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Crystal structure, Hirshfeld surface analysis, calculations of inter­molecular inter­action energies and energy frameworks and the DFT-optimized mol­ecular structure of 1-[(1-butyl-1H-1,2,3-triazol-4-yl)meth­yl]-3-(prop-1-en-2-yl)-1H-benzimidazol-2-one

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aLaboratory of Heterocyclic Organic Chemistry, Medicines Science Research Center, Pharmacochemistry Competence Center, Mohammed V University in Rabat, Faculté des Sciences, Av. Ibn Battouta, BP 1014, Rabat, Morocco, bUniversity of Zurich, Department of Chemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, cDepartment of Physics, Hacettepe University, 06800 Beytepe, Ankara, Türkiye, dLaboratory of Applied Organic Chemistry, Sidi Mohamed Ben Abdellah University, Faculty of Science And Technology, Road Immouzer, BP 2202 Fez, Morocco, eScience and Technology of Lille USR 3290, Villeneuve d'ascq cedex, France, fLaboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibnou Zohr University, Agadir, Morocco, and gLaboratory of Plant Chemistry, Organic and Bioorganic Synthesis, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta BP 1014 RP, Rabat, Morocco
*Correspondence e-mail: mustapha.zouhair@um5r.ac.ma

Edited by M. Weil, Vienna University of Technology, Austria (Received 15 March 2024; accepted 2 May 2024; online 14 May 2024)

This article is part of a collection of articles to commemorate the founding of the African Crystallographic Association and the 75th anniversary of the IUCr.

The benzimidazole entity of the title mol­ecule, C17H21N5O, is almost planar (r.m.s. deviation = 0.0262 Å). In the crystal, bifurcated C—H⋯O hydrogen bonds link individual mol­ecules into layers extending parallel to the ac plane. Two weak C—H⋯π(ring) inter­actions may also be effective in the stabilization of the crystal structure. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (57.9%), H⋯C/C⋯H (18.1%) and H⋯O/O⋯H (14.9%) inter­actions. Hydrogen bonding and van der Waals inter­actions are the most dominant forces in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization of the title compound is dominated via dispersion energy contributions. The mol­ecular structure optimized by density functional theory (DFT) at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined mol­ecular structure in the solid state.

1. Chemical context

Heterocyclic compounds comprising the benzimidazolone fragment have attracted inter­est due to their remarkable usefulness in various therapeutic applications. Extensive research has revealed several pharmacological and biological properties associated with these compounds, including anti­proliferative (Guillon et al., 2022[Guillon, J., Savrimoutou, S., Albenque-Rubio, S., Pinaud, N., Moreau, S. & Desplat, V. (2022). Molbank, M1333.]), anti­bacterial (Al-Ghulikah et al., 2023[Al-Ghulikah, H., Ghabi, A., haouas, A., Mtiraoui, H., Jeanneau, E. & Msaddek, M. (2023). Arab. J. Chem. 16, 104566.]; Saber et al., 2020[Saber, A., Sebbar, N. K., Sert, Y., Alzaqri, N., Hökelek, T., El Ghayati, L., Talbaoui, A., Mague, J. T., Baba, Y., Urrutigoîty, M. & Essassi, E. M. (2020). J. Mol. Struct. 1200, 127174.]), anti­cancer (Dimov et al., 2021[Dimov, S., Mavrova, A. T., Yancheva, D., Nikolova, B. & Tsoneva, I. (2021). Anticancer Agents Med. Chem. 21, 1441-1450.]) and anti­viral (Ferro et al., 2017[Ferro, S., Buemi, M. R., De Luca, L., Agharbaoui, F. E., Pannecouque, C. & Monforte, A. M. (2017). Bioorg. & Med. Chem. 25, 3861-3870.]) activities.

Our current studies focus on the syntheses of new benzimidazol-2-one derivatives by combining them with the 1,2,3-triazole moiety by using `click chemistry'. Specifically, the copper-catalysed azide-alkyne cyclo­addition (CuAAC) method has proved useful in obtaining the title compound, 1-[(1-butyl-1H-1,2,3-triazol-4-yl)meth­yl]-3-(prop-1-en-2-yl)-1H-benzimidazol-2-one (Fig. 1[link]). In this context, we determined its crystal structure, performed a Hirshfeld surface analysis and calculated inter­molecular inter­action energies and energy frameworks. A comparison of the experimentally determined mol­ecular structure in the solid state with the mol­ecular structure optimized by using density functional theory (DFT) at the B3LYP/6-311G(d,p) level was also carried out.

