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The title compound, C13H17N4O+·Cl, was synthesized from 1-(2-methoxy­ethyl)-5-nitro­benzimidazole and N-(2-chloro­ethyl)morpholine hydro­chloride in dimethyl­formamide. The crystal structure has been determined at 100 K and exhibits an intramolecular N—H...Cl, and intermolecular C—H...Cl and C—H...O interactions.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536804033240/lh6336sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536804033240/lh6336Isup2.hkl
Contains datablock I

CCDC reference: 262485

Key indicators

  • Single-crystal X-ray study
  • T = 100 K
  • Mean [sigma](C-C) = 0.001 Å
  • R factor = 0.027
  • wR factor = 0.069
  • Data-to-parameter ratio = 14.3

checkCIF/PLATON results

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Alert level C PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density .... 2.01
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 2 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: X-AREA (Stoe & Cie, 2002); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

1-[2-(5-Nitrobenzimidazol-1-yl)ethyl]morpholinium chloride top
Crystal data top
C13H17N4O3+·ClZ = 2
Mr = 312.76F(000) = 328
Triclinic, P1Dx = 1.512 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.0522 (5) ÅCell parameters from 23590 reflections
b = 9.9537 (8) Åθ = 2.8–29.3°
c = 9.9895 (7) ŵ = 0.30 mm1
α = 83.607 (6)°T = 100 K
β = 80.386 (6)°Prism, colorless
γ = 89.477 (6)°0.23 × 0.22 × 0.20 mm
V = 687.04 (9) Å3
Data collection top
Stoe IPDS-II
diffractometer
3692 independent reflections
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus3381 reflections with I > 2σ(I)
Plane graphite monochromatorRint = 0.027
Detector resolution: 6.67 pixels mm-1θmax = 29.1°, θmin = 2.8°
ω scansh = 99
Absorption correction: integration
(X-RED32; Stoe & Cie, 2002)
k = 1313
Tmin = 0.935, Tmax = 0.943l = 1313
14617 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.027Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.069All H-atom parameters refined
S = 1.06 w = 1/[σ2(Fo2) + (0.0336P)2 + 0.269P]
where P = (Fo2 + 2Fc2)/3
3692 reflections(Δ/σ)max < 0.001
258 parametersΔρmax = 0.42 e Å3
0 restraintsΔρmin = 0.21 e Å3
Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs 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
O10.73019 (14)0.07010 (8)0.42335 (10)0.0276 (3)
O20.62749 (13)0.04722 (8)0.25601 (9)0.0241 (3)
