organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890
Volume 68| Part 1| January 2012| Pages o79-o80

3-Carbamoylquinoxalin-1-ium chloride

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[Bailly, C., Echepare, S., Gago, F. & Waring, M. J. (1999). Anti-Cancer Drug Des. 14, 291-303.]); May et al. (2004[May, L. G., Madine, M. A. & Waring, M. J. (2004). Nucleic Acids Res. 32, 65-72.]); Mollegaard et al. (2000[Mollegaard, N. K., Bailly, C., Waring, M. J. & Nielsen, P. E. (2000). Biochemistry, 39, 9502-9507.]); Waring (1993[Waring, M. J. (1993). In Molecular aspects of anticancer drug-DNA interactions. Boca Raton, Florida, USA: CRC Press.]). For crystal structures of the mol­ecules triostin A, echinomycin and their derivatives, which all contain two quinoxalines, see: Hossain et al. (1982[Hossain, M. B., van der Helm, D., Olsen, R. K., Jones, P. G., Sheldrick, G. M., Egert, E., Kennard, O., Waring, M. J. & Viswamitra, M. A. (1982). J. Am. Chem. Soc. 104, 3401-3408.]); Sheldrick et al. (1984[Sheldrick, G. M., Guy, J. J., Kennard, O., Rivera, U. & Waring, M. J. (1984). J. Chem. Soc. Perkin Trans. 2, pp. 1601-1605.], 1995[Sheldrick, G. M., Heine, A., Schmidt-Bäse, K., Pohl, E., Jones, P. G., Paulus, E. & Waring, M. J. (1995). Acta Cryst. B51, 987-999.]); Viswamitra et al. (1981[Viswamitra, M. A., Kennard, O., Cruse, W. B. T., Egert, E., Sheldrick, G. M., Jones, P. G., Waring, M. J., Wakelin, L. P. G. & Olsen, R. K. (1981). Nature (London), 289, 817-819.]); Wang et al. (1984[Wang, A. H.-J., Ughetto, G., Quigley, G. J., Hakoshima, T., van der Marel, G. A., van Boom, J. H., Rich, A. (1984). Science, 225, 1115-1121.]); Ughetto et al. (1985[Ughetto, G., Wang, A. H.-J., Quigley, G. J., van der Marel, G. A., van Boom, J. H., Rich, A. (1985). Nucleic Acids Res. 13, 2305-2323.]). For a description of the Streptomycete producing the title compound, see: Castillo et al. (2003[Castillo, U., Harper, J. K., Strobel, G. A., Sears, J., Alesi, K., Ford, E., Lin, J., Hunter, M., Maranta, M., Ge, H., Yaver, D., Jensen, J. B., Porter, H., Robison, R., Miller, D., Hess, W. M., Condron, M. & Teplow, D. (2003). FEMS Microbiol. Lett. 224, 183-190.]).

[Scheme 1]

Experimental

Crystal data
  • C9H8N3O+·Cl

  • Mr = 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[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) Tmin = 0.913, Tmax = 0.971

  • 3671 measured reflections

  • 2147 independent reflections

  • 1798 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.25 e Å−3

  • Δρmin = −0.24 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Nonius (1998). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO-SMN; program(s) used to solve structure: SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]) and ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: SHELXL97.

Supporting information


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

Refinement top

All H atoms were refined independently with isotropic displacement parameters.

