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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 80| Part 10| October 2024| Pages 1075-1080
https://doi.org/10.1107/S2056989024008703

Crystal structure, Hirshfeld surface analysis, and calculations of inter­molecular inter­action energies and energy frameworks of 1-[(1-hexyl-1H-1,2,3-triazol-4-yl)meth­yl]-3-(1-methyl­ethen­yl)-benzimidazol-2-one

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Zakaria El Atrassi,a Zakaria Benzekri,a* Olivier Blacque,b Tuncer Hökelek,c Ahmed Mazzah,d Hassan Cherkaouia and Nada Kheira Sebbare,f

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 B, Winterthurerstrasse 190, 8057 Zurich, Switzerland, cDepartment of Physics, Hacettepe University, 06800 Beytepe, Ankara, Türkiye, dScience and Technology of Lille USR 3290, Villeneuve d'ascq cedex, France, eLaboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibnou Zohr University, Agadir, Morocco, and fLaboratory 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: z.benzekri@um5r.ac.ma

Edited by M. Weil, Vienna University of Technology, Austria (Received 12 August 2024; accepted 4 September 2024; online 30 September 2024)

The benzimidazole moiety in the title mol­ecule, C19H25N5O, is almost planar and oriented nearly perpendicular to the triazole ring. In the crystal, C—H⋯O hydrogen bonds link the mol­ecules into a network structure. There are no π–π inter­actions present but two weak C—H⋯π(ring) inter­actions are observed. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (62.0%), H⋯C/C⋯H (16.1%), H⋯N/N⋯H (13.7%) and H⋯O/O⋯H (7.5%) inter­actions. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated via the dispersion energy contributions in the title compound.

CCDC reference: 2381865

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1. Chemical context

Research into the properties of heterocyclic compounds, in particular benzimidazolo­nes, has become increasingly important. These compounds possess unique structural features and have shown a wide range of biological activities, including anti­proliferative (Guillon et al., 2022[Guillon, J., Savrimoutou, S., Albenque-Rubio, S., Pinaud, N., Moreau, S. & Desplat, V. (2022). Molbank, 2022, M1333.]), anti­bacterial (Al-Ghulikah et al., 2023[Al-Ghulikah, H., Ghabi, A., Mtiraoui, H., Jeanneau, E. & Msaddek, M. (2023). Arab. J. Chem. 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.]; Ibrahim et al., 2021[Ibrahim, S., Ghabi, A., Amiri, N., Mtiraoui, H., Hajji, M., Bel-Hadj-Tahar, R. & Msaddek, M. (2021). Monatsh. Chem. 152, 523-535.]), anti­cancer (Dimov et al., 2021[Dimov, S., Mavrova, A. T., Yancheva, D., Nikolova, B. & Tsoneva, I. (2021). Anticancer Agents Med. Chem. 21, 1441-1450.]), 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.]) and anti­depressant (Clayton et al., 2020[Clayton, A. H., Brown, L. & Kim, N. N. (2020). Opinion d'expert sur l'innocuité des Médicaments, 1-8.]) properties, and activities related to Alzheimer's disease (Mo et al., 2020[Mo, J., Chen, T., Yang, H., Guo, Y., Li, Q., Qiao, Y., Lin, H., Feng, F., Liu, W., Chen, Y., Liu, Z. & Sun, H. (2020). J. Enzyme Inhib. Med. Chem. 35, 330-343.]). Our research group recently made significant advances in synthesizing compounds that combine the 1,2,3-triazole moiety with benzimidazol-2-one derivatives.

Here we provide details of the synthesis and the mol­ecular and crystal structures of 1-[(1-hexyl-1H-1,2,3-triazol-4-yl)meth­yl]-3-(1-methyl­ethen­yl)benzimidazol-2-one, C19H25N5O. We have synthesized this compound using click chemistry, in particular by applying copper-catalysed azide–alkyne cyclo­addition (CuAAC). This approach not only ensures efficiency in the synthesis process but also facilitates the formation of complex mol­ecular structures (Fig. 1[link]). We also carried out Hirshfeld surface analysis and calculations of the inter­molecular inter­action energies and energy frameworks.

[Scheme 1]
[Figure 1]
Figure 1
Reaction scheme for the synthesis of benzimidazole derivatives using the CuAAC method.

