research communications
H-1,3-benzodiazol-2-yl}phenol
and Hirshfeld surface analysis of a new benzimidazole compound, 3-{1-[(2-hydroxyphenyl)methyl]-1aUnité de Recherche de Chimie de l'Environnement et Moléculaire Structurale (URCHEMS), Département de Chimie, Université Mentouri de Constantine, 25000 Constantine, Algeria, and bPharmaceutical Sciences Research Center CRSP, Constantine 25000, Algeria
*Correspondence e-mail: cherouana.aouatef@umc.edu.dz
This article is part of a collection of articles to commemorate the founding of the African Crystallographic Association and the 75th anniversary of the IUCr.
The title compound, C20H16N2O2, is composed of two monosubstituted benzene rings and one benzimidazole unit. The benzimidazole moiety subtends dihedral angles of 46.16 (7) and 77.45 (8)° with the benzene rings, which themselves form a dihedral angle of 54.34 (9)°. The features O—H⋯N and O—H⋯O hydrogen-bonding interactions, which together lead to the formation of two-dimensional hydrogen-bonded layers parallel to the (101) plane. In addition, π–π interactions also contribute to the crystal cohesion. Hirshfeld surface analysis indicates that the most significant contacts in the crystal packing are: H⋯H (47.5%), O⋯H/H⋯O (12.4%), N⋯H/H⋯N (6.1%), C⋯H/H⋯C (27.6%) and C⋯C (4.6%).
Keywords: benzimidazole; single crystal; X-ray diffraction; hydrogen bonding; intermolecular interactions; Hirshfeld surface analysis.
CCDC reference: 2311475
1. Chemical context
The benzimidazole unit comprises a phenyl ring fused to an imidazole ring. The first benzimidazole compound was prepared by Hoebrecker (1872). Benzimidazole is an important structural core in medicinal chemistry and this class of compounds displays a broad range of biological activities such as antimicrobial, antiviral, anticancer, anti-inflammatory, gastroprotective and analgesic (Spasov et al., 1999; Sevak et al., 2002; Demirayak et al., 2005). The use of benzimidazole derivatives with common drugs employed in the treatment of giardiasis has been reviewed (Harris et al., 2001). The coordination behavior of benzimidazole derivatives towards transition-metal ions was explored in order to increase their biological activity (Téllez et al., 2007). The present work describes the synthesis, structural characterization and Hirshfeld analysis of a new benzimidazole compound, 3-{1-[(2-hydroxyphenyl)methyl]-1H-1,3-benzodiazol-2-yl}phenol.
2. Structural commentary
The title compound is composed of two monosubstituted benzene rings and one benzimidazole unit (Fig. 1). The benzimidazole moiety subtends dihedral angles of 46.16 (7) and 77.45 (8)° with the benzene rings, which themselves form a dihedral angle of 54.34 (9)°. These angles are in agreement with those observed in similar structures (Quezada-Miriel et al., 2012; Shu-Ping Yang et al., 2007).
3. Supramolecular features
The crystal packing of the title compound reveals intermolecular hydrogen bonding, specifically O—H⋯O interactions involving benzene rings and O—H⋯N interaction between the benzimidazole moieties and benzene rings (Table 1). The molecules are self-assembled by intermolecular hydrogen bonds between the hydroxyl groups and the N1 atoms of the benzimidazole moieties, forming hydrogen-bonded ribbons with a C(8) graph-set motif (Etter et al., 1990; Bernstein et al., 1995) parallel to the (111) plane. The combination of the O—H⋯O and O—H⋯N hydrogen bonds leads to rings with R44 (18) and R44(38) graph-set motifs (Fig. 2). Further cohesion of the crystal packing is provided by π–π stacking interactions between C1–C6 benzene rings with centroid–centroid distances of 3.5957 (11) Å.
