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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2026 Jan 6;82(Pt 2):121–125. doi: 10.1107/S2056989025011466

The crystal structure of 2-(3-nitro­phen­yl)-1H-benzimidazole monohydrate revisited

Daimí González Caballero a, Mayra P Hernández Sánchez a, Javier Alcides Ellena b, Pedro Henrique de Oliveira Santiago b, Estael Ochoa Rodríguez c, Julio Duque Rodríguez a, Armando A Paneque Quevedo c,*
Editor: N Alvarez Failached
PMCID: PMC12874255  PMID: 41657506

The crystal structure of the title compound has been redetermined in the triclinic centrosymmetric space group P1. The benzene ring and the benzimidazole group are almost coplanar, with N—C—C—C torsion of 2.2 (3) and 5.9 (4)° in the two independent mol­ecules in the unit cell. The crystal structure features N—H⋯O and O—H⋯N hydrogen bonds and offset π–π stacking inter­actions.

Keywords: 2-(3-nitro­phen­yl)-1H-benzimidazole, single-crystal X-ray study, hydrogen bonding, π–π stacking

Abstract

The crystal structure of 2-(3-nitro­phen­yl)-1H-benzimidazole monohydrate, C13H9N3O2·H2O, has been investigated by single-crystal X-ray diffraction. The benzimidazole derivative had its structure studied previously, but it was described in the P1 space group [Sudha et al., (2023 ▸). J. Mol. Struct.1286, 135584]. Herein, we report a reexamination of this compound, which this time crystallized in the triclinic centrosymmetric space group P1. The benzene ring and the benzimidazole group are almost coplanar, with N—C—C—C torsion angles of −2.2 (3) and −5.9 (4)° in the two independent mol­ecules in the unit cell. The crystal structure features N—H⋯O and O—H⋯N hydrogen bonds and offset π–π stacking inter­actions.

1. Chemical context

Benzimidazoles are heterocyclic aromatic compounds of fused benzene and imidazole rings, which are very important for their applications in biochemistry and materials science. 2-Phenyl­benzimidazoles are known for their promising applications as pharmacophores. The structure of phenyl­benzimidazoles have been studied extensively due to their biological activities such as anti­cancer (Mostafa et al., 2019 ▸; Huynh et al., 2020 ▸), anti­viral (Ibba et al., 2021 ▸; Tonelli et al., 2010 ▸), anthelminthic (Escala et al., 2020 ▸) and anti­oxidant (Matysiak et al., 2019 ▸; Baldisserotto et al., 2020 ▸). The crystal structural analysis of these compounds is essential for understanding their physicochemical and biological properties.1.

The crystal structure of 2-(3-nitro­phen­yl)-1H-benzimidazole was previously reported by Sudha et al. (2023 ▸) and deposited in the Cambridge Structural Database [CSD (Groom et al., 2016 ▸) refcode SIBBEO, CCDC No. 2233191] in 2022. The mol­ecule was found to crystallize as a monohydrate in the triclinic crystal system, assigned to the P1 space group, with unit-cell parameters: a = 7.7366 (2) Å, b = 7.7604 (2) Å, c = 22.2948 (6) Å, α = 83.2940 (10)°, β = 86.0540 (10)° and γ = 65.7260 (10)° in a volume of 1211.55 (6) Å3. The crystal structure featured a network of inter­molecular hydrogen bonds, including C—H⋯O, N—H⋯O, and O—H⋯N inter­actions between the benzimidazole heterocycles and water mol­ecules.

A detailed analysis of the original refinement and the checkCIF PLATON report revealed two level G alerts that were unfortunately ignored, specifically, ALERT_2_G ADDSYM Detects New (Pseudo) Centre of Symmetry (97 % Fit) and ALERT_2_G ADDSYM Suggests Possible Pseudo/New Space Group (P-1 Check). These alerts indicated the detection of a new symmetry centre and suggested that the new space group might be PInline graphic. The omission of these alerts motivated us to review the reported structure. Herein, we present a revised crystal structure of 2-(3-nitro­phen­yl)-1H-benzimidazole. The compound was synthesized and structurally characterized by single-crystal X-ray diffraction analysis. The refined unit-cell parameters are consistent with those previously reported, confirming that the crystalline phase corresponds to the same compound. However, refinement in the space group PInline graphic revealed differences in the crystal packing, providing a structural model more consistent with the observed symmetry and tautomerism phenomenon typical of this kind of compound.

2. Structural commentary

Single crystals of the title compounds were obtained in reaction of o-phenyl­endi­amine and 3-nitro­benzaldehyde. The mol­ecule crystallizes in triclinic space group PInline graphic with two mol­ecules of 2-(3-nitro­phen­yl)-1H-benzimidazole and two mol­ecules of water in the asymmetric unit, as shown in Fig. 1 ▸. The 2-(3-nitro­phen­yl)-1H-benzimidazole mol­ecules are essentially planar, with torsion angles of −2.2 (3)° (N1A—C7A—C8A—C9A) and −5.9 (4)° (N1B—C7B—C8B—C9B) between the benzene and benzimidazole rings (Table 1 ▸).

Figure 1.

Figure 1

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The asymmetric unit of the title compound with displacement ellipsoids drawn at the 50% probability level. Atoms O4 and O4A have an occupancy of 0.5.

Table 1. Selected geometric parameters (Å, °).

