In the crystal of the title compound, molecules are linked by N—H⋯N hydrogen bonds into chains running parallel to the c axis.
Keywords: (1H-benzimidazol-2-yl)(morpholin-4-yl)methanethione, crystal structure, Hirshfeld surface analysis, Wilgerodt–Kindler reaction
Abstract
The title compound, C12H13N3OS, was synthesized via the Willgerodt–Kindler method. The benzimidozole moiety is essentially planar (r.m.s. deviation = 0.0084 Å). The thioamide group is inclined by 54.80 (14)° to the benzimidazole ring system. The morpholine ring is disordered over two sets of sites [ratio 0.841 (11):0.159 (11)], with chair conformations for both components. In the crystal, molecules are linked into N—H⋯N hydrogen-bonded chains running parallel to the c axis. Hirshfeld surface analysis was used to quantify the intermolecular interactions.
1. Chemical context
Benzimidazole is a biologically important compound and a useful structural motif for designing molecules of biochemical and pharmacological relevance. Numerous studies have confirmed that these molecules are effective against various strains of microorganisms (El Ashry et al., 2016 ▸). Likewise, substituted benzimidazole derivatives possess various biological activities, including antibacterial (Kazimierczuk et al., 2002 ▸), antifungal (Ansari & Lal, 2009 ▸), antinematode (Mavrova et al., 2006 ▸), antiviral (Pandey & Shukla, 1999 ▸), anticancer (Hranjec et al., 2011 ▸) and antiprotozoal (Mavrova et al., 2010 ▸) properties. Similarly, the morpholine moiety is a versatile and readily accessible synthetic building block; it is easily introduced as an amine reagent or can be built according to a variety of available synthetic methodologies. This versatile scaffold, appropriately substituted, possesses a wide range of biological activities (Walia et al., 2011 ▸). Additionally, most drugs containing a morpholine moiety in their structure have been found to exhibit significant biological properties (Basavaraja et al., 2010 ▸).
In this context, the title compound with its bifunctional properties (benzimidazole and morpholine derivative, respectively) was synthesized and structurally characterized. The bifunctional properties predispose its potential biological activity, and the three nitrogen and one sulfur atoms can be used in reactions as electrophilic or nucleophilic sites for the formation of heterocyclic compounds.
2. Structural commentary
The title compound crystallizes with one molecule in the asymmetric unit (Fig. 1 ▸). The benzimidazole ring system is essentially planar, with a maximum deviation of 0.013 (3) Å for C6 from the mean plane (r.m.s. deviation = 0.0084 Å). The length of the C1—N2 bond is 1.353 (3) Å, slightly shorter than an isolated single C—N bond (1.382 Å; Berno & Gambarotta, 1994 ▸), while that of the C1—N1 bond is 1.322 (3) Å, slightly longer than an isolated C=N double bond (1.281 Å; Schmaunz et al., 2014 ▸), and the N3—C8 bond length of 1.322 (3) Å is the same as that of C1—N1, indicating conjugation of the p-orbital electrons over the imidazole ring. The thioamide group makes a dihedral angle of 54.80 (14)° with the benzimidazole ring system. Both components of the disordered morpholine ring [occupancy ratio 0.841 (11):0.159 (11)] adopt chair conformations. The puckering parameters (Cremer & Pople, 1975 ▸) of the ring (main occupancy component) are Q = 0.521 (6) Å, θ = 176.8 (8)°, φ = 80 (8)°. Weak intramolecular C12—H12A⋯N1 and C9—H9B⋯S1 hydrogen bonds help to consolidate the conformation of the molecule (Table 1 ▸).
Figure 1.
The molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. Open bonds refer to the minor component of the disordered morpholide ring.
Table 1. Hydrogen-bond geometry (Å, °).
| D—H⋯A | D—H | H⋯A | D⋯A | D—H⋯A |
|---|---|---|---|---|
| N2—H2⋯N1i | 0.84 (4) | 2.07 (4) | 2.903 (3) | 169 (3) |
| C9—H9B⋯S1 | 0.97 | 2.60 | 3.070 (5) | 110 |
| C12—H12A⋯N1 | 0.97 | 2.48 | 3.131 (5) | 124 |
Symmetry code: (i)
.
