| Literature DB >> 30002901 |
Pinar Sen1, Sevgi Kansiz2, Necmi Dege2, Turganbay S Iskenderov3, S Zeki Yildiz4.
Abstract
In the title compound, C21H12N4O·H2O, the five-membered ring is essentially planar with a maximum deviation of 0.004 (2) Å. An N-H⋯O hydrogen bond connects the organic and water mol-ecules. In the crystal, O-H⋯N hydrogen bonds link mol-ecules into a two-dimensional network parallel to (100). Hirshfeld surface analyses and two-dimensional fingerprint plots were used to qu-antify the inter-molecular inter-actions present in the crystal, indicating that the most important contributions for the crystal packing are from H⋯H (28.7%), C⋯H/H⋯C (27.1%), N⋯H/H⋯N (26.4%), C⋯N/N⋯C (6.1%), O⋯H/H⋯O (3.7%) and C⋯C (6.0%) inter-actions.Entities:
Keywords: Hirshfeld surfaces; benzimidazole; crystal structure; hydrogen bonding
Year: 2018 PMID: 30002901 PMCID: PMC6038632 DOI: 10.1107/S2056989018008745
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of the title compound, showing the atom labelling. Displacement ellipsoids are drawn at the 20% probability level.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| N2—H2⋯O2 | 0.92 (2) | 1.86 (3) | 2.774 (3) | 171 (2) |
| O2—H2 | 0.85 | 2.17 | 2.876 (2) | 140 |
Symmetry code: (i) .
Figure 2A partial view of the crystal packing. Dashed lines denote the intermolecular N—H⋯O and O—H⋯N hydrogen bonding.
Figure 3The Hirshfeld surface mapped over d norm.
Figure 4Hirshfeld surfaces mapped over d norm to visualize the intermolecular interactions.
Figure 5Fingerprint plot for the title compound.
Figure 6Two-dimensional fingerprint plots with a d norm view for the H⋯H (28.7%), C⋯H/H⋯C (27.1%), N⋯H/H⋯N (26.4%) and O⋯H/H⋯O (3.7%) contacts in the title compound.
Figure 7The synthesis of the title compound.
Experimental details
| Crystal data | |
| Chemical formula | C21H12N4O·H2O |
|
| 354.36 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 296 |
|
| 8.7657 (6), 27.285 (2), 14.6938 (13) |
|
| 3514.4 (5) |
|
| 8 |
| Radiation type | Mo |
| μ (mm−1) | 0.09 |
| Crystal size (mm) | 0.79 × 0.39 × 0.18 |
| Data collection | |
| Diffractometer | STOE IPDS 2 |
| Absorption correction | Integration ( |
|
| 0.967, 0.988 |
| No. of measured, independent and observed [ | 33692, 3447, 1829 |
|
| 0.079 |
| (sin θ/λ)max (Å−1) | 0.617 |
| Refinement | |
|
| 0.044, 0.106, 0.91 |
| No. of reflections | 3447 |
| No. of parameters | 251 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.21, −0.25 |
Computer programs: X-AREA and X-RED (Stoe & Cie, 2004 ▸), SHELXL2017/1 (Sheldrick, 2015 ▸), ORTEP-3 for Windows and WinGX (Farrugia, 2012 ▸) and PLATON (Spek, 2009 ▸).