4. Hirshfeld surface analysis
Hirshfeld surface analysis was undertaken in order to better understand the intermolecular interactions within the ; Spackman et al., 2021). Hirshfeld surface analysis provides a three-dimensional picture of the intermolecular interactions. These interactions can be summarized by using fingerprint plots. The Hirshfeld surface of the title compound mapped over dnorm is shown in Fig. 3. The red spots on the surface indicate the presence of atoms in very close proximity to the outside of the surface, the white means that the atoms are in medium proximity while the blue areas are completely devoid of close contacts. The combination of the 3D Hirshfeld surface and the 2D fingerprint plots (Fig. 4), shows that intermolecular H⋯H contacts make the main contribution, corresponding to 47.5% of the total Hirshfeld surface (McKinnon et al., 2007) and that there are short intermolecular H⋯H contacts where de = di = 1 Å. In the fingerprint plot delineated into C⋯H/H⋯C contacts (27.6% of the total Hirshfeld surface) there are two short spikes. The red spots on the dnorm surface in Fig. 3 are due to the HO⋯O contacts corresponding to O—H⋯O and O—H⋯N hydrogen bonds. The O⋯H and N⋯H contacts represent 12.4% and 6.1% of the total Hirshfeld surface, respectively, Fig. 5. These contacts are manifested as sharp spikes at de + di = 1.8 Å for N⋯H and 1.9 Å for O⋯H. Finally, packing cohesion in this structure is also provided by C⋯N and C⋯C interactions, which correspond to π–π stacking interactions.
using graphical tools (Spackman & Jayatilaka, 20095. Synthesis and crystallization
All chemicals were commercially available, purchased from Sigma-Aldrich, and used as received without purification. 3-Hydroxybenzaldehyde (0.244 g, 2 mmol) and salicylaldehyde (0.244 g, 2 mmol) were added to an ethanolic solution of o-phenylenediamine (0.216 g, 2 mmol). The reaction mixture was stirred for 4 h under reflux at 348 K. The resulting brown solution was cooled in an ice bath. The obtained filtrate was left to evaporate slowly at room temperature, giving after two weeks colorless crystals suitable for single-crystal x-ray diffraction analysis.
6. Refinement
Crystal data, data collection and structure . All H atoms were located in difference electron-density maps and were treated as riding on their parent atoms with C—H = 0.93 Å, O—H = 0.84 Å and Uiso(H) = 1.2Ueq(C) or 1.5Ueq(O).
details are summarized in Table 2Supporting information
CCDC reference: 2311475
https://doi.org/10.1107/S2056989023010368/zn2033sup1.cif
