The crystal structure of the title compound, C17H14Cl2FN3O·H2O, is stabilized by hydrogen bonds. The morpholine ring exhibits a typical chair conformation, while the benzimidazole system is planar.
Supporting information
CCDC reference: 198333
Key indicators
- Single-crystal X-ray study
- T = 295 K
- Mean (C-C) = 0.003 Å
- R factor = 0.038
- wR factor = 0.106
- Data-to-parameter ratio = 14.3
checkCIF results
No syntax errors found
ADDSYM reports no extra symmetry
General Notes
ABSTY_01 Extra text has been found in the _exptl_absorpt_correction_type
field, which should be only a single keyword. A literature
citation should be included in the _exptl_absorpt_process_details
field.
In order to obtain 2-(2,4-Dichlorophenyl)-5-fluoro-6-morpholin-4-yl-1H-benzimidazole (Kuş, 2002), to a suspension of 4-fluoro-5-morpholin-4-yl-benzene-1,2-diamine (Sanna et al., 1998) (0,211 g, 1 mmol) in DMF (5 ml), the sodium metabisulfite adduct of 2,4-dichlorobenzaldehyde (0.191 g, 1 mmol) was added and the mixture was heated under a nitrogen atmosphere for 4 h at 333 K. Water was added to the reaction medium and the solid product obtained was collected by filtration and washed with water. The residue was chromatographed [EtOAc: n-hexane (1:2)] and recrystallized from ethanol, affording 0,311 mg (85%) of (I); m.p. 485–487 K. The assigned structure was substantiated by IR, 1H NMR and MS data.
The H atoms of N1 and water molecule were located from a difference Fourier map and refined freely. The other H atoms were positioned geometrically at distances 0.93 and 0.97 Å for methylene and aromatic H atoms, respectively, and refined riding on their parent atoms.
Data collection: CAD-4 EXPRESS (Enraf-Nonius, 1994); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP (Johnson, 1965); software used to prepare material for publication: PLATON (Spek, 2000).
Crystal data top
C17H14Cl2FN3O·H2O | Dx = 1.519 Mg m−3 |
Mr = 384.23 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, Pbca | Cell parameters from 25 reflections |
a = 7.4455 (7) Å | θ = 10.2–18.0° |
b = 15.310 (3) Å | µ = 0.41 mm−1 |
c = 29.487 (3) Å | T = 295 K |
V = 3361.2 (8) Å3 | Prism, light yellow |
Z = 8 | 0.48 × 0.36 × 0.24 mm |
F(000) = 1584 | |
Data collection top
Enraf-Nonius TurboCAD4 diffractometer | Rint = 0.079 |
non–profiled ω scans | θmax = 26.3°, θmin = 2.7° |
Absorption correction: psi scan (north et al., 1968) ? | h = 0→9 |
Tmin = 0.826, Tmax = 0.907 | k = 0→19 |
3893 measured reflections | l = 0→36 |
3403 independent reflections | 3 standard reflections every 120 min |
