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COMMUNICATIONS
ISSN: 2056-9890
Volume 77| Part 4| April 2021| Pages 396-401
https://doi.org/10.1107/S2056989021002723

Crystal structure, Hirshfeld surface analysis and density functional theory study of 6-methyl-2-[(5-methyl­isoxazol-3-yl)meth­yl]-1H-benzimidazole

CROSSMARK_Color_square_no_text.svg
Ahlam Idrissi,a Karim Chkirate,a Nadeem Abad,b* Bahia Djerrari,a Redouane Achour,a El Mokhtar Essassia and Luc Van Meerveltc

aLaboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco, bDepartment of Biochemistry, Faculty of Education & Science, Al-Baydha University, Yemen, and cKU Leuven, Chemistry Department, Celestijnenlaan 200F box 2404, Leuven, (Heverlee), B-3001, Belgium
*Correspondence e-mail: abadnadeem3@gmail.com

Edited by B. Therrien, University of Neuchâtel, Switzerland (Received 25 February 2021; accepted 12 March 2021; online 19 March 2021)

In the title mol­ecule, C13H13N3O, the isoxazole ring is inclined to the benzimidazole ring at a dihedral angle of 69.28 (14)°. In the crystal, N—H⋯N hydrogen bonds between neighboring benzimidazole rings form chains along the a-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (48.8%), H⋯C/C⋯H (20.9%) and H⋯N/N⋯H (19.3%) inter­actions. The optimized structure calculated using density functional theory at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated highest occupied mol­ecular orbital (HOMO) and lowest unoccupied mol­ecular orbital (LUMO) energy gap is 4.9266 eV.

CCDC reference: 2048487

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1. Chemical context

Nitro­gen-based structures have attracted increased attention in structural and inorganic chemistry in recent years because of their inter­esting properties (Lahmidi et al., 2018[Lahmidi, S., Sebbar, N. K., Hökelek, T., Chkirate, K., Mague, J. T. & Essassi, E. M. (2018). Acta Cryst. E74, 1833-1837.]; Chkirate et al., 2020a[Chkirate, K., Fettach, S., El Hafi, M., Karrouchi, K., Elotmani, B., Mague, J. T., Radi, S., Faouzi, M. E. A., Adarsh, N. N., Essassi, E. M. & Garcia, Y. (2020a). J. Inorg. Biochem. 208, 111092.]; Taia et al., 2020[Taia, A., Essaber, M., Aatif, A., Chkirate, K., Hökelek, T., Mague, J. T. & Sebbar, N. K. (2020). Acta Cryst. E76, 962-966.]; Al Ati et al., 2021[Al Ati, G., Chkirate, K., Mashrai, A., Mague, J. T., Ramli, Y., Achour, R. & Essassi, E. M. (2021). Acta Cryst. E77, 18-22.]). The benzimidazole family, particularly compounds containing the 2-methyl benzimidazole moiety, is important in medicinal chemistry because of their wide range of pharmacological applications including as anti­microbial and anti­tubercular agents (Ranjith et al., 2013[Ranjith, P. K., Rajeesh, P., Haridas, K. R., Susanta, N. K., Guru Row, T. N., Rishikesan, R. & Suchetha Kumari, N. (2013). Bioorg. Med. Chem. Lett. 23, 5228-5234.]), potential urease enzyme inhibitors (Menteşe et al., 2019[Menteşe, E., Emirik, M. & Sökmen, B. B. (2019). Bioorg. Chem. 86, 151-158.]) and anti­bacterial agents (Chkirate et al., 2020b[Chkirate, K., Karrouchi, K., Dege, N., Sebbar, N. K., Ejjoummany, A., Radi, S., Adarsh, N. N., Talbaoui, A., Ferbinteanu, M., Essassi, E. M. & Garcia, Y. (2020b). New J. Chem. 44, 2210-2221.]). In particular, isoxazolyl benzimidazole derivatives are used as analgesic and anti-inflammatory agents (Kankala et al., 2013[Kankala, S., Kankala, R. K., Gundepaka, P., Thota, N., Nerella, S., Gangula, M. R., Guguloth, H., Kagga, M., Vadde, R. & Vasam, C. S. (2013). Bioorg. Med. Chem. Lett. 23, 1306-1309.]). They are also potent and orally bioavailable bromo­domain BET inhibitors (Sperandio et al., 2019[Sperandio, D., Aktoudianakis, V., Babaoglu, K., Chen, X., Elbel, K., Chin, G., Corkey, B., Du, J., Jiang, B., Kobayashi, T., Mackman, R., Martinez, R., Yang, H., Zablocki, J., Kusam, S., Jordan, K., Webb, H., Bates, J. G., Lad, L., Mish, M., Niedziela-Majka, A., Metobo, S., Sapre, A., Hung, M., Jin, D., Fung, W., Kan, E., Eisenberg, G., Larson, N., Newby, Z. E. R., Lansdon, E., Tay, C., Neve, R. M., Shevick, S. L. & Breckenridge, D. G. (2019). Bioorg. Med. Chem. 27, 457-469.]). Given the wide range of therapeutic applications for such compounds, and in a continuation of the work already carried out on the synthesis of compounds resulting from 1,5-benzodiazepine (Chkirate et al., 2001[Chkirate, K., Regragui, R., Essassi, E. M. & Pierrot, M. (2001). Z. Kristallogr. New Cryst. Struct. 216, 635-636.], 2018[Chkirate, K., Sebbar, N. K., Hökelek, T., Krishnan, D., Mague, J. T. & Essassi, E. M. (2018). Acta Cryst. E74, 1669-1673.], 2019a[Chkirate, K., Fettach, S., Karrouchi, K., Sebbar, N. K., Essassi, E. M., Mague, J. T., Radi, S., Faouzi, M. E. A., Adarsh, N. N. & Garcia, Y. (2019a). J. Inorg. Biochem. 191, 21-28.],b[Chkirate, K., Kansiz, S., Karrouchi, K., Mague, J. T., Dege, N. & Essassi, E. M. (2019b). Acta Cryst. E75, 33-37.],c[Chkirate, K., Kansiz, S., Karrouchi, K., Mague, J. T., Dege, N. & Essassi, E. M. (2019c). Acta Cryst. E75, 154-158.], 2021[Chkirate, K., Azgaou, K., Elmsellem, H., El Ibrahimi, B., Sebbar, N. K., Anouar, E. H., Benmessaoud, M., El Hajjaji, S. & Essassi, E. M. (2021). J. Mol. Liq. 321, 114750.]), a similar approach gave the title compound, 6-methyl-2-[(5-methyl­isoxazol-3-yl)meth­yl]-1H-benzimidazole C13H13N3O (I)[link].