N1A—C1A 1.377 (3) N2A—C7A 1.328 (3)
N1A—C7A 1.358 (3) N2B—C7B 1.342 (3)
N1B—C7B 1.345 (3) N2B—C6B 1.385 (3)
N1B—C1B 1.386 (3) O2A—N3A 1.224 (3)
O1A—N3A 1.222 (3) N3A—C10A 1.470 (3)
N2A—C6A 1.392 (3)    
       
N1A—C7A—C8A—C9A −2.2 (3) N1B—C7B—C8B—C9B −5.9 (4)
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One of the benzimidazole mol­ecules has a hydrogen bond to a water mol­ecule and has bond lengths and angles within expected ranges and comparable to those of its nitro-substituted isomers (Li et al., 2005 ▸; Wu et al., 2009 ▸). The other benzimidazole mol­ecule has a hydrogen bond to a disordered water mol­ecule, which has two sets of atomic sites with an occupancy of 0.5. This disorder affects the proton bonded to the nitro­gen atom of the imidazole ring. That is, the bond distances reveal mol­ecules have half a hydrogen atom bonded to the nitro­gen N1B and the other half to N2B. The C7B—N1B [1.345 (3) Å] and C7B—N2B [1.342 (3) Å] bond lengths are inter­mediate between a single and a double bond (see Table 1 ▸), consistent with tautomerism. This phenomenon has been observed in this family of compounds using fluorescence and UV-vis spectroscopy (Mosquera et al., 1996 ▸).

3. Supra­molecular features

The crystal packing is consolidated by hydrogen-bond inter­actions between the 2-(3-nitro­phen­yl)-1H-benzimidazole mol­ecules and the water mol­ecules along two different crystallographic axes. Along the crystallographic b-axis, these hydrogen bonds are of the type O3—H3C⋯N2A, with donor–acceptor bond distances of 2.857 (4) Å (see Fig. 2 ▸, Table 2 ▸). Conversely, along the crystallographic a-axis, inter­actions of the type N2B—H2B⋯O4A are observed, with donor–acceptor distances of 2.812 (4) Å (see Fig. 2 ▸, Table 2 ▸).

Figure 2.

Figure 2

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Crystal packing of 2-(3-nitro­phen­yl)-1H-benzimidazole. Hydrogen bonds are indicated by dashed lines. (A) Hydrogen-bond inter­actions along the b axis and (B) along the a axis.

Table 2. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O3—H3C⋯N2Ai 0.87 1.99 2.857 (3) 173
N1A—H1A⋯O3 0.88 2.03 2.849 (3) 154
N1B—H1B⋯O4 0.88 1.91 2.776 (4) 168
N2B—H2B⋯O4Aii 0.88 1.96 2.812 (4) 162
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Symmetry codes: (i) Inline graphic; (ii) Inline graphic.

Furthermore, π–π stacking inter­actions are observed between benzene and benzimidazole rings, along to two different directions. Along the a axis, the centroid-to-centroid distance is 3.7956 (17) Å, with an inclination angle of 2.96 (9)°, while, along the b axis the centroid-to-centroid distances are 3.8810 (19) and 3.8496 (18) Å with inclination angles of 6.99 (10) and 6.88 (10)°, respectively (Fig. 3 ▸).

Figure 3.

Figure 3

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Anti-parallel offset π - π stacking (A) along the b axis and (B) along the c axis.

4. Comparative structural analysis

Comparative analysis of both compounds reveals that while the two structures crystallize in the triclinic system and share identical chemical formula and mol­ecular weight, they exhibit differences in their space groups. The lattice parameters show that the crystallographic axes and angles of the previously reported structure present slightly higher values than those determined in this work. These discrepancies can be attributed to differences in measurement conditions, specifically the temperature, as the literature data were recorded at 296 K, whereas our data were obtained at 200 K. This lower temperature induces less vibrational movement of atoms and the cell is determined with better precision. We also observed decreased values of both calculated density and linear absorption coefficient, which could be due to the volume differences of the unit cells. Additional parameters related to model adjustment and refinement show comparable magnitudes in both structural analyses.

The unit cell of the P1 structure contains four independent mol­ecules and four water mol­ecules acting as crystallization solvent. These adopt predominantly planar conformations, with torsion angles between the benzimidazole heterocycle and the phenyl ring of 1.2 (6), 3.9 (6), 3.0 (7), and 8.6 (7)°. In contrast, the presence of an inversion center in space group PInline graphic reduces the number of independent mol­ecules to two, with torsion angles of 2.2 (3) and 5.9 (4)°. In this packing arrangement, one water mol­ecule exhibits disorder, suggesting two possible crystalline packings. This disorder facilitated the identification of tautomerism in the benzimidazole mol­ecule, which is clearly reflected in the bond distances of the imidazole ring as discussed above.

The structural analysis of both compounds demonstrates that their solid-state packing is consolidated by a network of inter­molecular hydrogen bonds involving the water mol­ecules and 2-(3-nitro­phen­yl)-1H-benzimidazole. In the previously reported structure (space group P1), this packing develops predominantly along the crystallographic a-axis direction, with donor–acceptor distances of 3.372 (6) Å (C—H⋯O), 2.861 (5) Å (N—H⋯O), and 3.026 (5) Å (O—H⋯N), and corresponding bond angles of 155.7, 157 (4) and 166 (5)°, respectively.