2174 reflections with I > 2σ(I) | intensity decay: 4% |
Refinement top
Refinement on F2 | 5 restraints |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.038 | w = 1/[σ2(Fo2) + (0.0454P)2 + 1.0249P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.106 | (Δ/σ)max < 0.001 |
S = 1.02 | Δρmax = 0.23 e Å−3 |
3403 reflections | Δρmin = −0.32 e Å−3 |
238 parameters | |
Crystal data top
C17H14Cl2FN3O·H2O | V = 3361.2 (8) Å3 |
Mr = 384.23 | Z = 8 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 7.4455 (7) Å | µ = 0.41 mm−1 |
b = 15.310 (3) Å | T = 295 K |
c = 29.487 (3) Å | 0.48 × 0.36 × 0.24 mm |
Data collection top
Enraf-Nonius TurboCAD4 diffractometer | 2174 reflections with I > 2σ(I) |
Absorption correction: psi scan (north et al., 1968) ? | Rint = 0.079 |
Tmin = 0.826, Tmax = 0.907 | 3 standard reflections every 120 min |
3893 measured reflections | intensity decay: 4% |
3403 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.038 | 5 restraints |
wR(F2) = 0.106 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | Δρmax = 0.23 e Å−3 |
3403 reflections | Δρmin = −0.32 e Å−3 |
238 parameters | |
Special details top
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O2 | 0.4415 (3) | −0.16610 (12) | 0.09903 (7) | 0.0535 (5) | |
H1 | 0.133 (4) | 0.2013 (13) | 0.1179 (9) | 0.056 (8)* | |
H21 | 0.382 (4) | −0.1131 (15) | 0.1033 (10) | 0.068 (10)* | |
H22 | 0.572 (3) | −0.170 (3) | 0.0908 (15) | 0.150 (19)* | |
C2 | 0.2107 (3) | 0.07292 (15) | 0.13048 (8) | 0.0339 (5) | |
C4 | 0.2742 (4) | 0.00320 (17) | 0.01776 (8) | 0.0454 (7) | |
H4 | 0.3125 | −0.0544 | 0.0154 | 0.054* | |
C5 | 0.2488 (4) | 0.05422 (16) | −0.01928 (8) | 0.0419 (6) | |
C6 | 0.1896 (3) | 0.14190 (15) | −0.01880 (8) | 0.0346 (5) | |
C7 | 0.1546 (3) | 0.17945 (15) | 0.02315 (8) | 0.0338 (5) | |
H7 | 0.1151 | 0.2369 | 0.0255 | 0.041* | |
C8 | 0.1809 (3) | 0.12803 (14) | 0.06172 (8) | 0.0325 (5) | |
C9 | 0.2396 (3) | 0.04220 (16) | 0.05994 (8) | 0.0363 (6) | |
C10 | 0.0377 (4) | 0.15492 (17) | −0.09148 (9) | 0.0479 (7) | |
H10A | −0.0798 | 0.1671 | −0.0787 | 0.058* | |
H10B | 0.0494 | 0.0922 | −0.0951 | 0.058* | |
C11 | 0.0566 (4) | 0.19969 (18) | −0.13705 (9) | 0.0532 (7) | |
H11A | 0.1737 | 0.1864 | −0.1497 | 0.064* | |
H11B | −0.0338 | 0.1772 | −0.1576 | 0.064* | |
C12 | 0.1692 (4) | 0.32403 (17) | −0.10326 (9) | 0.0504 (7) | |
H12A | 0.1539 | 0.3867 | −0.1002 | 0.061* | |
H12B | 0.2872 | 0.3135 | −0.1161 | 0.061* | |
C13 | 0.1595 (4) | 0.28246 (16) | −0.05668 (8) | 0.0410 (6) | |
H13A | 0.2541 | 0.3057 | −0.0376 | 0.049* | |
