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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 78| Part 2| February 2022| Pages 211-215
https://doi.org/10.1107/S2056989022000585

The mol­ecular and crystal structures of 2-(3-hy­dr­oxy­prop­yl)benzimidazole and its nitrate salt

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Dilnoza Rakhmonova,a* Zukhra Kadirova,a Batirbay Torambetov,a Shakhnoza Kadirova,a Jamshid Ashurovb and Svitlana Shishkinac

aNational University of Uzbekistan named after Mirzo Ulugbek, 4 University St, Tashkent, 100174, Uzbekistan, bInstitute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, M. Ulugbek Str, 83, Tashkent, 700125, Uzbekistan, and cState Scientific Institution "Institute for Single Crystals" of National Academy of Sciences of Ukraine, 60 Nauky ave., 61001 Kharkiv, Ukraine
*Correspondence e-mail: d.rakhmonova81@mail.ru

Edited by D. Chopra, Indian Institute of Science Education and Research Bhopal, India (Received 18 November 2021; accepted 17 January 2022; online 20 January 2022)

2-(3-Hy­droxy­prop­yl)-1H-benzimidazole, C10H12N2O, which has potential biological activity, can be used as a ligand for complexation with metals. This compound is an electron donor, due to the lone pair of the nitro­gen atom in the imidazole ring. This nitro­gen atom also acts as a proton acceptor. In the crystalline phase, the nitrate salt, namely, 2-(3-hy­droxy­prop­yl)-1H-benzim­id­azol-3-ium nitrate, C10H13N2O+·NO3−, has been studied. The protonation of the 2-(3-hy­droxy­prop­yl)benzimidazole unit results in significant delocalization of the electron density within the imidazole ring. The salt formation leads to variations in the inter­molecular inter­actions, which were studied by analysis of the Hirshfeld surfaces and two-dimensional fingerprint plots.

CCDC references: 2142658; 2142657

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1. Chemical context

Benzimidazole derivatives and their complex compounds possess a wide spectrum of biological activity (Salahuddin et al., 2012[Salahuddin, Shaharyar, M. & Mazumder, A. (2012). Arab. J. Chem. 10, S157-S173.]), including anti­bacterial (Chkirate et al., 2020[Chkirate, K., Karrouchi, K., Dege, N., Kheira Sebbar, N., Ejjoummany, A., Radi, S., Adarsh, N. N., Talbaoui, A., Ferbinteanu, M., Essassi, E. M. & Garcia, Y. (2020). New J. Chem. 44, 2210-2221.]), anti­fungal (Khabnadideh et al., 2012[Khabnadideh, S., Rezaei, Z., Pakshir, K., Zomorodian, K. & Ghafari, N. (2012). Res. Pharm. Sci. 7, 65-72.]), anti­viral (Kharitonova et al., 2017[Kharitonova, M. I., Antonov, K. V., Fateev, I. V., Berzina, M. Ya., Kaushin, A. L., Paramonov, A. S., Kotovskaya, S. K., Andronova, V. L., Konstantinova, I. D., Galegov, G. A., Charushin, V. N. & Miroshnikov, A. I. (2017). Synthesis, 49, 1043-1052.]), anti­parasitic (Katti et al., 2019[Katti, S. A., Desai, K. S. & Loharkar, S. V. (2019). WJPR. 8, 1141-1151.]), anti-inflammatory and analgesic (Gaba et al., 2014[Gaba, M., Singh, S. & Mohan, C. (2014). Eur. J. Med. Chem. 76, 494-505.]) activities.

Nitro­gen-containing heterocycles can be lone-pair donors, forming complex compounds with a metal; in some, the nitro­gen heterocycle binds to the metal atom (Mottillo et al., 2015[Mottillo, C. & Friščić, T. (2015). Chem. Commun. 51, 8924-8927.]). The lone pair of the cyclic nitro­gen atom can be protonated, forming an organic cation (Yan et al., 2009[Yan, Z. Z., Hou, N., Liang, H. D., Zhao, S. L. & Tang, Y. (2009). X-ray Struct. Anal. Online, 25, 31-32.]; Yu et al., 2007[Yu, Q.-Y., Cai, Y.-P. & Ng, S. W. (2007). Acta Cryst. E63, o881-o882.], Bayar et al., 2018[Bayar, I., Khedhiri, L., Soudani, S., Lefebvre, F., Ferretti, V. & Ben Nasr, C. (2018). J. Mol. Struct. 1161, 486-496.]; Chen et al., 2010[Chen, S. H., Yang, F. R., Wang, M. T. & Wang, N. (2010). C. R. Chim. 13, 1391-1396.]). It has been shown (Pilipenko & Tananaiko, 1983[Pilipenko, A. T. & Tananaiko, M. M. (1983). Mixed-ligand and mixed-metal complexes and their application in analytical chemistry. Moscow: Chemistry.]) that compounds containing a protonated cation are formed as a result of the combination with counter-ions. Such compounds, also called ionic associates, are inter­mediate compounds between simple salts and complex (coordination) compounds. They have properties similar to those of mixed-ligand complexes, although the properties of the compound as a whole depends on many factors.