2. Structural commentary

The mol­ecular structure of the title compound is shown in Fig. 2[link]. The benzimidazole moiety is almost planar, the planar A (C1–C6) and B (N1/N2/C1/C2/C7) rings being oriented at a dihedral angle of 0.86 (5)°. Atoms O1 and C8 are 0.370 (10) Å and −0.0404 (16) Å, respectively, away from the least-squares plane of ring B. The planar triazole ring, C (N3–N5/C12/C13), is oriented almost perpendicular with respect to the benz­imidazole moiety at a dihedral angle of 87.57 (4)°, with atoms C11 and C14 lying 0.0044 (14) and 0.0463 (18) Å, respectively, from the least-squares plane of ring C. Bond lengths and angles in the whole mol­ecule are in characteristic ranges.

[Figure 2]
Figure 2
The mol­ecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. For clarity, only the major occupancy component of the disordered terminal propyl moiety of the hexyl chain is shown.

3. Supra­molecular features

In the crystal, C—H⋯O hydrogen bonds link the mol­ecules into a network structure (Table 1[link], Fig. 3[link]). There are no significant π–π inter­actions present, but two weak C—H⋯π(ring) inter­actions (Table 1[link]) are observed.

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C1–C6 ring.
D—H⋯A D—H H⋯A D⋯A D—H⋯A
C10—H10B⋯O1iv 0.99 (2) 2.31 (2) 3.284 (2) 168.8 (18)
C11—H11A⋯O1ii 0.99 2.37 3.3577 (17) 173
C11—H11B⋯Cg1i 0.99 2.76 3.5082 (18) 135
C15—H15B⋯Cg1ii 0.99 2.88 3.7599 (19) 152
Symmetry codes: (i) [x-1, y, z]; (ii) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (iv) [x+1, y, z].
[Figure 3]
Figure 3
A partial packing diagram. Inter­molecular C—H⋯O hydrogen bonds are shown as dashed lines.

4. Hirshfeld surface analysis

In order to qu­antify the inter­molecular inter­actions in the crystal 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.]). It is noted that only the major occupancy component of the disordered atoms at the terminal propyl moiety of the hexyl chain were taken into account for the analysis. 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 colours indicate distances shorter (in close contact) or longer (distant contact) than the van der Waals radii, respectively (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 the positive electrostatic potential (hydrogen-bond donors), while the red regions indicate the negative electrostatic potential (hydrogen-bond acceptors). Possible π–π stacking and C—H⋯π inter­actions can also be visualized using the shape-index surface, which can be used to identify characteristic packing modes, in particular, planar stacking arrangements and the presence of aromatic stacking inter­actions. The shape-index surface represents the C—H⋯π inter­actions as red p-holes, which are related to the electron ring inter­actions between the CH groups with the centroid of the aromatic rings of neighbouring mol­ecules. Fig. 6[link] clearly shows that there are C—H⋯π inter­actions present in the crystal packing of the title compound. On the other hand, the shape-index of the HS is a tool to visualize π–π stacking by the presence of adjacent red and blue triangles. If there are no adjacent red and/or blue triangles, then there are no π–π inter­actions, as Fig. 6[link] clearly suggests. 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 (McKinnon et al., 2007[McKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. pp. 3814-3816.]) are illustrated in Fig. 7[link]b–h, respectively, together with their relative contributions to the Hirshfeld surface. The most important inter­action is H⋯H (Table 2[link]) contributing 62.0% 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. As a result of the presence of C—H⋯π inter­actions (Table 1[link], Fig. 6[link]), the H⋯C/C⋯H contacts (Table 2[link]) contribute 16.1% to the overall crystal packing. H⋯N/N⋯H contacts (Fig. 7[link]d) make a 13.7% contribution to the HS, and the H⋯O/O⋯H contacts (Table 3[link] and Fig. 7[link]e) amount to 7.5% of the overall crystal packing. 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) contacts with 0.4%, 0.3% and 0.1% contributions, respectively, to the HS play a minor role.