H13B | 0.045 | 0.296 | −0.0427 | 0.049* | |
C14 | 0.2112 (3) | 0.06133 (16) | 0.18017 (8) | 0.0356 (6) | |
C15 | 0.1623 (4) | 0.12234 (16) | 0.21325 (8) | 0.0387 (6) | |
C16 | 0.1670 (4) | 0.10329 (16) | 0.25924 (8) | 0.0430 (6) | |
H16 | 0.134 | 0.1451 | 0.2806 | 0.052* | |
C17 | 0.2212 (4) | 0.02148 (17) | 0.27270 (8) | 0.0449 (7) | |
C18 | 0.2695 (4) | −0.04135 (17) | 0.24157 (9) | 0.0497 (7) | |
H18 | 0.3052 | −0.0966 | 0.251 | 0.06* | |
C19 | 0.2638 (4) | −0.02068 (16) | 0.19617 (9) | 0.0443 (6) | |
H19 | 0.2964 | −0.0632 | 0.1752 | 0.053* | |
Cl1 | 0.08997 (13) | 0.22705 (4) | 0.19919 (2) | 0.0626 (3) | |
Cl2 | 0.22726 (12) | −0.00354 (5) | 0.32997 (2) | 0.0651 (3) | |
F1 | 0.2899 (3) | 0.01926 (10) | −0.06064 (5) | 0.0644 (5) | |
N1 | 0.1615 (3) | 0.14605 (13) | 0.10721 (7) | 0.0351 (5) | |
N2 | 0.1796 (3) | 0.18785 (12) | −0.06074 (6) | 0.0341 (5) | |
N3 | 0.2587 (3) | 0.00853 (12) | 0.10326 (7) | 0.0389 (5) | |
O1 | 0.0371 (3) | 0.29124 (12) | −0.13328 (6) | 0.0526 (5) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O2 | 0.0563 (14) | 0.0337 (10) | 0.0704 (13) | −0.0020 (10) | 0.0069 (11) | −0.0007 (9) |
C2 | 0.0351 (14) | 0.0306 (12) | 0.0359 (13) | −0.0041 (11) | 0.0000 (10) | −0.0030 (10) |
C4 | 0.0626 (19) | 0.0325 (13) | 0.0410 (14) | 0.0075 (13) | 0.0058 (13) | −0.0048 (11) |
C5 | 0.0594 (17) | 0.0363 (13) | 0.0300 (12) | 0.0041 (12) | 0.0067 (12) | −0.0073 (10) |
C6 | 0.0352 (14) | 0.0330 (12) | 0.0357 (12) | −0.0021 (11) | 0.0020 (11) | 0.0005 (10) |
C7 | 0.0363 (14) | 0.0294 (12) | 0.0359 (12) | 0.0021 (11) | 0.0015 (11) | −0.0027 (10) |
C8 | 0.0327 (13) | 0.0299 (12) | 0.0350 (12) | −0.0022 (10) | 0.0013 (10) | −0.0044 (10) |
C9 | 0.0423 (14) | 0.0321 (12) | 0.0344 (12) | −0.0014 (11) | 0.0021 (11) | −0.0017 (10) |
C10 | 0.0517 (17) | 0.0462 (15) | 0.0458 (15) | −0.0092 (14) | −0.0077 (13) | −0.0026 (12) |
C11 | 0.068 (2) | 0.0495 (16) | 0.0417 (15) | −0.0008 (15) | −0.0164 (15) | −0.0018 (12) |
C12 | 0.072 (2) | 0.0354 (14) | 0.0442 (15) | 0.0002 (14) | −0.0039 (14) | 0.0020 (12) |
C13 | 0.0496 (16) | 0.0326 (12) | 0.0409 (14) | 0.0045 (12) | −0.0028 (12) | −0.0045 (11) |
C14 | 0.0376 (15) | 0.0333 (13) | 0.0360 (13) | −0.0047 (11) | −0.0001 (11) | −0.0012 (10) |
C15 | 0.0455 (15) | 0.0320 (13) | 0.0386 (14) | 0.0008 (12) | 0.0000 (12) | −0.0002 (10) |
C16 | 0.0531 (17) | 0.0391 (13) | 0.0369 (15) | 0.0019 (12) | 0.0018 (13) | −0.0053 (11) |
C17 | 0.0539 (18) | 0.0473 (16) | 0.0337 (14) | 0.0013 (13) | 0.0002 (12) | 0.0019 (11) |
C18 | 0.071 (2) | 0.0391 (14) | 0.0393 (15) | 0.0096 (14) | −0.0006 (14) | 0.0016 (11) |