In contrast, the structure proposed in this work (space group PInline graphic) exhibits a more robust packing motif that extends along both the a- and b- axis directions. This two-dimensional arrangement generates a more extensive hydrogen-bonded network, thereby enhancing the overall packing stability. In this case, the inter­actions are of the types O—H⋯N and N—H⋯O, and the donor–acceptor distances are significantly shorter, not exceeding 2.86 Å, which corresponds to stronger inter­molecular inter­actions.

Additionally, the crystal packing in both compounds features anti­parallel π - π stacking inter­actions between the mol­ecules of 2-(3-nitro­phen­yl)-1H-benzimidazole rings. In the previously reported structure, this stacking occurs predominantly along the crystallographic b axis, with centroid-to-centroid distances in the range of 3.854–3.914 Å and inclination angles between 1.353 and 1.677°. In parallel, a secondary overlap is observed along the a axis, with centroid-to-centroid distances of 3.814–3.819 Å and an inclination angle of 1.449°. Our structure also exhibits this type of π - π stacking inter­action, extending along the a and b-axis directions. The measured centroid-to-centroid distances of around 3.80 and 3.88 Å are similar to those previously documented.

5. Synthesis and crystallization

2-(3-Nitro­phen­yl)-1H-benzimidazole was synthesized by refluxing and stirring of o-phenyl­endi­amine (10.81 mg, 1 mmol) and 3-nitro­benzaldehyde (15.11 mg, 1 mmol) in 7 mL of aceto­nitrile for 7 h. The reaction progress was monitored for thin layer chromatography (TLC). The resulting solid was separated by vacuum filtration, purified by recrystallization and dried in a desiccator. Single crystals suitable for X-ray diffraction analysis were obtained by slow evaporation from an aceto­nitrile solution over a period of one week. The product was analyzed for NMR.

NMR 1H (DMSO d6, δ ppm): 13.28 (1H; s); 9.01 (1H; m); 8.61 (1H; d; J = 7.9 Hz); 8.32 (1H; dd; J = 8.2; 1.4 Hz); 7.85 (1H; t; J = 8.0); 7.5 (2H; m); 7.26 (2H; q; J = 6.0; 3.1 Hz)

NMR 13C (DMSO d6, δ ppm): 149.05; 148.35; 132.47; 131.72; 130.68; 122.65; 124.21; 120.82.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3 ▸. H atoms were located in difference-Fourier maps and refined at idealized positions using a riding model [Uiso(H) = 1.2 or 1.5Ueq].

Table 3. Experimental details.

Crystal data
Chemical formula C13H9N3O2·H2O
M r 257.25
Crystal system, space group Triclinic, PInline graphic
Temperature (K) 200
a, b, c (Å) 7.7169 (1), 7.7279 (1), 22.1425 (4)
α, β, γ (°) 83.171 (2), 85.664 (2), 65.266 (2)
V (Å3) 1190.34 (4)
Z 4
Radiation type Cu Kα
μ (mm−1) 0.88
Crystal size (mm) 0.26 × 0.16 × 0.08
 
Data collection
Diffractometer XtaLAB Synergy, Dualflex, HyPix
Absorption correction Multi-scan
Tmin, Tmax 0.949, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 22169, 5129, 4863
R int 0.033
(sin θ/λ)max (Å−1) 0.638
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.060, 0.143, 1.19
No. of reflections 5129
No. of parameters 362
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.26, −0.28
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Computer programs: CrysAlis PRO (Rigaku OD, 2023 ▸), SHELXT2018/2 (Sheldrick, 2015a ▸), SHELXL2018/3 (Sheldrick, 2015b ▸), OLEX2 (Dolomanov et al., 2009 ▸) and Mercury (Macrae et al., 2020 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989025011466/ny2017sup1.cif

e-82-00121-sup1.cif (26KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989025011466/ny2017Isup2.hkl

e-82-00121-Isup2.hkl (281.2KB, hkl)

Supporting information file. DOI: 10.1107/S2056989025011466/ny2017sup3.pdf

e-82-00121-sup3.pdf (110.9KB, pdf)
e-82-00121-Isup4.cml (4.8KB, cml)

Supporting information file. DOI: 10.1107/S2056989025011466/ny2017Isup4.cml

CCDC reference: 2432049

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors acknowledge the funding from the Plan Nacional de Ciencias Básicas (PNCB-PN223LH010–045) supported by CITMA (Cuban Ministry of Science and Environment). We would like to thank to Institute of Physics of Sao Carlos and FAPESP (Process numbers 17/15850–0 and 21/02522–0) providing the single-crystal XRD facility.

supplementary crystallographic information

2-(3-Nitrophenyl)-1H-benzimidazole monohydrate . Crystal data

C13H9N3O2·H2O Z = 4
Mr = 257.25 F(000) = 536
Triclinic, P1 Dx = 1.435 Mg m−3
a = 7.7169 (1) Å Cu Kα radiation, λ = 1.54184 Å
b = 7.7279 (1) Å Cell parameters from 14675 reflections
c = 22.1425 (4) Å θ = 6.0–79.3°
α = 83.171 (2)° µ = 0.88 mm−1
β = 85.664 (2)° T = 200 K
γ = 65.266 (2)° Block, light
V = 1190.34 (4) Å3 0.26 × 0.16 × 0.08 mm
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2-(3-Nitrophenyl)-1H-benzimidazole monohydrate . Data collection