O30.85763 (11)0.90840 (7)0.21328 (8)0.0159 (2)
N10.78503 (12)0.51776 (8)0.58133 (9)0.0132 (2)
N20.70521 (12)0.53469 (8)0.37100 (8)0.0111 (2)
N30.69205 (13)0.03821 (9)0.36281 (9)0.0155 (2)
N40.74863 (11)0.70253 (8)0.01066 (8)0.0097 (2)
C10.77324 (13)0.38996 (10)0.54127 (10)0.0112 (2)
C20.80100 (14)0.26446 (10)0.61276 (10)0.0134 (2)
C30.77557 (14)0.14967 (10)0.55176 (10)0.0140 (2)
C40.72227 (13)0.16227 (9)0.42217 (10)0.0121 (2)
C50.69425 (13)0.28445 (10)0.34640 (10)0.0112 (2)
C60.72237 (13)0.39783 (9)0.40996 (9)0.0101 (2)
C70.74371 (14)0.59865 (10)0.47766 (10)0.0131 (2)
C80.64118 (14)0.60099 (10)0.24937 (10)0.0130 (2)
C90.79803 (14)0.60362 (9)0.12404 (10)0.0114 (2)
C100.85402 (14)0.67119 (10)0.12549 (10)0.0118 (2)
C110.80831 (14)0.77585 (10)0.23740 (10)0.0136 (2)
C120.74573 (15)0.93997 (10)0.08845 (11)0.0157 (3)
C130.79196 (15)0.84529 (10)0.03084 (10)0.0137 (3)
Cl10.31412 (3)0.69009 (2)0.02117 (2)0.0131 (1)
H20.831 (2)0.2586 (15)0.7040 (15)0.018 (3)*
H30.790 (2)0.0606 (16)0.5972 (16)0.022 (4)*
H40.621 (2)0.6956 (15)0.0111 (15)0.022 (4)*
H50.661 (2)0.2889 (14)0.2591 (15)0.015 (3)*
H70.737 (2)0.6954 (15)0.4740 (14)0.016 (3)*
H8A0.527 (2)0.5561 (15)0.2346 (15)0.019 (3)*
H8B0.6072 (19)0.6899 (14)0.2691 (14)0.012 (3)*
H9A0.8047 (19)0.5160 (14)0.0913 (14)0.013 (3)*
H9B0.922 (2)0.6314 (14)0.1411 (14)0.012 (3)*
H10A0.815 (2)0.5832 (15)0.1382 (15)0.018 (3)*
H10B0.989 (2)0.6739 (13)0.1199 (14)0.012 (3)*
H11A0.886 (2)0.7583 (15)0.3240 (15)0.020 (3)*
H11B0.6719 (19)0.7723 (14)0.2430 (13)0.012 (3)*
H12A0.775 (2)1.0293 (15)0.0755 (15)0.020 (3)*
H12B0.608 (2)0.9332 (14)0.0911 (14)0.016 (3)*
H13A0.714 (2)0.8655 (14)0.1152 (14)0.016 (3)*
H13B0.928 (2)0.8499 (14)0.0364 (14)0.016 (3)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0424 (5)0.0088 (3)0.0336 (5)0.0010 (3)0.0135 (4)0.0002 (3)
O20.0343 (5)0.0182 (4)0.0240 (4)0.0029 (3)0.0134 (3)0.0083 (3)
O30.0192 (4)0.0132 (3)0.0141 (3)0.0023 (3)0.0018 (3)0.0027 (3)
N10.0139 (4)0.0127 (4)0.0127 (4)0.0009 (3)0.0010 (3)0.0020 (3)
N20.0128 (4)0.0092 (4)0.0107 (4)0.0006 (3)0.0016 (3)0.0004 (3)
N30.0164 (4)0.0107 (4)0.0194 (4)0.0000 (3)0.0023 (3)0.0023 (3)
N40.0099 (3)0.0086 (3)0.0104 (3)0.0002 (3)0.0013 (3)0.0003 (3)
C10.0100 (4)0.0121 (4)0.0109 (4)0.0008 (3)0.0005 (3)0.0008 (3)
C20.0143 (4)0.0144 (4)0.0109 (4)0.0000 (3)0.0026 (3)0.0014 (3)
C30.0148 (4)0.0119 (4)0.0144 (4)0.0009 (3)0.0021 (3)0.0023 (3)
C40.0123 (4)0.0094 (4)0.0145 (4)0.0001 (3)0.0013 (3)0.0019 (3)