C19 | 0.0597 (18) | 0.0343 (13) | 0.0389 (14) | 0.0044 (13) | 0.0030 (13) | −0.0052 (11) |
Cl1 | 0.1075 (7) | 0.0377 (4) | 0.0426 (4) | 0.0179 (4) | 0.0048 (4) | −0.0013 (3) |
Cl2 | 0.1003 (7) | 0.0616 (5) | 0.0335 (3) | 0.0178 (5) | −0.0003 (4) | 0.0039 (3) |
F1 | 0.1121 (16) | 0.0465 (10) | 0.0345 (8) | 0.0205 (9) | 0.0113 (9) | −0.0066 (7) |
N1 | 0.0418 (12) | 0.0311 (11) | 0.0324 (11) | 0.0014 (10) | 0.0018 (9) | −0.0032 (9) |
N2 | 0.0378 (12) | 0.0305 (10) | 0.0339 (10) | −0.0014 (9) | −0.0006 (9) | −0.0019 (8) |
N3 | 0.0485 (13) | 0.0323 (11) | 0.0360 (11) | −0.0002 (10) | 0.0022 (10) | −0.0010 (9) |
O1 | 0.0608 (13) | 0.0492 (11) | 0.0479 (11) | 0.0115 (10) | −0.0109 (10) | 0.0004 (8) |
Geometric parameters (Å, º) top
O2—H21 | 0.935 (18) | C11—H11A | 0.97 |
O2—H22 | 1.004 (18) | C11—H11B | 0.97 |
C2—N3 | 1.321 (3) | C12—O1 | 1.415 (3) |
C2—N1 | 1.363 (3) | C12—C13 | 1.516 (3) |
C2—C14 | 1.476 (3) | C12—H12A | 0.97 |
C4—C5 | 1.356 (4) | C12—H12B | 0.97 |
C4—C9 | 1.404 (3) | C13—N2 | 1.461 (3) |
C4—H4 | 0.93 | C13—H13A | 0.97 |
C5—F1 | 1.367 (3) | C13—H13B | 0.97 |
C5—C6 | 1.413 (3) | C14—C19 | 1.397 (4) |
C6—C7 | 1.389 (3) | C14—C15 | 1.399 (3) |
C6—N2 | 1.425 (3) | C15—C16 | 1.387 (3) |
C7—C8 | 1.397 (3) | C15—Cl1 | 1.741 (3) |
C7—H7 | 0.93 | C16—C17 | 1.375 (4) |
C8—N1 | 1.377 (3) | C16—H16 | 0.93 |
C8—C9 | 1.386 (3) | C17—C18 | 1.377 (4) |
C9—N3 | 1.385 (3) | C17—Cl2 | 1.732 (2) |
C10—N2 | 1.481 (3) | C18—C19 | 1.376 (4) |
C10—C11 | 1.515 (4) | C18—H18 | 0.93 |
C10—H10A | 0.97 | C19—H19 | 0.93 |
C10—H10B | 0.97 | N1—H1 | 0.927 (18) |
C11—O1 | 1.413 (3) | | |
| | | |
H21—O2—H22 | 123 (3) | C13—C12—H12A | 109.1 |
N3—C2—N1 | 112.3 (2) | O1—C12—H12B | 109.1 |
N3—C2—C14 | 120.9 (2) | C13—C12—H12B | 109.1 |
N1—C2—C14 | 126.8 (2) | H12A—C12—H12B | 107.8 |
C5—C4—C9 | 116.3 (2) | N2—C13—C12 | 109.7 (2) |
C5—C4—H4 | 121.9 | N2—C13—H13A | 109.7 |
C9—C4—H4 | 121.9 | C12—C13—H13A | 109.7 |
C4—C5—F1 | 117.5 (2) | N2—C13—H13B | 109.7 |
C4—C5—C6 | 125.6 (2) | C12—C13—H13B | 109.7 |
F1—C5—C6 | 116.8 (2) | H13A—C13—H13B | 108.2 |
C7—C6—C5 | 117.4 (2) | C19—C14—C15 | 115.9 (2) |
C7—C6—N2 | 124.0 (2) | C19—C14—C2 | 116.4 (2) |
C5—C6—N2 | 118.5 (2) | C15—C14—C2 | 127.7 (2) |
C6—C7—C8 | 117.8 (2) | C16—C15—C14 | 122.3 (2) |
C6—C7—H7 | 121.1 | C16—C15—Cl1 | 115.72 (19) |
C8—C7—H7 | 121.1 | C14—C15—Cl1 | 121.95 (19) |
N1—C8—C9 | 105.1 (2) | C17—C16—C15 | 118.8 (2) |
N1—C8—C7 | 131.7 (2) | C17—C16—H16 | 120.6 |
C9—C8—C7 | 123.2 (2) | C15—C16—H16 | 120.6 |
N3—C9—C8 | 110.5 (2) | C16—C17—C18 | 121.4 (2) |
