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Synthesis, crystal structure and Hirshfeld surface analysis of (1H-benzimidazol-2-yl)(morpholin-4-yl)methane­thione

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aInstitute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, M. Ulugbek Str. 83, Tashkent 700125, Uzbekistan, bTurin Polytechnic University in Tashkent, Kichik Khalka yuli str. 17, 100095 Tashkent, Uzbekistan, and cS. Yunusov Institute of Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, Mirzo Ulugbek str. 77, Tashkent 100170, Uzbekistan
*Correspondence e-mail: luqmonjohn@mail.ru

Edited by M. Weil, Vienna University of Technology, Austria (Received 30 June 2022; accepted 6 September 2022; online 8 September 2022)

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[El Ashry, E. S., El Kilany, Y., Nahas, N. M., Barakat, A., Al-Qurashi, N., Ghabbour, H. A. & Fun, H. K. (2016). Molecules, 21, 12. https://doi.org/10.3390/molecules21010012]). Likewise, substituted benzimidazole derivatives possess various bio­logical activities, including anti­bacterial (Kazimierczuk et al., 2002[Kazimierczuk, Z., Upcroft, J. A., Upcroft, P., Górska, A., Starościak, B. & Laudy, A. (2002). Acta Biochim. Pol. 49, 185-195.]), anti­fungal (Ansari & Lal, 2009[Ansari, K. F. & Lal, C. (2009). Eur. J. Med. Chem. 44, 2294-2299.]), anti­nematode (Mavrova et al., 2006[Mavrova, A. T., Anichina, K. K., Vuchev, D. I., Tsenov, J. A., Denkova, P. S., Kondeva, M. S. & Micheva, M. K. (2006). Eur. J. Med. Chem. 41, 1412-1420.]), anti­viral (Pandey & Shukla, 1999[Pandey, V. K. & Shukla, A. (1999). Indian J. Chem. 38, 1381-1383.]), anti­cancer (Hranjec et al., 2011[Hranjec, M., Starčević, K., Pavelić, S. K., Lučin, P., Pavelić, K. & Zamola, G. K. (2011). Eur. J. Med. Chem. 46, 2274-2279.]) and anti­protozoal (Mavrova et al., 2010[Mavrova, A. T., Vuchev, D., Anichina, K. & Vassilev, N. (2010). Eur. J. Med. Chem. 45, 5856-5861.]) 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[Walia, R., Hedaitullah, M., Naaz, S. F., Iqbal, K. & Lamba, H. S. (2011). Int. J. Res. Pharm. Chem, 1, 565-574.]). Additionally, most drugs containing a morpholine moiety in their structure have been found to exhibit significant biological properties (Basavaraja et al., 2010[Basavaraja, H. S., Jayadevaiah, K. V., Mumtaz, M. H., Vijay Kumar, M. M. J. & Basavaraj, P. (2010). J. Pharm. Sci. Res. 2, 5-12.]).

[Scheme 1]

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[link]). 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[Berno, P. & Gambarotta, S. (1994). Organometallics, 13, 2569-2571.]), 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[Schmaunz, C. E., Mayer, P. & Wanner, K. T. (2014). Synthesis, 46, 1630-1638.]), 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[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]) 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[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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+{\script{3\over 2}}, z+{\script{1\over 2}}].
[Figure 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.

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[link], Fig. 2[link]).

[Figure 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[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.]). The dnorm plots were mapped with a colour scale between −0.182 a.u. (blue) and 1.195 a.u. (red) and are shown Fig. 3[link]. The red spots indicate the contribution of N—H⋯N hydrogen bonds.

[Figure 3]
Figure 3
View of the three-dimensional Hirshfeld surface of the title compound plotted over dnorm.

The expanded two-dimensional fingerprint plots (Seth, 2014[Seth, S. K. (2014). J. Mol. Struct. 1064, 70-75.]; McKinnon et al., 2007[McKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. pp. 3814-3816.]) are displayed in Fig. 4[link] where de and di 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[link].

