3-Carbamoylquinoxalin-1-ium chloride

Harper, J.K.; Strobel, G.; Arif, A.M.

doi:10.1107/S1600536811052457

organic compounds

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Volume 68| Part 1| January 2012| Pages o79-o80

doi:10.1107/S1600536811052457

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3-Carbamoylquinoxalin-1-ium chloride

James K. Harper,^a ^* Gary Strobel ^b and Atta M. Arif ^c

^aUniversity of Central Florida, Department of Chemistry, 4000 Central Florida Blvd., Orlando, FL 32816, USA, ^bMontana State University, Department of Plant Sciences and Plant Patology, Bozeman, MT 59717, USA, and ^cUniversity of Utah, Department of Chemistry, 315 S. 1400 E. Rm. 2020, Salt Lake City, UT 84112, USA
^*Correspondence e-mail: james.harper@ucf.edu

(Received 15 November 2011; accepted 5 December 2011; online 10 December 2011)

The title compound, C₉H₈N₃O⁺·Cl⁻, was isolated from a liquid culture of streptomyces sp. In the cation, the ring system makes a dihedral angle of 0.2 (2)° with the amide group. The protonation creating the cation occurs at ome of the N atoms in the quinoxaline ring system. In the crystal, the ions are linked through N—H⋯O and N—H⋯Cl hydrogen bonds, forming a two-dimensional network parallel to (10 $[\overline{3}]$ ).

Related literature

For a description of the bioactivity and mode of action of compounds containing the quinoxaline moiety, see: Bailly et al. (1999 ); May et al. (2004 ); Mollegaard et al. (2000 ); Waring (1993 ). For crystal structures of the molecules triostin A, echinomycin and their derivatives, which all contain two quinoxalines, see: Hossain et al. (1982 ); Sheldrick et al. (1984 , 1995 ); Viswamitra et al. (1981 ); Wang et al. (1984 ); Ughetto et al. (1985 ). For a description of the Streptomycete producing the title compound, see: Castillo et al. (2003 ).

Experimental

Crystal data

C₉H₈N₃O⁺·Cl⁻
M_r = 209.63
Monoclinic, P 2₁ /n
a = 5.6476 (2) Å
b = 15.1045 (9) Å
c = 11.2556 (6) Å
β = 99.993 (3)°
V = 945.58 (8) Å³
Z = 4
Mo Kα radiation
μ = 0.37 mm⁻¹
T = 150 K
0.25 × 0.20 × 0.08 mm

Data collection

Nonius KappaCCD diffractometer
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997 ) T_min = 0.913, T_max = 0.971
3671 measured reflections
2147 independent reflections
1798 reflections with I > 2σ(I)
R_int = 0.018

Refinement

R[F² > 2σ(F²)] = 0.034
wR(F²) = 0.085
S = 1.05
2147 reflections
160 parameters
All H-atom parameters refined
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O1ⁱ	0.86 (2)	2.04 (2)	2.9008 (17)	173.5 (17)
N1—H1B⋯Cl1	0.90 (2)	2.44 (2)	3.2590 (13)	152.0 (17)
N3—H3N⋯Cl1ⁱⁱ	0.94 (2)	2.02 (2)	2.9501 (13)	169.8 (15)
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) $[x+{\script{3\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

Data collection: COLLECT (Nonius, 1998 ); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ); molecular graphics: WinGX (Farrugia, 1999 ) and ORTEP-3 (Farrugia, 1997 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811052457/lh5381sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811052457/lh5381Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811052457/lh5381Isup3.cml

checkCIF report

Comment top

The quinoxaline ring is an essential component of the DNA intercalators echinomycin and triostin A. The two quinoxaline rings present in each of these compounds bind the minor groove of double stranded DNA and thereby inhibit RNA synthesis (Bailly et al., 1999; May et al., 2004; Mollegaard et al., 2000; Waring, 1993). Presently, the quinoxaline ring has been characterized crystallographically only as part of a significantly larger molecular assembly (Hossain et al., 1982; Sheldrick et al.,1984; Sheldrick et al., 1995; Viswamitra et al., 1981; Wang et al., 1984; Ughetto et al., 1985). Accordingly, the resolution of the quinoxaline moieties currently established is relatively low. Here, characterization of a simpler quinoxaline ring system provides a higher resolution dataset for a compound having a substitution pattern identical to that found in the quinoxaline antibiotics. The conformation about the C1—C2 bond in the title compound is shown in Figure 1 and matches that reported for triostin A and echinomycin. Molecules in the crystal are linked through N1—H···O1ⁱ (see Table 1 for symmetry codes) hydrogen bonds as well as N1—H···Cl···H—N3 interaction. The structure viewed along the a axis is shown in figure 2.