| C21H12N4O·H2O | |
| Mo | |
| Orthorhombic, | Cell parameters from 17763 reflections |
| θ = 1.4–27.6° | |
| µ = 0.09 mm−1 | |
| Stick, red | |
| 0.79 × 0.39 × 0.18 mm | |
| STOE IPDS 2 diffractometer | 3447 independent reflections |
| Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus | 1829 reflections with |
| Detector resolution: 6.67 pixels mm-1 | |
| rotation method scans | θmax = 26.0°, θmin = 2.0° |
| Absorption correction: integration (X-RED32; Stoe & Cie, 2004) | |
| 33692 measured reflections |
| Refinement on | 0 restraints |
| Least-squares matrix: full | Hydrogen site location: mixed |
| H atoms treated by a mixture of independent and constrained refinement | |
| (Δ/σ)max < 0.001 | |
| 3447 reflections | Δρmax = 0.21 e Å−3 |
| 251 parameters | Δρmin = −0.25 e Å−3 |
| 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. |
| O1 | 0.69369 (16) | 0.65950 (6) | 0.29785 (11) | 0.0737 (5) | |
| N2 | 0.2691 (2) | 0.46625 (6) | 0.26099 (13) | 0.0612 (5) | |
| N1 | 0.3278 (2) | 0.47874 (7) | 0.11536 (11) | 0.0660 (5) | |
| C15 | 0.4616 (2) | 0.70114 (8) | 0.34035 (13) | 0.0556 (5) | |
| H15 | 0.401592 | 0.674922 | 0.321542 | 0.067* | |
| C8 | 0.4411 (2) | 0.53611 (7) | 0.22666 (14) | 0.0570 (5) | |
| C16 | 0.3945 (2) | 0.74273 (8) | 0.37607 (13) | 0.0555 (5) | |
| N3 | 0.1021 (3) | 0.74647 (8) | 0.38612 (15) | 0.0877 (7) | |
| C11 | 0.6078 (2) | 0.61778 (8) | 0.27451 (15) | 0.0617 (6) | |
| C7 | 0.3485 (2) | 0.49377 (7) | 0.20015 (14) | 0.0575 (5) | |
| C14 | 0.6179 (3) | 0.69884 (8) | 0.33284 (14) | 0.0595 (6) | |
| C5 | 0.1905 (3) | 0.43125 (8) | 0.21300 (14) | 0.0598 (6) | |
| C6 | 0.2289 (3) | 0.43919 (8) | 0.12231 (15) | 0.0626 (6) | |
| C20 | 0.2314 (3) | 0.74515 (8) | 0.38237 (15) | 0.0629 (6) | |
| C9 | 0.4841 (3) | 0.54391 (8) | 0.31609 (14) | 0.0636 (6) | |
| H9 | 0.455684 | 0.521444 | 0.360562 | 0.076* | |
| C17 | 0.4835 (3) | 0.78215 (8) | 0.40457 (14) | 0.0641 (6) | |
| C10 | 0.5683 (3) | 0.58453 (9) | 0.34017 (15) | 0.0669 (6) | |
| H10 | 0.597961 | 0.589294 | 0.400289 | 0.080* | |
| O2 | 0.2249 (4) | 0.46945 (10) | 0.44787 (13) | 0.1486 (11) | |
| H2B | 0.205614 | 0.441905 | 0.472290 | 0.223* | |
| H2C | 0.175029 | 0.490023 | 0.479514 | 0.223* | |
| C13 | 0.4861 (3) | 0.56973 (9) | 0.16191 (15) | 0.0728 (7) | |
| H13 | 0.460140 | 0.564674 | 0.101255 | 0.087* | |
| C19 | 0.7071 (3) | 0.73832 (10) | 0.35927 (16) | 0.0730 (7) | |
| H19 | 0.812628 | 0.736903 | 0.353160 | 0.088* | |
| C18 | 0.6397 (3) | 0.77925 (10) | 0.39428 (16) | 0.0796 (7) | |