[Scheme 1]

Besides the synthesis, we also report the mol­ecular and crystal structures along with the results of a Hirshfeld surface analysis and density functional theory computational calculations carried out at the B3LYP/6– 311 G(d,p) level.

2. Structural commentary

The title compound crystallizes in the ortho­rhom­bic space group Pbca with one mol­ecule in the asymmetric unit (Fig. 1[link]). The mol­ecule is not planar, as indicated by the torsion angles C4—C3—C6—C7 [−40.4 (4)°] and C3—C6—C7—N15 [−46.0 (4)°]. The best plane of the isoxazole ring (O1/N2/C3–C5; r.m.s. deviation = 0.003 Å) makes a dihedral angle of 69.28 (14)° with the best plane of the benzimidazole ring (C7/N8/C9–C14/N15; r.m.s. deviation = 0.015 Å). Both methyl groups are in the same plane as the ring to which they are attached [deviation of C17 from the isoxazole plane = 0.016 (6) Å, deviation of C16 from the benzimidazole ring = 0.067 (4) Å].

[Figure 1]
Figure 1
Mol­ecular structure of the title mol­ecule with the atom labeling scheme and 50% probability ellipsoids.

3. Supra­molecular features

The crystal packing is characterized by N—H⋯N and C—H⋯N inter­actions (Fig. 2[link], Table 1[link]). Chains of mol­ecules running in the a-axis direction are formed by N8—H8⋯N15i hydrogen bonds between neighboring benzimidazole rings [symmetry code: (i) −[{1\over 2}] + x, y, 3/2 – z]. Parallel chains inter­act through C4—H4⋯N2ii hydrogen bonds between neighboring isoxazole rings [symmetry code: (ii) 3/2 – x, [{1\over 2}] + y, z] resulting in the three-dimensional structure. The crystal packing contains no voids.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N8—H8⋯N15i 0.89 (3) 1.96 (3) 2.830 (3) 167 (2)
C4—H4⋯N2ii 0.93 2.57 3.447 (3) 157
Symmetry codes: (i) [x-{\script{1\over 2}}, y, -z+{\script{3\over 2}}]; (ii) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, z].
[Figure 2]
Figure 2
Partial crystal packing of the title compound. N—H⋯N hydrogen bonds are shown by blue dashed lines and C—H⋯N hydrogen bonds by gray dashed lines.