[Figure 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[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) gave one match for the benzimidazoyl-thio­carbonate moiety, CSD refcode FUTSOF (Ranskiy et al., 2016[Ranskiy, A. P., Didenko, N. O. & Gordienko, O. A. (2016). Ukrain. J. Chem, 82, 117-125.]). 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[Ramasamy, K., Malik, M. A., O'Brien, P. & Raftery, J. (2009). Dalton Trans. p. 2196-2200 .]), TACVIE (Bocheńska et al., 2010[Bocheńska, M., Kulesza, J., Chojnacki, J., Arnaud-Neu, F. & Hubscher-Bruder, V. (2010). J. Incl Phenom. Macrocycl Chem. 68, 75-83.]) and YABDAG (Pudovik et al., 1990[Pudovik, A. N., Khairullin, V. K., Vasyanina, M. A., Pokrovskaya, I. K., Kataeva, O. N., Litvinov, I. A. & Naumov, V. A. (1990). Izv. Akad. Nauk SSSR Ser. Khim. p. 2590.])].

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[Klingele, M. H. & Brooker, S. (2004). Eur. J. Org. Chem. pp. 3422-3434.]; Okamoto et al., 2007[Okamoto, K., Yamamoto, T. & Kanbara, T. (2007). Synlett, pp. 2687-2690.]), as shown in Fig. 5[link].

[Figure 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, Rf = 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, Rf = 0.25 (benzene:acetone 3:1 v:v).

1H NMR (400 MHz, DMSO-d6): 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-d6): 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[link]. 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[Fo > 4σ(Fo)] = 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 Uiso(H) = 1.2Ueq(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
Mr 247.31
Crystal system, space group Monoclinic, Ia
Temperature (K) 293
a, b, c (Å) 8.1644 (2), 15.9237 (3), 9.6936 (2)
β (°) 106.661 (2)
V3) 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[Rigaku OD (2020). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.])
Tmin, Tmax 0.568, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 5160, 1724, 1692
Rint 0.022
(sin θ/λ)max−1) 0.614
 
Refinement
R[F2 > 2σ(F2)], wR(F2), 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[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter −0.001 (13)
Computer programs: CrysAlis PRO (Rigaku OD, 2020[Rigaku OD (2020). 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.]), XP (Siemens, 1994[Siemens (1994). XP. Siemens Analytical X-Ray Instruments Inc., Madison, Wisconsin, USA.]), Mercury (Macrae et al. 2020[Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M. & Wood, P. A. (2020). J. Appl. Cryst. 53, 226-235.]) and PLATON (Spek, 2020[Spek, A. L. (2020). Acta Cryst. E76, 1-11.]).

Supporting information


Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2020); cell refinement: CrysAlis PRO (Rigaku OD, 2020); data reduction: CrysAlis PRO (Rigaku OD, 2020); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: XP (Siemens, 1994), Mercury (Macrae et al. 2020); software used to prepare material for publication: PLATON (Spek, 2020).