[Scheme 1]
[Figure 1]
Figure 1
Schematic synthesis procedure for obtaining benzimidazol-2-one derivatives.

2. Structural commentary

In the mol­ecular structure of the title compound (Fig. 2[link]), the benzimidazole entity is almost planar (r.m.s. deviation of atoms C1–C7/N1–N2/O1 is 0.0262 Å); rings A (C1–C6) and B (N1/N2/C1/C2/C7) are oriented at a dihedral angle of 1.20 (4)°. The triazole ring C (N3–N5/C12/C13) is oriented almost perpendicular to the benzimidazole fragment with dihedral angles of A/C = 85.36 (4)° and B/C = 86.52 (4)°. Atoms O1, C8 and C11 are −0.0139 (9) Å, 0.0759 (12) Å and −0.0632 (12) Å away, while atoms C11 and C14 are 0.0245 (11) Å and −0.0835 (13) Å away from the best least-squares planes of rings B and C, respectively. Hence, they appear almost coplanar with the corresponding ring planes.

[Figure 2]
Figure 2
The title mol­ecule with the atom-labelling scheme and displacement ellipsoids drawn at the 50% probability level.

3. Supra­molecular features

In the crystal, bifurcated C—H⋯O hydrogen bonds (Table 1[link], Fig. 3[link]) link individual mol­ecules into layers extending parallel to the ac plane. Two weak C—H⋯π(ring) inter­actions (Table 1[link]) may also be effective in the stabilization of the crystal packing.

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C1–C6 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
C10—H10B⋯O1i 0.987 (17) 2.303 (17) 3.2691 (16) 165.9 (13)
C11—H11B⋯O1ii 0.99 2.35 3.3346 (14) 171
C11—H11ACg1i 0.99 2.70 3.4833 (12) 136
C15—H15ACg1iii 0.99 2.90 3.8400 (13) 159
Symmetry codes: (i) [x-1, y, z]; (ii) [x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]; (iii) [x, -y-{\script{1\over 2}}, z-{\script{3\over 2}}].
[Figure 3]
Figure 3
A partial packing diagram of the title compound viewed down the a axis. Non-inter­acting hydrogen atoms were omitted for clarity.

4. Hirshfeld surface analysis

In order to visualize the inter­molecular inter­actions in the crystal structure of the title compound, a Hirshfeld surface (HS) analysis (Hirshfeld, 1977[Hirshfeld, H. L. (1977). Theor. Chim. Acta, 44, 129-138.]; Spackman & Jayatilaka, 2009[Spackman, M. A. & Jayatilaka, D. (2009). CrystEngComm, 11, 19-32.]) was carried out using CrystalExplorer (Spackman et al., 2021[Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D. & Spackman, M. A. (2021). J. Appl. Cryst. 54, 1006-1011.]). In the HS plotted over dnorm (Fig. 4[link]), the white surface indicates contacts with distances equal to the sum of van der Waals radii, and the red and blue surfaces contacts shorter (in close contact) or longer (distinct contact), respectively, than the van der Waals radii (Venkatesan et al., 2016[Venkatesan, P., Thamotharan, S., Ilangovan, A., Liang, H. & Sundius, T. (2016). Spectrochim. Acta A Mol. Biomol. Spectrosc. 153, 625-636.]). The bright-red spots indicate their roles as the respective donors and/or acceptors; they also appear as blue and red regions corresponding to positive and negative potentials on the HS mapped over electrostatic potential (Spackman et al., 2008[Spackman, M. A., McKinnon, J. J. & Jayatilaka, D. (2008). CrystEngComm, 10, 377-388.]; Jayatilaka et al., 2005[Jayatilaka, D., Grimwood, D. J., Lee, A., Lemay, A., Russel, A. J., Taylor, C., Wolff, S. K., Cassam-Chenai, P. & Whitton, A. (2005). TONTO - A System for Computational Chemistry. Available at: http://hirshfeldsurface.net/]), as shown in Fig. 5[link]. The blue regions indicate positive electrostatic potential (hydrogen-bond donors), while the red regions indicate negative electrostatic potential (hydrogen-bond acceptors). The shape-index of the HS does not reveal any relevant ππ inter­actions (Fig. 6[link]). However, the shape-index shows C—H⋯π inter­actions present as `red p-holes', which are related to the electron ring inter­actions between the CH groups and the centroids of the aromatic rings of neighbouring mol­ecules (Table 1[link]; Fig. 6[link]). The overall two-dimensional fingerprint plot, Fig. 7[link]a, and those delineated into H⋯H, H⋯C/C⋯H, H⋯N/N⋯H, H⋯O/ O⋯H, C⋯N/N⋯C, C⋯C and C⋯O/O⋯C inter­actions (McKinnon et al., 2007[McKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. pp. 3814-3816.]) are illustrated in Fig. 7[link]bh, respectively, together with their relative contributions to the HS. The most important inter­action is H⋯H contributing with 57.9% to the overall crystal packing, which is reflected in Fig. 7[link]b as widely scattered points of high density due to the large hydrogen content of the mol­ecule with the tip at de = di = 1.20 Å. As a result of the presence of C—H⋯π inter­actions, the H⋯C/C⋯H contacts contribute 18.1% to the overall crystal packing, as reflected in Fig. 7[link]c with the tips at de + di = 2.66 Å. The symmetrical pair of wings in the fingerprint plot delineated into H⋯N/N⋯H contacts (Fig. 7[link]d), with 14.9% contribution to the HS, has the tips at de + di = 2.66 Å. The symmetrical pair of spikes in the fingerprint plot delineated into H⋯O/O⋯H contacts (Fig. 7[link]e), 8.3% contribution to the HS, have the tips at de + di = 2.22 Å. Finally, the C⋯N/N⋯C (Fig. 7[link]f), C⋯C (Fig. 7[link]g) and C⋯O/O⋯C (Fig. 7[link]h) inter­actions make small contibutions of 0.4%, 0.2% and 0.1%, respectively, to the HS.