Related literature top

For a description of the bioactivity and mode of action of compounds containing the quinoxaline moiety, see: Bailly et al. (1999); May et al. (2004); Mollegaard et al. (2000); Waring (1993). For crystal structures of the molecules triostin A, echinomycin and their derivatives, which all contain two quinoxalines, see: Hossain et al. (1982); Sheldrick et al. (1984, 1995); Viswamitra et al. (1981); Wang et al. (1984); Ughetto et al. (1985). For a description of the Streptomycete producing the title compound, see: Castillo et al. (2003).

Experimental top

The title compound was obtained by liquid-liquid extraction (CH₂Cl₂/H₂O) of a culture of an endophytic Streptomyces sp. described elsewhere (Castillo et al., 2003). A crystal was grown by slow evaporation of a 1:1 mix of CHCl₃:MeOH

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: WinGX (Farrugia, 1999) and ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. Molecular structure of the title compound. Displacement ellipsoids are shown at the 50% probability level on non-hydrogen atoms.
	Fig. 2. Part of the crystal structure viewed along the a axis. The dashed lines indicate N—H···O and N—H···Cl hydrogen bonds.

3-Carbamoylquinoxalin-1-ium chloride top

Crystal data top

C₉H₈N₃O⁺·Cl⁻	F(000) = 432
M_r = 209.63	D_x = 1.473 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 1998 reflections
a = 5.6476 (2) Å	θ = 1.0–27.5°
b = 15.1045 (9) Å	µ = 0.37 mm⁻¹
c = 11.2556 (6) Å	T = 150 K
β = 99.993 (3)°	Plate, pale yellow
V = 945.58 (8) Å³	0.25 × 0.20 × 0.08 mm
Z = 4

Data collection top

Nonius KappaCCD diffractometer	2147 independent reflections
Radiation source: fine-focus sealed tube	1798 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.018
ϕ and ω scans	θ_max = 27.5°, θ_min = 3.9°
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997)	h = −7→7
T_min = 0.913, T_max = 0.971	k = −18→19
3671 measured reflections	l = −14→14

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.034	All H-atom parameters refined
wR(F²) = 0.085	w = 1/[σ²(F_o²) + (0.0397P)² + 0.2499P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max < 0.001
2147 reflections	Δρ_max = 0.25 e Å⁻³
160 parameters	Δρ_min = −0.24 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.012 (4)

Crystal data top

C₉H₈N₃O⁺·Cl⁻	V = 945.58 (8) Å³
M_r = 209.63	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 5.6476 (2) Å	µ = 0.37 mm⁻¹
b = 15.1045 (9) Å	T = 150 K
c = 11.2556 (6) Å	0.25 × 0.20 × 0.08 mm
β = 99.993 (3)°

Data collection top

Nonius KappaCCD diffractometer	2147 independent reflections
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997)	1798 reflections with I > 2σ(I)
T_min = 0.913, T_max = 0.971	R_int = 0.018
3671 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.034	0 restraints
wR(F²) = 0.085	All H-atom parameters refined
S = 1.05	Δρ_max = 0.25 e Å⁻³
2147 reflections	Δρ_min = −0.24 e Å⁻³
160 parameters

Special details top

Experimental. The program DENZO-SMN (Otwinowski & Minor, 1997) uses a scaling algorithm that effectively corrects for absorption effects. High redundancy data were used in the scaling program hence the 'multi-scan' code word was used. No transmission coefficients are available from the program (only scale factors for each frame). The scale factors in the experimental table are calculated from the 'size' command in the SHELXL97 input file.

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s 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 > σ(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 (Å²) top