4. Hirshfeld surface analysis

The CrystalExplorer program (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). CrystalExplorer17. The University of Western Australia.]) was used to investigate and visualize the inter­molecular inter­actions of (I)[link]. The Hirshfeld surface plotted over dnorm in the range −0.61 49 to 1.3177 a.u. is shown in Fig. 3[link]a. The red spots are close contacts with a negative dnorm value and represent N—H⋯N and C—H⋯N inter­actions. The white regions representing contacts equal to the van der Waals separation and a dnorm value of zero are indicative of the H⋯H inter­actions. The electrostatic potential using the STO-3G basis set at the Hartree–Fock level of theory and mapped on the Hirshfeld surface over the range ± 0.05 a.u. clearly shows the positions of close inter­molecular contacts in the compound (Fig. 3[link]b). The positive electrostatic potential (blue region) over the surface indicates hydrogen-donor potential, whereas the hydrogen-bond acceptors are represented by negative electrostatic potential (red region). The shape-index (Fig. 4[link]) generated in the ranges −1 to 1 Å reveals that there are no significant π–π inter­actions (normally indicated by adjacent red and blue triangles).

[Figure 3]
Figure 3
(a) View of the three-dimensional Hirshfeld surface of the title compound, plotted over dnorm in the range −0.6149 to 1.3177 a.u. (b) View of the three-dimensional Hirshfeld surface of the title compound plotted over electrostatic potential energy in the range −0.0500 to 0.0500 a.u. using the STO-3 G basis set at the Hartree–Fock level of theory.
[Figure 4]
Figure 4
Hirshfeld surface of the title compound plotted over shape-index.

The overall two-dimensional fingerprint plot (McKinnon et al., 2007[McKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. 3814-3816.]) is shown in Fig. 5[link]a, while those delineated into H⋯H, H⋯C/C⋯H, H⋯N/N⋯H, H⋯O/O⋯H, C⋯C and C⋯N/N⋯C contacts are illustrated in Fig. 5[link]b–g, respectively, together with their relative contributions to the Hirshfeld surface (HS). The most important inter­action is H⋯H, contributing 48.8% to the overall crystal packing, which is reflected in Fig. 5[link]b as widely scattered points of high density due to the large hydrogen content of the mol­ecule, with the tip at de = di = 1.28 Å. In the presence of C—H inter­actions, the pair of characteristic wings in the fingerprint plot delineated into H⋯C/C⋯H contacts (20.9% contribution to the HS), Fig. 5[link]c, has the tips at de + di = 2.69 Å. The pair of scattered points of spikes in the fingerprint plot delineated into H⋯N/N⋯H, Fig. 5[link]d (19.3%), have the tips at de + di = 1.81 Å. The H⋯O/O⋯H contacts, Fig. 5[link]e (9.6%), have the tips at de + di = 2.65 Å. The C⋯C contacts, Fig. 5[link]f, contribute 0.9% to the HS and appear as a pair of scattered points of spikes with the tips at de + di = 3.60 Å. Finally, the C⋯N/N⋯C contacts, Fig. 5[link]g, make only a 0.5% contribution to the HS and have a low-density distribution of points.

[Figure 5]
Figure 5
The full two-dimensional fingerprint plots for the title compound, showing (a) all inter­actions, and delineated into (b) H⋯H, (c) H⋯C/C⋯H, (d) H⋯N/N⋯H, (e) H⋯O/O⋯H, (f) C⋯C and (g) C⋯N/N⋯C inter­actions. The di and de values are the closest inter­nal and external distances (in Å) from given points on the Hirshfeld surface.

5. Density Functional Theory calculations

The structure in the gas phase of the title compound was optimized by means of density functional theory. The density functional theory calculation was performed by the hybrid B3LYP method and the 6–311 G(d,p) basis-set, which is based on Becke's model (Becke, 1993[Becke, A. D. (1993). J. Chem. Phys. 98, 5648-5652.]) and considers a mixture of the exact (Hartree–Fock) and density functional theory exchange utilizing the B3 functional, together with the LYP correlation functional (Lee et al., 1988[Lee, C., Yang, W. & Parr, R. G. (1988). Phys. Rev. B, 37, 785-789.]). After obtaining the converged geometry, the harmonic vibrational frequencies were calculated at the same theoretical level to confirm that the number of imaginary frequencies is zero for the stationary point. Both the geometry optimization and harmonic vibrational frequency analysis of the title compound were performed with the GAUSSIAN 09 program (Frisch et al., 2009[Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J. A. Jr, Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Rega, N., Millam, J. M., Klene, M., Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, O., Foresman, J. B., Ortiz, J. V., Cioslowski, J. & Fox, D. J. (2009). GAUSSIAN09. Revision A.02. Gaussian Inc, Wallingford, CT, USA.]). The theoretical and experimental results related to bond lengths and angles are in good agreement, as well as with the results of the previous structural study of 5,6-dimethyl-2-[(5-methyl-1,2-oxazol-3-yl)meth­yl]-1-(prop-2-en-1-yl)-1H-benzimidazole, (III) (Benyahya et al., 2017[Benyahya, M. A., El Azzaoui, B., Sebbar, N. K., Ouzidan, Y., Essassi, E. M. & Mague, J. T. (2017). IUCrData, 2, x170647.]) and 5-methyl-3-(1-(2-pyridyl­meth­yl)-1H-benzimidazol-2-ylmeth­yl)isoxazole, (IV) (Doumbia et al., 2009[Doumbia, M. L., Bouhfid, R., Essassi, E. M. & El Ammari, L. (2009). Acta Cryst. E65, o2714-o2715.]), which are summarized in Table 2[link]. Calculated numerical values for title compound including electronegativity (χ), hardness (η), ionization potential (I), dipole moment (μ), electron affinity (A), electrophilicity (ω) and softness (σ) are collated in Table 3[link]. The electron transition from the highest occupied mol­ecular orbital (HOMO) to the lowest unoccupied mol­ecular orbital (LUMO) energy level is shown in Fig. 6[link]. The HOMO and LUMO are localized in the plane extending over the whole 6-methyl-2-[(5-methyl­isoxazol-3-yl)meth­yl]-1H-benzimidazole system. The energy band gap [ΔE = ELUMO - EHOMO] of the mol­ecule is 4.9266 eV, and the frontier mol­ecular orbital energies, EHOMO and ELUMO, are −5.8170 and −0.8904 eV, respectively.