[Figure 4]
Figure 4
View of the three-dimensional HS of the title compound plotted over dnorm.
[Figure 5]
Figure 5
View of the three-dimensional HS of the title compound plotted over electrostatic potential energy using the STO-3 G basis set at the Hartree–Fock level of theory. Hydrogen-bond donors and acceptors are shown as blue and red regions around the atoms corresponding to positive and negative potentials, respectively.
[Figure 6]
Figure 6
HS of the title compound plotted over shape-index.
[Figure 7]
Figure 7
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⋯N/N⋯C, (g) C⋯C and (h) C⋯O/O⋯C inter­actions. The di and de values are the closest inter­nal and external distances (in Å) from given points on the Hirshfeld surface.

The nearest neighbour environment of a mol­ecule can be determined from the colour patches on the HS based on how close to other mol­ecules they are. The HS representations with the function dnorm plotted onto the surface are shown for the H⋯H, H⋯C/C⋯H and H⋯N/N⋯H inter­actions in Fig. 8[link]ac, respectively. The HS analysis confirms the importance of H-atom contacts in establishing the packing. The large number of H⋯H, H⋯C/C⋯H and H⋯N/N⋯H inter­actions suggest that van der Waals and hydrogen-bonding inter­actions play the major roles in the crystal packing (Hathwar et al., 2015[Hathwar, V. R., Sist, M., Jørgensen, M. R. V., Mamakhel, A. H., Wang, X., Hoffmann, C. M., Sugimoto, K., Overgaard, J. & Iversen, B. B. (2015). IUCrJ, 2, 563-574.]).

[Figure 8]
Figure 8
The HS representations with the function dnorm plotted onto the surface for (a) H⋯H, (b) H⋯C/C⋯H and (c) H⋯N/N⋯H inter­actions.

5. Inter­action energy calculations and energy frameworks

The inter­molecular inter­action energies were calculated using the CE–B3LYP/6–311G(d,p) energy model available in CrystalExplorer (Spackman et al., 2021[Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D. & Spackman, M. A. (2021). J. Appl. Cryst. 54, 1006-1011.]), where a cluster of mol­ecules is generated by applying crystallographic symmetry operations with respect to a selected central mol­ecule within a radius of 3.8 Å by default (Turner et al., 2014[Turner, M. J., Grabowsky, S., Jayatilaka, D. & Spackman, M. A. (2014). J. Phys. Chem. Lett. 5, 4249-4255.]). The total inter­molecular energy (Etot) is the sum of electrostatic (Eele), polarization (Epol), dispersion (Edis) and exchange-repulsion (Erep) energies (Turner et al., 2015[Turner, M. J., Thomas, S. P., Shi, M. W., Jayatilaka, D. & Spackman, M. A. (2015). Chem. Commun. 51, 3735-3738.]) with scale factors of 1.057, 0.740, 0.871 and 0.618, respectively (Mackenzie et al., 2017[Mackenzie, C. F., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). IUCrJ, 4, 575-587.]). Hydrogen-bonding inter­action energies (in kJ mol−1) were calculated as −32.1 (Eele), −9.4 (Epol), −53.7 (Edis), 48.4 (Erep) and −57.7 (Etot) for C10—H10B⋯O1 and −21.0 (Eele), −7.7 (Epol), −65.2 (Edis), 51.6 (Erep) and −52.8 (Etot) for the C11—H11B⋯O1 hydrogen bond. Energy frameworks combine the calculation of inter­molecular inter­action energies with a graphical representation of their magnitude (Turner et al., 2015[Turner, M. J., Thomas, S. P., Shi, M. W., Jayatilaka, D. & Spackman, M. A. (2015). Chem. Commun. 51, 3735-3738.]). Energies between mol­ecular pairs are represented as cylinders joining the centroids of pairs of mol­ecules with the cylinder radius proportional to the relative strength of the corresponding inter­action energy. Energy frameworks were constructed for Eele (red cylinders), Edis (green cylinders) and Etot (blue cylinders) (Fig. 9[link]ac). The evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated via dispersion energies in the crystal structure of the title compound.