XtaLAB Synergy, Dualflex, HyPix diffractometer 4863 reflections with I > 2σ(I)
Detector resolution: 10.0000 pixels mm-1 Rint = 0.033
ω scans θmax = 79.5°, θmin = 4.0°
Absorption correction: multi-scan h = −6→9
Tmin = 0.949, Tmax = 1.000 k = −9→9
22169 measured reflections l = −28→28
5129 independent reflections
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2-(3-Nitrophenyl)-1H-benzimidazole monohydrate . Refinement

Refinement on F2 H-atom parameters constrained
Least-squares matrix: full w = 1/[σ2(Fo2) + (0.0147P)2 + 1.5554P] where P = (Fo2 + 2Fc2)/3
R[F2 > 2σ(F2)] = 0.060 (Δ/σ)max < 0.001
wR(F2) = 0.143 Δρmax = 0.26 e Å−3
S = 1.19 Δρmin = −0.28 e Å−3
5129 reflections Extinction correction: SHELXL-2018/3 (Sheldrick 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
362 parameters Extinction coefficient: 0.0033 (3)
0 restraints
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2-(3-Nitrophenyl)-1H-benzimidazole monohydrate . Special details

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.
Refinement. The data collection was performed at 200 K on a Rigaku Synergy-S Dualflex diffractometer, equipped with an HyPix-6000HE detector and using a CuKα (1.54184 Å) radiation. The CrysAlisPro software was used for the cell refinement, data collection and reduction, and multi-scan absorption correction. The structure was solved by the intrinsic phasing method from SHELXT, and the non-hydrogen atoms were refined considering anisotropic displacement parameters by the full-matrix least-squares on F2 method from SHELXL, with both included in Olex2. The hydrogen atoms were located from Fourier difference maps and refined at idealized positions using a riding model [Uiso(H) = 1.2 or 1.5Ueq]. Olex2 and Mercury were employed to prepare the material for publication.Data collection: CrysAlis Pro 1.171.43.118a (Rigaku Oxford Diffraction, 2023); cell refinement: CrysAlisPro 1.171.43.118a (Rigaku Oxford Diffraction, 2023); data reduction: CrysAlis Pro 1.171.43.118a (Rigaku Oxford Diffraction, 2023); multi-scan absorption correction: CrysAlisPro (Rigaku Oxford Diffraction, 2023); program(s) used to solve structure: ShelXT 2018/2 (Sheldrick, 2015b); program(s) used to refine structure: ShelXL 2019/2 (Sheldrick, 2015a); interface graphics: Olex2 1.5 (Dolomanov et al., 2009); software used to prepare material for publication: Mercury (Cambridge Crystallographic Data Centre, 2023) and Olex2 1.5 (Dolomanov et al., 2009).The single crystal data for the title compound were submitted to the Cambridge Crystallographic Data Center (CCDC number: 2432049).
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2-(3-Nitrophenyl)-1H-benzimidazole monohydrate . Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq Occ. (<1)
O3 0.1736 (3) 0.0751 (3) 0.46534 (9) 0.0403 (4)
H3C 0.164738 −0.026839 0.455811 0.060*
H3D 0.073870 0.128480 0.488832 0.060*
N1A 0.1889 (3) 0.4351 (3) 0.42963 (9) 0.0283 (4)
H1A 0.222925 0.310951 0.436817 0.034*
N1B 0.3379 (3) 0.7820 (3) 1.02554 (9) 0.0304 (4)