| H18 | 0.700081 | 0.805688 | 0.411514 | 0.095* | |
| C1 | 0.1650 (3) | 0.40948 (9) | 0.05537 (17) | 0.0779 (7) | |
| H1 | 0.189956 | 0.413927 | −0.005580 | 0.093* | |
| C12 | 0.5683 (3) | 0.61047 (9) | 0.18562 (16) | 0.0729 (7) | |
| H12 | 0.597142 | 0.633031 | 0.141412 | 0.087* | |
| C21 | 0.4137 (3) | 0.82420 (10) | 0.44552 (17) | 0.0822 (8) | |
| C4 | 0.0891 (3) | 0.39499 (8) | 0.23910 (17) | 0.0754 (7) | |
| H4 | 0.063662 | 0.390196 | 0.299896 | 0.090* | |
| N4 | 0.3579 (3) | 0.85731 (10) | 0.47866 (17) | 0.1136 (9) | |
| C3 | 0.0277 (3) | 0.36651 (9) | 0.17176 (19) | 0.0827 (7) | |
| H3 | −0.040521 | 0.341761 | 0.187190 | 0.099* | |
| C2 | 0.0650 (3) | 0.37372 (9) | 0.08091 (19) | 0.0822 (7) | |
| H2A | 0.021084 | 0.353825 | 0.036701 | 0.099* | |
| H2 | 0.259 (3) | 0.4705 (9) | 0.3227 (17) | 0.085 (8)* |
| O1 | 0.0442 (9) | 0.0814 (11) | 0.0956 (11) | −0.0072 (9) | 0.0038 (8) | −0.0091 (9) |
| N2 | 0.0693 (13) | 0.0588 (11) | 0.0555 (11) | 0.0030 (9) | 0.0003 (10) | 0.0023 (10) |
| N1 | 0.0762 (13) | 0.0634 (12) | 0.0585 (11) | 0.0056 (10) | 0.0011 (10) | 0.0022 (9) |
| C15 | 0.0494 (14) | 0.0554 (13) | 0.0620 (12) | −0.0078 (10) | −0.0041 (10) | −0.0002 (10) |
| C8 | 0.0545 (13) | 0.0530 (13) | 0.0633 (13) | 0.0111 (11) | −0.0010 (10) | 0.0039 (10) |
| C16 | 0.0581 (14) | 0.0553 (13) | 0.0532 (12) | −0.0051 (11) | −0.0036 (10) | 0.0025 (10) |
| N3 | 0.0663 (15) | 0.0929 (16) | 0.1039 (17) | 0.0086 (13) | 0.0019 (13) | −0.0076 (12) |
| C11 | 0.0458 (13) | 0.0665 (14) | 0.0728 (15) | 0.0047 (11) | 0.0039 (11) | −0.0020 (12) |
| C7 | 0.0594 (14) | 0.0550 (13) | 0.0582 (13) | 0.0133 (11) | −0.0004 (11) | 0.0047 (10) |
| C14 | 0.0536 (15) | 0.0676 (15) | 0.0572 (12) | −0.0049 (12) | 0.0003 (11) | −0.0017 (11) |
| C5 | 0.0635 (15) | 0.0510 (12) | 0.0651 (13) | 0.0095 (12) | −0.0034 (11) | 0.0033 (11) |
| C6 | 0.0676 (15) | 0.0568 (13) | 0.0632 (13) | 0.0097 (12) | −0.0030 (12) | 0.0003 (11) |
| C20 | 0.0639 (17) | 0.0579 (14) | 0.0668 (14) | 0.0009 (12) | −0.0017 (13) | −0.0041 (11) |
| C9 | 0.0660 (15) | 0.0651 (14) | 0.0597 (13) | 0.0066 (12) | 0.0051 (11) | 0.0027 (11) |
| C17 | 0.0725 (17) | 0.0634 (15) | 0.0563 (12) | −0.0144 (13) | −0.0031 (11) | −0.0020 (11) |
| C10 | 0.0606 (15) | 0.0779 (16) | 0.0620 (13) | 0.0063 (13) | 0.0017 (11) | −0.0049 (12) |
| O2 | 0.264 (3) | 0.1188 (17) | 0.0633 (11) | −0.079 (2) | 0.0336 (15) | −0.0127 (11) |
| C13 | 0.0824 (17) | 0.0731 (16) | 0.0628 (13) | −0.0058 (14) | −0.0087 (13) | 0.0085 (12) |