[Scheme 1]

In the present paper we report the mol­ecular and crystal structures of 2-(3-hy­droxy­prop­yl)benzimidazole (BIZ) and its nitrate salt (BIZHNO3), which were determined to study the influence of protonation.

2. Structural commentary

Analysis of the mol­ecular structures of the title compounds revealed that the C7—N1 and C7—N2 bonds have different lengths [N1—C7 = 1.322 (4) Å and N2—C7 = 1.352 (4) Å] in the neutral BIZ mol­ecule (Fig. 1[link]) but are equal within standard uncertainties [N1—C7 = 1.329 (2) Å and N2—C7 = 1.331 (2) Å] in its protonated form in BIZHNO3 (Fig. 2[link]). Such a delocalization of the electron density during protonation allows the structure of protonated BIZ mol­ecule to be described as a superposition of two resonance structures, as shown in the scheme below.

[Scheme 2]
[Figure 1]
Figure 1
Mol­ecular structure of the neutral 2-(3-hy­droxy­prop­yl)benzimidazole mol­ecule in the BIZ structure. Displacement ellipsoids are shown at the 50% probability level.
[Figure 2]
Figure 2
Mol­ecular structure of the 2-(3-hy­droxy­prop­yl)benzimidazole nitrate salt in the BIZHNO3 structure. Displacement ellipsoids are shown at the 50% probability level.

The neutral and protonated BIZ mol­ecules differ in the conformation of the hy­droxy­alkyl substituent (Figs. 1[link] and 2[link]). In the neutral BIZ mol­ecule, the hy­droxy­alkyl substituent is almost coplanar to the benzimidazole fragment [the N2—C7—C8—C9 torsion angle is 15.3 (4)°]. The hy­droxy­alkyl subs­tituent has an all-trans conformation [C7—C8—C9—C10 and C8—C9—C10—O1 = −179.8 (3) and −178.7 (3)°, respectively]. In the protonated BIZ mol­ecule, the hy­droxy­alkyl substituent is rotated orthogonally to the benzimidazole fragments [N2—C7—C8—C9 = 103.1 (2)°] and has an ap−,−sc conformation [C7—C8—C9—C10 and C8—C9—C10—O1 = −179.3 (2) and −62.3 (2)°, respectively].

3. Supra­molecular features

In the crystal, BIZ mol­ecules are linked by O—H⋯N and N—H⋯O hydrogen bonds (Table 1[link]). The zigzag chains formed by the N–H⋯O hydrogen bonds propagate in the [100] direction (Fig. 3[link], on the left). These chains are connected by O—H⋯N hydrogen bonds in the [010] and [001] directions (Fig. 3[link], on the right; the chains are highlighted in blue). In addition, weak C3—H⋯C3 (π) inter­actions (Table 1[link]) are observed between the BIZ mol­ecules.

Table 1
Hydrogen-bond geometry (Å, °) for BIZ[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N2—H2N⋯O1i 0.84 (3) 1.95 (3) 2.772 (3) 165 (3)
O1—H1⋯N1ii 0.85 (4) 1.90 (4) 2.741 (3) 169 (4)
C3—H3⋯C3iii 0.97 (4) 2.87 (4) 3.770 (4) 154 (3)
Symmetry codes: (i) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]; (ii) [-x+{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]; (iii) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z].
[Figure 3]
Figure 3
Crystal packing of the neutral mol­ecules in the BIZ structure. Projection in the [100] direction.

In the crystal of the nitrate salt, the protonated BIZ mol­ecules are connected by N—H⋯O hydrogen bonds (Table 2[link]), forming centrosymmetric dimers (Fig. 4[link]). These dimers are linked by the bridging nitrate anions in the [001] direction via N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds (Fig. 5[link]). Stacking inter­actions of the head-to-tail type between the imidazole rings of BIZH+ mol­ecules are observed in the [010] direction, the distance between π-systems being 3.502 (2) Å.

Table 2
Hydrogen-bond geometry (Å, °) for BIZHNO3[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N2—H2N⋯O2 0.86 (2) 1.90 (2) 2.755 (2) 173 (2)
N1—H1N⋯O1i 0.91 (2) 1.78 (2) 2.696 (2) 177 (2)
O1—H1O⋯O2ii 0.90 (3) 2.06 (3) 2.866 (2) 149 (3)
O1—H1O⋯O4ii 0.90 (3) 2.14 (3) 2.951 (3) 150 (3)
C5—H5⋯O4iii 0.93 2.43 3.251 (3) 147
Symmetry codes: (i) [-x+2, -y+1, -z+1]; (ii) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iii) [-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{3\over 2}}].
[Figure 4]
Figure 4
Hydrogen-bonded centrosymmetric dimer of the cations in the nitrate salt. Hydrogen bonds are shown by the cyan lines.
[Figure 5]
Figure 5
Crystal packing of the 2-(3-hy­droxy­prop­yl)benzimidazole nitrate salt in the BIZHNO3 structure. Projection in the [010] direction. Hydrogen bonds are shown by cyan lines.