3. Supramolecular features
In the crystal, molecules are linked by N2—H2⋯N1 hydrogen bonds into chains running parallel to the c axis (Table 1 ▸, Fig. 2 ▸).
Figure 2.
A view of the crystal packing of the title compound along the a axis. Intermolecular N—H⋯N hydrogen bonds are indicated by blue dotted lines. Only the major component of the disordered morpholide ring is shown.
Analysis and calculations of the Hirshfeld surface were carried out with CrystalExplorer17.5 (Spackman et al., 2021 ▸). The d norm plots were mapped with a colour scale between −0.182 a.u. (blue) and 1.195 a.u. (red) and are shown Fig. 3 ▸. The red spots indicate the contribution of N—H⋯N hydrogen bonds.
Figure 3.
View of the three-dimensional Hirshfeld surface of the title compound plotted over d norm.
The expanded two-dimensional fingerprint plots (Seth, 2014 ▸; McKinnon et al., 2007 ▸) are displayed in Fig. 4 ▸ where d e and d i are the respective distances to the nearest nuclei outside and inside the surface from the Hirshfeld surface. The most important contributions to the crystal packing originate from H⋯H contacts (46.4%), followed by C⋯H/H⋯C contacts (21.0%) and S⋯H/H⋯S contacts (15.7%). Numerical data for other contributions are given in Fig. 4 ▸.
Figure 4.
Two-dimensional fingerprint plots of the title compound, showing (a) all interactions, and delineated into (b) H⋯H, (c) C⋯H/H⋯C, (d) S⋯H/H⋯S, (e) N⋯H/H⋯N and (f) O⋯H/H⋯O interactions.
4. Database survey
A search in the Cambridge Structural Database (CSD, version 2022; Groom et al., 2016 ▸) gave one match for the benzimidazoyl-thiocarbonate moiety, CSD refcode FUTSOF (Ranskiy et al., 2016 ▸). In the latter compound, the N and S atoms are bound to a CuII cation. The corresponding N—C bond lengths within the benzimidazole ring exhibit little difference from those the of title compound, except that the C8—S1 bond length is slightly longer [1.708 (7) Å] than in the title compound [1.658 (3) Å]. Another search in the CSD for the morpholin-4-yl-thiocarbonate moiety gave 54 hits, with atomic coordinates not available for five of these structures. In all of the structures, the morpholine ring has a chair conformation, with three structures showing disorder of the morpholine ring [CSD refcodes: QOVVUT (Ramasamy et al., 2009 ▸), TACVIE (Bocheńska et al., 2010 ▸) and YABDAG (Pudovik et al., 1990 ▸)].
5. Synthesis and crystallization
1H-Benzimidazol-2-yl(morpholin-4-yl)methanethione was synthesized using a previously reported procedure with minor modifications (Klingele & Brooker, 2004 ▸; Okamoto et al., 2007 ▸), as shown in Fig. 5 ▸.
Figure 5.
Schematic synthesis of 1H-benzimidazol-2-yl(morpholin-4-yl)methanethione (2).
Method (i): A reaction mixture consisting of 1.32 g (10 mmol) of 2-methylbenzimidazole (1), 1.68 ml (1.7 g, d = 1.01 g ml−1, 20 mmol) of morpholine and 0.96 g (30 mmol) of sulfur was heated in a round-bottomed flask at 448–453 K for 18 h. The excess of morpholine was evaporated, and the residue was treated with methanol. The resulting solid was filtered off and recrystallized from benzene, resulting in 1.52 g (61%) of morpholide (2). Melting point 513–515 K, R f = 0.25 (benzene:acetone 3:1 v:v).
