
Br3	0.0370 (5)	0.0460 (5)	0.0333 (4)	0.0011 (3)	−0.0044 (3)	−0.0048 (3)

Geometric parameters (Å, º)

C1—N1	1.346 (7)	C7—N2	1.394 (7)
C1—C2	1.359 (9)	C8—C9	1.387 (8)
C1—H1	0.9500	C8—H8	0.9500
C2—C3	1.368 (9)	C9—C10	1.385 (9)
C2—H2	0.9500	C9—Br3	1.907 (6)
C3—C4	1.372 (10)	C10—C11	1.362 (8)
C3—H3	0.9500	C10—N3	1.449 (7)
C4—C5	1.384 (8)	C11—C12	1.405 (8)
C4—H4	0.9500	C11—H11	0.9500
C5—N1	1.374 (7)	C12—N1	1.462 (7)
C5—C6	1.471 (9)	N2—H2A	0.8800
C6—O1	1.225 (7)	N3—H1N3	0.9100
C6—N2	1.361 (8)	N3—H2N3	0.9100
C7—C12	1.361 (8)	N3—H3N3	0.9100
C7—C8	1.395 (8)
N1—C1—C2	122.3 (6)	C8—C9—C10	120.5 (6)
N1—C1—H1	118.9	C8—C9—Br3	117.1 (5)
C2—C1—H1	118.9	C10—C9—Br3	122.4 (4)
C1—C2—C3	119.2 (7)	C11—C10—C9	120.5 (5)
C1—C2—H2	120.4	C11—C10—N3	119.0 (6)
C3—C2—H2	120.4	C9—C10—N3	120.5 (5)
C2—C3—C4	119.6 (6)	C10—C11—C12	119.2 (6)
C2—C3—H3	120.2	C10—C11—H11	120.4
C4—C3—H3	120.2	C12—C11—H11	120.4
C3—C4—C5	120.4 (6)	C7—C12—C11	120.7 (6)
C3—C4—H4	119.8	C7—C12—N1	119.1 (5)
C5—C4—H4	119.8	C11—C12—N1	120.2 (5)
N1—C5—C4	119.0 (6)	C1—N1—C5	119.5 (5)
N1—C5—C6	122.3 (5)	C1—N1—C12	122.5 (5)
C4—C5—C6	118.7 (6)	C5—N1—C12	118.0 (5)
O1—C6—N2	122.2 (6)	C6—N2—C7	123.2 (5)
O1—C6—C5	122.1 (6)	C6—N2—H2A	118.4
N2—C6—C5	115.7 (5)	C7—N2—H2A	118.4
C12—C7—C8	120.2 (5)	C10—N3—H1N3	109.5
C12—C7—N2	121.4 (5)	C10—N3—H2N3	109.5
C8—C7—N2	118.5 (6)	H1N3—N3—H2N3	109.5
C9—C8—C7	119.0 (6)	C10—N3—H3N3	109.5
C9—C8—H8	120.5	H1N3—N3—H3N3	109.5
C7—C8—H8	120.5	H2N3—N3—H3N3	109.5
N1—C1—C2—C3	0.9 (10)	N2—C7—C12—C11	−179.2 (5)
C1—C2—C3—C4	−0.7 (11)	C8—C7—C12—N1	178.6 (5)
C2—C3—C4—C5	−1.5 (11)	N2—C7—C12—N1	−1.1 (9)
C3—C4—C5—N1	3.4 (10)	C10—C11—C12—C7	−1.4 (9)
C3—C4—C5—C6	−175.0 (6)	C10—C11—C12—N1	−179.5 (5)
N1—C5—C6—O1	−172.7 (6)	C2—C1—N1—C5	1.1 (9)
C4—C5—C6—O1	5.7 (9)	C2—C1—N1—C12	−178.7 (6)
N1—C5—C6—N2	6.4 (8)	C4—C5—N1—C1	−3.2 (9)
C4—C5—C6—N2	−175.2 (6)	C6—C5—N1—C1	175.2 (5)
C12—C7—C8—C9	0.6 (9)	C4—C5—N1—C12	176.5 (5)
N2—C7—C8—C9	−179.7 (5)	C6—C5—N1—C12	−5.1 (8)
C7—C8—C9—C10	−0.9 (9)	C7—C12—N1—C1	−178.0 (6)
C7—C8—C9—Br3	−179.4 (4)	C11—C12—N1—C1	0.1 (9)
C8—C9—C10—C11	0.1 (9)	C7—C12—N1—C5	2.3 (8)
Br3—C9—C10—C11	178.4 (4)	C11—C12—N1—C5	−179.6 (5)
C8—C9—C10—N3	−179.5 (5)	O1—C6—N2—C7	174.0 (6)
Br3—C9—C10—N3	−1.1 (8)	C5—C6—N2—C7	−5.1 (8)
C9—C10—C11—C12	1.1 (9)	C12—C7—N2—C6	2.7 (9)
N3—C10—C11—C12	−179.3 (5)	C8—C7—N2—C6	−177.0 (5)
C8—C7—C12—C11	0.6 (9)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···Br1^i	0.88	2.46	3.322 (5)	167
N3—H1N3···Br2^ii	0.91	2.53	3.432 (5)	171
N3—H2N3···Br2^iii	0.91	2.42	3.287 (5)	160
N3—H3N3···Br1	0.91	2.50	3.374 (5)	162
C2—H2···Br2^iv	0.95	2.91	3.813 (6)	160
C3—H3···Br1^v	0.95	2.85	3.752 (7)	160
C8—H8···Br1^i	0.95	2.86	3.672 (6)	144
C11—H11···Br2^ii	0.95	2.80	3.639 (6)	148

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