4. Hirshfeld surface analysis

Hirshfeld surface analysis (Turner et al., 2017[Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). Turner CrystalExplorer17. University of Western Australia. https://Hirshfeldsurface.net]) is one of the modern methods allowing inter­molecular inter­actions to be studied in a more analytical way. This method appears to be effective for comparing the capability of the neutral BIZ mol­ecule and its protonated form to participate in inter­molecular inter­actions of different types. The Hirshfeld surfaces were calculated for the BIZ and BIZH+ mol­ecules using a standard high surface resolution, mapped over dnorm (Fig. 6[link]). Bright-red spots are observed for all the donors and acceptors of strong hydrogen bonds in the two structures under study, indicating their participation in inter­molecular inter­actions. It should be noted that the bright-red spot on the N1 atom in the BIZ mol­ecule indicates its capability to be protonated or participate in complexation with a metal.

[Figure 6]
Figure 6
Hirshfeld surfaces mapped over dnorm (top) and two-dimensional fingerprint plots (bottom) of the neutral 2-(3-hy­droxy­prop­yl)benzimidazole mol­ecule and its protonated cation in the structures of BIZ and BIZHNO3.

The two-dimensional fingerprint plots constructed for the BIZ and BIZH+ mol­ecules show that the hydrogen bonds are stronger in the structure of the nitrate salt (see the sharp spikes in Fig. 6[link]). To compare inter­molecular inter­actions of different types in the structures under study, we have analysed their contributions to the total Hirshfeld surfaces (Fig. 7[link]). As can be seen from the histogram, the protonation of the BIZ mol­ecule and presence of the nitrate anion results in a significant increase of the contribution of O⋯H/H⋯O inter­actions associated with X—H⋯O hydrogen bonds. In addition, the contributions of N⋯C/C⋯N and C⋯C inter­actions indicate that stacking between imidazole rings also increases in the BIZHNO3 structure (Fig. 7[link]). A significant decrease in the contribution of N⋯H/H⋯N inter­actions (X—H⋯N bonding) in the BIZHNO3 structure can be explained by the protonation of the N1 atom, which participates as proton acceptor of hydrogen bonds in the BIZ structure. The different contributions of C⋯H/H⋯C inter­actions associated with X—H⋯C (π) hydrogen bonds coincide with the presence of a C—H⋯C(π) hydrogen bond in the BIZ structure (Table 1[link]) and the absence of similar inter­actions in the BIZHNO3 structure (Table 2[link]). The nitrate anions act as bridging moieties in the BIZHNO3 structure, which results in an increase in the distances between BIZH+ mol­ecules. This fact can explain the decrease in the contribution of H⋯H inter­actions in the BIZHNO3 structure (Fig. 7[link]).

[Figure 7]
Figure 7
Relative contributions of the strongest inter­molecular inter­actions (in %) to the total Hirshfeld surface of the neutral mol­ecule and its cation in the structures of BIZ and BIZHNO3.

5. Database survey

A search of the Cambridge Structural Database (CSD, version 5.42, update of November 2020; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) revealed three structures containing the BIZ mol­ecule [refcodes FIYXAN and FIYXER (Elmali et al., 2005[Elmali, A., Elerman, Y., Eren, G., Gümüş, F. & Svoboda, I. (2005). Z. Naturforsch. Teil B, 60, 164-168.]) and RIYNUL (Zhao et al., 2019[Zhao, Y., Han, X., Yu, F., Wei, D., Cheng, Q., Meng, X., Ding, J. & Hou, H. (2019). Chem. Eur. J. 25, 5246-5250.])]. Two of these structures (FIYXAN and FIYXER) contain protonated BIZ mol­ecules, which form salts with PtCl42− or PtCl62− anions. In the RIYNUL structure, the BIZ mol­ecule forms a coordination bond with the Cd atom.

In addition, three structures with a close analogue of the BIZ mol­ecule containing a carb­oxy­lic group instead of a hydroxyl group were found in the CSD [refcodes JOQROZ (Fu et al., 2016[Fu, W.-W., Liu, Y.-Y., Zhang, Y.-H., Xu, L., Zhang, J.-L. & Wei, H.-B. (2016). Synth. React. Inorg. Met.-Org. Nano-Met. Chem. 46, 1857-1860.]), NOVCEI (Liu et al., 2015[Liu, Z., Zheng, S. & Feng, S. (2015). Acta Cryst. E71, m5-m6.]) and TILGOL (Zeng et al., 2007[Zeng, M.-H., Yao, M.-X., Liang, H. & Ng, S. W. (2007). J. Coord. Chem. 60, 1983-1987.])]. In all of these structures, the organic ligand forms an N—M+ coordination bond with participation of the N2 atom of the imidazole ring.