Table 2
Comparison of selected (X-ray and DFT bond lengths and angles (Å, °) in the title compound and related structures

  X-ray B3LYP/6–311G(d,p) (III)a (IV)b
O1—N2 1.413 (3) 1.3949 1.417 1.4100
O1—C5 1.339 (4) 1.3481 1.356 1.3526
N2—C3 1.299 (3) 1.3115 1.304 1.3044
C3—C6 1.488 (4) 1.5065 1.501 1.504
C5—C17 1.485 (4) 1.4868 1.476 1.478
C6—C7 1.488 (4) 1.5026 1.498 1.494
C7—N8 1.349 (3) 1.3755 1.377 1.3720
C7—N15 1.320 (3) 1.3092 1.312 1.3079
N8—C9 1.371 (3) 1.3814 1.386 1.3840
C11—C16 1.500 (4) 1.5112 1.504 –
C14—N15 1.391 (3) 1.388 1.400 1.3880
         
C5—O1—N2 108.2 (2) 109.1398 108.37 108.57
C3—N2—O1 105.5 (2) 106.0707 105.15 105.28
N2—C3—C4 111.3 (2) 111.0906 112.00 111.51
N2—C3—C6 118.9 (2) 120.8172 120.16 119.88
O1—C5—C17 117.0 (3) 116.8621 116.33 115.90
C4—C5—O1 109.5 (3) 109.3513 109.34 109.15
N8—C7—C6 121.7 (2) 122.8089 123.02 122.62
N15—C7—C6 125.6 (2) 123.8733 123.28 124.10
N15—C7—N8 112.7 (2) 113.2373 113.69 113.28
C7—N8—C9 107.59 (19) 106.9514 106.09 106.49
N8—C9—C14 105.29 (19) 104.6015 105.63 105.05
C13—C14—N15 130.8 (2) 130.4265 129.98 129.63
N15—C14—C9 109.67 (19) 110.2891 110.23 110.42
C7—N15—C14 104.72 (19) 104.9141 104.36 104.75
Notes: (a) Results of the previous DFT-optimized geometry of 5,6-dimethyl-2-[(5-methyl-1,2-oxazol-3-yl)meth­yl]-1-(prop-2-en-1-yl)-1H-benzimidazole (Benyahya et al., 2017[Benyahya, M. A., El Azzaoui, B., Sebbar, N. K., Ouzidan, Y., Essassi, E. M. & Mague, J. T. (2017). IUCrData, 2, x170647.]); (b) results of the previous crystallographic study of 5-methyl-3-(1-(2-pyridyl­meth­yl)-1H-benzimidazol-2-ylmeth­yl)isoxazole (Doumbia et al., 2009[Doumbia, M. L., Bouhfid, R., Essassi, E. M. & El Ammari, L. (2009). Acta Cryst. E65, o2714-o2715.])

Table 3
Calculated energies

Mol­ecular Energy Title Compound
Total Energy TE (eV) −20214.1624
EHOMO (eV) −5.8170
ELUMO (eV) −0.8904
Gap, ΔE (eV) 4.9266
Dipole moment, μ (Debye) 4.4403
Ionization potential, I (eV) 5.8170
Electron affinity, A 0.8904
Electronegativity, χ 3.3537
Hardness, η 2.4633
Electrophilicity, index ω 2.2830
Softness, σ 0.4060
Fraction of electron transferred, ΔN 0.7401
[Figure 6]
Figure 6
The energy band gap of 6-methyl-2-[(5-methyl­isoxazol-3-yl)meth­yl]-1H-benzimidazole.