Method (ii): 1.32 g (10 mmol) of 2-methylbenzimidazole, 0.92 ml (0.93 g, d = 1.01 g ml−1, 11.0 mmol) of morpholine, 0.96 g (30 mmol) of sulfur, 0.11 g (0.46 mmol) Na2S·9H2O and 5 ml of DMSO were mixed and heated in an oil bath at 403–408 K for 10 h. The reaction mixture was cooled to 343 K and extracted three times with 30 ml of a 5%wt NaOH solution. The extracts were combined and filtered. The filtrate was adjusted to pH 5–6 with H2SO4. The precipitate was filtered off and dried, then recrystallized from benzene and dried again. Yield 1.91 g (77.0%). Melting point 513–515 K, R f = 0.25 (benzene:acetone 3:1 v:v).
1H NMR (400 MHz, DMSO-d 6): 12.9 (1H, s, NH), 7.7 (1H, d, J = 8.0, H-4), 7.54 (1H, d, J = 7.9, H-7), 7.24–7.33 (2H, m, H-5,6), 4.37 (2H, br.t., J = 4.7, NCH2-morpholine), 4.22 (2H, br.t., J = 4.7, NCH2-morpholine), 3.82 (2H, br.t., J = 4.9, OCH2-morpholine), 3.71 (2H, br.t., J = 4.8, OCH2-morpholine). 13C NMR (400 MHz, DMSO-d 6): 50.19 (NCH2-morpholine), 52.95 (NCH2-morpholine), 65.94 (OCH2-morpholine), 66.62 (OCH2-morpholine), 112.2 (C-3a), 120.06 (C-4), 121.3 (C-5), 122.6 (C-6), 124.0 (C-7), 133.9 (C-7a), 142.2 (C-2), 148.9 (C=S). IR (ν, cm−1): 1614 (C=N), 1377 (C=S).
A single crystal suitable for X-ray diffraction was selected from crystals obtained by method (ii).
6. Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. Refinement of the structure with an ordered model gave remaining electron difference peaks about 0.5, 0.26 and 0.24 e− Å−3 near the morpholide ring, resulting in R1[F o > 4σ(F o)] = 0.039. Introduction of a disorder model including split positions for C9, C10, C11 and C12 of the morpholide ring resulted in a occupancy ratio of 0.841 (11):0.159 (11) for the major and minor components (atoms of the minor component denoted by the B). For atom pair C10/C10B, the SHELXL command EADP was used. All C-bound H atoms were positioned geometrically, with C—H = 0.96 Å (for methylene H atoms) and C—H = 0.93 Å (for aromatic H atoms), and were refined with U iso(H) = 1.2U eq(C). The H atom bound to N2 was located in a difference-Fourier map, and its coordinates and isotropic displacement parameter refined freely.
Table 2. Experimental details.
| Crystal data | |
| Chemical formula | C12H13N3OS |
| M r | 247.31 |
| Crystal system, space group | Monoclinic, I a |
| Temperature (K) | 293 |
| a, b, c (Å) | 8.1644 (2), 15.9237 (3), 9.6936 (2) |
| β (°) | 106.661 (2) |
| V (Å3) | 1207.33 (5) |
| Z | 4 |
| Radiation type | Cu Kα |
| μ (mm−1) | 2.28 |
| Crystal size (mm) | 0.30 × 0.25 × 0.14 |
| Data collection | |
| Diffractometer | XtaLAB Synergy, Single source at home/near, HyPix3000 |
| Absorption correction | Multi-scan (CrysAlis PRO; Rigaku OD, 2020 ▸) |
| T min, T max | 0.568, 1.000 |
| No. of measured, independent and observed [I > 2σ(I)] reflections | 5160, 1724, 1692 |
| R int | 0.022 |
| (sin θ/λ)max (Å−1) | 0.614 |
| Refinement | |
| R[F 2 > 2σ(F 2)], wR(F 2), S | 0.030, 0.079, 1.10 |
| No. of reflections | 1724 |
| No. of parameters | 189 |
| No. of restraints | 2 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.17, −0.19 |
| Absolute structure | Flack x determined using 531 quotients [(I +)−(I −)]/[(I +)+(I −)] (Parsons et al., 2013 ▸) |
| Absolute structure parameter | −0.001 (13) |
Supplementary Material
Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989022008933/wm5654sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989022008933/wm5654Isup2.hkl
Supporting information file. DOI: 10.1107/S2056989022008933/wm5654Isup3.cml
CCDC reference: 2165380
Additional supporting information: crystallographic information; 3D view; checkCIF report
Acknowledgments
The authors are grateful to the Institute of Bioorganic Chemistry, Academy Sciences of Uzbekistan, for providing laboratory facilities.