Table 2
Selected interatomic distances (Å)

O1⋯C9 3.185 (2) C7⋯H9C 2.85
O1⋯H10Bi 2.31 (2) H3⋯C7ii 2.80
O1⋯H11B 2.72 C10⋯H9Ciii 2.80
O1⋯H9C 2.60 H16B⋯H19A 2.41
H3⋯O1ii 2.69 H17A⋯H19Ai 2.36
H11A⋯O1ii 2.37 H17B⋯H19C 2.41
C3⋯H11A 2.87    
Symmetry codes: (i) [x-1, y, z]; (ii) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (iii) [x+1, y, z].

Table 3
Experimental details

Crystal data
Chemical formula C19H25N5O
Mr 339.44
Crystal system, space group Monoclinic, P21/c
Temperature (K) 160
a, b, c (Å) 5.7820 (3), 26.5057 (14), 11.7704 (5)
β (°) 90.407 (4)
V (Å3) 1803.84 (15)
Z 4
Radiation type Cu Kα
μ (mm−1) 0.64
Crystal size (mm) 0.25 × 0.14 × 0.09
 
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.]) based on expressions derived by Clark & Reid (1995[Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897.])]
Tmin, Tmax 0.901, 0.951
No. of measured, independent and observed [I > 2σ(I)] reflections 21177, 3808, 3160
Rint 0.052
(sin θ/λ)max (Å−1) 0.632
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.045, 0.127, 1.03
No. of reflections 3808
No. of parameters 257
No. of restraints 42
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.25, −0.26
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.]).
[Figure 4]
Figure 4
View of the three-dimensional Hirshfeld surface of the title compound plotted over dnorm.
[Figure 5]
Figure 5
View of the three-dimensional Hirshfeld surface 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, respectively, around the atoms corresponding to positive and negative potentials.
[Figure 6]
Figure 6
Hirshfeld surface 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 Hirshfeld surface representations of contact patches plotted onto the surface are shown for the H⋯H, H⋯C/C⋯H, H⋯N/N⋯H and H⋯O/O⋯H inter­actions in Fig. 8[link]a–d, respectively.

[Figure 8]
Figure 8
The Hirshfeld surface representation of contact patches plotted onto the surface for (a) H⋯H, (b) H⋯C/C⋯H, (c) H⋯N/N⋯H and H⋯O/O⋯H inter­actions.

The Hirshfeld surface analysis confirms the importance of H-atom contacts in establishing the crystal packing, as shown by the large number of H⋯H, H⋯C/C⋯H, H⋯N/N⋯H and H⋯O/O⋯H inter­actions (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.]).

5. Inter­action energy calculations and energy frameworks

The inter­molecular inter­action energies were calculated using the CE–B3LYP/6–31G(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 the 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 to be −32.5 (Eele), −9.2 (Epol), −60.5 (Edis), 54.9(Erep) and 59.9 (Etot) for the C10—H10B⋯O1, and −19.8 (Eele), −7.5 (Epol), −72.3 (Edis), 50.3 (Erep) and −58.3 (Etot) for the C11—H11A⋯O1 hydrogen-bonding inter­actions. 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]a–c). The evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated by the dispersion energy contributions in the crystal structure of the title compound.

[Figure 9]
Figure 9
The energy frameworks for a cluster of mol­ecules of title compound viewed down the c-axis direction 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. Database survey

A survey of the Cambridge Structural Database (CSD, updated July 2024; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) found several mol­ecules that are similar to the title compound. These include: formula I in Fig. 10[link] (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.]), formula II with R1 = –C(CH3)=CH2, R2 = –C6H9, and R3 = –H (CSD refcode ROPKOA; El Atrassi et al., 2024[El Atrassi, Z., Zouhair, M., Blacque, O., Hökelek, T., Haoudi, A., Mazzah, A., Cherkaoui, H. & Sebbar, N. K. (2024). Acta Cryst. E80, 601-606.]), formula 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.]), formula 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.]) and formula V 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.]). Most of the identified compounds exhibit an almost planar benzimidazol-2-one ring system, with the dihedral angle between the constituent rings being less than 1°, or the nitro­gen atom bearing the exocyclic substituent being less than 0.03 Å from the mean plane of the remaining nine atoms.

[Figure 10]
Figure 10
Related compounds.

7. Synthesis and crystallization

2.87 mmol of compound 1 (Fig. 1[link]) and 0.45 mmol of 1-azido­hexane were dissolved in 10 ml of ethanol. This solution was added into 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. After filtration and concentration of the solution under reduced pressure, the obtained residue was chromatographed on a silica gel column using ethyl acetate/hexane (3/1 v/v) as the eluent. The resulting solid was filtered, washed with water, dried, and recrystallized from ethanol. The title compound 2 was obtained in a yield of 87%.

8. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. The H10A and H10B hydrogen atoms were located in a difference-Fourier map, and were refined isotropically. The other C-bound hydrogen-atom positions were calculated geometrically at distances of 0.95 Å (for aromatic CH), 0.99 Å (for CH2) and 0.98 Å (for CH3) and refined using a riding model by applying the constraints Uiso(H) = k×Ueq(C), where k = 1.2 for CH and CH2 and k = 1.5 for CH3. The terminal propyl moiety of the hexyl chain is disordered over two positions (H17A, H17B, C18A, H18A, H18B, C19A, H19A, H19B, H19C, H17C, H17D, C18B, H18C, H18D, C19B, H19D, H19E, H19F) with a refined occupancy ratio of 0.821 (5):0.179 (5).

Supporting information

CCDC reference: 2381865

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989024008703/wm5732sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989024008703/wm5732Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989024008703/wm5732Isup3.cdx

Supporting information file. DOI: https://doi.org/10.1107/S2056989024008703/wm5732Isup4.cml

checkCIF report


Computing details top

1-[(1-Hexyl-1H-1,2,3-triazol-4-yl)methyl]-3-(1-methylethenyl)benzimidazol-2-one top
Crystal data top
C19H25N5OF(000) = 728
Mr = 339.44Dx = 1.250 Mg m−3
Monoclinic, P21/cCu Kα radiation, λ = 1.54184 Å
a = 5.7820 (3) ÅCell parameters from 8532 reflections
b = 26.5057 (14) Åθ = 3.3–76.2°
c = 11.7704 (5) ŵ = 0.64 mm−1
β = 90.407 (4)°T = 160 K
V = 1803.84 (15) Å3Plate, colourless
Z = 40.25 × 0.14 × 0.09 mm
Data collection top
SuperNova, Dual, Cu at home/near, Atlas
diffractometer		3808 independent reflections
Radiation source: micro-focus sealed X-ray tube, SuperNova (Cu) X-ray Source3160 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.052
Detector resolution: 10.3801 pixels mm-1θmax = 77.0°, θmin = 3.3°
ω scansh = −7→7
Absorption correction: analytical
[CrysAlisPro (Rigaku OD, 2023) based on expressions derived by Clark & Reid (1995)]		k = −33→29
Tmin = 0.901, Tmax = 0.951l = −14→10
21177 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)] = 0.045 w = 1/[σ2(Fo2) + (0.0636P)2 + 0.5249P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.127(Δ/σ)max < 0.001
S = 1.03Δρmax = 0.25 e Å−3
3808 reflectionsΔρmin = −0.26 e Å−3
257 parametersExtinction correction: SHELXL (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
42 restraintsExtinction coefficient: 0.0036 (4)
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.

Refinement. 1. Fixed Uiso At 1.2 times of: All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups At 1.5 times of: All C(H,H,H) groups 2. Restrained distances C18B-C19B ~ C19A-C18A ~ C18B-C17 ~ C18A-C17 with sigma of 0.005 3. Uiso/Uaniso restraints and constraints C18A ~ C19A ~ C18B ~ C19B: within 3A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 3A 4. Others Sof(H17C)=Sof(H17D)=Sof(C18B)=Sof(H18C)=Sof(H18D)=Sof(C19B)=Sof(H19D)= Sof(H19E)=Sof(H19F)=1-FVAR(1) Sof(H17A)=Sof(H17B)=Sof(C18A)=Sof(H18A)=Sof(H18B)=Sof(C19A)=Sof(H19A)= Sof(H19B)=Sof(H19C)=FVAR(1) 5.a Secondary CH2 refined with riding coordinates: C11(H11A,H11B), C14(H14A,H14B), C15(H15A,H15B), C16(H16A,H16B), C17(H17A, H17B), C17(H17C,H17D), C18A(H18A,H18B), C18B(H18C,H18D) 5.b Aromatic/amide H refined with riding coordinates: C3(H3), C4(H4), C5(H5), C6(H6), C13(H13) 5.c Idealised Me refined as rotating group: C9(H9A,H9B,H9C), C19A(H19A,H19B,H19C), C19B(H19D,H19E,H19F)