(1H-Benzimidazol-2-yl)(morpholin-4-yl)methanethione top
Crystal data top
C12H13N3OSDx = 1.361 Mg m3
Mr = 247.31Melting point: 513(2) K
Monoclinic, IaCu Kα radiation, λ = 1.54184 Å
a = 8.1644 (2) ÅCell parameters from 4375 reflections
b = 15.9237 (3) Åθ = 5.5–71.1°
c = 9.6936 (2) ŵ = 2.28 mm1
β = 106.661 (2)°T = 293 K
V = 1207.33 (5) Å3Needle, colourless
Z = 40.30 × 0.25 × 0.14 mm
F(000) = 520
Data collection top
XtaLAB Synergy, Single source at home/near, HyPix3000
diffractometer
1724 independent reflections
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source1692 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.022
Detector resolution: 10.0000 pixels mm-1θmax = 71.3°, θmin = 5.5°
ω scansh = 910
Absorption correction: multi-scan
(CrysAlisPro; Rigaku OD, 2020)
k = 1919
Tmin = 0.568, Tmax = 1.000l = 911
5160 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)] = 0.030 w = 1/[σ2(Fo2) + (0.0448P)2 + 0.2955P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.079(Δ/σ)max < 0.001
S = 1.10Δρmax = 0.17 e Å3
1724 reflectionsΔρmin = 0.19 e Å3
189 parametersAbsolute structure: Flack x determined using 531 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
2 restraintsAbsolute structure parameter: 0.001 (13)
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*/UeqOcc. (<1)
S10.43314 (11)0.91597 (4)0.55516 (11)0.0555 (2)
O10.9333 (3)0.79690 (17)0.3720 (4)0.0726 (8)
N10.3522 (3)0.69924 (13)0.3950 (2)0.0334 (4)
N20.3362 (3)0.72781 (14)0.6169 (3)0.0354 (5)
H20.350 (4)0.754 (2)0.695 (4)0.038 (8)*
N30.6584 (3)0.81395 (16)0.4919 (4)0.0555 (8)
C10.3992 (3)0.74997 (16)0.5073 (3)0.0316 (5)
C20.1490 (4)0.6052 (2)0.6418 (4)0.0490 (7)
H2B0.14290.61680.73420.059*
C30.0676 (4)0.5366 (2)0.5648 (4)0.0540 (8)
H3A0.00480.50120.60660.065*
C40.0767 (4)0.51882 (19)0.4256 (4)0.0498 (7)
H4A0.02100.47160.37800.060*
C50.1663 (3)0.56963 (17)0.3576 (3)0.0397 (6)
H5A0.17080.55810.26470.048*
C60.2502 (3)0.63938 (15)0.4345 (3)0.0320 (5)
C70.2407 (3)0.65587 (16)0.5736 (3)0.0337 (5)
C80.5083 (3)0.82515 (16)0.5156 (3)0.0377 (6)
C90.7777 (7)0.8840 (3)0.4960 (9)0.0661 (16)0.841 (11)
H9A0.87050.88230.58480.079*0.841 (11)
H9B0.71870.93730.49160.079*0.841 (11)
C100.8473 (9)0.8753 (4)0.3682 (10)0.078 (2)0.841 (11)
H10A0.75410.87900.27990.093*0.841 (11)
H10B0.92630.92090.36860.093*0.841 (11)
C110.8153 (7)0.7297 (3)0.3658 (7)0.0530 (12)0.841 (11)
H11A0.87220.67640.36370.064*0.841 (11)
H11B0.72130.73430.27820.064*0.841 (11)
C120.7468 (6)0.7322 (2)0.4947 (7)0.0466 (11)0.841 (11)
H12A0.66750.68630.49030.056*0.841 (11)
H12B0.83970.72700.58280.056*0.841 (11)
C9B0.715 (5)0.8869 (14)0.398 (5)0.067 (10)0.159 (11)
H9C0.66800.87800.29570.080*0.159 (11)
H9D0.68400.94250.42360.080*0.159 (11)