supplementary crystallographic information
Crystal data
| C12H13N3OS | Dx = 1.361 Mg m−3 |
| Mr = 247.31 | Melting point: 513(2) K |
| Monoclinic, Ia | Cu Kα radiation, λ = 1.54184 Å |
| a = 8.1644 (2) Å | Cell parameters from 4375 reflections |
| b = 15.9237 (3) Å | θ = 5.5–71.1° |
| c = 9.6936 (2) Å | µ = 2.28 mm−1 |
| β = 106.661 (2)° | T = 293 K |
| V = 1207.33 (5) Å3 | Needle, colourless |
| Z = 4 | 0.30 × 0.25 × 0.14 mm |
| F(000) = 520 |
Data collection
| XtaLAB Synergy, Single source at home/near, HyPix3000 diffractometer | 1724 independent reflections |
| Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source | 1692 reflections with I > 2σ(I) |
| Mirror monochromator | Rint = 0.022 |
| Detector resolution: 10.0000 pixels mm-1 | θmax = 71.3°, θmin = 5.5° |
| ω scans | h = −9→10 |
| Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2020) | k = −19→19 |
| Tmin = 0.568, Tmax = 1.000 | l = −9→11 |
| 5160 measured reflections |
Refinement
| Refinement on F2 | Hydrogen site location: mixed |
| Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
| R[F2 > 2σ(F2)] = 0.030 | w = 1/[σ2(Fo2) + (0.0448P)2 + 0.2955P] where P = (Fo2 + 2Fc2)/3 |
| wR(F2) = 0.079 | (Δ/σ)max < 0.001 |
| S = 1.10 | Δρmax = 0.17 e Å−3 |
| 1724 reflections | Δρmin = −0.19 e Å−3 |
| 189 parameters | Absolute structure: Flack x determined using 531 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
| 2 restraints | Absolute structure parameter: −0.001 (13) |
Special details
| Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
| x | y | z | Uiso*/Ueq | Occ. (<1) | |
| S1 | 0.43314 (11) | 0.91597 (4) | 0.55516 (11) | 0.0555 (2) | |
| O1 | 0.9333 (3) | 0.79690 (17) | 0.3720 (4) | 0.0726 (8) | |
| N1 | 0.3522 (3) | 0.69924 (13) | 0.3950 (2) | 0.0334 (4) | |
| N2 | 0.3362 (3) | 0.72781 (14) | 0.6169 (3) | 0.0354 (5) | |
| H2 | 0.350 (4) | 0.754 (2) | 0.695 (4) | 0.038 (8)* | |
| N3 | 0.6584 (3) | 0.81395 (16) | 0.4919 (4) | 0.0555 (8) | |
| C1 | 0.3992 (3) | 0.74997 (16) | 0.5073 (3) | 0.0316 (5) | |
| C2 | 0.1490 (4) | 0.6052 (2) | 0.6418 (4) | 0.0490 (7) | |
| H2B | 0.1429 | 0.6168 | 0.7342 | 0.059* | |
| C3 | 0.0676 (4) | 0.5366 (2) | 0.5648 (4) | 0.0540 (8) | |
| H3A | 0.0048 | 0.5012 | 0.6066 | 0.065* | |