[Figure 9]
Figure 9
The energy frameworks for a cluster of mol­ecules of the title compound viewed down the c axis, showing (a) electrostatic energy, (b) dispersion energy and (c) total energy diagrams. The cylindrical radius is proportional to the relative strength of the corresponding energies and they were adjusted to the same scale factor of 80 with cut-off value of 5 kJ mol−1 within 2×2×2 unit cells.

6. DFT calculations

The mol­ecular structure in the gas phase was optimized using density functional theory (DFT) with the B3LYP functional and 6-311G(d,p) basis-set calculations, as implemented in GAUSSIAN 09 (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. Gaussian Inc., Wallingford, CT, USA.]). The optimized parameters, including bond lengths and angles, showed satisfactory agreement with the experimental structural data (Table 2[link]). The largest differences between the calculated and experimental values were observed for the C1—N1 (0.04 Å), N1—C7 and N1—C8 (0.02 Å) bond lengths, the N4—N3—C12 (0.82°) bond angle and the torsion angle N3—C12—C13—N5 (0.3°). These differences may be due to the fact that the calculations are based on an isolated mol­ecule at 0 K, while the experimental results were obtained from inter­acting mol­ecules in the solid state, where intra- and inter­molecular inter­actions with neighbouring mol­ecules are present.

Table 2
Comparison of selected (X-ray and DFT) bond length and angles (Å, °)

Bonds/angles X-ray B3LYP/6–311G(d,p)
C1—N1 1.3992 (14) 1.352
N1—C7 1.3847 (14) 1.364
N1—C8 1.4402 (14) 1.461
O1—C7 1.2250 (13) 1.235
C2—N2 1.3919 (13) 1.378
N2—C7 1.3770 (14) 1.382
N2—C11 1.4568 (14) 1.438
N3—N4 1.3222 (14) 1.311
N4—N3—C12 108.94 (9) 108.12
N3—N4—N5 106.93 (9) 106.47
N4—N5—C13 111.07 (9) 111.64
N4—N5—C14 120.09 (9) 120.71
C13—N5—C14 128.71 (10) 128.48
N2—C7—N1 106.56 (9) 106.29
N3—N4—N5—C13 0.00 (13) 0.02
N3—C12—C13—N5 –0.12 (12) 0.18
C1—N1—C7—O1 –178.68 (11) –178.74
C1—N1—C7—N2 0.08 (12) 0.07

7. Database survey

A survey of the Cambridge Structural Database (CSD, updated March 2024; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) indicates that there are several mol­ecules similar to the title compound (Fig. 10[link]). These include I (CSD refcode YIVWUZ; Zouhair et al., 2023[Zouhair, M., El Ghayati, L., El Monfalouti, H., Abchihi, H., Hökelek, T., Ahmed, M., Mague, J. T. & Sebbar, N. K. (2023). Acta Cryst. E79, 1179-1182.]), II with R1 = –C6H9, R2 = –C6H5 and R3 = H (CSD refcode PAZFOO; Adardour et al., 2017[Adardour, M., Loughzail, M., Dahaoui, S., Baouid, A. & Berraho, M. (2017). IUCrData, 2, x170907.]), III with R1 = –C(CH3)=CH2, R2 = –C10H22 and R3 = –H (CSD refcode ETAJOB; Saber et al., 2021[Saber, A., Anouar, E. H., Sebbar, G., Ibrahimi, B. E., Srhir, M., Hökelek, T., Mague, J. T., Ghayati, L. E., Sebbar, N. K. & Essassi, E. M. (2021). J. Mol. Struct. 1242, 130719.]) and IV with R1 = –CH2C6H5, R2 = -C12H26 and R3 = H (CSD refcode ETAKAO; Saber et al., 2021[Saber, A., Anouar, E. H., Sebbar, G., Ibrahimi, B. E., Srhir, M., Hökelek, T., Mague, J. T., Ghayati, L. E., Sebbar, N. K. & Essassi, E. M. (2021). J. Mol. Struct. 1242, 130719.]). The benzimidazol-2-one unit in all of these compounds is almost planar, with the dihedral angle between the constituent rings being less than 1°, or having the nitro­gen atom bearing the exocyclic substituent less than 0.03 Å from the mean plane of the remaining nine atoms.