C10B0.901 (5)0.873 (2)0.447 (5)0.078 (2)0.159 (11)
H10C0.93950.86540.55040.093*0.159 (11)
H10D0.96050.92110.42210.093*0.159 (11)
C11B0.872 (4)0.7315 (17)0.446 (4)0.057 (7)0.159 (11)
H11C0.91410.73990.54950.069*0.159 (11)
H11D0.91100.67720.42310.069*0.159 (11)
C12B0.688 (4)0.7353 (11)0.400 (4)0.047 (7)0.159 (11)
H12C0.63720.68450.42430.057*0.159 (11)
H12D0.64450.74550.29710.057*0.159 (11)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0713 (5)0.0311 (3)0.0723 (5)0.0025 (3)0.0340 (4)0.0069 (4)
O10.0627 (14)0.0675 (16)0.104 (2)0.0080 (12)0.0499 (15)0.0086 (15)
N10.0392 (10)0.0334 (10)0.0311 (11)0.0016 (8)0.0157 (9)0.0017 (8)
N20.0419 (12)0.0381 (11)0.0294 (12)0.0055 (9)0.0151 (9)0.0052 (10)
N30.0524 (15)0.0346 (13)0.092 (2)0.0092 (10)0.0407 (16)0.0091 (13)
C10.0349 (13)0.0307 (11)0.0307 (12)0.0001 (9)0.0121 (10)0.0004 (9)
C20.0532 (17)0.0567 (16)0.0425 (16)0.0104 (14)0.0226 (14)0.0030 (14)
C30.0517 (17)0.0498 (16)0.064 (2)0.0166 (14)0.0231 (16)0.0053 (15)
C40.0434 (15)0.0411 (15)0.065 (2)0.0097 (11)0.0154 (14)0.0078 (14)
C50.0369 (12)0.0408 (13)0.0410 (15)0.0029 (10)0.0105 (11)0.0085 (12)
C60.0314 (11)0.0330 (11)0.0325 (12)0.0012 (9)0.0107 (10)0.0017 (10)
C70.0351 (11)0.0350 (11)0.0329 (13)0.0020 (10)0.0127 (10)0.0002 (10)
C80.0460 (14)0.0318 (12)0.0375 (14)0.0042 (10)0.0153 (12)0.0009 (10)
C90.066 (3)0.052 (2)0.094 (5)0.027 (2)0.045 (3)0.021 (3)
C100.093 (4)0.057 (2)0.108 (5)0.012 (3)0.067 (5)0.003 (4)
C110.047 (3)0.052 (2)0.061 (3)0.0026 (18)0.017 (2)0.007 (2)
C120.0397 (19)0.0437 (19)0.059 (3)0.0014 (16)0.019 (2)0.0024 (19)
C9B0.09 (2)0.030 (9)0.11 (3)0.002 (11)0.07 (2)0.009 (14)
C10B0.093 (4)0.057 (2)0.108 (5)0.012 (3)0.067 (5)0.003 (4)
C11B0.049 (14)0.062 (14)0.058 (17)0.015 (10)0.010 (12)0.002 (13)
C12B0.050 (13)0.029 (8)0.08 (2)0.005 (8)0.040 (14)0.002 (10)
Geometric parameters (Å, º) top
S1—C81.658 (3)C5—C61.402 (3)
O1—C101.427 (7)C5—H5A0.9300
O1—C111.430 (5)C6—C71.399 (4)
O1—C11B1.43 (3)C9—C101.511 (10)
O1—C10B1.48 (4)C9—H9A0.9700
N1—C11.322 (3)C9—H9B0.9700
N1—C61.390 (3)C10—H10A0.9700
N2—C11.353 (3)C10—H10B0.9700
N2—C71.382 (3)C11—C121.508 (8)
N2—H20.84 (4)C11—H11A0.9700
N3—C81.322 (3)C11—H11B0.9700
N3—C91.475 (5)C12—H12A0.9700
N3—C121.485 (5)C12—H12B0.9700
N3—C12B1.60 (2)C9B—C10B1.47 (6)
N3—C9B1.62 (2)C9B—H9C0.9700
C1—C81.480 (3)C9B—H9D0.9700
C2—C31.380 (5)C10B—H10C0.9700
C2—C71.390 (4)C10B—H10D0.9700
C2—H2B0.9300C11B—C12B1.44 (4)
C3—C41.401 (5)C11B—H11C0.9700
C3—H3A0.9300C11B—H11D0.9700
C4—C51.379 (4)C12B—H12C0.9700
C4—H4A0.9300C12B—H12D0.9700
C10—O1—C11109.5 (4)O1—C10—C9110.9 (6)
C11B—O1—C10B102 (2)O1—C10—H10A109.5
C1—N1—C6104.3 (2)C9—C10—H10A109.5
C1—N2—C7106.6 (2)O1—C10—H10B109.5
C1—N2—H2127 (2)C9—C10—H10B109.5
C7—N2—H2127 (2)H10A—C10—H10B108.0