6. Database survey

A search of the Cambridge Structural Database (CSD version 5.40, updated March 2020; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) with the 2-methyl­benzimidazole fragment yielded multiple matches. Of these, three had an isoxazol-3-yl substituent comparable to (I)[link] and they are shown in Fig. 7[link]. The first compound (II) (refcode REQZIW; Attar et al., 2001[Attar, K. H., Azaoui, B. E., Benchidmi, M., Essassi, E. M. & Pierrot, M. (2001). Acta Cryst. E57, o809-o810.]) has no substituent on the phenyl ring. For the second one (III) (refcode FECPIP; Benyahya et al., 2017[Benyahya, M. A., El Azzaoui, B., Sebbar, N. K., Ouzidan, Y., Essassi, E. M. & Mague, J. T. (2017). IUCrData, 2, x170647.]) the phenyl ring is disubstituted with an allyl substituent on nitro­gen 1. The third one (IV) (refcode PUGLAF; Doumbia et al., 2009[Doumbia, M. L., Bouhfid, R., Essassi, E. M. & El Ammari, L. (2009). Acta Cryst. E65, o2714-o2715.]) carries pyridin-2-ylmethyl on nitro­gen 1. The benzimidazole and isoxazole moieties are planar and make a dihedral angle of 76,15 (4)° in REQZIW. In FECPIP, the benzimidazole moiety is slightly non-planar, as indicated by the dihedral angle of 1.3 (1)° between the five- and six-membered rings. The isoxazole ring is planar to within 0.005 (1) Å and makes a dihedral angle of 89.78 (8)° with the benzimidazole ring. On the other hand, in PUGLAF, the fused-ring system is essentially planar, with a maximum deviation of 0.019 (1) Å. It forms inter­planar angles of 70.03 (7)° with the isoxazole ring and 81.68 (7)° with the pyridine ring. The two latter rings are also planar, the maximum deviations from the mean planes being 0.0028 (15) and 0.0047 (12) Å. In (I)[link], The isoxazole ring is inclined to the mean plane of the benzimidazole ring by 69.28 (14)° which is approximately the same as in PUGLAF, but less tilted than in REQZIW and FECPIP.

[Figure 7]
Figure 7
Structural fragments (II), (III) and (IV) used in the database survey.

7. Synthesis and crystallization

(Z)-7-Methyl-4-(2-oxo­propyl­idene)-1,5-benzodiazepin-2-one (2.3 g, 0.01 mol) and hydroxyl­amine hydro­chloride (0.7 g, 0.01 mol) were brought to reflux in 40 ml of methanol for 2 h. After neutralization with NaHCO3, the compound that precipitated was filtered and recrystallized from ethyl acetate. The product was dissolved to saturation in ethyl acetate and crystals were obtained by evaporation at room temperature. yield: 70%; m.p. 465–467 K; IR [KBr, γ(cm−1)]: γNH = 3416; γCH = 3012–3263; γC=N–C=C= 1525–1672; 1H NMR [300MHz, DMSO-d6, δ(ppm)]: 2.32 (s, 3H, CH3 isoxazole); 2.57 (s, 3H, CH3 benzimidazole); 4.23 (s, 2H, CH2); 6.22 (s, 1H, CH isoxazole); 7.00–7.60 (m, 3H, CHar); 5.0 (s, 1H, NH). 13C NMR [75MHz, DMSO-d6, δ(ppm)]: 13.2 (CH3 isoxazole); 24.3 (CH3 benzimidazole); 26.7 (CH2); 101.8 (CH isoxazole); 115.2–125.8 (CH ar­yl); 132.7–169.6 (C quaternary).

8. Refinement

Crystal data, data collection and structure details refinement are given in Table 4[link]. Hydrogen atoms were located in the first difference-Fourier map. C-bound H atoms were positioned geometrically (C—H = 0.93–0.97 Å) and included as riding contributions with Uiso(H) = 1.2Ueq(C) (1.5 for methyl groups). At the end of the refinement, the final difference Fourier map showed no residual peaks of chemical significance.