[Figure 10]
Figure 10
Related mol­ecular fragments for searching the CSD database.

8. Synthesis and crystallization

To a solution of 2.87 mmol of 1-(prop-1-en-2-yl)-3-(prop-2-yn­yl)-1H-benzimidazol-2-one and 0.45 mmol of 1-azido­butane in 10 ml of ethanol were added 1.64 mmol of CuSO4 and 3.73 mmol of sodium ascorbate dissolved in 10 ml of distilled water. The reaction mixture was stirred for 10 h at room temperature and monitored by TLC. After filtration and concentration of the solution under reduced pressure, the residue obtained was chromatographed on a silica gel column using ethyl acetate/hexane (3/1) as eluent. The resulting solid was filtered off, washed with water, dried, and then recrystallized from ethanol, yield: 73%.

9. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. Methyl­ene hydrogens attached to C10 were located in a difference-Fourier map, and were included as riding contributions in idealized positions with Uiso(H) = 1.2Ueq(C). Aromatic H atoms were treated the same way, and methyl H atoms with Uiso(H) = 1.5Ueq(C).

Table 3
Experimental details

Crystal data
Chemical formula C17H21N5O
Mr 311.39
Crystal system, space group Monoclinic, P21/c
Temperature (K) 160
a, b, c (Å) 5.7032 (1), 24.2184 (5), 11.8683 (2)
β (°) 91.312 (2)
V3) 1638.85 (5)
Z 4
Radiation type Cu Kα
μ (mm−1) 0.66
Crystal size (mm) 0.19 × 0.12 × 0.05
 
Data collection
Diffractometer SuperNova, Dual, Cu at home/near, Atlas
Absorption correction Analytical [CrysAlis PRO (Rigaku OD, 2023[Rigaku, OD (2023). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England..]) using a multifaceted crystal model (Clark & Reid, 1995[Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897.])]
Tmin, Tmax 0.894, 0.971
No. of measured, independent and observed [I > 2σ(I)] reflections 19825, 3435, 2968
Rint 0.034
(sin θ/λ)max−1) 0.631
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.034, 0.086, 1.05
No. of reflections 3435
No. of parameters 219
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.22, −0.21
Computer programs: CrysAlis PRO (Rigaku OD, 2023[Rigaku, OD (2023). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England..]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), 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.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Computing details top