N3—C9—C4 | 129.8 (2) | C16—C17—Cl2 | 119.4 (2) |
C8—C9—C4 | 119.7 (2) | C18—C17—Cl2 | 119.2 (2) |
N2—C10—C11 | 108.8 (2) | C19—C18—C17 | 118.7 (2) |
N2—C10—H10A | 109.9 | C19—C18—H18 | 120.7 |
C11—C10—H10A | 109.9 | C17—C18—H18 | 120.7 |
N2—C10—H10B | 109.9 | C18—C19—C14 | 122.9 (2) |
C11—C10—H10B | 109.9 | C18—C19—H19 | 118.5 |
H10A—C10—H10B | 108.3 | C14—C19—H19 | 118.5 |
O1—C11—C10 | 111.7 (2) | C2—N1—C8 | 107.31 (19) |
O1—C11—H11A | 109.3 | C2—N1—H1 | 129.8 (17) |
C10—C11—H11A | 109.3 | C8—N1—H1 | 122.4 (17) |
O1—C11—H11B | 109.3 | C6—N2—C13 | 115.07 (18) |
C10—C11—H11B | 109.3 | C6—N2—C10 | 113.62 (19) |
H11A—C11—H11B | 107.9 | C13—N2—C10 | 108.3 (2) |
O1—C12—C13 | 112.6 (2) | C2—N3—C9 | 104.77 (19) |
O1—C12—H12A | 109.1 | C11—O1—C12 | 109.3 (2) |
| | | |
C9—C4—C5—F1 | 176.9 (2) | Cl1—C15—C16—C17 | 179.4 (2) |
C9—C4—C5—C6 | −0.6 (4) | C15—C16—C17—C18 | −0.4 (4) |
C4—C5—C6—C7 | 0.1 (4) | C15—C16—C17—Cl2 | −179.8 (2) |
F1—C5—C6—C7 | −177.3 (2) | C16—C17—C18—C19 | 0.4 (4) |
C4—C5—C6—N2 | 176.5 (3) | Cl2—C17—C18—C19 | 179.9 (2) |
F1—C5—C6—N2 | −1.0 (4) | C17—C18—C19—C14 | 0.0 (4) |
C5—C6—C7—C8 | 0.2 (4) | C15—C14—C19—C18 | −0.5 (4) |
N2—C6—C7—C8 | −176.0 (2) | C2—C14—C19—C18 | −179.5 (2) |
C6—C7—C8—N1 | 178.8 (2) | N3—C2—N1—C8 | −0.7 (3) |
C6—C7—C8—C9 | 0.0 (4) | C14—C2—N1—C8 | −179.7 (2) |
N1—C8—C9—N3 | −0.9 (3) | C9—C8—N1—C2 | 1.0 (3) |
C7—C8—C9—N3 | 178.1 (2) | C7—C8—N1—C2 | −178.0 (3) |
N1—C8—C9—C4 | −179.5 (2) | C7—C6—N2—C13 | 10.1 (3) |
C7—C8—C9—C4 | −0.5 (4) | C5—C6—N2—C13 | −166.0 (2) |
C5—C4—C9—N3 | −177.6 (3) | C7—C6—N2—C10 | −115.6 (3) |
C5—C4—C9—C8 | 0.7 (4) | C5—C6—N2—C10 | 68.3 (3) |
N2—C10—C11—O1 | −60.6 (3) | C12—C13—N2—C6 | 174.4 (2) |
O1—C12—C13—N2 | 57.9 (3) | C12—C13—N2—C10 | −57.2 (3) |
N3—C2—C14—C19 | −0.3 (4) | C11—C10—N2—C6 | −172.2 (2) |
N1—C2—C14—C19 | 178.6 (2) | C11—C10—N2—C13 | 58.6 (3) |
N3—C2—C14—C15 | −179.2 (2) | N1—C2—N3—C9 | 0.1 (3) |
N1—C2—C14—C15 | −0.2 (4) | C14—C2—N3—C9 | 179.2 (2) |
C19—C14—C15—C16 | 0.6 (4) | C8—C9—N3—C2 | 0.5 (3) |
C2—C14—C15—C16 | 179.4 (3) | C4—C9—N3—C2 | 178.9 (3) |
C19—C14—C15—Cl1 | −179.0 (2) | C10—C11—O1—C12 | 59.0 (3) |
C2—C14—C15—Cl1 | −0.1 (4) | C13—C12—O1—C11 | −57.6 (3) |
C14—C15—C16—C17 | −0.1 (4) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···Cl1 | 0.93 (2) | 2.45 (3) | 3.029 (2) | 121 (2) |
C19—H19···N3 | 0.93 | 2.41 | 2.776 (3) | 104 |
C10—H10B···F1 | 0.97 | 2.34 | 2.944 (3) | 120 |
N1—H1···O2i | 0.93 (2) | 2.18 (2) | 2.986 (3) | 145 (2) |
O2—H21···N3 | 0.93 (2) | 2.07 (2) | 3.002 (3) | 172 (3) |
O2—H22···N2ii | 1.00 (2) | 2.07 (3) | 3.057 (3) | 168 (4) |