6. Synthesis and crystallization

All chemicals were obtained from commercial sources and used directly without further purification. 1,2-Phenyl­enedi­amine (2.16 g, 0.02 mol) was dissolved in hydro­chloric acid (25 mL, 4 M) at 373 K, and γ-hy­droxy­butyric acid (2.82 g, 0.02 mol) was added to the solution. The mixture was heated with reflux for 6 h at 398 K. After cooling to room temperature, the mixture was neutralized using NaOH (pH 7–9). The product was dissolved in aqueous ethanol and treated with activated carbon for purification. The 2-hy­droxy­propyl­benzimidazole precipitate was filtered off and dried in air. Pale-beige single crystals of the title compound suitable for X-ray diffraction analysis were recrystallized from ethanol solution by slow evaporation, yield 80%, m.p. 437 K.

Synthesis of the [BIZH+]NO3− salt:

A weighed portion of copper nitrate (3 × 10 −3 mol) was dissolved in a minimum amount of water and mixed with an alcoholic saturated solution of the ligand (6 × 10 −3 mol) while heating in a water bath. The solution turned green. The solution was then acidified with nitric acid to pH 5 to prevent the precipitation of hydroxides. The reaction was carried out for 40 minutes while heating in a water bath, after which the reaction mixture was allowed to crystallize. After three days, the precipitated light-yellow crystals were separated, washed with ethanol, and dried in air. The product yield was 62%, m.p. 371–373 K.

[Scheme 3]

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. All hydrogen atoms were located in difference-Fourier maps. All of the hydrogen atoms in the BIZ structure and H atoms participating in strong hydrogen bonds in the BIZHNO3 structure were refined using an isotropic approximation. Other hydrogen atoms in the BIZHNO3 structure were refined as riding with Csp2—H = 0.97 Å, Uiso(H) = 1.2Ueq(C) for the methyl­ene fragments or Car—H = 0.93 Å, Uiso(H) = 1.2Ueq(C) for the aromatic rings.

Table 3
Experimental details

  BIZ BIZHNO3
Crystal data
Chemical formula C10H12N2O C10H13N2O+·NO3−
Mr 176.22 239.23
Crystal system, space group Orthorhombic, P212121 Monoclinic, P21/n
Temperature (K) 293 293
a, b, c (Å) 5.852 (2), 12.437 (3), 12.444 (3) 8.5100 (3), 8.2525 (4), 16.5130 (7)
α, β, γ (°) 90, 90, 90 90, 93.760 (4), 90
V (Å3) 905.7 (4) 1157.19 (9)
Z 4 4
Radiation type Cu Kα Cu Kα
μ (mm−1) 0.69 0.91
Crystal size (mm) 0.12 × 0.10 × 0.08 0.12 × 0.10 × 0.08
 
Data collection
Diffractometer Oxford Diffraction Xcallibur, Ruby Oxford Diffraction Xcalibur, Ruby
Absorption correction Multi-scan (CrysAlis PRO; Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]) Multi-scan (CrysAlis PRO; Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.])
Tmin, Tmax 0.958, 1.000 0.739, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 3945, 1371, 1191 4122, 2345, 1644
Rint 0.029 0.021
θmax (°) 62.0 75.8
(sin θ/λ)max (Å−1) 0.573 0.629
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.091, 1.06 0.044, 0.128, 1.04
No. of reflections 1371 2345
No. of parameters 166 167
H-atom treatment All H-atom parameters refined H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.11, −0.19 0.16, −0.15
Absolute structure Flack x determined using 428 quotients [(I+)−(I−)]/[(I+)+(I−)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.]) –
Absolute structure parameter 0.1 (3) –
Computer programs: CrysAlis PRO (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2016/6 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Supporting information

CCDC references: 2142658; 2142657

Crystal structure: contains datablocks BIZ, BIZHNO3. DOI: https://doi.org/10.1107/S2056989022000585/dx2040sup1.cif

Structure factors: contains datablock BIZ. DOI: https://doi.org/10.1107/S2056989022000585/dx2040BIZsup2.hkl

Structure factors: contains datablock BIZHNO3. DOI: https://doi.org/10.1107/S2056989022000585/dx2040BIZHNO3sup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989022000585/dx2040BIZsup4.cml

Supporting information file. DOI: https://doi.org/10.1107/S2056989022000585/dx2040BIZHNO3sup5.cml

checkCIF report


Computing details top

For both structures, data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell refinement: CrysAlis PRO (Oxford Diffraction, 2009); data reduction: CrysAlis PRO (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2016/6 (Sheldrick, 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