1-[(1-Butyl-1H-1,2,3-triazol-4-yl)methyl]-3-(prop-1-en-2-yl)-1H-benzimidazol-2-one top
Crystal data top
C17H21N5OF(000) = 664
Mr = 311.39Dx = 1.262 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54184 Å
a = 5.7032 (1) ÅCell parameters from 10273 reflections
b = 24.2184 (5) Åθ = 3.6–76.4°
c = 11.8683 (2) ŵ = 0.66 mm1
β = 91.312 (2)°T = 160 K
V = 1638.85 (5) Å3Plate, colourless
Z = 40.19 × 0.12 × 0.05 mm
Data collection top
SuperNova, Dual, Cu at home/near, Atlas
diffractometer
3435 independent reflections
Radiation source: micro-focus sealed X-ray tube, SuperNova (Cu) X-ray Source2968 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.034
Detector resolution: 10.3801 pixels mm-1θmax = 76.8°, θmin = 3.7°
ω scansh = 77
Absorption correction: analytical
[CrysAlisPro (Rigaku OD, 2023) using a multifaceted crystal model (Clark & Reid, 1995)]
k = 3026
Tmin = 0.894, Tmax = 0.971l = 1414
19825 measured reflections
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.034 w = 1/[σ2(Fo2) + (0.0353P)2 + 0.4935P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.086(Δ/σ)max = 0.001
S = 1.05Δρmax = 0.22 e Å3
3435 reflectionsΔρmin = 0.21 e Å3
219 parametersExtinction correction: SHELXL (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.0018 (2)
Primary atom site location: dual
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
C10.57633 (19)0.82949 (4)0.42568 (9)0.0208 (2)
N10.71001 (16)0.82797 (4)0.52597 (8)0.0223 (2)
O11.04428 (14)0.77946 (4)0.58607 (6)0.02597 (19)
C20.68397 (19)0.79364 (4)0.35005 (9)0.0202 (2)
N20.87645 (16)0.77053 (4)0.40675 (7)0.0203 (2)
N31.17211 (17)0.63652 (4)0.43348 (9)0.0262 (2)
C30.5972 (2)0.78704 (5)0.24096 (9)0.0252 (2)
H30.6718760.7632570.1891860.030*
C40.3964 (2)0.81658 (5)0.21003 (10)0.0298 (3)
H40.3321480.8127480.1358910.036*
N41.08726 (18)0.59076 (4)0.47758 (9)0.0300 (2)
C50.2882 (2)0.85168 (5)0.28603 (11)0.0302 (3)
H50.1511750.8712230.2625650.036*
N50.85618 (17)0.59867 (4)0.48951 (8)0.0245 (2)
C60.3761 (2)0.85880 (5)0.39558 (10)0.0264 (2)
H60.3018920.8826960.4472980.032*
C70.89510 (19)0.79157 (5)0.51438 (9)0.0206 (2)
H10A0.459 (3)0.8759 (7)0.7493 (13)0.037 (4)*
H10B0.365 (3)0.8256 (7)0.6610 (13)0.041 (4)*
C80.6746 (2)0.86076 (5)0.62539 (9)0.0235 (2)
C90.8628 (2)0.90232 (6)0.65046 (12)0.0349 (3)
H9A1.0136150.8833710.6608270.052*
H9B0.8258040.9224500.7194420.052*
H9C0.8723460.9283620.5875280.052*
C100.4838 (2)0.85325 (5)0.68373 (11)0.0296 (3)
C111.03801 (19)0.72874 (5)0.36645 (9)0.0221 (2)
H11A1.2008950.7403170.3848750.027*
H11B1.0214800.7259300.2834270.027*
C120.99452 (19)0.67315 (5)0.41755 (9)0.0201 (2)
C130.79133 (19)0.64923 (5)0.45341 (9)0.0230 (2)
H130.6385780.6648930.4528760.028*
C140.7134 (2)0.55616 (5)0.54332 (11)0.0289 (3)
H14A0.7467150.5198270.5089670.035*
H14B0.5452340.5645070.5297050.035*
C150.7638 (2)0.55325 (5)0.66936 (11)0.0297 (3)
H15A0.7336830.5898590.7032380.036*
H15B0.9314690.5443000.6827160.036*
C160.6139 (3)0.51012 (6)0.72697 (12)0.0392 (3)
H16A0.4461950.5190930.7138030.047*
H16B0.6438180.4735030.6930860.047*