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
C10.7940 (2)0.17577 (5)0.68604 (12)0.0308 (3)
O10.33103 (18)0.21779 (4)0.52367 (8)0.0364 (3)
N10.6614 (2)0.17482 (5)0.58607 (10)0.0326 (3)
N20.4944 (2)0.22890 (5)0.70261 (9)0.0296 (3)
C20.6863 (2)0.20966 (5)0.75975 (11)0.0291 (3)
N30.2200 (2)0.35163 (5)0.66222 (11)0.0374 (3)
C30.7721 (3)0.21852 (6)0.86806 (12)0.0352 (3)
H30.6982980.2413660.9183180.042*
N40.3129 (2)0.39205 (5)0.61517 (13)0.0424 (3)
C40.9712 (3)0.19248 (7)0.90008 (13)0.0393 (4)
H41.0350840.1977300.9737120.047*
C51.0783 (3)0.15899 (6)0.82652 (14)0.0399 (4)
H51.2136100.1417010.8511270.048*
N50.5415 (2)0.38392 (5)0.60927 (11)0.0357 (3)
C60.9922 (3)0.15015 (6)0.71767 (13)0.0356 (3)
H61.0666300.1274660.6672510.043*
C70.4775 (2)0.20804 (6)0.59617 (12)0.0303 (3)
C80.7004 (3)0.14433 (6)0.48692 (12)0.0352 (3)
C90.5113 (3)0.10808 (7)0.45822 (17)0.0492 (4)
H9A0.4935850.0838420.5204220.074*
H9B0.5500580.0900190.3882450.074*
H9C0.3661450.1265810.4471460.074*
C100.8948 (3)0.14965 (7)0.43056 (15)0.0442 (4)
H10A0.931 (4)0.1277 (8)0.3654 (18)0.056 (6)*
H10B1.012 (4)0.1741 (9)0.4565 (18)0.058 (6)*
C110.3375 (3)0.26838 (6)0.74017 (12)0.0323 (3)
H11A0.3490850.2717780.8237790.039*
H11B0.1766460.2586180.7209650.039*
C120.3908 (2)0.31811 (6)0.68620 (11)0.0301 (3)
C130.5969 (3)0.33859 (6)0.65264 (13)0.0340 (3)
H130.7463670.3239220.6587260.041*
C140.6934 (3)0.42141 (6)0.55722 (15)0.0424 (4)
H14A0.8555240.4096260.5630880.051*
H14B0.6812530.4535260.5996970.051*
C150.6340 (3)0.43082 (6)0.43358 (15)0.0421 (4)
H15A0.4750250.4445260.4279210.051*
H15B0.6375410.3984160.3917830.051*
C160.8018 (3)0.46769 (7)0.37858 (17)0.0480 (4)
H16A0.8070030.4990650.4241500.058*
H16B0.9587430.4527640.3794780.058*
C170.7356 (4)0.48077 (8)0.25675 (17)0.0586 (5)
H17A0.5815330.4970620.2576990.070*0.821 (5)
H17B0.7193830.4488520.2137610.070*0.821 (5)
H17C0.6133560.5068770.2526060.070*0.179 (5)
H17D0.6880900.4507290.2124040.070*0.179 (5)
C18A0.9007 (5)0.51525 (10)0.1912 (3)0.0583 (8)0.821 (5)
H18A0.8194760.5292840.1239580.070*0.821 (5)
H18B0.9484340.5437630.2403900.070*0.821 (5)
C19A1.1136 (5)0.48654 (11)0.1530 (3)0.0744 (10)0.821 (5)
H19A1.1955780.4731570.2196400.112*0.821 (5)
H19B1.2159440.5093270.1113070.112*0.821 (5)
H19C1.0665830.4586000.1034480.112*0.821 (5)
C18B0.9733 (13)0.5011 (6)0.2206 (8)0.058 (3)0.179 (5)
H18C1.0050390.5340400.2570900.070*0.179 (5)