2-(3-Hydroxypropyl)-1H-benzimidazole (BIZ) top
Crystal data top
C10H12N2ODx = 1.292 Mg m−3
Mr = 176.22Cu Kα radiation, λ = 1.54178 Å
Orthorhombic, P212121Cell parameters from 1839 reflections
a = 5.852 (2) Åθ = 5.2–32.4°
b = 12.437 (3) ŵ = 0.69 mm−1
c = 12.444 (3) ÅT = 293 K
V = 905.7 (4) Å3Block, colorless
Z = 40.12 × 0.10 × 0.08 mm
F(000) = 376
Data collection top
Oxford Diffraction Xcallibur, Ruby
diffractometer		1371 independent reflections
Radiation source: Enhance (Cu) X-ray Source1191 reflections with I > 2σ(I)
Detector resolution: 10.2576 pixels mm-1Rint = 0.029
ω scansθmax = 62.0°, θmin = 5.0°
Absorption correction: multi-scan
(CrysAlisPro; Oxford Diffraction, 2009)		h = −6→6
Tmin = 0.958, Tmax = 1.000k = −13→11
3945 measured reflectionsl = −12→14
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.039All H-atom parameters refined
wR(F2) = 0.091 w = 1/[σ2(Fo2) + (0.0573P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
1371 reflectionsΔρmax = 0.11 e Å−3
166 parametersΔρmin = −0.19 e Å−3
0 restraintsAbsolute structure: Flack x determined using 428 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Primary atom site location: difference Fourier mapAbsolute structure parameter: 0.1 (3)
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O1−0.0261 (5)0.38855 (16)0.5824 (2)0.0635 (7)
H1−0.080 (6)0.439 (3)0.621 (3)0.083 (14)*
N10.6471 (4)0.43719 (19)0.2047 (2)0.0470 (6)
N20.6271 (4)0.2901 (2)0.3056 (2)0.0457 (7)
H2N0.587 (5)0.243 (2)0.350 (3)0.045 (9)*
C10.8204 (5)0.3668 (2)0.1742 (2)0.0454 (7)
C20.9878 (6)0.3766 (3)0.0962 (3)0.0559 (9)
H20.994 (6)0.444 (3)0.051 (3)0.068 (10)*
C31.1430 (6)0.2942 (3)0.0847 (3)0.0631 (9)
H31.268 (7)0.297 (3)0.034 (3)0.076 (11)*
C41.1335 (6)0.2037 (3)0.1499 (3)0.0616 (10)
H41.232 (6)0.148 (3)0.144 (3)0.081 (12)*
C50.9683 (6)0.1915 (3)0.2277 (3)0.0555 (9)
H50.961 (6)0.128 (3)0.274 (3)0.075 (11)*
C60.8096 (5)0.2745 (2)0.2377 (2)0.0446 (7)
C70.5365 (5)0.3875 (2)0.2830 (2)0.0427 (7)
C80.3317 (6)0.4331 (3)0.3370 (3)0.0505 (8)
H8A0.369 (6)0.511 (3)0.353 (3)0.076 (11)*
H8B0.206 (6)0.431 (3)0.286 (3)0.059 (9)*
C90.2555 (6)0.3800 (3)0.4403 (3)0.0485 (8)
H9A0.376 (6)0.382 (3)0.493 (3)0.055 (9)*
H9B0.220 (5)0.307 (3)0.428 (3)0.049 (8)*
C100.0467 (6)0.4349 (3)0.4844 (3)0.0507 (8)
H10A0.073 (5)0.512 (3)0.495 (3)0.051 (8)*
H10B−0.086 (6)0.432 (3)0.432 (3)0.069 (10)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0956 (18)0.0401 (12)0.0547 (14)0.0140 (12)0.0202 (13)0.0041 (11)
N10.0527 (15)0.0425 (12)0.0457 (15)−0.0018 (11)−0.0032 (13)0.0034 (11)
N20.0518 (15)0.0398 (13)0.0454 (16)−0.0046 (11)−0.0032 (12)0.0091 (12)
C10.0476 (17)0.0427 (15)0.0459 (18)−0.0053 (14)−0.0035 (14)−0.0040 (13)
C20.064 (2)0.0517 (18)0.052 (2)−0.0131 (17)0.0045 (16)−0.0032 (16)
C30.060 (2)0.066 (2)0.064 (2)−0.0104 (18)0.0101 (19)−0.016 (2)