C170.6652 (3)0.50730 (6)0.85305 (13)0.0462 (4)
H17A0.8322010.4995710.8664920.069*
H17B0.5713370.4778380.8861960.069*
H17C0.6252250.5426860.8877570.069*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0202 (5)0.0196 (5)0.0226 (5)0.0020 (4)0.0017 (4)0.0017 (4)
N10.0207 (4)0.0248 (5)0.0214 (5)0.0030 (4)0.0015 (3)0.0022 (4)
O10.0235 (4)0.0322 (4)0.0221 (4)0.0034 (3)0.0036 (3)0.0013 (3)
C20.0193 (5)0.0188 (5)0.0223 (5)0.0020 (4)0.0008 (4)0.0037 (4)
N20.0203 (4)0.0214 (5)0.0193 (4)0.0022 (4)0.0003 (3)0.0006 (3)
N30.0205 (5)0.0255 (5)0.0329 (5)0.0027 (4)0.0022 (4)0.0050 (4)
C30.0283 (6)0.0252 (6)0.0220 (5)0.0036 (5)0.0017 (4)0.0010 (4)
C40.0309 (6)0.0318 (6)0.0262 (6)0.0047 (5)0.0081 (5)0.0067 (5)
N40.0223 (5)0.0254 (5)0.0424 (6)0.0038 (4)0.0038 (4)0.0068 (4)
C50.0233 (6)0.0291 (6)0.0379 (7)0.0002 (5)0.0072 (5)0.0086 (5)
N50.0203 (5)0.0228 (5)0.0302 (5)0.0011 (4)0.0002 (4)0.0026 (4)
C60.0224 (5)0.0235 (6)0.0332 (6)0.0016 (4)0.0008 (4)0.0028 (5)
C70.0195 (5)0.0215 (5)0.0210 (5)0.0009 (4)0.0010 (4)0.0019 (4)
C80.0248 (5)0.0214 (5)0.0241 (5)0.0025 (4)0.0027 (4)0.0035 (4)
C90.0308 (6)0.0317 (7)0.0422 (7)0.0055 (5)0.0005 (5)0.0098 (5)
C100.0275 (6)0.0325 (6)0.0290 (6)0.0029 (5)0.0018 (5)0.0057 (5)
C110.0221 (5)0.0224 (5)0.0219 (5)0.0022 (4)0.0042 (4)0.0016 (4)
C120.0198 (5)0.0220 (5)0.0186 (5)0.0017 (4)0.0012 (4)0.0008 (4)
C130.0189 (5)0.0234 (5)0.0268 (5)0.0019 (4)0.0007 (4)0.0022 (4)
C140.0259 (6)0.0237 (6)0.0372 (7)0.0056 (5)0.0001 (5)0.0038 (5)
C150.0291 (6)0.0242 (6)0.0358 (7)0.0014 (5)0.0025 (5)0.0029 (5)
C160.0488 (8)0.0292 (7)0.0401 (7)0.0074 (6)0.0097 (6)0.0037 (5)
C170.0656 (10)0.0335 (7)0.0399 (8)0.0074 (7)0.0122 (7)0.0062 (6)
Geometric parameters (Å, º) top
C1—N11.3992 (14)C8—C101.3158 (17)
C1—C21.4007 (15)C9—H9A0.9800
C1—C61.3847 (16)C9—H9B0.9800
N1—C71.3847 (14)C9—H9C0.9800
N1—C81.4402 (14)C10—H10A0.966 (16)
O1—C71.2250 (13)C10—H10B0.987 (17)
C2—N21.3919 (13)C11—H11A0.9900
C2—C31.3846 (16)C11—H11B0.9900
N2—C71.3770 (14)C11—C121.4995 (15)
N2—C111.4568 (14)C12—C131.3719 (15)
N3—N41.3222 (14)C13—H130.9500
N3—C121.3564 (14)C14—H14A0.9900
C3—H30.9500C14—H14B0.9900
C3—C41.3924 (17)C14—C151.5184 (17)
C4—H40.9500C15—H15A0.9900
C4—C51.3938 (19)C15—H15B0.9900
N4—N51.3424 (13)C15—C161.5218 (17)
C5—H50.9500C16—H16A0.9900
C5—C61.3933 (17)C16—H16B0.9900
N5—C131.3464 (15)C16—C171.520 (2)
N5—C141.4678 (15)C17—H17A0.9800
C6—H60.9500C17—H17B0.9800
C8—C91.4965 (16)C17—H17C0.9800
N1—C1—C2106.90 (9)H9B—C9—H9C109.5
C6—C1—N1131.54 (11)H10A—C10—H10B119.5 (13)
C6—C1—C2121.57 (10)C8—C10—H10A119.0 (9)
C1—N1—C8126.77 (9)C8—C10—H10B121.5 (9)
C7—N1—C1109.51 (9)N2—C11—H11A109.1
C7—N1—C8123.64 (9)N2—C11—H11B109.1
N2—C2—C1106.96 (9)N2—C11—C12112.28 (9)
C3—C2—C1121.22 (10)H11A—C11—H11B107.9
C3—C2—N2131.81 (11)C12—C11—H11A109.1
C2—N2—C11128.19 (9)C12—C11—H11B109.1
C7—N2—C2110.06 (9)N3—C12—C11120.90 (10)
C7—N2—C11121.71 (9)N3—C12—C13108.30 (10)
N4—N3—C12108.94 (9)C13—C12—C11130.79 (10)
C2—C3—H3121.3N5—C13—C12104.77 (10)
C2—C3—C4117.47 (11)N5—C13—H13127.6