	x	y	z	U_iso*/U_eq
Cl1	0.08949 (6)	0.30272 (3)	0.19526 (3)	0.03255 (15)
O1	0.76925 (19)	0.43611 (7)	0.55896 (10)	0.0336 (3)
N1	0.4423 (2)	0.39023 (9)	0.42509 (12)	0.0269 (3)
N2	0.6771 (2)	0.23505 (8)	0.39555 (10)	0.0234 (3)
N3	1.1403 (2)	0.21019 (8)	0.51784 (11)	0.0248 (3)
C1	0.6625 (3)	0.38080 (9)	0.48828 (13)	0.0247 (3)
C2	0.7884 (2)	0.29539 (9)	0.46906 (12)	0.0234 (3)
C3	1.0240 (3)	0.28321 (10)	0.53318 (13)	0.0254 (3)
C4	1.0391 (2)	0.14589 (9)	0.43990 (12)	0.0237 (3)
C5	1.1680 (3)	0.06898 (10)	0.42012 (14)	0.0289 (3)
C6	1.0562 (3)	0.00651 (11)	0.34196 (14)	0.0338 (4)
C7	0.8153 (3)	0.01774 (11)	0.28407 (14)	0.0331 (4)
C8	0.6884 (3)	0.09223 (10)	0.30207 (13)	0.0276 (3)
C9	0.7997 (2)	0.15942 (9)	0.37975 (12)	0.0229 (3)
H1A	0.370 (3)	0.4397 (13)	0.4318 (16)	0.036 (5)*
H1B	0.381 (4)	0.3498 (15)	0.3699 (19)	0.051 (6)*
H3	1.102 (3)	0.3227 (12)	0.5857 (17)	0.035 (5)*
H3N	1.290 (3)	0.2011 (11)	0.5682 (17)	0.034 (5)*
H5	1.324 (3)	0.0634 (12)	0.4615 (16)	0.035 (5)*
H6	1.139 (3)	−0.0467 (12)	0.3273 (15)	0.032 (4)*
H7	0.738 (3)	−0.0276 (13)	0.2325 (17)	0.041 (5)*
H8	0.523 (3)	0.1023 (10)	0.2602 (15)	0.027 (4)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0270 (2)	0.0419 (2)	0.0258 (2)	−0.00693 (15)	−0.00344 (14)	−0.00243 (15)
O1	0.0323 (6)	0.0264 (5)	0.0365 (6)	0.0033 (4)	−0.0097 (5)	−0.0054 (5)
N1	0.0258 (6)	0.0235 (6)	0.0284 (7)	0.0029 (5)	−0.0037 (5)	−0.0018 (5)
N2	0.0240 (6)	0.0249 (6)	0.0205 (6)	−0.0011 (5)	0.0015 (5)	0.0019 (5)
N3	0.0217 (6)	0.0290 (6)	0.0225 (6)	0.0013 (5)	0.0000 (5)	0.0016 (5)
C1	0.0263 (7)	0.0231 (7)	0.0228 (7)	−0.0001 (6)	−0.0011 (5)	0.0023 (6)
C2	0.0235 (7)	0.0251 (7)	0.0212 (7)	−0.0014 (5)	0.0030 (5)	0.0016 (5)
C3	0.0244 (7)	0.0268 (7)	0.0232 (7)	−0.0009 (6)	−0.0007 (6)	−0.0007 (6)
C4	0.0253 (7)	0.0258 (7)	0.0204 (7)	−0.0011 (5)	0.0051 (5)	0.0029 (5)
C5	0.0286 (8)	0.0315 (8)	0.0274 (8)	0.0053 (6)	0.0075 (6)	0.0033 (6)
C6	0.0433 (9)	0.0288 (8)	0.0321 (8)	0.0056 (7)	0.0144 (7)	−0.0001 (7)
C7	0.0428 (9)	0.0303 (8)	0.0279 (8)	−0.0050 (7)	0.0102 (7)	−0.0071 (7)
C8	0.0296 (8)	0.0314 (8)	0.0220 (7)	−0.0046 (6)	0.0052 (6)	−0.0018 (6)
C9	0.0257 (7)	0.0246 (7)	0.0189 (7)	−0.0008 (6)	0.0050 (5)	0.0022 (5)

Geometric parameters (Å, º) top

O1—C1	1.2361 (17)	C3—H3	0.900 (19)
N1—C1	1.3285 (18)	C4—C5	1.409 (2)
N1—H1A	0.86 (2)	C4—C9	1.4178 (19)
N1—H1B	0.90 (2)	C5—C6	1.368 (2)
N2—C2	1.3154 (18)	C5—H5	0.928 (17)
N2—C9	1.3635 (18)	C6—C7	1.413 (2)
N3—C3	1.3104 (19)	C6—H6	0.957 (18)
N3—C4	1.3660 (19)	C7—C8	1.368 (2)
N3—H3N	0.94 (2)	C7—H7	0.95 (2)
C1—C2	1.5066 (19)	C8—C9	1.414 (2)
C2—C3	1.411 (2)	C8—H8	0.980 (16)