C40.055 (2)0.057 (2)0.073 (3)0.0039 (17)−0.0013 (18)−0.0160 (19)
C50.059 (2)0.0442 (17)0.063 (2)0.0022 (15)−0.0082 (18)−0.0027 (17)
C60.0465 (16)0.0425 (15)0.0448 (18)−0.0059 (13)−0.0059 (14)−0.0025 (13)
C70.0468 (16)0.0404 (14)0.0409 (16)−0.0043 (13)−0.0073 (14)−0.0007 (13)
C80.0551 (18)0.0509 (17)0.0455 (18)0.0022 (16)−0.0049 (16)0.0033 (14)
C90.058 (2)0.0418 (18)0.046 (2)0.0018 (14)−0.0023 (15)−0.0023 (15)
C100.0614 (19)0.0441 (17)0.0467 (19)0.0030 (16)−0.0008 (17)0.0035 (15)
Geometric parameters (Å, º) top
O1—C101.414 (4)C4—C51.376 (5)
O1—H10.85 (4)C4—H40.91 (4)
N1—C71.322 (4)C5—C61.394 (4)
N1—C11.393 (4)C5—H50.98 (4)
N2—C71.352 (4)C7—C81.486 (5)
N2—C61.376 (4)C8—C91.513 (4)
N2—H2N0.84 (3)C8—H8A1.02 (4)
C1—C21.385 (4)C8—H8B0.97 (3)
C1—C61.395 (4)C9—C101.503 (5)
C2—C31.377 (5)C9—H9A0.96 (4)
C2—H21.01 (4)C9—H9B0.94 (3)
C3—C41.389 (5)C10—H10A0.98 (3)
C3—H30.97 (4)C10—H10B1.01 (4)
C10—O1—H1107 (3)C5—C6—C1121.9 (3)
C7—N1—C1105.3 (2)N1—C7—N2112.3 (3)
C7—N2—C6107.6 (3)N1—C7—C8123.4 (3)
C7—N2—H2N131 (2)N2—C7—C8124.3 (3)
C6—N2—H2N121 (2)C7—C8—C9117.1 (3)
C2—C1—N1130.6 (3)C7—C8—H8A106 (2)
C2—C1—C6120.1 (3)C9—C8—H8A109 (2)
N1—C1—C6109.3 (3)C7—C8—H8B107 (2)
C3—C2—C1118.3 (3)C9—C8—H8B109 (2)
C3—C2—H2123 (2)H8A—C8—H8B109 (3)
C1—C2—H2119 (2)C10—C9—C8110.6 (3)
C2—C3—C4121.1 (4)C10—C9—H9A109.7 (19)
C2—C3—H3123 (2)C8—C9—H9A111 (2)
C4—C3—H3116 (2)C10—C9—H9B108.7 (19)
C5—C4—C3121.9 (4)C8—C9—H9B110.1 (19)
C5—C4—H4115 (2)H9A—C9—H9B107 (3)
C3—C4—H4123 (2)O1—C10—C9112.0 (3)
C4—C5—C6116.7 (3)O1—C10—H10A109.1 (19)
C4—C5—H5122 (2)C9—C10—H10A111.5 (19)
C6—C5—H5121 (2)O1—C10—H10B108 (2)
N2—C6—C5132.6 (3)C9—C10—H10B112 (2)
N2—C6—C1105.5 (3)H10A—C10—H10B104 (3)
C7—N1—C1—C2179.9 (3)N1—C1—C6—N20.5 (3)
C7—N1—C1—C6−0.5 (3)C2—C1—C6—C52.1 (4)
N1—C1—C2—C3178.5 (3)N1—C1—C6—C5−177.5 (3)
C6—C1—C2—C3−1.0 (4)C1—N1—C7—N20.3 (3)
C1—C2—C3—C4−0.4 (5)C1—N1—C7—C8−177.9 (3)
C2—C3—C4—C50.8 (5)C6—N2—C7—N10.0 (3)
C3—C4—C5—C60.2 (5)C6—N2—C7—C8178.2 (3)
C7—N2—C6—C5177.5 (3)N1—C7—C8—C9−166.7 (3)
C7—N2—C6—C1−0.3 (3)N2—C7—C8—C915.3 (4)
C4—C5—C6—N2−179.1 (3)C7—C8—C9—C10−179.8 (3)
C4—C5—C6—C1−1.7 (5)C8—C9—C10—O1−178.7 (3)
C2—C1—C6—N2−179.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···O1i0.84 (3)1.95 (3)2.772 (3)165 (3)
O1—H1···N1ii0.85 (4)1.90 (4)2.741 (3)169 (4)
C3—H3···C3iii0.97 (4)2.87 (4)3.770 (4)154 (3)
Symmetry codes: (i) x+1/2, −y+1/2, −z+1; (ii) −x+1/2, −y+1, z+1/2; (iii) x+1/2, −y+1/2, −z.
2-(3-Hydroxypropyl)-1H-benzimidazol-3-ium nitrate (BIZHNO3) top
Crystal data top
C10H13N2O+·NO3−F(000) = 504
Mr = 239.23Dx = 1.373 Mg m−3
Monoclinic, P21/nCu Kα radiation, λ = 1.54184 Å
a = 8.5100 (3) ÅCell parameters from 1670 reflections
b = 8.2525 (4) Åθ = 5.2–75.5°
c = 16.5130 (7) ŵ = 0.91 mm−1
β = 93.760 (4)°T = 293 K
V = 1157.19 (9) Å3Block, colorless
Z = 40.12 × 0.10 × 0.08 mm
Data collection top
Oxford Diffraction Xcalibur, Ruby