| C4 | 0.0767 (4) | 0.51882 (19) | 0.4256 (4) | 0.0498 (7) | |
| H4A | 0.0210 | 0.4716 | 0.3780 | 0.060* | |
| C5 | 0.1663 (3) | 0.56963 (17) | 0.3576 (3) | 0.0397 (6) | |
| H5A | 0.1708 | 0.5581 | 0.2647 | 0.048* | |
| C6 | 0.2502 (3) | 0.63938 (15) | 0.4345 (3) | 0.0320 (5) | |
| C7 | 0.2407 (3) | 0.65587 (16) | 0.5736 (3) | 0.0337 (5) | |
| C8 | 0.5083 (3) | 0.82515 (16) | 0.5156 (3) | 0.0377 (6) | |
| C9 | 0.7777 (7) | 0.8840 (3) | 0.4960 (9) | 0.0661 (16) | 0.841 (11) |
| H9A | 0.8705 | 0.8823 | 0.5848 | 0.079* | 0.841 (11) |
| H9B | 0.7187 | 0.9373 | 0.4916 | 0.079* | 0.841 (11) |
| C10 | 0.8473 (9) | 0.8753 (4) | 0.3682 (10) | 0.078 (2) | 0.841 (11) |
| H10A | 0.7541 | 0.8790 | 0.2799 | 0.093* | 0.841 (11) |
| H10B | 0.9263 | 0.9209 | 0.3686 | 0.093* | 0.841 (11) |
| C11 | 0.8153 (7) | 0.7297 (3) | 0.3658 (7) | 0.0530 (12) | 0.841 (11) |
| H11A | 0.8722 | 0.6764 | 0.3637 | 0.064* | 0.841 (11) |
| H11B | 0.7213 | 0.7343 | 0.2782 | 0.064* | 0.841 (11) |
| C12 | 0.7468 (6) | 0.7322 (2) | 0.4947 (7) | 0.0466 (11) | 0.841 (11) |
| H12A | 0.6675 | 0.6863 | 0.4903 | 0.056* | 0.841 (11) |
| H12B | 0.8397 | 0.7270 | 0.5828 | 0.056* | 0.841 (11) |
| C9B | 0.715 (5) | 0.8869 (14) | 0.398 (5) | 0.067 (10) | 0.159 (11) |
| H9C | 0.6680 | 0.8780 | 0.2957 | 0.080* | 0.159 (11) |
| H9D | 0.6840 | 0.9425 | 0.4236 | 0.080* | 0.159 (11) |
| C10B | 0.901 (5) | 0.873 (2) | 0.447 (5) | 0.078 (2) | 0.159 (11) |
| H10C | 0.9395 | 0.8654 | 0.5504 | 0.093* | 0.159 (11) |
| H10D | 0.9605 | 0.9211 | 0.4221 | 0.093* | 0.159 (11) |
| C11B | 0.872 (4) | 0.7315 (17) | 0.446 (4) | 0.057 (7) | 0.159 (11) |
| H11C | 0.9141 | 0.7399 | 0.5495 | 0.069* | 0.159 (11) |
| H11D | 0.9110 | 0.6772 | 0.4231 | 0.069* | 0.159 (11) |
| C12B | 0.688 (4) | 0.7353 (11) | 0.400 (4) | 0.047 (7) | 0.159 (11) |
| H12C | 0.6372 | 0.6845 | 0.4243 | 0.057* | 0.159 (11) |
| H12D | 0.6445 | 0.7455 | 0.2971 | 0.057* | 0.159 (11) |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| S1 | 0.0713 (5) | 0.0311 (3) | 0.0723 (5) | 0.0025 (3) | 0.0340 (4) | −0.0069 (4) |
| O1 | 0.0627 (14) | 0.0675 (16) | 0.104 (2) | −0.0080 (12) | 0.0499 (15) | −0.0086 (15) |
| N1 | 0.0392 (10) | 0.0334 (10) | 0.0311 (11) | −0.0016 (8) | 0.0157 (9) | −0.0017 (8) |
| N2 | 0.0419 (12) | 0.0381 (11) | 0.0294 (12) | −0.0055 (9) | 0.0151 (9) | −0.0052 (10) |