C1—N1—H1A	117.3 (12)	N3—C4—C9	117.53 (13)
C1—N1—H1B	120.9 (13)	C5—C4—C9	121.29 (13)
H1A—N1—H1B	121.2 (18)	C6—C5—C4	118.49 (15)
C2—N2—C9	117.67 (12)	C6—C5—H5	123.5 (11)
C3—N3—C4	121.30 (13)	C4—C5—H5	118.0 (11)
C3—N3—H3N	117.5 (10)	C5—C6—C7	120.93 (15)
C4—N3—H3N	120.9 (10)	C5—C6—H6	120.4 (10)
O1—C1—N1	125.36 (13)	C7—C6—H6	118.6 (10)
O1—C1—C2	118.78 (12)	C8—C7—C6	121.19 (15)
N1—C1—C2	115.85 (12)	C8—C7—H7	118.8 (11)
N2—C2—C3	122.45 (13)	C6—C7—H7	120.0 (11)
N2—C2—C1	119.85 (12)	C7—C8—C9	119.58 (14)
C3—C2—C1	117.69 (12)	C7—C8—H8	122.4 (9)
N3—C3—C2	119.48 (13)	C9—C8—H8	118.0 (9)
N3—C3—H3	116.4 (12)	N2—C9—C8	120.04 (13)
C2—C3—H3	124.2 (12)	N2—C9—C4	121.50 (13)
N3—C4—C5	121.17 (13)	C8—C9—C4	118.46 (13)

C9—N2—C2—C3	−1.7 (2)	C9—C4—C5—C6	−0.6 (2)
C9—N2—C2—C1	179.05 (12)	C4—C5—C6—C7	−1.3 (2)
O1—C1—C2—N2	179.06 (13)	C5—C6—C7—C8	1.6 (2)
N1—C1—C2—N2	−1.63 (19)	C6—C7—C8—C9	0.1 (2)
O1—C1—C2—C3	−0.2 (2)	C2—N2—C9—C8	179.78 (13)
N1—C1—C2—C3	179.12 (13)	C2—N2—C9—C4	−0.14 (19)
C4—N3—C3—C2	0.7 (2)	C7—C8—C9—N2	178.09 (13)
N2—C2—C3—N3	1.5 (2)	C7—C8—C9—C4	−2.0 (2)
C1—C2—C3—N3	−179.26 (12)	N3—C4—C9—N2	2.22 (19)
C3—N3—C4—C5	177.53 (13)	C5—C4—C9—N2	−177.80 (12)
C3—N3—C4—C9	−2.5 (2)	N3—C4—C9—C8	−177.70 (12)
N3—C4—C5—C6	179.33 (13)	C5—C4—C9—C8	2.3 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1ⁱ	0.86 (2)	2.04 (2)	2.9008 (17)	173.5 (17)
N1—H1B···Cl1	0.90 (2)	2.44 (2)	3.2590 (13)	152.0 (17)
N3—H3N···Cl1ⁱⁱ	0.94 (2)	2.02 (2)	2.9501 (13)	169.8 (15)

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

Experimental details

Crystal data
Chemical formula	C₉H₈N₃O⁺·Cl⁻
M_r	209.63
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	150
a, b, c (Å)	5.6476 (2), 15.1045 (9), 11.2556 (6)
β (°)	99.993 (3)
V (Å³)	945.58 (8)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.37
Crystal size (mm)	0.25 × 0.20 × 0.08

Data collection
Diffractometer	Nonius KappaCCD diffractometer
Absorption correction	Multi-scan (DENZO-SMN; Otwinowski & Minor, 1997)
T_min, T_max	0.913, 0.971
No. of measured, independent and observed [I > 2σ(I)] reflections	3671, 2147, 1798
R_int	0.018
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.034, 0.085, 1.05
No. of reflections	2147
No. of parameters	160
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.25, −0.24

Computer programs: COLLECT (Nonius, 1998), DENZO-SMN (Otwinowski & Minor, 1997), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), WinGX (Farrugia, 1999) and ORTEP-3 (Farrugia, 1997).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1ⁱ	0.86 (2)	2.04 (2)	2.9008 (17)	173.5 (17)
N1—H1B···Cl1	0.90 (2)	2.44 (2)	3.2590 (13)	152.0 (17)
N3—H3N···Cl1ⁱⁱ	0.94 (2)	2.02 (2)	2.9501 (13)	169.8 (15)

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

References

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Volume 68| Part 1| January 2012| Pages o79-o80

doi:10.1107/S1600536811052457

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