contains datablocks global, I. DOI:Supporting information file. DOI: https://doi.org/10.1107/S2056989023010368/zn2033Isup2.cml
C20H16N2O2 | F(000) = 664 |
Mr = 316.35 | Least Squares Treatment of 25 SET4 setting angles. |
Monoclinic, P21/n | Dx = 1.322 Mg m−3 |
Hall symbol: -P 2yn | Mo Kα radiation, λ = 0.71073 Å |
a = 10.6474 (3) Å | Cell parameters from 33506 reflections |
b = 13.2429 (3) Å | θ = 2.4–30.1° |
c = 11.4176 (3) Å | µ = 0.09 mm−1 |
β = 99.067 (1)° | T = 100 K |
V = 1589.79 (7) Å3 | Prism, colourless |
Z = 4 | 0.1 × 0.1 × 0.08 mm |
Nonius KappaCCD diffractometer | 2866 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.056 |
Graphite monochromator | θmax = 30.1°, θmin = 2.4° |
ω scans | h = −15→14 |
33506 measured reflections | k = −17→18 |
4650 independent reflections | l = −15→16 |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.059 | H-atom parameters constrained |
wR(F2) = 0.190 | W = 1/[Σ2(FO2) + (0.1027P)2 + 0.1399P] WHERE P = (FO2 + 2FC2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
4643 reflections | Δρmax = 0.50 e Å−3 |
217 parameters | Δρmin = −0.30 e Å−3 |
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 esds are taken into account in the estimation of distances, angles and torsion angles |
x | y | z | Uiso*/Ueq | ||
O1 | 0.71485 (14) | 0.50588 (12) | 0.85134 (15) | 0.0674 (6) | |
O2 | 0.86823 (12) | 0.19463 (10) | 0.75574 (10) | 0.0484 (4) | |
N1 | 0.50090 (14) | 0.18753 (11) | 1.12414 (12) | 0.0415 (4) | |
N2 | 0.64015 (13) | 0.13212 (10) | 1.01162 (12) | 0.0365 (4) | |
C1 | 0.54208 (16) | 0.30396 (13) | 0.96699 (14) | 0.0393 (5) | |
C2 | 0.64184 (18) | 0.36170 (13) | 0.93853 (15) | 0.0434 (5) | |
C3 | 0.61480 (19) | 0.45154 (14) | 0.87656 (16) | 0.0470 (6) | |
C4 | 0.49058 (19) | 0.48277 (14) | 0.84368 (16) | 0.0496 (6) | |
C5 | 0.3922 (2) | 0.42579 (16) | 0.87286 (17) | 0.0524 (6) | |
C6 | 0.41675 (19) | 0.33701 (15) | 0.93432 (16) | 0.0475 (6) | |
C7 | 0.56219 (15) | 0.20898 (13) | 1.03474 (14) | 0.0376 (5) | |
C8 | 0.62905 (16) | 0.05631 (12) | 1.09273 (15) | 0.0386 (5) | |
C9 | 0.54146 (16) | 0.09200 (13) | 1.16216 (15) | 0.0405 (5) | |
C10 | 0.50993 (19) | 0.03349 (15) | 1.25517 (17) | 0.0504 (6) | |
C11 | 0.5675 (2) | −0.05921 (16) | 1.27507 (19) | 0.0584 (7) | |
C12 | 0.6536 (2) | −0.09453 (14) | 1.20405 (19) | 0.0573 (7) | |
C13 | 0.68637 (19) | −0.03791 (14) | 1.11183 (17) | 0.0485 (6) | |
C14 | 0.71836 (15) | 0.12707 (14) | 0.91676 (14) | 0.0389 (5) | |
C15 | 0.85421 (16) | 0.16113 (12) | 0.95674 (14) | 0.0353 (5) | |
C16 | 0.91028 (19) | 0.16091 (16) | 1.07445 (16) | 0.0500 (6) | |