Table 4
Experimental details

Crystal data
Chemical formula C13H13N3O
Mr 227.26
Crystal system, space group Orthorhombic, Pbca
Temperature (K) 294
a, b, c (Å) 9.6545 (6), 11.2437 (6), 22.9108 (14)
V (Å3) 2487.0 (3)
Z 8
Radiation type Mo Kα
μ (mm−1) 0.08
Crystal size (mm) 0.35 × 0.2 × 0.2
 
Data collection
Diffractometer Rigaku Oxford Diffraction SuperNova, Single source at offset/far, Eos
Absorption correction Multi-scan (CrysAlis PRO; Rigaku OD, 2018[Rigaku OD (2018). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.])
Tmin, Tmax 0.883, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 13352, 2519, 1723
Rint 0.024
(sin θ/λ)max (Å−1) 0.625
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.064, 0.203, 1.05
No. of reflections 2519
No. of parameters 160
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.33, −0.26
Computer programs: CrysAlis PRO (Rigaku OD, 2018[Rigaku OD (2018). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2016/4 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). 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 reference: 2048487

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989021002723/tx2037sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989021002723/tx2037Isup2.hkl

checkCIF report


Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2018); cell refinement: CrysAlis PRO (Rigaku OD, 2018); data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016/4 (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

6-Methyl-2-[(5-methylisoxazol-3-yl)methyl]-1H-benzimidazole top
Crystal data top
C13H13N3ODx = 1.214 Mg m−3
Mr = 227.26Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PbcaCell parameters from 3531 reflections
a = 9.6545 (6) Åθ = 2.9–23.3°
b = 11.2437 (6) ŵ = 0.08 mm−1
c = 22.9108 (14) ÅT = 294 K
V = 2487.0 (3) Å3Prism, brown
Z = 80.35 × 0.2 × 0.2 mm
F(000) = 960
Data collection top
Rigaku Oxford Diffraction SuperNova, Single source at offset/far, Eos
diffractometer		2519 independent reflections
Radiation source: micro-focus sealed X-ray tube, SuperNova (Mo) X-ray Source1723 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.024
Detector resolution: 15.9631 pixels mm-1θmax = 26.4°, θmin = 2.8°
ω scansh = −10→12
Absorption correction: multi-scan
(CrysAlisPro; Rigaku OD, 2018)		k = −14→13
Tmin = 0.883, Tmax = 1.000l = −28→28
13352 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.064H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.203 w = 1/[σ2(Fo2) + (0.0963P)2 + 0.6658P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
2519 reflectionsΔρmax = 0.33 e Å−3
160 parametersΔρmin = −0.26 e Å−3
0 restraints
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
O10.8450 (3)0.0193 (2)0.57078 (9)0.1116 (8)
N20.7873 (3)−0.0264 (2)0.62282 (11)0.0916 (8)
C30.7336 (2)0.0646 (2)0.64943 (11)0.0649 (6)
C40.7542 (3)0.1693 (2)0.61779 (12)0.0852 (9)
H40.7261970.2456150.6280500.102*
C50.8227 (4)0.1368 (3)0.56964 (12)0.0962 (10)
C60.6621 (3)0.0459 (3)0.70624 (12)0.0802 (8)
H6A0.5629910.0422860.6994890.096*
H6B0.690721−0.0300270.7223080.096*
C70.6914 (2)0.1410 (2)0.74970 (10)0.0628 (6)
N80.5894 (2)0.19185 (18)0.78133 (8)0.0616 (5)
C90.6490 (2)0.2765 (2)0.81631 (9)0.0578 (6)
C100.5943 (3)0.3565 (2)0.85619 (10)0.0727 (7)
H100.4999990.3576060.8645180.087*
C110.6850 (3)0.4350 (3)0.88328 (11)0.0815 (8)