H18D1.0974400.4771640.2423050.070*0.179 (5)
C19B0.960 (2)0.5068 (5)0.0915 (8)0.061 (3)0.179 (5)
H19D0.9663380.4734230.0559160.092*0.179 (5)
H19E1.0905190.5272340.0653720.092*0.179 (5)
H19F0.8145450.5234670.0704340.092*0.179 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0308 (7)0.0297 (7)0.0318 (7)−0.0014 (5)0.0010 (5)0.0029 (5)
O10.0368 (6)0.0420 (6)0.0302 (5)0.0042 (5)−0.0033 (4)0.0014 (4)
N10.0334 (6)0.0346 (7)0.0297 (6)0.0030 (5)0.0000 (5)−0.0028 (5)
N20.0316 (6)0.0307 (6)0.0266 (5)0.0029 (5)0.0013 (4)0.0008 (5)
C20.0296 (7)0.0292 (7)0.0285 (6)−0.0014 (5)0.0013 (5)0.0035 (5)
N30.0307 (6)0.0369 (7)0.0446 (7)0.0047 (5)0.0007 (5)0.0037 (5)
C30.0370 (8)0.0387 (8)0.0300 (7)−0.0022 (6)0.0002 (6)0.0017 (6)
N40.0321 (7)0.0360 (7)0.0590 (8)0.0054 (5)0.0015 (6)0.0074 (6)
C40.0387 (8)0.0443 (9)0.0347 (7)−0.0047 (7)−0.0056 (6)0.0082 (6)
C50.0324 (7)0.0404 (9)0.0468 (9)0.0000 (6)−0.0054 (6)0.0115 (7)
N50.0300 (6)0.0326 (7)0.0445 (7)0.0013 (5)−0.0004 (5)0.0008 (5)
C60.0330 (7)0.0318 (8)0.0420 (8)0.0015 (6)0.0005 (6)0.0024 (6)
C70.0316 (7)0.0314 (7)0.0280 (6)−0.0004 (6)0.0021 (5)0.0029 (5)
C80.0366 (8)0.0344 (8)0.0346 (7)0.0044 (6)−0.0017 (6)−0.0050 (6)
C90.0455 (9)0.0438 (10)0.0582 (10)−0.0026 (8)−0.0012 (8)−0.0141 (8)
C100.0405 (9)0.0512 (10)0.0411 (8)0.0039 (7)0.0032 (7)−0.0106 (7)
C110.0324 (7)0.0350 (8)0.0296 (6)0.0050 (6)0.0052 (5)0.0008 (6)
C120.0304 (7)0.0326 (7)0.0275 (6)0.0039 (5)−0.0004 (5)−0.0026 (5)
C130.0290 (7)0.0346 (8)0.0385 (7)0.0045 (6)−0.0012 (6)0.0013 (6)
C140.0358 (8)0.0348 (8)0.0567 (10)−0.0045 (6)−0.0001 (7)0.0035 (7)
C150.0354 (8)0.0372 (8)0.0538 (9)0.0006 (6)0.0048 (7)0.0046 (7)
C160.0436 (9)0.0369 (9)0.0636 (11)−0.0008 (7)0.0124 (8)0.0025 (8)
C170.0648 (12)0.0539 (12)0.0574 (11)−0.0017 (10)0.0196 (9)0.0042 (9)
C18A0.0807 (19)0.0386 (15)0.0561 (17)0.0058 (12)0.0190 (14)0.0133 (11)
C19A0.0639 (17)0.0589 (17)0.101 (2)−0.0032 (13)0.0307 (16)0.0218 (15)
C18B0.093 (7)0.039 (6)0.042 (5)−0.009 (5)0.012 (5)0.009 (4)
C19B0.077 (7)0.059 (6)0.047 (5)−0.002 (5)0.011 (5)0.012 (5)
Geometric parameters (Å, º) top
C1—N11.4000 (18)C11—C121.496 (2)
C1—C21.398 (2)C12—C131.370 (2)
C1—C61.381 (2)C13—H130.9500
O1—C71.2257 (18)C14—H14A0.9900
N1—C71.3862 (18)C14—H14B0.9900
N1—C81.4386 (18)C14—C151.514 (2)
N2—C21.3901 (18)C15—H15A0.9900
N2—C71.3723 (18)C15—H15B0.9900
N2—C111.4560 (18)C15—C161.525 (2)