C12—H12A···F1i | 0.97 | 2.38 | 3.257 (3) | 150 |
C12—H12A···Cl2iii | 0.97 | 2.78 | 3.408 (3) | 123 |
Symmetry codes: (i) −x+1/2, y+1/2, z; (ii) −x+1, −y, −z; (iii) x, −y+1/2, z−1/2. |
Experimental details
Crystal data |
Chemical formula | C17H14Cl2FN3O·H2O |
Mr | 384.23 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 295 |
a, b, c (Å) | 7.4455 (7), 15.310 (3), 29.487 (3) |
V (Å3) | 3361.2 (8) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.41 |
Crystal size (mm) | 0.48 × 0.36 × 0.24 |
|
Data collection |
Diffractometer | Enraf-Nonius TurboCAD4 diffractometer |
Absorption correction | Psi scan (North et al., 1968) |
Tmin, Tmax | 0.826, 0.907 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3893, 3403, 2174 |
Rint | 0.079 |
(sin θ/λ)max (Å−1) | 0.623 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.106, 1.02 |
No. of reflections | 3403 |
No. of parameters | 238 |
No. of restraints | 5 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.23, −0.32 |
Selected geometric parameters (Å, º) topC2—N3 | 1.321 (3) | C6—N2 | 1.425 (3) |
C2—N1 | 1.363 (3) | C15—Cl1 | 1.741 (3) |
C2—C14 | 1.476 (3) | C17—Cl2 | 1.732 (2) |
C5—F1 | 1.367 (3) | | |
| | | |
N3—C2—N1 | 112.3 (2) | O1—C12—C13 | 112.6 (2) |
N3—C2—C14 | 120.9 (2) | N2—C13—C12 | 109.7 (2) |
N1—C2—C14 | 126.8 (2) | C19—C14—C2 | 116.4 (2) |
C4—C5—F1 | 117.5 (2) | C14—C15—Cl1 | 121.95 (19) |
C5—C6—N2 | 118.5 (2) | C16—C17—Cl2 | 119.4 (2) |
N1—C8—C9 | 105.1 (2) | C2—N1—C8 | 107.31 (19) |
N3—C9—C8 | 110.5 (2) | C13—N2—C10 | 108.3 (2) |
N2—C10—C11 | 108.8 (2) | C2—N3—C9 | 104.77 (19) |
O1—C11—C10 | 111.7 (2) | C11—O1—C12 | 109.3 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···Cl1 | 0.93 (2) | 2.45 (3) | 3.029 (2) | 120.5 (19) |
C19—H19···N3 | 0.9300 | 2.4050 | 2.776 (3) | 103.68 |
C10—H10B···F1 | 0.9700 | 2.3427 | 2.944 (3) | 119.49 |
N1—H1···O2i | 0.93 (2) | 2.18 (2) | 2.986 (3) | 145 (2) |
O2—H21···N3 | 0.93 (2) | 2.07 (2) | 3.002 (3) | 172 (3) |
O2—H22···N2ii | 1.00 (2) | 2.07 (3) | 3.057 (3) | 168 (4) |
C12—H12A···F1i | 0.9700 | 2.3790 | 3.257 (3) | 150.22 |
C12—H12A···Cl2iii | 0.9700 | 2.7808 | 3.408 (3) | 123.05 |
Symmetry codes: (i) −x+1/2, y+1/2, z; (ii) −x+1, −y, −z; (iii) x, −y+1/2, z−1/2. |