C120.8243 (3)0.4291 (3)0.87071 (12)0.0855 (9)
H120.8837420.4818160.8894380.103*
C130.8799 (3)0.3491 (3)0.83190 (11)0.0785 (8)
H130.9746280.3471480.8245630.094*
C140.7902 (2)0.2713 (2)0.80401 (10)0.0615 (6)
N150.81476 (19)0.18510 (19)0.76175 (9)0.0678 (6)
C160.6344 (5)0.5270 (4)0.92565 (15)0.1269 (13)
H16A0.6382580.6040860.9077630.190*
H16B0.6918720.5262140.9598310.190*
H16C0.5405000.5093870.9364870.190*
C170.8775 (7)0.2031 (4)0.51859 (15)0.174 (2)
H17A0.9758820.1919380.5160940.261*
H17B0.8574620.2862700.5230700.261*
H17C0.8345130.1741110.4835890.261*
H80.501 (3)0.182 (2)0.7723 (11)0.079 (8)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.153 (2)0.0868 (15)0.0948 (15)−0.0016 (13)0.0324 (14)−0.0116 (12)
N20.118 (2)0.0609 (13)0.0961 (16)0.0068 (12)0.0172 (14)0.0016 (12)
C30.0657 (15)0.0504 (12)0.0785 (15)−0.0017 (10)−0.0074 (12)−0.0070 (11)
C40.121 (2)0.0538 (14)0.0809 (18)−0.0009 (14)−0.0090 (17)−0.0022 (12)
C50.150 (3)0.0717 (18)0.0673 (17)−0.0246 (18)−0.0082 (17)−0.0019 (14)
C60.0720 (17)0.0801 (18)0.0885 (18)−0.0208 (13)0.0074 (13)−0.0092 (14)
C70.0463 (13)0.0698 (14)0.0724 (14)−0.0068 (11)0.0015 (10)0.0054 (11)
N80.0404 (11)0.0732 (13)0.0711 (12)−0.0031 (9)−0.0037 (9)0.0051 (10)
C90.0494 (12)0.0671 (14)0.0569 (12)0.0038 (10)−0.0035 (10)0.0105 (10)
C100.0704 (16)0.0799 (17)0.0678 (14)0.0137 (13)−0.0001 (12)0.0093 (13)
C110.103 (2)0.0806 (18)0.0608 (15)0.0105 (16)−0.0089 (14)0.0014 (12)
C120.094 (2)0.093 (2)0.0687 (16)−0.0185 (16)−0.0220 (15)0.0013 (14)
C130.0649 (16)0.099 (2)0.0717 (15)−0.0169 (14)−0.0119 (13)0.0017 (15)
C140.0528 (13)0.0738 (15)0.0580 (12)−0.0059 (10)−0.0080 (10)0.0101 (11)
N150.0453 (11)0.0817 (14)0.0763 (13)−0.0062 (9)0.0034 (9)−0.0031 (10)
C160.157 (3)0.126 (3)0.097 (2)0.025 (3)−0.003 (2)−0.029 (2)
C170.311 (7)0.140 (3)0.072 (2)−0.080 (4)0.008 (3)0.011 (2)
Geometric parameters (Å, º) top
O1—N21.413 (3)C9—C141.393 (3)
O1—C51.339 (4)C10—H100.9300
N2—C31.299 (3)C10—C111.390 (4)
C3—C41.396 (4)C11—C121.377 (4)
C3—C61.488 (4)C11—C161.500 (4)
C4—H40.9300C12—H120.9300
C4—C51.337 (4)C12—C131.374 (4)
C5—C171.485 (4)C13—H130.9300
C6—H6A0.9700C13—C141.386 (3)
C6—H6B0.9700C14—N151.391 (3)
C6—C71.488 (4)C16—H16A0.9600
C7—N81.349 (3)C16—H16B0.9600
C7—N151.320 (3)C16—H16C0.9600
N8—C91.371 (3)C17—H17A0.9600
N8—H80.88 (3)C17—H17B0.9600
C9—C101.387 (3)C17—H17C0.9600
C5—O1—N2108.2 (2)C9—C10—C11117.8 (3)
C3—N2—O1105.5 (2)C11—C10—H10121.1
N2—C3—C4111.3 (2)C10—C11—C16121.4 (3)
N2—C3—C6118.9 (2)C12—C11—C10119.4 (3)
C4—C3—C6129.7 (2)C12—C11—C16119.2 (3)
C3—C4—H4127.2C11—C12—H12118.4
C5—C4—C3105.6 (3)C13—C12—C11123.3 (3)
C5—C4—H4127.2C13—C12—H12118.4
O1—C5—C17117.0 (3)C12—C13—H13121.1
C4—C5—O1109.5 (3)C12—C13—C14117.8 (3)
C4—C5—C17133.5 (3)C14—C13—H13121.1
C3—C6—H6A108.9C13—C14—C9119.5 (2)
C3—C6—H6B108.9C13—C14—N15130.8 (2)
H6A—C6—H6B107.7N15—C14—C9109.67 (19)
C7—C6—C3113.3 (2)C7—N15—C14104.72 (19)
C7—C6—H6A108.9C11—C16—H16A109.5
C7—C6—H6B108.9C11—C16—H16B109.5
N8—C7—C6121.7 (2)C11—C16—H16C109.5
N15—C7—C6125.6 (2)H16A—C16—H16B109.5
N15—C7—N8112.7 (2)H16A—C16—H16C109.5
C7—N8—C9107.59 (19)H16B—C16—H16C109.5
C7—N8—H8121.4 (17)C5—C17—H17A109.5
C9—N8—H8129.2 (17)C5—C17—H17B109.5
N8—C9—C10132.5 (2)C5—C17—H17C109.5
N8—C9—C14105.29 (19)H17A—C17—H17B109.5
C10—C9—C14122.2 (2)H17A—C17—H17C109.5
C9—C10—H10121.1H17B—C17—H17C109.5
O1—N2—C3—C4−0.7 (3)N8—C7—N15—C14−0.4 (3)