| C19 | 0.0528 (15) | 0.098 (2) | 0.0683 (14) | −0.0241 (14) | −0.0033 (11) | −0.0065 (13) |
| C18 | 0.085 (2) | 0.0824 (18) | 0.0709 (15) | −0.0335 (16) | −0.0013 (14) | −0.0168 (13) |
| C1 | 0.0890 (18) | 0.0737 (16) | 0.0710 (15) | 0.0085 (15) | −0.0049 (14) | −0.0034 (13) |
| C12 | 0.0713 (17) | 0.0743 (16) | 0.0731 (15) | −0.0070 (13) | −0.0037 (13) | 0.0125 (12) |
| C21 | 0.112 (2) | 0.0648 (16) | 0.0694 (15) | −0.0126 (16) | −0.0029 (14) | −0.0104 (13) |
| C4 | 0.0823 (18) | 0.0674 (15) | 0.0764 (15) | 0.0009 (14) | 0.0025 (14) | 0.0061 (13) |
| N4 | 0.157 (2) | 0.0810 (16) | 0.1027 (18) | 0.0009 (17) | −0.0028 (17) | −0.0252 (14) |
| C3 | 0.0792 (18) | 0.0662 (16) | 0.103 (2) | −0.0019 (13) | −0.0046 (16) | −0.0015 (15) |
| C2 | 0.087 (2) | 0.0679 (17) | 0.0922 (19) | 0.0068 (15) | −0.0177 (16) | −0.0126 (14) |
| O1—C14 | 1.363 (2) | C9—C10 | 1.378 (3) |
| O1—C11 | 1.407 (2) | C9—H9 | 0.9300 |
| N2—C7 | 1.359 (3) | C17—C18 | 1.379 (3) |
| N2—C5 | 1.373 (3) | C17—C21 | 1.433 (4) |
| N2—H2 | 0.92 (2) | C10—H10 | 0.9300 |
| N1—C7 | 1.324 (3) | O2—H2B | 0.8500 |
| N1—C6 | 1.388 (3) | O2—H2C | 0.8500 |
| C15—C14 | 1.376 (3) | C13—C12 | 1.370 (3) |
| C15—C16 | 1.382 (3) | C13—H13 | 0.9300 |
| C15—H15 | 0.9300 | C19—C18 | 1.364 (3) |
| C8—C13 | 1.379 (3) | C19—H19 | 0.9300 |
| C8—C9 | 1.383 (3) | C18—H18 | 0.9300 |
| C8—C7 | 1.465 (3) | C1—C2 | 1.364 (3) |
| C16—C17 | 1.393 (3) | C1—H1 | 0.9300 |
| C16—C20 | 1.435 (3) | C12—H12 | 0.9300 |
| N3—C20 | 1.135 (3) | C21—N4 | 1.137 (3) |
| C11—C12 | 1.366 (3) | C4—C3 | 1.368 (3) |
| C11—C10 | 1.369 (3) | C4—H4 | 0.9300 |
| C14—C19 | 1.387 (3) | C3—C2 | 1.388 (4) |
| C5—C4 | 1.384 (3) | C3—H3 | 0.9300 |
| C5—C6 | 1.391 (3) | C2—H2A | 0.9300 |
| C6—C1 | 1.392 (3) | ||
| C14—O1—C11 | 117.92 (16) | C18—C17—C16 | 118.6 (2) |
| C7—N2—C5 | 107.66 (18) | C18—C17—C21 | 121.0 (2) |
| C7—N2—H2 | 129.0 (15) | C16—C17—C21 | 120.4 (2) |
| C5—N2—H2 | 123.1 (15) | C11—C10—C9 | 119.2 (2) |
| C7—N1—C6 | 104.91 (18) | C11—C10—H10 | 120.4 |
| C14—C15—C16 | 119.5 (2) | C9—C10—H10 | 120.4 |
| C14—C15—H15 | 120.3 | H2B—O2—H2C | 104.5 |
| C16—C15—H15 | 120.3 | C12—C13—C8 | 121.0 (2) |
| C13—C8—C9 | 118.4 (2) | C12—C13—H13 | 119.5 |
| C13—C8—C7 | 119.96 (19) | C8—C13—H13 | 119.5 |
| C9—C8—C7 | 121.66 (19) | C18—C19—C14 | 119.8 (2) |
| C15—C16—C17 | 120.7 (2) | C18—C19—H19 | 120.1 |
| C15—C16—C20 | 119.1 (2) | C14—C19—H19 | 120.1 |
| C17—C16—C20 | 120.2 (2) | C19—C18—C17 | 121.2 (2) |
| C12—C11—C10 | 120.9 (2) | C19—C18—H18 | 119.4 |