H1B 0.227011 0.792387 1.014005 0.037* 0.5
O1A 0.4550 (3) −0.0745 (3) 0.60162 (10) 0.0465 (5)
N2A 0.1397 (3) 0.7325 (3) 0.44496 (9) 0.0301 (4)
N2B 0.6441 (3) 0.7347 (3) 1.02223 (9) 0.0329 (4)
H2B 0.761161 0.709550 1.008309 0.039* 0.5
O2A 0.5774 (4) −0.0252 (3) 0.67853 (10) 0.0596 (6)
O2B 0.2185 (4) 0.6574 (4) 0.75537 (10) 0.0613 (6)
N3A 0.4913 (3) 0.0301 (3) 0.63092 (10) 0.0376 (5)
N3B 0.2103 (3) 0.6730 (3) 0.80954 (11) 0.0412 (5)
O1B 0.0731 (3) 0.6836 (5) 0.84205 (12) 0.0777 (9)
C1A 0.1094 (3) 0.5468 (3) 0.37720 (11) 0.0285 (5)
C6A 0.0788 (3) 0.7335 (3) 0.38728 (11) 0.0287 (5)
C7A 0.2053 (3) 0.5510 (3) 0.46826 (10) 0.0265 (4)
C8A 0.2879 (3) 0.4819 (3) 0.52868 (10) 0.0276 (5)
C10B 0.3731 (4) 0.6794 (4) 0.83806 (12) 0.0339 (5)
C7B 0.4986 (3) 0.7414 (3) 0.99100 (11) 0.0290 (5)
C8B 0.5112 (3) 0.7108 (3) 0.92656 (11) 0.0307 (5)
C9A 0.3495 (3) 0.2896 (3) 0.55094 (11) 0.0293 (5)
H9A 0.338751 0.199813 0.527338 0.035*
C10A 0.4261 (3) 0.2330 (3) 0.60782 (11) 0.0295 (5)
C1B 0.3815 (3) 0.8043 (3) 1.08291 (11) 0.0314 (5)
C13A 0.3078 (3) 0.6093 (3) 0.56450 (11) 0.0306 (5)
H13A 0.266785 0.740398 0.549665 0.037*
C2A 0.0621 (4) 0.5032 (4) 0.32333 (12) 0.0347 (5)
H2A 0.084461 0.376064 0.316944 0.042*
C6B 0.5735 (3) 0.7754 (3) 1.08070 (11) 0.0317 (5)
C11A 0.4476 (4) 0.3572 (4) 0.64416 (11) 0.0336 (5)
H11A 0.501960 0.313291 0.683143 0.040*
C9B 0.3581 (3) 0.7054 (3) 0.89880 (11) 0.0317 (5)
H9B 0.244353 0.719626 0.921598 0.038*
C5A −0.0028 (4) 0.8848 (4) 0.34244 (12) 0.0362 (5)
H5A −0.024451 1.011989 0.348411 0.043*
C12A 0.3870 (4) 0.5463 (4) 0.62149 (11) 0.0346 (5)
H12A 0.399535 0.634844 0.645215 0.042*
C13B 0.6752 (4) 0.6906 (4) 0.89100 (12) 0.0384 (6)
H13B 0.781149 0.694671 0.909055 0.046*
C5B 0.6598 (4) 0.7897 (4) 1.13177 (12) 0.0379 (6)
H5B 0.789997 0.769988 1.130611 0.045*
C3A −0.0190 (4) 0.6546 (4) 0.27960 (12) 0.0396 (6)
H3A −0.054207 0.631380 0.242171 0.048*
C2B 0.2696 (4) 0.8484 (4) 1.13590 (12) 0.0396 (6)
H2BA 0.139295 0.868184 1.137329 0.048*
C4B 0.5475 (4) 0.8338 (4) 1.18425 (12) 0.0426 (6)
H4B 0.601705 0.845371 1.219862 0.051*
C4A −0.0507 (4) 0.8418 (4) 0.28922 (12) 0.0404 (6)
H4A −0.106953 0.942141 0.258042 0.049*
C11B 0.5328 (4) 0.6592 (4) 0.80230 (12) 0.0430 (6)
H11B 0.538312 0.641906 0.760319 0.052*
C3B 0.3561 (4) 0.8619 (4) 1.18614 (12) 0.0432 (6)
H3B 0.283808 0.891098 1.223132 0.052*
C12B 0.6848 (4) 0.6649 (5) 0.82983 (13) 0.0476 (7)
H12B 0.797537 0.651013 0.806462 0.057*
O4 −0.0338 (5) 0.8428 (6) 1.0039 (2) 0.0461 (9) 0.5
H4C −0.099853 0.776852 1.000548 0.069* 0.5
H4D −0.117933 0.960993 1.002400 0.069* 0.5
O4A 0.0352 (5) 0.6490 (6) 1.0048 (2) 0.0435 (9) 0.5
H4AA 0.110804 0.695421 1.016520 0.065* 0.5
H4AB 0.111454 0.538147 0.993016 0.065* 0.5
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2-(3-Nitrophenyl)-1H-benzimidazole monohydrate . Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
O3 0.0460 (11) 0.0307 (9) 0.0514 (11) −0.0228 (8) 0.0142 (8) −0.0142 (8)
N1A 0.0307 (10) 0.0220 (9) 0.0334 (10) −0.0112 (7) 0.0003 (8) −0.0069 (7)