diffractometer		2345 independent reflections
Radiation source: Enhance (Cu) X-ray Source1644 reflections with I > 2σ(I)
Detector resolution: 10.2576 pixels mm-1Rint = 0.021
ω scansθmax = 75.8°, θmin = 5.4°
Absorption correction: multi-scan
(CrysAlisPro; Oxford Diffraction, 2009)		h = −9→10
Tmin = 0.739, Tmax = 1.000k = −10→8
4122 measured reflectionsl = −20→18
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.044H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.128 w = 1/[σ2(Fo2) + (0.0715P)2 + 0.0026P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
2345 reflectionsΔρmax = 0.16 e Å−3
167 parametersΔρmin = −0.15 e Å−3
0 restraintsExtinction correction: SHELXL2016/6 (Sheldrick 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: difference Fourier mapExtinction coefficient: 0.0075 (11)
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O11.12121 (17)0.57042 (19)0.61912 (9)0.0691 (5)
H1O1.102 (4)0.662 (3)0.6461 (18)0.112 (10)*
O20.4689 (2)0.27088 (18)0.74998 (8)0.0732 (5)
O30.4922 (3)0.5257 (2)0.74234 (10)0.1045 (7)
O40.3822 (2)0.4195 (2)0.84232 (10)0.1011 (6)
N10.65129 (19)0.34198 (19)0.47832 (10)0.0519 (4)
H1N0.726 (3)0.374 (3)0.4442 (14)0.075 (7)*
N20.54243 (17)0.29223 (18)0.59032 (9)0.0477 (4)
H2N0.527 (3)0.290 (3)0.6412 (13)0.065 (6)*
C10.5164 (2)0.2529 (2)0.45731 (11)0.0464 (4)
C20.4513 (3)0.1965 (2)0.38345 (12)0.0591 (5)
H20.4982090.2169500.3351750.071*
N30.4465 (2)0.4091 (2)0.77860 (10)0.0616 (4)
C30.3151 (3)0.1095 (2)0.38500 (13)0.0663 (6)
H30.2686650.0693830.3365210.080*
C40.2433 (2)0.0789 (2)0.45704 (14)0.0641 (6)
H40.1495660.0206390.4552430.077*
C50.3081 (2)0.1330 (2)0.53068 (12)0.0541 (5)
H50.2614440.1113990.5789150.065*
C60.44674 (19)0.22143 (19)0.52923 (10)0.0444 (4)
C70.6645 (2)0.3629 (2)0.55826 (11)0.0486 (4)
C80.7967 (2)0.4460 (2)0.60431 (12)0.0576 (5)
H8A0.7655740.4716620.6583170.069*
H8B0.8191600.5471040.5774200.069*
C90.9449 (2)0.3426 (2)0.61118 (13)0.0567 (5)
H9A0.9219760.2409860.6374220.068*
H9B0.9766650.3181460.5571670.068*
C101.0784 (2)0.4255 (3)0.65864 (12)0.0618 (5)
H10A1.0471140.4508540.7126360.074*
H10B1.1684140.3532860.6640510.074*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0677 (10)0.0726 (10)0.0693 (9)−0.0224 (8)0.0217 (7)−0.0162 (8)
O20.1068 (13)0.0561 (8)0.0580 (8)0.0013 (8)0.0154 (8)−0.0021 (7)
O30.1610 (19)0.0591 (10)0.0956 (13)−0.0156 (11)0.0260 (13)0.0054 (9)
O40.1175 (15)0.1153 (15)0.0749 (11)0.0069 (12)0.0408 (10)−0.0192 (10)
N10.0507 (9)0.0494 (8)0.0569 (9)−0.0031 (7)0.0136 (7)0.0017 (7)
N20.0479 (8)0.0489 (8)0.0468 (8)−0.0003 (6)0.0071 (7)−0.0006 (7)
C10.0469 (9)0.0403 (8)0.0521 (9)0.0048 (7)0.0040 (7)0.0032 (7)
C20.0714 (13)0.0556 (11)0.0498 (10)0.0078 (10)−0.0003 (9)0.0008 (9)
N30.0658 (11)0.0633 (10)0.0556 (10)0.0006 (8)0.0026 (8)−0.0041 (8)
C30.0695 (14)0.0583 (12)0.0681 (13)0.0051 (10)−0.0170 (11)−0.0093 (10)