C2—C31.385 (2)C16—H16A0.9900
N3—N41.3219 (19)C16—H16B0.9900
N3—C121.3567 (18)C16—C171.522 (3)
C3—H30.9500C17—H17A0.9900
C3—C41.392 (2)C17—H17B0.9900
N4—N51.3414 (18)C17—H17C0.9900
C4—H40.9500C17—H17D0.9900
C4—C51.389 (2)C17—C18A1.534 (3)
C5—H50.9500C17—C18B1.539 (5)
C5—C61.391 (2)C18A—H18A0.9900
N5—C131.343 (2)C18A—H18B0.9900
N5—C141.464 (2)C18A—C19A1.518 (3)
C6—H60.9500C19A—H19A0.9800
C8—C91.492 (2)C19A—H19B0.9800
C8—C101.317 (2)C19A—H19C0.9800
C9—H9A0.9800C18B—H18C0.9900
C9—H9B0.9800C18B—H18D0.9900
C9—H9C0.9800C18B—C19B1.528 (5)
C10—H10A0.99 (2)C19B—H19D0.9800
C10—H10B0.99 (2)C19B—H19E0.9800
C11—H11A0.9900C19B—H19F0.9800
C11—H11B0.9900
O1···C93.185 (2)C7···H9C2.85
O1···H10Bi2.31 (2)H3···C7ii2.80
O1···H11B2.72C10···H9Ciii2.80
O1···H9C2.60H16B···H19A2.41
H3···O1ii2.69H17A···H19Ai2.36
H11A···O1ii2.37H17B···H19C2.41
C3···H11A2.87
C2—C1—N1106.82 (12)C12—C13—H13127.5
C6—C1—N1131.78 (14)N5—C14—H14A109.1
C6—C1—C2121.40 (14)N5—C14—H14B109.1
C1—N1—C8127.15 (12)N5—C14—C15112.42 (14)
C7—N1—C1109.41 (12)H14A—C14—H14B107.9
C7—N1—C8123.43 (12)C15—C14—H14A109.1
C2—N2—C11127.86 (12)C15—C14—H14B109.1
C7—N2—C2110.20 (12)C14—C15—H15A109.2
C7—N2—C11121.76 (12)C14—C15—H15B109.2
N2—C2—C1107.03 (12)C14—C15—C16111.90 (15)
C3—C2—C1121.46 (14)H15A—C15—H15B107.9
C3—C2—N2131.51 (14)C16—C15—H15A109.2
N4—N3—C12108.69 (12)C16—C15—H15B109.2
C2—C3—H3121.5C15—C16—H16A109.0
C2—C3—C4117.09 (14)C15—C16—H16B109.0
C4—C3—H3121.5H16A—C16—H16B107.8
N3—N4—N5107.16 (12)C17—C16—C15112.93 (16)
C3—C4—H4119.3C17—C16—H16A109.0
C5—C4—C3121.32 (14)C17—C16—H16B109.0
C5—C4—H4119.3C16—C17—H17A108.0
C4—C5—H5119.2C16—C17—H17B108.0
C4—C5—C6121.57 (15)C16—C17—H17C112.4
C6—C5—H5119.2C16—C17—H17D112.4
N4—N5—C13110.89 (13)C16—C17—C18A117.2 (2)
N4—N5—C14120.47 (13)C16—C17—C18B97.0 (4)
C13—N5—C14128.61 (13)H17A—C17—H17B107.2
C1—C6—C5117.16 (14)H17C—C17—H17D109.9
C1—C6—H6121.4C18A—C17—H17A108.0
C5—C6—H6121.4C18A—C17—H17B108.0
O1—C7—N1126.94 (13)C18B—C17—H17C112.4
O1—C7—N2126.51 (14)C18B—C17—H17D112.4
N2—C7—N1106.53 (12)C17—C18A—H18A109.4
N1—C8—C9115.25 (13)C17—C18A—H18B109.4
C10—C8—N1119.20 (15)H18A—C18A—H18B108.0
C10—C8—C9125.55 (15)C19A—C18A—C17111.0 (2)
C8—C9—H9A109.5C19A—C18A—H18A109.4
C8—C9—H9B109.5C19A—C18A—H18B109.4
C8—C9—H9C109.5C18A—C19A—H19A109.5
H9A—C9—H9B109.5C18A—C19A—H19B109.5
H9A—C9—H9C109.5C18A—C19A—H19C109.5
H9B—C9—H9C109.5H19A—C19A—H19B109.5
C8—C10—H10A120.9 (13)H19A—C19A—H19C109.5