C17 | 1.0337 (2) | 0.19263 (17) | 1.10898 (18) | 0.0565 (7) | |
C18 | 1.10283 (19) | 0.22691 (18) | 1.02536 (18) | 0.0561 (7) | |
C19 | 1.04917 (17) | 0.22814 (16) | 0.90709 (17) | 0.0505 (6) | |
C20 | 0.92539 (16) | 0.19490 (12) | 0.87220 (14) | 0.0364 (5) | |
H1 | 0.69016 | 0.56161 | 0.82622 | 0.1010* | |
H2 | 0.90990 | 0.22934 | 0.71643 | 0.0730* | |
H2A | 0.72555 | 0.34062 | 0.96058 | 0.0520* | |
H4 | 0.47340 | 0.54263 | 0.80161 | 0.0590* | |
H5 | 0.30871 | 0.44742 | 0.85090 | 0.0630* | |
H6 | 0.34993 | 0.29882 | 0.95425 | 0.0570* | |
H10 | 0.45194 | 0.05650 | 1.30205 | 0.0600* | |
H11 | 0.54868 | −0.09918 | 1.33701 | 0.0700* | |
H12 | 0.68991 | −0.15799 | 1.21930 | 0.0690* | |
H13 | 0.74390 | −0.06162 | 1.06486 | 0.0580* | |
H14A | 0.68017 | 0.16920 | 0.85120 | 0.0470* | |
H14B | 0.71891 | 0.05813 | 0.88814 | 0.0470* | |
H16 | 0.86349 | 0.13880 | 1.13176 | 0.0600* | |
H17 | 1.06999 | 0.19081 | 1.18856 | 0.0680* | |
H18 | 1.18584 | 0.24933 | 1.04831 | 0.0670* | |
H19 | 1.09626 | 0.25138 | 0.85055 | 0.0610* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0589 (9) | 0.0611 (9) | 0.0872 (12) | 0.0017 (7) | 0.0269 (8) | 0.0158 (8) |
O2 | 0.0457 (7) | 0.0684 (8) | 0.0323 (6) | −0.0122 (6) | 0.0096 (5) | 0.0031 (5) |
N1 | 0.0386 (8) | 0.0533 (8) | 0.0348 (7) | 0.0000 (6) | 0.0125 (6) | −0.0014 (6) |
N2 | 0.0342 (7) | 0.0432 (7) | 0.0342 (7) | −0.0025 (6) | 0.0118 (6) | −0.0014 (5) |
C1 | 0.0426 (9) | 0.0459 (9) | 0.0300 (8) | 0.0020 (7) | 0.0080 (7) | −0.0044 (6) |
C2 | 0.0446 (10) | 0.0482 (9) | 0.0383 (9) | 0.0035 (8) | 0.0092 (8) | −0.0003 (7) |
C3 | 0.0536 (11) | 0.0493 (10) | 0.0407 (10) | −0.0016 (8) | 0.0157 (8) | −0.0028 (7) |
C4 | 0.0579 (12) | 0.0499 (10) | 0.0395 (10) | 0.0095 (9) | 0.0034 (8) | 0.0003 (8) |
C5 | 0.0495 (11) | 0.0612 (11) | 0.0446 (10) | 0.0083 (9) | 0.0012 (8) | −0.0028 (9) |
C6 | 0.0458 (10) | 0.0550 (10) | 0.0418 (10) | 0.0037 (8) | 0.0072 (8) | −0.0037 (8) |
C7 | 0.0346 (8) | 0.0475 (9) | 0.0312 (8) | −0.0019 (7) | 0.0068 (6) | −0.0039 (6) |
C8 | 0.0349 (8) | 0.0438 (8) | 0.0370 (9) | −0.0085 (7) | 0.0058 (7) | −0.0033 (7) |
C9 | 0.0365 (9) | 0.0489 (9) | 0.0371 (9) | −0.0074 (7) | 0.0089 (7) | −0.0024 (7) |
C10 | 0.0487 (11) | 0.0623 (11) | 0.0426 (10) | −0.0139 (9) | 0.0146 (8) | 0.0028 (8) |
C11 | 0.0643 (13) | 0.0582 (12) | 0.0519 (12) | −0.0225 (10) | 0.0063 (10) | 0.0102 (9) |
C12 | 0.0674 (14) | 0.0410 (9) | 0.0600 (12) | −0.0101 (9) | −0.0006 (10) | 0.0029 (9) |
C13 | 0.0506 (11) | 0.0445 (9) | 0.0505 (11) | −0.0031 (8) | 0.0081 (9) | −0.0044 (8) |