O1—N2—C3—C6179.3 (2)N8—C9—C10—C11−177.5 (2)
N2—O1—C5—C40.0 (4)N8—C9—C14—C13178.6 (2)
N2—O1—C5—C17179.1 (3)N8—C9—C14—N150.5 (2)
N2—C3—C4—C50.7 (3)C9—C10—C11—C12−1.3 (4)
N2—C3—C6—C7139.7 (3)C9—C10—C11—C16178.2 (3)
C3—C4—C5—O1−0.4 (4)C9—C14—N15—C7−0.1 (3)
C3—C4—C5—C17−179.3 (4)C10—C9—C14—C13−0.6 (3)
C3—C6—C7—N8133.7 (2)C10—C9—C14—N15−178.7 (2)
C3—C6—C7—N15−46.0 (4)C10—C11—C12—C130.5 (4)
C4—C3—C6—C7−40.4 (4)C11—C12—C13—C140.3 (4)
C5—O1—N2—C30.4 (3)C12—C13—C14—C9−0.3 (4)
C6—C3—C4—C5−179.3 (3)C12—C13—C14—N15177.4 (2)
C6—C7—N8—C9−179.1 (2)C13—C14—N15—C7−177.9 (3)
C6—C7—N15—C14179.3 (2)C14—C9—C10—C111.4 (3)
C7—N8—C9—C10178.4 (2)N15—C7—N8—C90.7 (3)
C7—N8—C9—C14−0.7 (2)C16—C11—C12—C13−179.0 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N8—H8···N15i0.89 (3)1.96 (3)2.830 (3)167 (2)
C4—H4···N2ii0.932.573.447 (3)157
Symmetry codes: (i) x−1/2, y, −z+3/2; (ii) −x+3/2, y+1/2, z.
Comparison of selected (X-ray and DFT bond lengths and angles (Å, °) in the title compound and related structures top
X-rayB3LYP/6–311G(d,p)(III)a(IV)b
O1—N21.413 (3)1.39491.4171.4100
O1—C51.339 (4)1.34811.3561.3526
N2—C31.299 (3)1.31151.3041.3044
C3—C61.488 (4)1.50651.5011.504
C5—C171.485 (4)1.48681.4761.478
C6—C71.488 (4)1.50261.4981.494
C7—N81.349 (3)1.37551.3771.3720
C7—N151.320 (3)1.30921.3121.3079
N8—C91.371 (3)1.38141.3861.3840
C11—C161.500 (4)1.51121.504–
C14—N151.391 (3)1.3881.4001.3880
C5—O1—N2108.2 (2)109.1398108.37108.57
C3—N2—O1105.5 (2)106.0707105.15105.28
N2—C3—C4111.3 (2)111.0906112.00111.51
N2—C3—C6118.9 (2)120.8172120.16119.88
O1—C5—C17117.0 (3)116.8621116.33115.90
C4—C5—O1109.5 (3)109.3513109.34109.15
N8—C7—C6121.7 (2)122.8089123.02122.62
N15—C7—C6125.6 (2)123.8733123.28124.10
N15—C7—N8112.7 (2)113.2373113.69113.28
C7—N8—C9107.59 (19)106.9514106.09106.49
N8—C9—C14105.29 (19)104.6015105.63105.05
C13—C14—N15130.8 (2)130.4265129.98129.63
N15—C14—C9109.67 (19)110.2891110.23110.42
C7—N15—C14104.72 (19)104.9141104.36104.75
Notes: (a) Results of the previous DFT-optimized geometry of 5,6-dimethyl-2-[(5-methyl-1,2-oxazol-3-yl)methyl]-1-(prop-2-en-1-yl)-1H-benzimidazole (Benyahya et al., 2017); () results of the previous crystallographic study of 5-methyl-3-(1-(2-pyridylmethyl)-1H-benzimidazol-2-ylmethyl)isoxazole (Doumbia et al., 2009)
Calculated energies top
Molecular EnergyTitle Compound
Total Energy TE (eV)-20214.1624
EHOMO (eV)-5.8170
ELUMO (eV)-0.8904
Gap, ΔE (eV)4.9266
Dipole moment, µ (Debye)4.4403
Ionization potential, I (eV)5.8170
Electron affinity, A0.8904
Electronegativity, χ3.3537
Hardness, η2.4633
Electrophilicity, index ω2.2830
Softness, σ0.4060
Fraction of electron transferred, ΔN0.7401
 

Acknowledgements

LVM thanks the Hercules Foundation for supporting the purchase of the diffractometer through project AKUL/09/0035. Authors contributions are as follows. Conceptualization, AI; methodology, AI; investigation, KC and NA; theoretical calculations, KC; writing (original draft) KC; writing (review and editing of the manuscript), NA; formal analysis, BD; supervision, EME and RA; crystal-structure determination and validation, LVM.

References

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ISSN: 2056-9890
Volume 77| Part 4| April 2021| Pages 396-401
https://doi.org/10.1107/S2056989021002723
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