N1B 0.0247 (9) 0.0357 (10) 0.0320 (10) −0.0130 (8) −0.0022 (8) −0.0045 (8)
O1A 0.0507 (11) 0.0275 (9) 0.0630 (13) −0.0183 (8) 0.0018 (9) −0.0054 (8)
N2A 0.0339 (10) 0.0251 (9) 0.0336 (10) −0.0140 (8) 0.0023 (8) −0.0065 (8)
N2B 0.0255 (9) 0.0387 (11) 0.0354 (11) −0.0145 (8) −0.0031 (8) −0.0015 (9)
O2A 0.0797 (16) 0.0382 (11) 0.0486 (13) −0.0131 (11) −0.0161 (11) 0.0073 (9)
O2B 0.0766 (16) 0.0832 (17) 0.0396 (12) −0.0453 (14) −0.0113 (11) −0.0113 (11)
N3A 0.0390 (11) 0.0278 (10) 0.0408 (12) −0.0100 (9) 0.0061 (9) −0.0029 (9)
N3B 0.0368 (12) 0.0446 (13) 0.0417 (13) −0.0138 (10) −0.0077 (10) −0.0097 (10)
O1B 0.0372 (12) 0.140 (3) 0.0651 (16) −0.0377 (15) 0.0009 (11) −0.0412 (17)
C1A 0.0238 (10) 0.0293 (11) 0.0336 (12) −0.0119 (9) 0.0030 (9) −0.0067 (9)
C6A 0.0270 (11) 0.0278 (11) 0.0317 (12) −0.0114 (9) 0.0035 (9) −0.0063 (9)
C7A 0.0259 (10) 0.0247 (10) 0.0311 (11) −0.0122 (9) 0.0053 (8) −0.0083 (8)
C8A 0.0258 (10) 0.0269 (11) 0.0317 (11) −0.0126 (9) 0.0050 (9) −0.0063 (9)
C10B 0.0329 (12) 0.0327 (12) 0.0375 (13) −0.0140 (10) −0.0051 (10) −0.0042 (10)
C7B 0.0258 (11) 0.0299 (11) 0.0323 (12) −0.0125 (9) −0.0031 (9) −0.0014 (9)
C8B 0.0307 (11) 0.0283 (11) 0.0322 (12) −0.0116 (9) −0.0014 (9) −0.0019 (9)
C9A 0.0289 (11) 0.0260 (11) 0.0357 (12) −0.0135 (9) 0.0039 (9) −0.0083 (9)
C10A 0.0268 (11) 0.0253 (11) 0.0360 (12) −0.0115 (9) 0.0055 (9) −0.0033 (9)
C1B 0.0297 (12) 0.0317 (12) 0.0327 (12) −0.0126 (9) −0.0025 (9) −0.0026 (9)
C13A 0.0348 (12) 0.0266 (11) 0.0336 (12) −0.0158 (9) 0.0040 (9) −0.0058 (9)
C2A 0.0339 (12) 0.0338 (12) 0.0379 (13) −0.0137 (10) −0.0001 (10) −0.0111 (10)
C6B 0.0284 (11) 0.0313 (12) 0.0350 (12) −0.0122 (9) −0.0018 (9) −0.0014 (9)
C11A 0.0355 (12) 0.0362 (13) 0.0311 (12) −0.0170 (10) 0.0009 (10) −0.0038 (10)
C9B 0.0254 (11) 0.0331 (12) 0.0354 (12) −0.0110 (9) 0.0001 (9) −0.0044 (9)
C5A 0.0384 (13) 0.0285 (12) 0.0407 (14) −0.0135 (10) 0.0026 (10) −0.0027 (10)
C12A 0.0441 (14) 0.0343 (12) 0.0315 (12) −0.0215 (11) 0.0034 (10) −0.0086 (10)
C13B 0.0329 (13) 0.0487 (15) 0.0405 (14) −0.0226 (11) 0.0046 (10) −0.0109 (11)
C5B 0.0315 (12) 0.0426 (14) 0.0401 (14) −0.0157 (11) −0.0078 (10) −0.0005 (11)
C3A 0.0373 (13) 0.0464 (15) 0.0346 (13) −0.0152 (11) −0.0020 (10) −0.0091 (11)
C2B 0.0308 (12) 0.0480 (15) 0.0392 (14) −0.0153 (11) 0.0021 (10) −0.0068 (11)
C4B 0.0482 (16) 0.0470 (15) 0.0342 (13) −0.0197 (13) −0.0111 (11) −0.0032 (11)
C4A 0.0394 (14) 0.0401 (14) 0.0372 (14) −0.0134 (11) −0.0021 (11) 0.0031 (11)
C11B 0.0518 (16) 0.0517 (16) 0.0329 (13) −0.0278 (13) 0.0060 (11) −0.0121 (12)
C3B 0.0456 (15) 0.0507 (16) 0.0327 (13) −0.0188 (13) 0.0037 (11) −0.0087 (11)
C12B 0.0443 (15) 0.0659 (19) 0.0438 (16) −0.0327 (14) 0.0145 (12) −0.0192 (14)
O4 0.0229 (17) 0.043 (2) 0.071 (3) −0.0129 (15) −0.0067 (17) −0.001 (2)
O4A 0.0249 (17) 0.045 (2) 0.061 (3) −0.0140 (16) −0.0002 (16) −0.0096 (18)
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2-(3-Nitrophenyl)-1H-benzimidazole monohydrate . Geometric parameters (Å, º)