C14 | 0.0360 (9) | 0.0501 (9) | 0.0325 (8) | −0.0039 (7) | 0.0117 (7) | −0.0054 (7) |
C15 | 0.0343 (8) | 0.0411 (8) | 0.0317 (8) | 0.0004 (6) | 0.0085 (6) | −0.0022 (6) |
C16 | 0.0484 (11) | 0.0690 (12) | 0.0331 (9) | −0.0117 (9) | 0.0076 (8) | 0.0055 (8) |
C17 | 0.0517 (12) | 0.0776 (14) | 0.0362 (10) | −0.0147 (10) | −0.0051 (8) | 0.0049 (9) |
C18 | 0.0373 (10) | 0.0784 (13) | 0.0500 (11) | −0.0128 (9) | −0.0007 (8) | 0.0048 (10) |
C19 | 0.0382 (10) | 0.0718 (12) | 0.0432 (10) | −0.0084 (9) | 0.0120 (8) | 0.0076 (9) |
C20 | 0.0370 (9) | 0.0427 (8) | 0.0304 (8) | 0.0018 (7) | 0.0077 (7) | −0.0008 (6) |
O1—C3 | 1.354 (3) | C14—C15 | 1.515 (2) |
O2—C20 | 1.372 (2) | C15—C20 | 1.392 (2) |
N1—C7 | 1.326 (2) | C15—C16 | 1.382 (2) |
N1—C9 | 1.384 (2) | C16—C17 | 1.377 (3) |
O1—H1 | 0.8200 | C17—C18 | 1.372 (3) |
N2—C7 | 1.365 (2) | C18—C19 | 1.381 (3) |
N2—C14 | 1.468 (2) | C19—C20 | 1.387 (3) |
O2—H2 | 0.8200 | C2—H2A | 0.9300 |
N2—C8 | 1.384 (2) | C4—H4 | 0.9300 |
C1—C6 | 1.398 (3) | C5—H5 | 0.9300 |
C1—C2 | 1.388 (3) | C6—H6 | 0.9300 |
C1—C7 | 1.475 (2) | C10—H10 | 0.9300 |
C2—C3 | 1.391 (3) | C11—H11 | 0.9300 |
C3—C4 | 1.380 (3) | C12—H12 | 0.9300 |
C4—C5 | 1.374 (3) | C13—H13 | 0.9300 |
C5—C6 | 1.373 (3) | C14—H14A | 0.9700 |
C8—C13 | 1.391 (2) | C14—H14B | 0.9700 |
C8—C9 | 1.398 (2) | C16—H16 | 0.9300 |
C9—C10 | 1.398 (3) | C17—H17 | 0.9300 |
C10—C11 | 1.375 (3) | C18—H18 | 0.9300 |
C11—C12 | 1.397 (3) | C19—H19 | 0.9300 |
C12—C13 | 1.382 (3) | ||
C7—N1—C9 | 105.67 (14) | C17—C18—C19 | 119.99 (19) |
C3—O1—H1 | 109.00 | C18—C19—C20 | 120.34 (18) |
C7—N2—C14 | 127.55 (14) | C15—C20—C19 | 119.96 (15) |
C8—N2—C14 | 125.38 (14) | O2—C20—C15 | 117.67 (15) |
C7—N2—C8 | 107.03 (13) | O2—C20—C19 | 122.37 (15) |
C20—O2—H2 | 109.00 | C1—C2—H2A | 120.00 |
C6—C1—C7 | 117.43 (16) | C3—C2—H2A | 120.00 |
C2—C1—C6 | 119.90 (16) | C3—C4—H4 | 120.00 |
C2—C1—C7 | 122.65 (15) | C5—C4—H4 | 120.00 |
C1—C2—C3 | 119.05 (17) | C4—C5—H5 | 120.00 |
C2—C3—C4 | 120.49 (18) | C6—C5—H5 | 120.00 |
O1—C3—C2 | 117.14 (18) | C1—C6—H6 | 120.00 |
O1—C3—C4 | 122.37 (17) | C5—C6—H6 | 120.00 |
C3—C4—C5 | 120.27 (18) | C9—C10—H10 | 121.00 |
C4—C5—C6 | 120.21 (19) | C11—C10—H10 | 121.00 |
C1—C6—C5 | 120.08 (18) | C10—C11—H11 | 119.00 |
N1—C7—C1 | 122.56 (15) | C12—C11—H11 | 119.00 |
N1—C7—N2 | 112.15 (15) | C11—C12—H12 | 119.00 |
N2—C7—C1 | 125.24 (14) | C13—C12—H12 | 119.00 |
N2—C8—C13 | 132.39 (16) | C8—C13—H13 | 122.00 |
C9—C8—C13 | 121.99 (16) | C12—C13—H13 | 122.00 |
N2—C8—C9 | 105.62 (14) | N2—C14—H14A | 109.00 |
C8—C9—C10 | 120.33 (16) | N2—C14—H14B | 109.00 |