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
[Figure 1] Fig. 1. Molecular structure of the title compound. Displacement ellipsoids are shown at the 50% probability level on non-hydrogen atoms.
[Figure 2] 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+·ClF(000) = 432
Mr = 209.63Dx = 1.473 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 1998 reflections
a = 5.6476 (2) Åθ = 1.0–27.5°
b = 15.1045 (9) ŵ = 0.37 mm1
c = 11.2556 (6) ÅT = 150 K
β = 99.993 (3)°Plate, pale yellow
V = 945.58 (8) Å30.25 × 0.20 × 0.08 mm
Z = 4
Data collection top
Nonius KappaCCD
diffractometer
2147 independent reflections
Radiation source: fine-focus sealed tube1798 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.018
ϕ and ω scansθmax = 27.5°, θmin = 3.9°
Absorption correction: multi-scan
(DENZO-SMN; Otwinowski & Minor, 1997)
h = 77
Tmin = 0.913, Tmax = 0.971k = 1819
3671 measured reflectionsl = 1414
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.034All H-atom parameters refined
wR(F2) = 0.085 w = 1/[σ2(Fo2) + (0.0397P)2 + 0.2499P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
2147 reflectionsΔρmax = 0.25 e Å3
160 parametersΔρmin = 0.24 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.012 (4)
Crystal data top
C9H8N3O+·ClV = 945.58 (8) Å3
Mr = 209.63Z = 4
Monoclinic, P21/nMo Kα radiation
a = 5.6476 (2) ŵ = 0.37 mm1
b = 15.1045 (9) ÅT = 150 K
c = 11.2556 (6) Å0.25 × 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)
Tmin = 0.913, Tmax = 0.971Rint = 0.018
3671 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0340 restraints
wR(F2) = 0.085All H-atom parameters refined
S = 1.05Δρmax = 0.25 e Å3
2147 reflectionsΔρmin = 0.24 e Å3
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
xyzUiso*/Ueq
Cl10.08949 (6)0.30272 (3)0.19526 (3)0.03255 (15)
O10.76925 (19)0.43611 (7)0.55896 (10)0.0336 (3)
N10.4423 (2)0.39023 (9)0.42509 (12)0.0269 (3)
N20.6771 (2)0.23505 (8)0.39555 (10)0.0234 (3)
N31.1403 (2)0.21019 (8)0.51784 (11)0.0248 (3)
C10.6625 (3)0.38080 (9)0.48828 (13)0.0247 (3)
C20.7884 (2)0.29539 (9)0.46906 (12)0.0234 (3)
C31.0240 (3)0.28321 (10)0.53318 (13)0.0254 (3)
C41.0391 (2)0.14589 (9)0.43990 (12)0.0237 (3)
C51.1680 (3)0.06898 (10)0.42012 (14)0.0289 (3)
C61.0562 (3)0.00651 (11)0.34196 (14)0.0338 (4)
C70.8153 (3)0.01774 (11)0.28407 (14)0.0331 (4)
C80.6884 (3)0.09223 (10)0.30207 (13)0.0276 (3)
C90.7997 (2)0.15942 (9)0.37975 (12)0.0229 (3)
H1A0.370 (3)0.4397 (13)0.4318 (16)0.036 (5)*
H1B0.381 (4)0.3498 (15)0.3699 (19)0.051 (6)*
H31.102 (3)0.3227 (12)0.5857 (17)0.035 (5)*
H3N1.290 (3)0.2011 (11)0.5682 (17)0.034 (5)*
H51.324 (3)0.0634 (12)0.4615 (16)0.035 (5)*
H61.139 (3)0.0467 (12)0.3273 (15)0.032 (4)*
H70.738 (3)0.0276 (13)0.2325 (17)0.041 (5)*
H80.523 (3)0.1023 (10)0.2602 (15)0.027 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0270 (2)0.0419 (2)0.0258 (2)0.00693 (15)0.00344 (14)0.00243 (15)
O10.0323 (6)0.0264 (5)0.0365 (6)0.0033 (4)0.0097 (5)0.0054 (5)
N10.0258 (6)0.0235 (6)0.0284 (7)0.0029 (5)0.0037 (5)0.0018 (5)
N20.0240 (6)0.0249 (6)0.0205 (6)0.0011 (5)0.0015 (5)0.0019 (5)
N30.0217 (6)0.0290 (6)0.0225 (6)0.0013 (5)0.0000 (5)0.0016 (5)