C4—C3—H3121.3C12—C13—H13127.6
C3—C4—H4119.5N5—C14—H14A109.3
C3—C4—C5121.10 (11)N5—C14—H14B109.3
C5—C4—H4119.5N5—C14—C15111.53 (10)
N3—N4—N5106.93 (9)H14A—C14—H14B108.0
C4—C5—H5119.2C15—C14—H14A109.3
C6—C5—C4121.62 (11)C15—C14—H14B109.3
C6—C5—H5119.2C14—C15—H15A109.1
N4—N5—C13111.07 (9)C14—C15—H15B109.1
N4—N5—C14120.09 (9)C14—C15—C16112.28 (11)
C13—N5—C14128.71 (10)H15A—C15—H15B107.9
C1—C6—C5117.01 (11)C16—C15—H15A109.1
C1—C6—H6121.5C16—C15—H15B109.1
C5—C6—H6121.5C15—C16—H16A109.2
O1—C7—N1127.03 (10)C15—C16—H16B109.2
O1—C7—N2126.40 (10)H16A—C16—H16B107.9
N2—C7—N1106.56 (9)C17—C16—C15112.07 (12)
N1—C8—C9114.85 (10)C17—C16—H16A109.2
C10—C8—N1119.21 (11)C17—C16—H16B109.2
C10—C8—C9125.91 (11)C16—C17—H17A109.5
C8—C9—H9A109.5C16—C17—H17B109.5
C8—C9—H9B109.5C16—C17—H17C109.5
C8—C9—H9C109.5H17A—C17—H17B109.5
H9A—C9—H9B109.5H17A—C17—H17C109.5
H9A—C9—H9C109.5H17B—C17—H17C109.5
C1—N1—C7—O1178.68 (11)C3—C2—N2—C114.13 (19)
C1—N1—C7—N20.08 (12)C3—C4—C5—C60.16 (19)
C1—N1—C8—C9112.17 (13)C4—C5—C6—C10.11 (18)
C1—N1—C8—C1066.21 (16)N4—N3—C12—C11178.92 (10)
C1—C2—N2—C71.17 (12)N4—N3—C12—C130.13 (13)
C1—C2—N2—C11176.71 (10)N4—N5—C13—C120.08 (13)
C1—C2—C3—C41.20 (17)N4—N5—C14—C1571.86 (14)
N1—C1—C2—N21.18 (12)N5—C14—C15—C16178.92 (11)
N1—C1—C2—C3178.09 (10)C6—C1—N1—C7179.65 (12)
N1—C1—C6—C5178.57 (12)C6—C1—N1—C83.6 (2)
C2—C1—N1—C70.79 (12)C6—C1—C2—N2179.20 (10)
C2—C1—N1—C8175.93 (10)C6—C1—C2—C31.53 (17)
C2—C1—C6—C50.93 (17)C7—N1—C8—C964.12 (15)
C2—N2—C7—N10.68 (12)C7—N1—C8—C10117.50 (13)
C2—N2—C7—O1179.46 (11)C7—N2—C11—C1272.83 (13)
C2—N2—C11—C12104.83 (12)C8—N1—C7—O14.47 (18)
C2—C3—C4—C50.38 (18)C8—N1—C7—N2176.77 (10)
N2—C2—C3—C4179.74 (11)C11—N2—C7—N1177.36 (9)
N2—C11—C12—N3150.31 (10)C11—N2—C7—O11.41 (17)
N2—C11—C12—C1330.88 (16)C11—C12—C13—N5178.80 (11)
N3—N4—N5—C130.00 (13)C12—N3—N4—N50.08 (13)
N3—N4—N5—C14176.20 (10)C13—N5—C14—C15103.59 (14)
N3—C12—C13—N50.12 (12)C14—N5—C13—C12175.86 (11)
C3—C2—N2—C7177.99 (12)C14—C15—C16—C17179.91 (12)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C1–C6 ring.
D—H···AD—HH···AD···AD—H···A
C10—H10B···O1i0.987 (17)2.303 (17)3.2691 (16)165.9 (13)
C11—H11B···O1ii0.992.353.3346 (14)171
C11—H11A···Cg1i0.992.703.4833 (12)136
C15—H15A···Cg1iii0.992.903.8400 (13)159
Symmetry codes: (i) x1, y, z; (ii) x, y+3/2, z1/2; (iii) x, y1/2, z3/2.
Comparison of selected (X-ray and DFT) bond length and angles (Å, °) top
Bonds/anglesX-rayB3LYP/6-311G(d,p)
C1—N11.3992 (14)1.352
N1—C71.3847 (14)1.364
N1—C81.4402 (14)1.461
O1—C71.2250 (13)1.235
C2—N21.3919 (13)1.378
N2—C71.3770 (14)1.382
N2—C111.4568 (14)1.438
N3—N41.3222 (14)1.311
N4—N3—C12108.94 (9)108.12
N3—N4—N5106.93 (9)106.47
N4—N5—C13111.07 (9)111.64
N4—N5—C14120.09 (9)120.71
C13—N5—C14128.71 (10)128.48
N2—C7—N1106.56 (9)106.29
N3—N4—N5—C130.00 (13)0.02
N3—C12—C13—N5–0.12 (12)0.18
C1—N1—C7—O1–178.68 (11)–178.74
C1—N1—C7—N20.08 (12)0.07
 

Funding information

TH is grateful to Hacettepe University Scientific Research Project Unit (grant No. 013 D04 602 004).

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