N1—C9—C8 | 109.52 (15) | C15—C14—H14A | 109.00 |
N1—C9—C10 | 130.13 (16) | C15—C14—H14B | 109.00 |
C9—C10—C11 | 117.80 (18) | H14A—C14—H14B | 108.00 |
C10—C11—C12 | 121.29 (19) | C15—C16—H16 | 119.00 |
C11—C12—C13 | 121.90 (18) | C17—C16—H16 | 119.00 |
C8—C13—C12 | 116.69 (18) | C16—C17—H17 | 120.00 |
N2—C14—C15 | 112.94 (13) | C18—C17—H17 | 120.00 |
C16—C15—C20 | 118.44 (16) | C17—C18—H18 | 120.00 |
C14—C15—C16 | 122.54 (15) | C19—C18—H18 | 120.00 |
C14—C15—C20 | 119.02 (14) | C18—C19—H19 | 120.00 |
C15—C16—C17 | 121.63 (18) | C20—C19—H19 | 120.00 |
C16—C17—C18 | 119.63 (19) | ||
C9—N1—C7—N2 | 0.45 (19) | C3—C4—C5—C6 | −0.4 (3) |
C9—N1—C7—C1 | 178.12 (15) | C4—C5—C6—C1 | −0.3 (3) |
C7—N1—C9—C8 | −0.12 (19) | N2—C8—C9—N1 | −0.25 (19) |
C7—N1—C9—C10 | 178.39 (19) | N2—C8—C9—C10 | −178.92 (16) |
C8—N2—C7—N1 | −0.62 (19) | C13—C8—C9—N1 | 179.53 (16) |
C8—N2—C7—C1 | −178.22 (15) | C13—C8—C9—C10 | 0.9 (3) |
C14—N2—C7—N1 | 177.32 (15) | N2—C8—C13—C12 | 179.02 (18) |
C14—N2—C7—C1 | −0.3 (3) | C9—C8—C13—C12 | −0.7 (3) |
C7—N2—C8—C9 | 0.51 (18) | N1—C9—C10—C11 | −178.49 (18) |
C7—N2—C8—C13 | −179.25 (19) | C8—C9—C10—C11 | −0.1 (3) |
C14—N2—C8—C9 | −177.49 (15) | C9—C10—C11—C12 | −0.7 (3) |
C14—N2—C8—C13 | 2.8 (3) | C10—C11—C12—C13 | 0.9 (3) |
C7—N2—C14—C15 | 94.94 (19) | C11—C12—C13—C8 | −0.2 (3) |
C8—N2—C14—C15 | −87.5 (2) | N2—C14—C15—C16 | 22.2 (2) |
C6—C1—C2—C3 | −0.6 (3) | N2—C14—C15—C20 | −157.17 (15) |
C7—C1—C2—C3 | −178.60 (16) | C14—C15—C16—C17 | −179.68 (19) |
C2—C1—C6—C5 | 0.8 (3) | C20—C15—C16—C17 | −0.3 (3) |
C7—C1—C6—C5 | 178.91 (17) | C14—C15—C20—O2 | −0.6 (2) |
C2—C1—C7—N1 | 134.27 (18) | C14—C15—C20—C19 | 178.84 (16) |
C2—C1—C7—N2 | −48.4 (2) | C16—C15—C20—O2 | −179.98 (16) |
C6—C1—C7—N1 | −43.8 (2) | C16—C15—C20—C19 | −0.6 (3) |
C6—C1—C7—N2 | 133.60 (18) | C15—C16—C17—C18 | 1.0 (3) |
C1—C2—C3—O1 | 179.55 (16) | C16—C17—C18—C19 | −0.9 (3) |
C1—C2—C3—C4 | −0.1 (3) | C17—C18—C19—C20 | 0.0 (3) |
O1—C3—C4—C5 | −179.00 (18) | C18—C19—C20—O2 | −179.92 (19) |
C2—C3—C4—C5 | 0.6 (3) | C18—C19—C20—C15 | 0.7 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O2i | 0.82 | 2.04 | 2.861 (2) | 173 |
O2—H2···N1ii | 0.82 | 1.89 | 2.7124 (19) | 178 |
C16—H16···N2 | 0.93 | 2.55 | 2.878 (2) | 101 |
Symmetry codes: (i) −x+3/2, y+1/2, −z+3/2; (ii) x+1/2, −y+1/2, z−1/2. |
Acknowledgements
The authors acknowledge the Algerian Ministry of Higher Education and Scientific Research, the Algerian Directorate-General for Scientific Research and Technological Development for support.
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