C10.0263 (7)0.0231 (7)0.0228 (7)0.0001 (6)0.0011 (5)0.0023 (6)
C20.0235 (7)0.0251 (7)0.0212 (7)0.0014 (5)0.0030 (5)0.0016 (5)
C30.0244 (7)0.0268 (7)0.0232 (7)0.0009 (6)0.0007 (6)0.0007 (6)
C40.0253 (7)0.0258 (7)0.0204 (7)0.0011 (5)0.0051 (5)0.0029 (5)
C50.0286 (8)0.0315 (8)0.0274 (8)0.0053 (6)0.0075 (6)0.0033 (6)
C60.0433 (9)0.0288 (8)0.0321 (8)0.0056 (7)0.0144 (7)0.0001 (7)
C70.0428 (9)0.0303 (8)0.0279 (8)0.0050 (7)0.0102 (7)0.0071 (7)
C80.0296 (8)0.0314 (8)0.0220 (7)0.0046 (6)0.0052 (6)0.0018 (6)
C90.0257 (7)0.0246 (7)0.0189 (7)0.0008 (6)0.0050 (5)0.0022 (5)
Geometric parameters (Å, º) top
O1—C11.2361 (17)C3—H30.900 (19)
N1—C11.3285 (18)C4—C51.409 (2)
N1—H1A0.86 (2)C4—C91.4178 (19)
N1—H1B0.90 (2)C5—C61.368 (2)
N2—C21.3154 (18)C5—H50.928 (17)
N2—C91.3635 (18)C6—C71.413 (2)
N3—C31.3104 (19)C6—H60.957 (18)
N3—C41.3660 (19)C7—C81.368 (2)
N3—H3N0.94 (2)C7—H70.95 (2)
C1—C21.5066 (19)C8—C91.414 (2)
C2—C31.411 (2)C8—H80.980 (16)
C1—N1—H1A117.3 (12)N3—C4—C9117.53 (13)
C1—N1—H1B120.9 (13)C5—C4—C9121.29 (13)
H1A—N1—H1B121.2 (18)C6—C5—C4118.49 (15)
C2—N2—C9117.67 (12)C6—C5—H5123.5 (11)
C3—N3—C4121.30 (13)C4—C5—H5118.0 (11)
C3—N3—H3N117.5 (10)C5—C6—C7120.93 (15)
C4—N3—H3N120.9 (10)C5—C6—H6120.4 (10)
O1—C1—N1125.36 (13)C7—C6—H6118.6 (10)
O1—C1—C2118.78 (12)C8—C7—C6121.19 (15)
N1—C1—C2115.85 (12)C8—C7—H7118.8 (11)
N2—C2—C3122.45 (13)C6—C7—H7120.0 (11)
N2—C2—C1119.85 (12)C7—C8—C9119.58 (14)
C3—C2—C1117.69 (12)C7—C8—H8122.4 (9)
N3—C3—C2119.48 (13)C9—C8—H8118.0 (9)
N3—C3—H3116.4 (12)N2—C9—C8120.04 (13)
C2—C3—H3124.2 (12)N2—C9—C4121.50 (13)
N3—C4—C5121.17 (13)C8—C9—C4118.46 (13)
C9—N2—C2—C31.7 (2)C9—C4—C5—C60.6 (2)
C9—N2—C2—C1179.05 (12)C4—C5—C6—C71.3 (2)
O1—C1—C2—N2179.06 (13)C5—C6—C7—C81.6 (2)
N1—C1—C2—N21.63 (19)C6—C7—C8—C90.1 (2)
O1—C1—C2—C30.2 (2)C2—N2—C9—C8179.78 (13)
N1—C1—C2—C3179.12 (13)C2—N2—C9—C40.14 (19)
C4—N3—C3—C20.7 (2)C7—C8—C9—N2178.09 (13)
N2—C2—C3—N31.5 (2)C7—C8—C9—C42.0 (2)
C1—C2—C3—N3179.26 (12)N3—C4—C9—N22.22 (19)
C3—N3—C4—C5177.53 (13)C5—C4—C9—N2177.80 (12)
C3—N3—C4—C92.5 (2)N3—C4—C9—C8177.70 (12)
N3—C4—C5—C6179.33 (13)C5—C4—C9—C82.3 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O1i0.86 (2)2.04 (2)2.9008 (17)173.5 (17)
N1—H1B···Cl10.90 (2)2.44 (2)3.2590 (13)152.0 (17)
N3—H3N···Cl1ii0.94 (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 formulaC9H8N3O+·Cl
Mr209.63
Crystal system, space groupMonoclinic, P21/n
Temperature (K)150
a, b, c (Å)5.6476 (2), 15.1045 (9), 11.2556 (6)
β (°) 99.993 (3)
V3)945.58 (8)
Z4
Radiation typeMo Kα
µ (mm1)0.37
Crystal size (mm)0.25 × 0.20 × 0.08
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
(DENZO-SMN; Otwinowski & Minor, 1997)
Tmin, Tmax0.913, 0.971
No. of measured, independent and
observed [I > 2σ(I)] reflections
3671, 2147, 1798
Rint0.018
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.034, 0.085, 1.05
No. of reflections2147
No. of parameters160
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N1—H1A···O1i0.86 (2)2.04 (2)2.9008 (17)173.5 (17)
N1—H1B···Cl10.90 (2)2.44 (2)3.2590 (13)152.0 (17)
N3—H3N···Cl1ii0.94 (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
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