C40.0478 (11)0.0521 (11)0.0911 (16)−0.0028 (9)−0.0055 (10)−0.0061 (10)
C50.0473 (10)0.0466 (10)0.0691 (12)−0.0012 (8)0.0096 (9)0.0020 (9)
C60.0433 (9)0.0393 (8)0.0509 (9)0.0033 (7)0.0041 (7)0.0011 (7)
C70.0453 (9)0.0427 (9)0.0582 (10)0.0022 (7)0.0057 (8)−0.0029 (8)
C80.0489 (11)0.0524 (10)0.0715 (13)−0.0021 (8)0.0041 (9)−0.0132 (9)
C90.0548 (11)0.0457 (9)0.0685 (11)0.0003 (8)−0.0027 (9)−0.0031 (9)
C100.0558 (11)0.0662 (12)0.0622 (12)0.0003 (10)−0.0053 (9)−0.0056 (10)
Geometric parameters (Å, º) top
O1—C101.421 (2)C3—C41.396 (3)
O1—H1O0.90 (3)C3—H30.9300
O2—N31.254 (2)C4—C51.376 (3)
O3—N31.211 (2)C4—H40.9300
O4—N31.220 (2)C5—C61.389 (2)
N1—C71.329 (2)C5—H50.9300
N1—C11.388 (2)C7—C81.484 (2)
N1—H1N0.91 (2)C8—C91.521 (3)
N2—C71.331 (2)C8—H8A0.9700
N2—C61.384 (2)C8—H8B0.9700
N2—H2N0.86 (2)C9—C101.502 (3)
C1—C61.386 (2)C9—H9A0.9700
C1—C21.387 (3)C9—H9B0.9700
C2—C31.365 (3)C10—H10A0.9700
C2—H20.9300C10—H10B0.9700
C10—O1—H1O114.7 (19)N2—C6—C1106.33 (15)
C7—N1—C1109.37 (16)N2—C6—C5132.01 (17)
C7—N1—H1N124.0 (14)C1—C6—C5121.66 (17)
C1—N1—H1N126.4 (14)N1—C7—N2108.73 (16)
C7—N2—C6109.41 (15)N1—C7—C8125.51 (17)
C7—N2—H2N125.0 (15)N2—C7—C8125.72 (17)
C6—N2—H2N125.6 (15)C7—C8—C9112.10 (15)
C6—C1—C2121.46 (17)C7—C8—H8A109.2
C6—C1—N1106.16 (15)C9—C8—H8A109.2
C2—C1—N1132.37 (18)C7—C8—H8B109.2
C3—C2—C1116.80 (19)C9—C8—H8B109.2
C3—C2—H2121.6H8A—C8—H8B107.9
C1—C2—H2121.6C10—C9—C8112.27 (16)
O3—N3—O4123.2 (2)C10—C9—H9A109.2
O3—N3—O2118.34 (18)C8—C9—H9A109.2
O4—N3—O2118.47 (18)C10—C9—H9B109.2
C2—C3—C4122.06 (19)C8—C9—H9B109.2
C2—C3—H3119.0H9A—C9—H9B107.9
C4—C3—H3119.0O1—C10—C9110.57 (17)
C5—C4—C3121.47 (19)O1—C10—H10A109.5
C5—C4—H4119.3C9—C10—H10A109.5
C3—C4—H4119.3O1—C10—H10B109.5
C4—C5—C6116.53 (18)C9—C10—H10B109.5
C4—C5—H5121.7H10A—C10—H10B108.1
C6—C5—H5121.7
C7—N1—C1—C60.46 (19)N1—C1—C6—C5−179.68 (15)
C7—N1—C1—C2−178.67 (19)C4—C5—C6—N2−179.65 (17)
C6—C1—C2—C30.4 (3)C4—C5—C6—C1−0.3 (3)
N1—C1—C2—C3179.40 (19)C1—N1—C7—N2−0.6 (2)
C1—C2—C3—C40.4 (3)C1—N1—C7—C8177.29 (16)
C2—C3—C4—C5−1.1 (3)C6—N2—C7—N10.50 (19)
C3—C4—C5—C61.0 (3)C6—N2—C7—C8−177.38 (16)
C7—N2—C6—C1−0.21 (18)N1—C7—C8—C9−74.5 (2)
C7—N2—C6—C5179.26 (18)N2—C7—C8—C9103.1 (2)
C2—C1—C6—N2179.09 (16)C7—C8—C9—C10−179.28 (17)
N1—C1—C6—N2−0.15 (18)C8—C9—C10—O1−62.3 (2)
C2—C1—C6—C5−0.4 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···O20.86 (2)1.90 (2)2.755 (2)173 (2)
N1—H1N···O1i0.91 (2)1.78 (2)2.696 (2)177 (2)
O1—H1O···O2ii0.90 (3)2.06 (3)2.866 (2)149 (3)
O1—H1O···O4ii0.90 (3)2.14 (3)2.951 (3)150 (3)
C5—H5···O4iii0.932.433.251 (3)147
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+3/2, y+1/2, −z+3/2; (iii) −x+1/2, y−1/2, −z+3/2.
 

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ISSN: 2056-9890
Volume 78| Part 2| February 2022| Pages 211-215
https://doi.org/10.1107/S2056989022000585
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