C8—C10—H10B120.1 (13)H19B—C19A—H19C109.5
H10A—C10—H10B118.8 (17)C17—C18B—H18C110.6
N2—C11—H11A109.2C17—C18B—H18D110.6
N2—C11—H11B109.2H18C—C18B—H18D108.7
N2—C11—C12111.94 (11)C19B—C18B—C17105.7 (7)
H11A—C11—H11B107.9C19B—C18B—H18C110.6
C12—C11—H11A109.2C19B—C18B—H18D110.6
C12—C11—H11B109.2C18B—C19B—H19D109.5
N3—C12—C11120.90 (13)C18B—C19B—H19E109.5
N3—C12—C13108.30 (13)C18B—C19B—H19F109.5
C13—C12—C11130.80 (13)H19D—C19B—H19E109.5
N5—C13—C12104.97 (13)H19D—C19B—H19F109.5
N5—C13—H13127.5H19E—C19B—H19F109.5
C1—N1—C7—O1177.74 (14)C4—C5—C6—C1−0.6 (2)
C1—N1—C7—N2−0.87 (16)N5—C14—C15—C16−176.78 (13)
C1—N1—C8—C9118.16 (17)C6—C1—N1—C7−179.65 (15)
C1—N1—C8—C10−61.0 (2)C6—C1—N1—C81.2 (3)
C1—C2—C3—C40.4 (2)C6—C1—C2—N2179.77 (13)
N1—C1—C2—N2−0.88 (15)C6—C1—C2—C3−0.8 (2)
N1—C1—C2—C3178.54 (13)C7—N1—C8—C9−60.8 (2)
N1—C1—C6—C5−178.31 (15)C7—N1—C8—C10120.01 (18)
N2—C2—C3—C4179.71 (15)C7—N2—C2—C10.37 (16)
N2—C11—C12—N3147.34 (13)C7—N2—C2—C3−178.97 (15)
N2—C11—C12—C13−32.5 (2)C7—N2—C11—C12−74.12 (17)
C2—C1—N1—C71.10 (16)C8—N1—C7—O1−3.1 (2)
C2—C1—N1—C8−178.02 (14)C8—N1—C7—N2178.29 (13)
C2—C1—C6—C50.9 (2)C11—N2—C2—C1−174.74 (13)
C2—N2—C7—O1−178.31 (14)C11—N2—C2—C35.9 (2)
C2—N2—C7—N10.30 (16)C11—N2—C7—O1−2.8 (2)
C2—N2—C11—C12100.48 (16)C11—N2—C7—N1175.77 (12)
C2—C3—C4—C5−0.2 (2)C11—C12—C13—N5179.73 (14)
N3—N4—N5—C13−0.26 (18)C12—N3—N4—N50.17 (17)
N3—N4—N5—C14177.91 (14)C13—N5—C14—C15116.89 (18)
N3—C12—C13—N5−0.12 (16)C14—N5—C13—C12−177.75 (15)
C3—C4—C5—C60.3 (2)C14—C15—C16—C17−175.78 (15)
N4—N3—C12—C11−179.90 (13)C15—C16—C17—C18A−176.58 (17)
N4—N3—C12—C13−0.03 (17)C15—C16—C17—C18B−161.5 (6)
N4—N5—C13—C120.23 (17)C16—C17—C18A—C19A76.2 (3)
N4—N5—C14—C15−60.9 (2)C16—C17—C18B—C19B168.8 (9)
Symmetry codes: (i) x−1, y, z; (ii) x, −y+1/2, z+1/2; (iii) x+1, y, z.
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···O1iii0.99 (2)2.31 (2)3.284 (2)168.8 (18)
C11—H11A···O1ii0.992.373.3577 (17)173
C11—H11B···Cg1i0.992.763.5082 (18)135
C15—H15B···Cg1ii0.992.883.7599 (19)152
Symmetry codes: (i) x−1, y, z; (ii) x, −y+1/2, z+1/2; (iii) x+1, y, z.
 

Funding information

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

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ISSN: 2056-9890
Volume 80| Part 10| October 2024| Pages 1075-1080
https://doi.org/10.1107/S2056989024008703
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