| N3 | 0.0524 (15) | 0.0346 (13) | 0.092 (2) | −0.0092 (10) | 0.0407 (16) | −0.0091 (13) |
| C1 | 0.0349 (13) | 0.0307 (11) | 0.0307 (12) | −0.0001 (9) | 0.0121 (10) | −0.0004 (9) |
| C2 | 0.0532 (17) | 0.0567 (16) | 0.0425 (16) | −0.0104 (14) | 0.0226 (14) | 0.0030 (14) |
| C3 | 0.0517 (17) | 0.0498 (16) | 0.064 (2) | −0.0166 (14) | 0.0231 (16) | 0.0053 (15) |
| C4 | 0.0434 (15) | 0.0411 (15) | 0.065 (2) | −0.0097 (11) | 0.0154 (14) | −0.0078 (14) |
| C5 | 0.0369 (12) | 0.0408 (13) | 0.0410 (15) | −0.0029 (10) | 0.0105 (11) | −0.0085 (12) |
| C6 | 0.0314 (11) | 0.0330 (11) | 0.0325 (12) | 0.0012 (9) | 0.0107 (10) | −0.0017 (10) |
| C7 | 0.0351 (11) | 0.0350 (11) | 0.0329 (13) | −0.0020 (10) | 0.0127 (10) | −0.0002 (10) |
| C8 | 0.0460 (14) | 0.0318 (12) | 0.0375 (14) | −0.0042 (10) | 0.0153 (12) | −0.0009 (10) |
| C9 | 0.066 (3) | 0.052 (2) | 0.094 (5) | −0.027 (2) | 0.045 (3) | −0.021 (3) |
| C10 | 0.093 (4) | 0.057 (2) | 0.108 (5) | −0.012 (3) | 0.067 (5) | −0.003 (4) |
| C11 | 0.047 (3) | 0.052 (2) | 0.061 (3) | 0.0026 (18) | 0.017 (2) | −0.007 (2) |
| C12 | 0.0397 (19) | 0.0437 (19) | 0.059 (3) | 0.0014 (16) | 0.019 (2) | −0.0024 (19) |
| C9B | 0.09 (2) | 0.030 (9) | 0.11 (3) | 0.002 (11) | 0.07 (2) | 0.009 (14) |
| C10B | 0.093 (4) | 0.057 (2) | 0.108 (5) | −0.012 (3) | 0.067 (5) | −0.003 (4) |
| C11B | 0.049 (14) | 0.062 (14) | 0.058 (17) | 0.015 (10) | 0.010 (12) | −0.002 (13) |
| C12B | 0.050 (13) | 0.029 (8) | 0.08 (2) | −0.005 (8) | 0.040 (14) | 0.002 (10) |
Geometric parameters (Å, º)
| S1—C8 | 1.658 (3) | C5—C6 | 1.402 (3) |
| O1—C10 | 1.427 (7) | C5—H5A | 0.9300 |
| O1—C11 | 1.430 (5) | C6—C7 | 1.399 (4) |
| O1—C11B | 1.43 (3) | C9—C10 | 1.511 (10) |
| O1—C10B | 1.48 (4) | C9—H9A | 0.9700 |
| N1—C1 | 1.322 (3) | C9—H9B | 0.9700 |
| N1—C6 | 1.390 (3) | C10—H10A | 0.9700 |
| N2—C1 | 1.353 (3) | C10—H10B | 0.9700 |
| N2—C7 | 1.382 (3) | C11—C12 | 1.508 (8) |
| N2—H2 | 0.84 (4) | C11—H11A | 0.9700 |
| N3—C8 | 1.322 (3) | C11—H11B | 0.9700 |
| N3—C9 | 1.475 (5) | C12—H12A | 0.9700 |
| N3—C12 | 1.485 (5) | C12—H12B | 0.9700 |
| N3—C12B | 1.60 (2) | C9B—C10B | 1.47 (6) |
| N3—C9B | 1.62 (2) | C9B—H9C | 0.9700 |
| C1—C8 | 1.480 (3) | C9B—H9D | 0.9700 |