C50.0105 (4)0.0118 (4)0.0109 (4)0.0003 (3)0.0014 (3)0.0004 (3)
C60.0090 (4)0.0101 (4)0.0102 (4)0.0004 (3)0.0002 (3)0.0010 (3)
C70.0138 (4)0.0114 (4)0.0136 (4)0.0004 (3)0.0003 (3)0.0023 (3)
C80.0122 (4)0.0138 (4)0.0117 (4)0.0021 (3)0.0011 (3)0.0031 (3)
C90.0119 (4)0.0106 (4)0.0110 (4)0.0014 (3)0.0016 (3)0.0017 (3)
C100.0125 (4)0.0116 (4)0.0106 (4)0.0013 (3)0.0001 (3)0.0015 (3)
C110.0145 (4)0.0146 (4)0.0116 (4)0.0001 (3)0.0026 (3)0.0002 (3)
C120.0207 (5)0.0099 (4)0.0161 (5)0.0012 (3)0.0036 (4)0.0005 (3)
C130.0196 (5)0.0082 (4)0.0137 (4)0.0013 (3)0.0041 (4)0.0010 (3)
Cl10.0105 (1)0.0154 (1)0.0136 (1)0.0006 (1)0.0029 (1)0.0013 (1)
Geometric parameters (Å, º) top
O1—N31.2265 (13)C8—C91.5239 (14)
O2—N31.2222 (13)C10—C111.5145 (14)
O3—C111.4237 (12)C12—C131.5128 (15)
O3—C121.4250 (13)C2—H20.965 (15)
N1—C11.3826 (13)C3—H30.963 (16)
N1—C71.3102 (13)C5—H50.937 (15)
N2—C61.3844 (12)C7—H70.961 (15)
N2—C71.3657 (13)C8—H8A0.965 (14)
N2—C81.4543 (13)C8—H8B0.948 (14)
N3—C41.4601 (13)C9—H9A0.963 (14)
N4—C91.5002 (12)C9—H9B0.967 (14)
N4—C101.5007 (13)C10—H10A0.949 (15)
N4—C131.4985 (13)C10—H10B0.964 (14)
N4—H40.903 (14)C11—H11A0.976 (15)
C1—C21.3973 (14)C11—H11B0.974 (14)
C1—C61.4104 (13)C12—H12A0.942 (15)
C2—C31.3800 (14)C12—H12B0.979 (14)
C3—C41.3994 (14)C13—H13A0.966 (14)
C4—C51.3898 (14)C13—H13B0.972 (14)
C5—C61.3863 (13)
Cl1···N43.0517 (9)C5···H11Bi3.017 (14)
Cl1···C83.5457 (11)C5···H10Bxi2.898 (14)
Cl1···C9i3.5562 (10)C5···H11Axi2.962 (14)
Cl1···H13Bii3.131 (14)C7···H11Aix2.975 (15)
Cl1···H42.151 (14)C8···H13A2.829 (14)
Cl1···H8A2.996 (15)C8···H53.100 (14)
Cl1···H10Bii2.899 (14)C10···H9Axi3.071 (14)
Cl1···H5i2.760 (15)C13···H8B2.817 (14)
Cl1···H9Bii2.862 (14)H2···Cl1iii2.865 (15)
Cl1···H2iii2.865 (15)H3···O3x2.399 (16)
Cl1···H12Aiv2.947 (15)H3···O12.376 (16)
Cl1···H9Ai2.652 (14)H4···Cl12.151 (14)
Cl1···H10Ai2.929 (15)H4···H8A2.49 (2)
O1···C7v3.2845 (13)H4···H8B2.56 (2)
O1···C4vi3.3909 (14)H4···H11B2.535 (19)
O2···C13v3.2462 (13)H4···H12B2.48 (2)
O2···C12i3.3412 (14)H5···H11Bi2.47 (2)
O3···N42.8684 (11)H5···O22.424 (14)
O3···C3vii3.2840 (13)H5···Cl1i2.760 (15)
O1···H7v2.334 (15)H5···C83.100 (14)
O1···H32.376 (16)H7···H11Aix2.56 (2)
O2···H13Av2.425 (14)H7···O1xii2.334 (15)
O2···H52.424 (14)H7···H8B2.38 (2)
O2···H11Bi2.770 (14)H8A···Cl12.996 (15)
O2···H12Bi2.519 (14)H8A···N1iii2.672 (15)
O3···H3vii2.399 (16)H8A···C1iii2.907 (15)
N1···N1viii3.2282 (12)H8A···H42.49 (2)
N1···C1viii3.2520 (13)H8B···H72.38 (2)