O3—H3C 0.8695 C1B—C6B 1.401 (3)
O3—H3D 0.8706 C1B—C2B 1.391 (4)
N1A—H1A 0.8800 C13A—H13A 0.9500
N1A—C1A 1.377 (3) C13A—C12A 1.387 (3)
N1A—C7A 1.358 (3) C2A—H2A 0.9500
N1B—H1B 0.8800 C2A—C3A 1.381 (4)
N1B—C7B 1.345 (3) C6B—C5B 1.393 (3)
N1B—C1B 1.386 (3) C11A—H11A 0.9500
O1A—N3A 1.222 (3) C11A—C12A 1.376 (4)
N2A—C6A 1.392 (3) C9B—H9B 0.9500
N2A—C7A 1.328 (3) C5A—H5A 0.9500
N2B—H2B 0.8800 C5A—C4A 1.377 (4)
N2B—C7B 1.342 (3) C12A—H12A 0.9500
N2B—C6B 1.385 (3) C13B—H13B 0.9500
O2A—N3A 1.224 (3) C13B—C12B 1.384 (4)
O2B—N3B 1.214 (3) C5B—H5B 0.9500
N3A—C10A 1.470 (3) C5B—C4B 1.383 (4)
N3B—O1B 1.213 (3) C3A—H3A 0.9500
N3B—C10B 1.469 (3) C3A—C4A 1.403 (4)
C1A—C6A 1.404 (3) C2B—H2BA 0.9500
C1A—C2A 1.390 (3) C2B—C3B 1.376 (4)
C6A—C5A 1.397 (3) C4B—H4B 0.9500
C7A—C8A 1.468 (3) C4B—C3B 1.399 (4)
C8A—C9A 1.395 (3) C4A—H4A 0.9500
C8A—C13A 1.398 (3) C11B—H11B 0.9500
C10B—C9B 1.373 (3) C11B—C12B 1.382 (4)
C10B—C11B 1.375 (4) C3B—H3B 0.9500
C7B—C8B 1.463 (3) C12B—H12B 0.9500
C8B—C9B 1.390 (3) O4—H4C 0.8699
C8B—C13B 1.400 (3) O4—H4D 0.8700
C9A—H9A 0.9500 O4A—H4AA 0.8695
C9A—C10A 1.376 (3) O4A—H4AB 0.8700
C10A—C11A 1.390 (3)
H3C—O3—H3D 104.5 C12A—C13A—H13A 119.7
C1A—N1A—H1A 126.1 C1A—C2A—H2A 121.8
C7A—N1A—H1A 126.1 C3A—C2A—C1A 116.5 (2)
C7A—N1A—C1A 107.73 (19) C3A—C2A—H2A 121.8
C7B—N1B—H1B 126.8 N2B—C6B—C1B 107.5 (2)
C7B—N1B—C1B 106.38 (19) N2B—C6B—C5B 131.4 (2)
C1B—N1B—H1B 126.8 C5B—C6B—C1B 121.1 (2)
C7A—N2A—C6A 105.17 (19) C10A—C11A—H11A 121.3
C7B—N2B—H2B 126.8 C12A—C11A—C10A 117.5 (2)
C7B—N2B—C6B 106.5 (2) C12A—C11A—H11A 121.3
C6B—N2B—H2B 126.8 C10B—C9B—C8B 119.2 (2)
O1A—N3A—O2A 123.4 (2) C10B—C9B—H9B 120.4
O1A—N3A—C10A 118.0 (2) C8B—C9B—H9B 120.4
O2A—N3A—C10A 118.6 (2) C6A—C5A—H5A 121.4
O2B—N3B—C10B 119.3 (2) C4A—C5A—C6A 117.3 (2)
O1B—N3B—O2B 123.2 (2) C4A—C5A—H5A 121.4
O1B—N3B—C10B 117.5 (2) C13A—C12A—H12A 119.5
N1A—C1A—C6A 105.3 (2) C11A—C12A—C13A 120.9 (2)
N1A—C1A—C2A 132.1 (2) C11A—C12A—H12A 119.5
C2A—C1A—C6A 122.6 (2) C8B—C13B—H13B 119.6
N2A—C6A—C1A 109.5 (2) C12B—C13B—C8B 120.8 (2)
N2A—C6A—C5A 130.3 (2) C12B—C13B—H13B 119.6
C5A—C6A—C1A 120.2 (2) C6B—C5B—H5B 121.5
N1A—C7A—C8A 123.5 (2) C4B—C5B—C6B 117.0 (2)
N2A—C7A—N1A 112.3 (2) C4B—C5B—H5B 121.5
N2A—C7A—C8A 124.2 (2) C2A—C3A—H3A 119.3
C9A—C8A—C7A 121.1 (2) C2A—C3A—C4A 121.5 (2)
C9A—C8A—C13A 119.0 (2) C4A—C3A—H3A 119.3
C13A—C8A—C7A 119.8 (2) C1B—C2B—H2BA 121.5
C9B—C10B—N3B 118.5 (2) C3B—C2B—C1B 117.0 (2)
C9B—C10B—C11B 123.4 (2) C3B—C2B—H2BA 121.5
C11B—C10B—N3B 118.1 (2) C5B—C4B—H4B 119.2
N1B—C7B—C8B 123.5 (2) C5B—C4B—C3B 121.6 (2)
N2B—C7B—N1B 112.3 (2) C3B—C4B—H4B 119.2
N2B—C7B—C8B 124.3 (2) C5A—C4A—C3A 122.1 (2)
C9B—C8B—C7B 120.6 (2) C5A—C4A—H4A 119.0
C9B—C8B—C13B 118.3 (2) C3A—C4A—H4A 119.0
C13B—C8B—C7B 121.1 (2) C10B—C11B—H11B 121.3
C8A—C9A—H9A 120.7 C10B—C11B—C12B 117.4 (2)
C10A—C9A—C8A 118.5 (2) C12B—C11B—H11B 121.3
C10A—C9A—H9A 120.7 C2B—C3B—C4B 121.8 (3)
C9A—C10A—N3A 118.2 (2) C2B—C3B—H3B 119.1
C9A—C10A—C11A 123.4 (2) C4B—C3B—H3B 119.1
C11A—C10A—N3A 118.4 (2) C13B—C12B—H12B 119.6
N1B—C1B—C6B 107.4 (2) C11B—C12B—C13B 120.9 (3)
N1B—C1B—C2B 131.0 (2) C11B—C12B—H12B 119.6
C2B—C1B—C6B 121.6 (2) H4C—O4—H4D 104.5