| C12—C11—O1 | 119.1 (2) | C17—C18—H18 | 119.4 |
| C10—C11—O1 | 120.0 (2) | C2—C1—C6 | 118.7 (2) |
| N1—C7—N2 | 112.18 (19) | C2—C1—H1 | 120.6 |
| N1—C7—C8 | 124.8 (2) | C6—C1—H1 | 120.6 |
| N2—C7—C8 | 122.99 (19) | C11—C12—C13 | 119.7 (2) |
| O1—C14—C15 | 123.5 (2) | C11—C12—H12 | 120.2 |
| O1—C14—C19 | 116.3 (2) | C13—C12—H12 | 120.2 |
| C15—C14—C19 | 120.2 (2) | N4—C21—C17 | 179.4 (3) |
| N2—C5—C4 | 132.6 (2) | C3—C4—C5 | 117.3 (2) |
| N2—C5—C6 | 105.2 (2) | C3—C4—H4 | 121.4 |
| C4—C5—C6 | 122.1 (2) | C5—C4—H4 | 121.4 |
| N1—C6—C5 | 110.03 (19) | C4—C3—C2 | 121.5 (2) |
| N1—C6—C1 | 130.7 (2) | C4—C3—H3 | 119.3 |
| C5—C6—C1 | 119.3 (2) | C2—C3—H3 | 119.3 |
| N3—C20—C16 | 178.8 (3) | C1—C2—C3 | 121.1 (2) |
| C10—C9—C8 | 120.9 (2) | C1—C2—H2A | 119.4 |
| C10—C9—H9 | 119.5 | C3—C2—H2A | 119.4 |
| C8—C9—H9 | 119.5 | ||
| C14—C15—C16—C17 | −0.1 (3) | C7—C8—C9—C10 | −178.5 (2) |
| C14—C15—C16—C20 | 179.04 (19) | C15—C16—C17—C18 | 1.6 (3) |
| C14—O1—C11—C12 | 99.2 (2) | C20—C16—C17—C18 | −177.6 (2) |
| C14—O1—C11—C10 | −82.4 (2) | C15—C16—C17—C21 | −177.0 (2) |
| C6—N1—C7—N2 | 0.1 (2) | C20—C16—C17—C21 | 3.8 (3) |
| C6—N1—C7—C8 | −177.8 (2) | C12—C11—C10—C9 | −1.7 (3) |
| C5—N2—C7—N1 | −0.5 (2) | O1—C11—C10—C9 | 179.93 (19) |
| C5—N2—C7—C8 | 177.44 (19) | C8—C9—C10—C11 | 0.9 (3) |
| C13—C8—C7—N1 | 14.5 (3) | C9—C8—C13—C12 | −1.4 (3) |
| C9—C8—C7—N1 | −166.3 (2) | C7—C8—C13—C12 | 177.8 (2) |
| C13—C8—C7—N2 | −163.2 (2) | O1—C14—C19—C18 | 179.5 (2) |
| C9—C8—C7—N2 | 16.0 (3) | C15—C14—C19—C18 | 1.1 (3) |
| C11—O1—C14—C15 | −4.8 (3) | C14—C19—C18—C17 | 0.4 (4) |
| C11—O1—C14—C19 | 176.87 (19) | C16—C17—C18—C19 | −1.7 (4) |
| C16—C15—C14—O1 | −179.49 (18) | C21—C17—C18—C19 | 176.9 (2) |
| C16—C15—C14—C19 | −1.2 (3) | N1—C6—C1—C2 | −177.4 (2) |
| C7—N2—C5—C4 | −177.5 (2) | C5—C6—C1—C2 | 0.7 (3) |
| C7—N2—C5—C6 | 0.7 (2) | C10—C11—C12—C13 | 1.0 (3) |
| C7—N1—C6—C5 | 0.4 (2) | O1—C11—C12—C13 | 179.3 (2) |
| C7—N1—C6—C1 | 178.7 (2) | C8—C13—C12—C11 | 0.6 (4) |
| N2—C5—C6—N1 | −0.7 (2) | N2—C5—C4—C3 | 178.5 (2) |
| C4—C5—C6—N1 | 177.75 (19) | C6—C5—C4—C3 | 0.5 (3) |
| N2—C5—C6—C1 | −179.20 (19) | C5—C4—C3—C2 | −0.2 (4) |
| C4—C5—C6—C1 | −0.8 (3) | C6—C1—C2—C3 | −0.5 (4) |
| C13—C8—C9—C10 | 0.7 (3) | C4—C3—C2—C1 | 0.2 (4) |
| H··· | ||||
| N2—H2···O2 | 0.92 (2) | 1.86 (3) | 2.774 (3) | 171 (2) |
| O2—H2 | 0.85 | 2.17 | 2.876 (2) | 140 |
| C15—H15···O1ii | 0.93 | 2.56 | 3.306 (2) | 137 |
| C19—H19···N3iii | 0.93 | 2.60 | 3.491 (3) | 162 |