N1···C8iii3.3487 (13)H8B···H13A2.24 (2)
N1···N22.2526 (12)H8B···C132.817 (14)
N1···C11ix3.3239 (13)H8B···H42.56 (2)
N2···N12.2526 (12)H8B···C2iii2.974 (14)
N2···C1iii3.4392 (13)H8B···C1iii3.070 (14)
N4···O32.8684 (11)H9A···H10A2.31 (2)
N4···Cl13.0517 (9)H9A···H10Bxi2.396 (19)
N1···H11Aix2.810 (15)H9A···Cl1i2.652 (14)
N1···H8Aiii2.672 (15)H9A···C10xi3.071 (14)
C1···N2iii3.4392 (13)H9B···H10B2.559 (19)
C1···N1viii3.2520 (13)H9B···Cl1xiv2.862 (14)
C1···C8iii3.3044 (14)H9B···H13B2.30 (2)
C1···C7viii3.3824 (14)H10A···H9A2.31 (2)
C2···C8iii3.5092 (14)H10A···Cl1i2.929 (15)
C2···C7viii3.4378 (14)H10B···H9B2.559 (19)
C3···O3x3.2840 (13)H10B···H13B2.462 (19)
C4···C11xi3.5339 (14)H10B···C5xi2.898 (14)
C4···O1vi3.3909 (14)H10B···Cl1xiv2.899 (14)
C5···C11xi3.5614 (14)H10B···H9Axi2.396 (19)
C5···C7iii3.5439 (14)H11A···C4xi2.860 (14)
C5···C10xi3.5601 (14)H11A···C7xiii2.975 (15)
C6···C7iii3.2923 (14)H11A···C5xi2.962 (14)
C7···C1viii3.3824 (14)H11A···N1xiii2.810 (15)
C7···O1xii3.2845 (13)H11A···H7xiii2.56 (2)
C7···C6iii3.2923 (14)H11A···C3xi3.078 (15)
C7···C5iii3.5439 (14)H11B···H12B2.317 (19)
C7···C2viii3.4378 (14)H11B···H42.535 (19)
C8···C1iii3.3044 (14)H11B···C5i3.017 (14)
C8···C2iii3.5092 (14)H11B···H5i2.47 (2)
C8···Cl13.5457 (11)H11B···O2i2.770 (14)
C8···N1iii3.3487 (13)H12A···H13Bxv2.53 (2)
C9···Cl1i3.5562 (10)H12A···Cl1iv2.947 (15)
C10···C5xi3.5601 (14)H12B···H11B2.317 (19)
C11···N1xiii3.3239 (13)H12B···H42.48 (2)
C11···C5xi3.5614 (14)H12B···O2i2.519 (14)
C11···C4xi3.5339 (14)H13A···O2xii2.425 (14)
C12···O2i3.3412 (14)H13A···C82.829 (14)
C13···O2xii3.2462 (13)H13A···H8B2.24 (2)
C1···H8Aiii2.907 (15)H13B···H10B2.462 (19)
C1···H8Biii3.070 (14)H13B···H12Axv2.53 (2)
C2···H8Biii2.974 (14)H13B···Cl1xiv3.131 (14)
C3···H11Axi3.078 (15)H13B···H9B2.30 (2)
C4···H11Axi2.860 (14)
C11—O3—C12109.12 (8)C4—C3—H3118.9 (9)
C1—N1—C7104.00 (8)C4—C5—H5122.2 (9)
C6—N2—C7105.88 (8)C6—C5—H5123.3 (9)
C6—N2—C8128.79 (8)N1—C7—H7124.9 (8)
C7—N2—C8125.08 (8)N2—C7—H7120.5 (8)
O1—N3—O2123.14 (9)N2—C8—H8A109.5 (9)
O1—N3—C4118.49 (9)N2—C8—H8B105.8 (8)
O2—N3—C4118.36 (9)C9—C8—H8A110.7 (9)
C9—N4—C10111.11 (7)C9—C8—H8B110.9 (8)
C9—N4—C13111.83 (7)H8A—C8—H8B108.0 (12)
C10—N4—C13109.43 (7)N4—C9—H9A106.8 (8)
C13—N4—H4107.9 (10)N4—C9—H9B106.4 (8)
C9—N4—H4107.7 (9)C8—C9—H9A109.1 (8)
C10—N4—H4108.8 (9)C8—C9—H9B113.0 (8)
N1—C1—C2129.05 (9)H9A—C9—H9B111.1 (12)
N1—C1—C6110.52 (8)N4—C10—H10A107.2 (9)
C2—C1—C6120.41 (9)N4—C10—H10B106.3 (8)