C8A—C13A—H13A 119.7 H4AA—O4A—H4AB 104.5
C12A—C13A—C8A 120.7 (2)
N1A—C1A—C6A—N2A 0.1 (2) C7A—N2A—C6A—C1A 0.3 (2)
N1A—C1A—C6A—C5A −179.5 (2) C7A—N2A—C6A—C5A 179.9 (2)
N1A—C1A—C2A—C3A 179.3 (2) C7A—C8A—C9A—C10A 179.8 (2)
N1A—C7A—C8A—C9A −2.2 (3) C7A—C8A—C13A—C12A −179.5 (2)
N1A—C7A—C8A—C13A 177.0 (2) C8A—C9A—C10A—N3A −179.8 (2)
N1B—C7B—C8B—C9B −5.9 (4) C8A—C9A—C10A—C11A −0.8 (3)
N1B—C7B—C8B—C13B 172.6 (2) C8A—C13A—C12A—C11A 0.0 (4)
N1B—C1B—C6B—N2B −0.4 (3) C10B—C11B—C12B—C13B −0.2 (5)
N1B—C1B—C6B—C5B 179.6 (2) C7B—N1B—C1B—C6B 0.0 (3)
N1B—C1B—C2B—C3B −179.5 (3) C7B—N1B—C1B—C2B 179.5 (3)
O1A—N3A—C10A—C9A −8.1 (3) C7B—N2B—C6B—C1B 0.6 (3)
O1A—N3A—C10A—C11A 172.9 (2) C7B—N2B—C6B—C5B −179.4 (3)
N2A—C6A—C5A—C4A −179.5 (2) C7B—C8B—C9B—C10B 179.0 (2)
N2A—C7A—C8A—C9A 178.3 (2) C7B—C8B—C13B—C12B −178.9 (3)
N2A—C7A—C8A—C13A −2.6 (3) C8B—C13B—C12B—C11B 0.2 (5)
N2B—C7B—C8B—C9B 175.0 (2) C9A—C8A—C13A—C12A −0.3 (3)
N2B—C7B—C8B—C13B −6.5 (4) C9A—C10A—C11A—C12A 0.5 (4)
N2B—C6B—C5B—C4B 179.8 (3) C10A—C11A—C12A—C13A −0.1 (4)
O2A—N3A—C10A—C9A 172.5 (2) C1B—N1B—C7B—N2B 0.3 (3)
O2A—N3A—C10A—C11A −6.6 (3) C1B—N1B—C7B—C8B −178.8 (2)
O2B—N3B—C10B—C9B 177.2 (3) C1B—C6B—C5B—C4B −0.1 (4)
O2B—N3B—C10B—C11B −2.7 (4) C1B—C2B—C3B—C4B 0.3 (4)
N3A—C10A—C11A—C12A 179.5 (2) C13A—C8A—C9A—C10A 0.7 (3)
N3B—C10B—C9B—C8B 179.7 (2) C2A—C1A—C6A—N2A 179.9 (2)
N3B—C10B—C11B—C12B −179.8 (3) C2A—C1A—C6A—C5A 0.3 (4)
O1B—N3B—C10B—C9B −2.9 (4) C2A—C3A—C4A—C5A 0.0 (4)
O1B—N3B—C10B—C11B 177.2 (3) C6B—N2B—C7B—N1B −0.6 (3)
C1A—N1A—C7A—N2A 0.7 (3) C6B—N2B—C7B—C8B 178.6 (2)
C1A—N1A—C7A—C8A −178.8 (2) C6B—C1B—C2B—C3B −0.1 (4)
C1A—C6A—C5A—C4A 0.1 (4) C6B—C5B—C4B—C3B 0.3 (4)
C1A—C2A—C3A—C4A 0.3 (4) C9B—C10B—C11B—C12B 0.3 (4)
C6A—N2A—C7A—N1A −0.7 (3) C9B—C8B—C13B—C12B −0.4 (4)
C6A—N2A—C7A—C8A 178.9 (2) C13B—C8B—C9B—C10B 0.5 (4)
C6A—C1A—C2A—C3A −0.5 (4) C5B—C4B—C3B—C2B −0.5 (5)
C6A—C5A—C4A—C3A −0.3 (4) C2B—C1B—C6B—N2B −179.9 (2)
C7A—N1A—C1A—C6A −0.5 (2) C2B—C1B—C6B—C5B 0.0 (4)
C7A—N1A—C1A—C2A 179.7 (2) C11B—C10B—C9B—C8B −0.4 (4)
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2-(3-Nitrophenyl)-1H-benzimidazole monohydrate . Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
O3—H3C···N2Ai 0.87 1.99 2.857 (3) 173
N1A—H1A···O3 0.88 2.03 2.849 (3) 154
N1B—H1B···O4 0.88 1.91 2.776 (4) 168
N2B—H2B···O4Aii 0.88 1.96 2.812 (4) 162
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Symmetry codes: (i) x, y−1, z; (ii) x+1, y, z.

References

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989025011466/ny2017sup1.cif

e-82-00121-sup1.cif (26KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989025011466/ny2017Isup2.hkl

e-82-00121-Isup2.hkl (281.2KB, hkl)

Supporting information file. DOI: 10.1107/S2056989025011466/ny2017sup3.pdf

e-82-00121-sup3.pdf (110.9KB, pdf)
e-82-00121-Isup4.cml (4.8KB, cml)

Supporting information file. DOI: 10.1107/S2056989025011466/ny2017Isup4.cml

CCDC reference: 2432049

Additional supporting information: crystallographic information; 3D view; checkCIF report

Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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