| C2—C3 | 1.380 (5) | C10B—H10C | 0.9700 |
| C2—C7 | 1.390 (4) | C10B—H10D | 0.9700 |
| C2—H2B | 0.9300 | C11B—C12B | 1.44 (4) |
| C3—C4 | 1.401 (5) | C11B—H11C | 0.9700 |
| C3—H3A | 0.9300 | C11B—H11D | 0.9700 |
| C4—C5 | 1.379 (4) | C12B—H12C | 0.9700 |
| C4—H4A | 0.9300 | C12B—H12D | 0.9700 |
| C10—O1—C11 | 109.5 (4) | O1—C10—C9 | 110.9 (6) |
| C11B—O1—C10B | 102 (2) | O1—C10—H10A | 109.5 |
| C1—N1—C6 | 104.3 (2) | C9—C10—H10A | 109.5 |
| C1—N2—C7 | 106.6 (2) | O1—C10—H10B | 109.5 |
| C1—N2—H2 | 127 (2) | C9—C10—H10B | 109.5 |
| C7—N2—H2 | 127 (2) | H10A—C10—H10B | 108.0 |
| C8—N3—C9 | 122.1 (3) | O1—C11—C12 | 110.5 (4) |
| C8—N3—C12 | 125.8 (3) | O1—C11—H11A | 109.5 |
| C9—N3—C12 | 110.4 (3) | C12—C11—H11A | 109.5 |
| C8—N3—C12B | 120.0 (9) | O1—C11—H11B | 109.5 |
| C8—N3—C9B | 115.3 (10) | C12—C11—H11B | 109.5 |
| C12B—N3—C9B | 97.8 (16) | H11A—C11—H11B | 108.1 |
| N1—C1—N2 | 113.7 (2) | N3—C12—C11 | 107.6 (4) |
| N1—C1—C8 | 124.5 (2) | N3—C12—H12A | 110.2 |
| N2—C1—C8 | 121.8 (2) | C11—C12—H12A | 110.2 |
| C3—C2—C7 | 116.4 (3) | N3—C12—H12B | 110.2 |
| C3—C2—H2B | 121.8 | C11—C12—H12B | 110.2 |
| C7—C2—H2B | 121.8 | H12A—C12—H12B | 108.5 |
| C2—C3—C4 | 122.0 (3) | C10B—C9B—N3 | 99 (3) |
| C2—C3—H3A | 119.0 | C10B—C9B—H9C | 112.1 |
| C4—C3—H3A | 119.0 | N3—C9B—H9C | 112.1 |
| C5—C4—C3 | 121.6 (3) | C10B—C9B—H9D | 112.1 |
| C5—C4—H4A | 119.2 | N3—C9B—H9D | 112.1 |
| C3—C4—H4A | 119.2 | H9C—C9B—H9D | 109.7 |
| C4—C5—C6 | 117.2 (3) | C9B—C10B—O1 | 106 (3) |
| C4—C5—H5A | 121.4 | C9B—C10B—H10C | 110.5 |
| C6—C5—H5A | 121.4 | O1—C10B—H10C | 110.5 |
| N1—C6—C7 | 109.9 (2) | C9B—C10B—H10D | 110.5 |
| N1—C6—C5 | 129.6 (2) | O1—C10B—H10D | 110.5 |
| C7—C6—C5 | 120.5 (2) | H10C—C10B—H10D | 108.7 |
| N2—C7—C2 | 132.2 (3) | O1—C11B—C12B | 107 (2) |
| N2—C7—C6 | 105.4 (2) | O1—C11B—H11C | 110.3 |
| C2—C7—C6 | 122.4 (2) | C12B—C11B—H11C | 110.3 |
| N3—C8—C1 | 117.1 (2) | O1—C11B—H11D | 110.3 |
| N3—C8—S1 | 125.5 (2) | C12B—C11B—H11D | 110.3 |
| C1—C8—S1 | 117.5 (2) | H11C—C11B—H11D | 108.5 |
| N3—C9—C10 | 108.0 (5) | C11B—C12B—N3 | 100 (3) |
| N3—C9—H9A | 110.1 | C11B—C12B—H12C | 111.8 |
| C10—C9—H9A | 110.1 | N3—C12B—H12C | 111.8 |
| N3—C9—H9B | 110.1 | C11B—C12B—H12D | 111.8 |
| C10—C9—H9B | 110.1 | N3—C12B—H12D | 111.8 |