C1—C2—C3118.15 (9)C11—C10—H10A111.6 (9)
C2—C3—C4119.46 (9)C11—C10—H10B110.5 (8)
C3—C4—C5124.68 (9)H10A—C10—H10B111.1 (12)
N3—C4—C5117.62 (9)O3—C11—H11A106.8 (9)
N3—C4—C3117.70 (8)O3—C11—H11B109.3 (8)
C4—C5—C6114.46 (9)C10—C11—H11A108.9 (9)
N2—C6—C1104.95 (8)C10—C11—H11B110.1 (8)
N2—C6—C5132.20 (9)H11A—C11—H11B110.5 (11)
C1—C6—C5122.83 (9)O3—C12—H12A108.5 (9)
N1—C7—N2114.65 (9)O3—C12—H12B111.0 (8)
N2—C8—C9111.71 (8)C13—C12—H12A109.0 (9)
N4—C9—C8110.25 (8)C13—C12—H12B108.8 (8)
N4—C10—C11110.06 (8)H12A—C12—H12B108.8 (12)
O3—C11—C10111.16 (8)N4—C13—H13A107.8 (8)
O3—C12—C13110.70 (8)N4—C13—H13B107.1 (8)
N4—C13—C12109.55 (8)C12—C13—H13A110.7 (8)
C1—C2—H2120.6 (9)C12—C13—H13B110.8 (8)
C3—C2—H2121.2 (9)H13A—C13—H13B110.9 (12)
C2—C3—H3121.7 (9)
C12—O3—C11—C1062.09 (10)C10—N4—C9—C8158.44 (8)
C11—O3—C12—C1363.17 (10)C13—N4—C9—C878.96 (9)
C7—N1—C1—C2179.13 (10)C9—N4—C13—C12178.13 (8)
C7—N1—C1—C60.28 (11)N1—C1—C6—N20.49 (11)
C1—N1—C7—N20.04 (13)N1—C1—C6—C5177.83 (9)
C7—N2—C6—C5177.61 (10)N1—C1—C2—C3178.18 (10)
C8—N2—C6—C1174.79 (9)C2—C1—C6—C51.13 (15)
C8—N2—C6—C53.31 (17)C6—C1—C2—C30.56 (14)
C7—N2—C8—C9108.94 (10)C2—C1—C6—N2179.45 (9)
C6—N2—C8—C977.76 (12)C1—C2—C3—C40.39 (14)
C7—N2—C6—C10.49 (10)C2—C3—C4—C50.90 (15)
C8—N2—C7—N1174.93 (9)C2—C3—C4—N3178.46 (9)
C6—N2—C7—N10.35 (12)C3—C4—C5—C60.38 (14)
O1—N3—C4—C5174.53 (10)N3—C4—C5—C6178.99 (8)
O2—N3—C4—C56.43 (14)C4—C5—C6—N2178.45 (10)
O1—N3—C4—C36.06 (14)C4—C5—C6—C10.64 (14)
O2—N3—C4—C3172.98 (9)N2—C8—C9—N4165.05 (8)
C13—N4—C10—C1153.61 (10)N4—C10—C11—O357.91 (10)
C9—N4—C10—C11177.59 (8)O3—C12—C13—N459.99 (11)
C10—N4—C13—C1254.58 (10)
Symmetry codes: (i) x+1, y+1, z; (ii) x1, y, z; (iii) x+1, y+1, z+1; (iv) x+1, y+2, z; (v) x, y1, z; (vi) x+1, y, z+1; (vii) x, y+1, z1; (viii) x+2, y+1, z+1; (ix) x, y, z+1; (x) x, y1, z+1; (xi) x+2, y+1, z; (xii) x, y+1, z; (xiii) x, y, z1; (xiv) x+1, y, z; (xv) x+2, y+2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4···Cl10.903 (14)2.151 (14)3.0517 (9)176.0 (12)
C3—H3···O3x0.963 (16)2.399 (16)3.2840 (13)152.6 (13)
C5—H5···Cl1i0.937 (15)2.760 (15)3.6627 (10)162.1 (12)
C7—H7···O1xii0.961 (15)2.334 (15)3.2845 (13)169.9 (12)
C9—H9A···Cl1i0.963 (14)2.652 (14)3.5562 (10)156.6 (11)
C12—H12B···O2i0.979 (14)2.519 (14)3.3412 (14)141.5 (11)
C13—H13A···O2xii0.966 (14)2.425 (14)3.2462 (13)142.6 (11)
Symmetry codes: (i) x+1, y+1, z; (x) x, y1, z+1; (xii) x, y+1, z.
 

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