The benzimidazole nucleus, which is a useful structure for further molecular exploration and for the development of new pharmaceutical compounds, has received much attention in recent years (Mann et al., 2001; Nakano et al., 2000). Owing to the versatility of this heterocycle, we are focusing our research efforts on new and potent benzimidazole derivatives. In our previous studies we described the synthesis and antimicrobial activities of some benzimidazole derivatives (Göker et al., 2001; Kuş et al., 2001). 2-(substituted phenyl)- benzimidazoles have different pharmaceutical activities such as antibacterial, antiviral, antitumoral and anti-inflammatory (Coburn et al., 1987; Roth et al., 1997; Chen et al., 1993; Denny et al., 1993; Evans et al., 1996).
To evaluate their antimicrobial activities, we synthesized 2-(2,4-Dichlorophenyl)-5-fluoro-6-morpholin-4-yl-1H-benzimidazole and its analogues. The synthesis and physical and spectroscopic data of this compound, which has a substituted phenyl ring at the 2 position of the benzimidazole nucleus, has been reported by us (Kuş, 2002). In this research, the X-ray structure of its monohydrate, (I), was determined in order to establish its conformation.
The intramolecular bond distances and angles (Table 1) for the benzimidazole moiety of (I) are in good agreement with those observed in other benzimidazole derivatives (Göker et al., 1995; Özbey et al., 1998; Kendi et al., 1999; Vasudevan et al., 1994; Balasubramanian et al., 1996). The bond lengths C15—Cl1 and C17—Cl2 (Table 1) are within the expected range (Allen et al., 1987).
As expected, the benzimidazole ring system is essentially planar [maximum deviation 0.017 (3) Å for C9], with a dihedral angle of 1.54 (9) Å between the imidazole and the benzene ring planes. The F atom lies −0.077 (2) Å from the least-squares plane defined by all the atoms of the two fused rings. In the molecule, the benzimidazole system is coplanar with the phenyl substituent owing to the hydrogen bonding between the imidazole N atoms and the chlorine and one of the carbon atoms of the phenyl moiety (Table 2). The dihedral angle between the best planes of these rings is 0.15 (7)°, so the structure is almost planar except for the morpholin ring, as shown in Fig. 1. The dichlorophenyl ring is planar and the Cl1 atom is situated 0.0240 (9) Å above this plane.
The morpholin ring deviates from planarity, with atoms N2 and O1 displaced from the C10/C11/C12/C13 mean plane by 0.689 (2) and −0.645 (2) Å, respectively. The dihedral angle between the best planes of the morpholin ring and the benzimidazole ring is 40.8 (1)°. The puckering parameters (Cremer & Pople, 1975) of this ring are Q=0.581 (2) Å, θ=177.1 (3)° and ϕ=-43 (5)°, thus the morpholin ring adopts a chair conformation.
The crystal structure of the title compound is stabilized by intra- and intermolecular hydrogen bonds (Table 2, Fig. 2).