| H9A—C9—H9B | 108.4 | H12C—C12B—H12D | 109.5 |
| C6—N1—C1—N2 | 0.1 (3) | C12—N3—C8—S1 | 162.8 (4) |
| C6—N1—C1—C8 | −179.1 (2) | C12B—N3—C8—S1 | −156.9 (15) |
| C7—N2—C1—N1 | 0.6 (3) | C9B—N3—C8—S1 | −40.3 (19) |
| C7—N2—C1—C8 | 179.8 (2) | N1—C1—C8—N3 | −55.2 (4) |
| C7—C2—C3—C4 | 0.1 (5) | N2—C1—C8—N3 | 125.7 (3) |
| C2—C3—C4—C5 | −0.7 (5) | N1—C1—C8—S1 | 125.4 (2) |
| C3—C4—C5—C6 | 0.9 (4) | N2—C1—C8—S1 | −53.7 (3) |
| C1—N1—C6—C7 | −0.7 (3) | C8—N3—C9—C10 | −135.7 (5) |
| C1—N1—C6—C5 | −179.5 (3) | C12—N3—C9—C10 | 58.2 (9) |
| C4—C5—C6—N1 | 178.1 (3) | C11—O1—C10—C9 | 61.3 (8) |
| C4—C5—C6—C7 | −0.5 (4) | N3—C9—C10—O1 | −59.2 (9) |
| C1—N2—C7—C2 | 179.1 (3) | C10—O1—C11—C12 | −62.0 (8) |
| C1—N2—C7—C6 | −1.0 (3) | C8—N3—C12—C11 | 135.6 (4) |
| C3—C2—C7—N2 | −179.8 (3) | C9—N3—C12—C11 | −58.9 (7) |
| C3—C2—C7—C6 | 0.3 (5) | O1—C11—C12—N3 | 60.2 (6) |
| N1—C6—C7—N2 | 1.1 (3) | C8—N3—C9B—C10B | 157 (2) |
| C5—C6—C7—N2 | 180.0 (2) | C12B—N3—C9B—C10B | −74 (3) |
| N1—C6—C7—C2 | −179.0 (3) | N3—C9B—C10B—O1 | 76 (3) |
| C5—C6—C7—C2 | −0.1 (4) | C11B—O1—C10B—C9B | −73 (4) |
| C9—N3—C8—C1 | 179.5 (5) | C10B—O1—C11B—C12B | 74 (4) |
| C12—N3—C8—C1 | −16.6 (5) | O1—C11B—C12B—N3 | −77 (3) |
| C12B—N3—C8—C1 | 23.7 (15) | C8—N3—C12B—C11B | −160.0 (16) |
| C9B—N3—C8—C1 | 140.3 (19) | C9B—N3—C12B—C11B | 75 (3) |
| C9—N3—C8—S1 | −1.1 (6) |
Hydrogen-bond geometry (Å, º)
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H2···N1i | 0.84 (4) | 2.07 (4) | 2.903 (3) | 169 (3) |
| C9—H9B···S1 | 0.97 | 2.60 | 3.070 (5) | 110 |
| C12—H12A···N1 | 0.97 | 2.48 | 3.131 (5) | 124 |
Symmetry code: (i) x, −y+3/2, z+1/2.
Funding Statement
This work was supported financially by the Ministry of Innovative Development of Uzbekistan (grant No. F-FA-2021-408 ‘Study of the laws of the introduction of pharmacophore fragments into the molecule on the basis of modern cross-coupling and heterocyclization reactions’).
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989022008933/wm5654sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989022008933/wm5654Isup2.hkl
Supporting information file. DOI: 10.1107/S2056989022008933/wm5654Isup3.cml
CCDC reference: 2165380
Additional supporting information: crystallographic information; 3D view; checkCIF report