C8—N3—C9122.1 (3)O1—C11—C12110.5 (4)
C8—N3—C12125.8 (3)O1—C11—H11A109.5
C9—N3—C12110.4 (3)C12—C11—H11A109.5
C8—N3—C12B120.0 (9)O1—C11—H11B109.5
C8—N3—C9B115.3 (10)C12—C11—H11B109.5
C12B—N3—C9B97.8 (16)H11A—C11—H11B108.1
N1—C1—N2113.7 (2)N3—C12—C11107.6 (4)
N1—C1—C8124.5 (2)N3—C12—H12A110.2
N2—C1—C8121.8 (2)C11—C12—H12A110.2
C3—C2—C7116.4 (3)N3—C12—H12B110.2
C3—C2—H2B121.8C11—C12—H12B110.2
C7—C2—H2B121.8H12A—C12—H12B108.5
C2—C3—C4122.0 (3)C10B—C9B—N399 (3)
C2—C3—H3A119.0C10B—C9B—H9C112.1
C4—C3—H3A119.0N3—C9B—H9C112.1
C5—C4—C3121.6 (3)C10B—C9B—H9D112.1
C5—C4—H4A119.2N3—C9B—H9D112.1
C3—C4—H4A119.2H9C—C9B—H9D109.7
C4—C5—C6117.2 (3)C9B—C10B—O1106 (3)
C4—C5—H5A121.4C9B—C10B—H10C110.5
C6—C5—H5A121.4O1—C10B—H10C110.5
N1—C6—C7109.9 (2)C9B—C10B—H10D110.5
N1—C6—C5129.6 (2)O1—C10B—H10D110.5
C7—C6—C5120.5 (2)H10C—C10B—H10D108.7
N2—C7—C2132.2 (3)O1—C11B—C12B107 (2)
N2—C7—C6105.4 (2)O1—C11B—H11C110.3
C2—C7—C6122.4 (2)C12B—C11B—H11C110.3
N3—C8—C1117.1 (2)O1—C11B—H11D110.3
N3—C8—S1125.5 (2)C12B—C11B—H11D110.3
C1—C8—S1117.5 (2)H11C—C11B—H11D108.5
N3—C9—C10108.0 (5)C11B—C12B—N3100 (3)
N3—C9—H9A110.1C11B—C12B—H12C111.8
C10—C9—H9A110.1N3—C12B—H12C111.8
N3—C9—H9B110.1C11B—C12B—H12D111.8
C10—C9—H9B110.1N3—C12B—H12D111.8
H9A—C9—H9B108.4H12C—C12B—H12D109.5
C6—N1—C1—N20.1 (3)C12—N3—C8—S1162.8 (4)
C6—N1—C1—C8179.1 (2)C12B—N3—C8—S1156.9 (15)
C7—N2—C1—N10.6 (3)C9B—N3—C8—S140.3 (19)
C7—N2—C1—C8179.8 (2)N1—C1—C8—N355.2 (4)
C7—C2—C3—C40.1 (5)N2—C1—C8—N3125.7 (3)
C2—C3—C4—C50.7 (5)N1—C1—C8—S1125.4 (2)
C3—C4—C5—C60.9 (4)N2—C1—C8—S153.7 (3)
C1—N1—C6—C70.7 (3)C8—N3—C9—C10135.7 (5)
C1—N1—C6—C5179.5 (3)C12—N3—C9—C1058.2 (9)
C4—C5—C6—N1178.1 (3)C11—O1—C10—C961.3 (8)
C4—C5—C6—C70.5 (4)N3—C9—C10—O159.2 (9)
C1—N2—C7—C2179.1 (3)C10—O1—C11—C1262.0 (8)
C1—N2—C7—C61.0 (3)C8—N3—C12—C11135.6 (4)
C3—C2—C7—N2179.8 (3)C9—N3—C12—C1158.9 (7)
C3—C2—C7—C60.3 (5)O1—C11—C12—N360.2 (6)
N1—C6—C7—N21.1 (3)C8—N3—C9B—C10B157 (2)
C5—C6—C7—N2180.0 (2)C12B—N3—C9B—C10B74 (3)
N1—C6—C7—C2179.0 (3)N3—C9B—C10B—O176 (3)
C5—C6—C7—C20.1 (4)C11B—O1—C10B—C9B73 (4)
C9—N3—C8—C1179.5 (5)C10B—O1—C11B—C12B74 (4)
C12—N3—C8—C116.6 (5)O1—C11B—C12B—N377 (3)
C12B—N3—C8—C123.7 (15)C8—N3—C12B—C11B160.0 (16)
C9B—N3—C8—C1140.3 (19)C9B—N3—C12B—C11B75 (3)
C9—N3—C8—S11.1 (6)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···N1i0.84 (4)2.07 (4)2.903 (3)169 (3)
C9—H9B···S10.972.603.070 (5)110
C12—H12A···N10.972.483.131 (5)124
Symmetry code: (i) x, y+3/2, z+1/2.
 

Acknowledgements

The authors are grateful to the Institute of Bioorganic Chemistry, Academy Sciences of Uzbekistan, for providing laboratory facilities.

Funding information

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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