Skip to main content
NCBI home page
Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2022 May 10;78(Pt 6):554–558. doi: 10.1107/S2056989022004741

Crystal structure and Hirshfeld surface analysis of 5-amino-5′-bromo-2′-oxo-2,3-di­hydro-1H-spiro­[imidazo[1,2-a]pyridine-7,3′-indoline]-6,8-dicarbo­nitrile dimethyl sulfoxide disolvate

Farid N Naghiyev a, Victor N Khrustalev b,c, Anton P Novikov b, Mehmet Akkurt d, Rovnag M Rzayev e, Anzurat A Akobirshoeva f,*, Ibrahim G Mamedov a
Editor: A S Batsanovg
PMCID: PMC9431780  PMID: 36072149

Inter­molecular N—H⋯O, C—H⋯O and C—H⋯N hydrogen bonds form a three-dimensional network in the crystal, connecting mol­ecules through the O atoms of solvent mol­ecules.

Keywords: crystal structure; spiro­[imidazo[1,2-a]pyridine; hydrogen bonds; dimethyl sulfoxide; disorder; Hirshfeld surface analysis

Abstract

In the title compound, C16H11BrN6O·2C2H6OS, the 1,2,3,7-tetra­hydro­imid­azo[1,2-a]pyridine ring system and the oxindole moiety are both nearly planar [maximum deviations = 0.042 (2) and 0.115 (2) Å, respectively] and their planes form a dihedral angle of 86.04 (5)° with each other. Inter­molecular N—H⋯O, C—H⋯O and C—H⋯N hydrogen bonds link mol­ecules in the crystal through the O atoms of the solvent mol­ecules, generating a three-dimensional network. A Hirshfeld surface analysis was performed to further analyse the inter­molecular inter­actions.

1. Chemical context

C—C and C—N bond-forming reactions represent a significant synthetic class because they play critical roles in various applications in different fields of chemistry (Yadigarov et al., 2009 ▸; Abdelhamid et al., 2011 ▸; Yin et al., 2020 ▸; Khalilov et al., 2021 ▸). Nitro­gen heterocycles, particularly those including the spiro­[imidazo[1,2-a]pyridine] moiety, play a key role in medi­cinal chemistry (Han et al., 2008 ▸; Mamedov et al., 2020 ▸; Samaneh et al., 2021 ▸). The conjugate addition to oxo­in­dol­inylidenemalono­nitriles has been well studied in simple two-component reactions with respect to producing spiro derivatives (Lu et al., 2012 ▸; Jun et al., 2019 ▸). We have previously reported the three-component reaction of 2-(2-oxoindolin-3-yl­idene)malono­nitrile with malono­nitrile and ethyl­enedi­amine which resulted in 5-amino-2′-oxo-2,3-di­hydro-1H-spiro­[imidazo[1,2-a]pyridine-7,3′-indoline]-6,8-dicarbo­nitrile (Magerramov et al., 2018 ▸). In the framework of our ongoing structural studies (Naghiyev et al., 2020 ▸, 2021a ▸,b ▸), herein the crystal structure and Hirshfeld surface analysis of 5-amino-5′-bromo-2′-oxo-2,3-di­hydro-1H-spiro­[imidazo[1,2-a]pyridine-7,3′-indoline]-6,8-dicarbo­nitrile, (1), is reported.

2. Structural commentary

In the title compound, (1) (see Scheme and Fig. 1 ▸), the 1,2,3,7-tetra­hydro­imidazo[1,2-a]pyridine ring system (N1/N4/C2/C3/C5–C8/C8A) and the oxindole moiety (O1/N2/C1/C7/C11–C16) are nearly planar, with maximum deviations of 0.042 (2) Å for C3 and 0.115 (2) Å for O1. These ring systems make a dihedral angle of 86.04 (5)° with each other. The cyano (–C≡N) and amine (NH2) groups form an inter­molecular hydrogen bond with one dimethyl sulfoxide (DMSO) group, giving an S(10) motif (Bernstein et al., 1995 ▸) (Table 1 ▸). 2.

Figure 1.

Figure 1

Open in a new tab

The title mol­ecule with the labelling scheme and displacement ellipsoids drawn at the 50% probability level. The minor components of the disorder are not shown.

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1⋯O2A i 0.90 1.98 2.855 (4) 165
N1—H1⋯O2B i 0.90 2.00 2.87 (4) 160
N2—H2⋯O2A ii 0.90 1.91 2.793 (5) 166
N2—H2⋯O2B ii 0.90 1.94 2.82 (5) 166
N5—H5A⋯O3A iii 0.90 2.20 3.034 (3) 155
N5—H5B⋯O3A 0.90 2.06 2.918 (3) 160
C2—H2B⋯N9iv 0.99 2.59 3.469 (4) 148
C19A—H19A⋯N9 0.98 2.41 3.114 (5) 128
C19A—H19C⋯O1v 0.98 2.52 3.392 (4) 148
C20A—H20B⋯O1v 0.98 2.46 3.359 (4) 152
Open in a new tab

Symmetry codes: (i) Inline graphic ; (ii) Inline graphic ; (iii) Inline graphic ; (iv) Inline graphic ; (v) Inline graphic .

3. Supra­molecular features and Hirshfeld surface analysis

In the crystal, mol­ecules are linked through the O atoms of the DMSO solvent mol­ecules by inter­molecular N—H⋯O and C—H⋯O hydrogen bonds which, together with C—H⋯N hydrogen bonds, form a three-dimensional (3D) network (Table 1 ▸ and Fig. 2 ▸). The π-cloud of the C8A—N1 bond (which has some multiple-bond character) acts as an electron donor to Br1 in a kind of ‘halogen bond’, with a Br1⋯C8A(−x + 1, −y + 1, −z) distance of 3.284 (2) Å.

Figure 2.

Figure 2

Open in a new tab

A view of the mol­ecular packing of (1) along the a-axis direction.

The Hirshfeld surfaces were calculated and the two-dimensional (2D) fingerprint plots generated using CrystalExplorer (Version 17.5; Turner et al., 2017 ▸). Fig. 3 ▸ shows the 3D Hirshfeld surface of (1) with d norm (normalized contact distance) plotted over the range from −0.6206 to 1.3180 a.u. The inter­actions given in Table 1 ▸ play a key role in the mol­ecular packing of (1).

Figure 3.

Figure 3

Open in a new tab

View of the 3D Hirshfeld surface of (1) plotted over d norm in the range from −0.6206 to 1.3180 a.u.

The overall 2D fingerprint plot for (1) is given in Fig. 4 ▸(a), and those delineated into H⋯H, N⋯H/H⋯N, O⋯H/H⋯O, C⋯H/H⋯C and Br⋯H/H⋯Br contacts are shown in Figs. 4 ▸(b)–(f). The percentage contributions to the Hirshfeld surfaces from the various inter­atomic contacts are as follows: H⋯H [Fig. 4 ▸(b); 27.1%], N⋯H/H⋯N [Fig. 4 ▸(c); 23.8%], O⋯H/H⋯O [Fig. 4 ▸(d); 15.7%], C⋯H/H⋯C [Fig. 4 ▸(e); 13.2%] and Br⋯H/H⋯Br [Fig. 4 ▸(f); 10.2%]. Other minor contributions to the Hirshfeld surface are from Br⋯C/C⋯Br (3.9%), Br⋯N/N⋯Br (2.0%), C⋯C (1.5%), S⋯C/C⋯S (0.8%), S⋯H/H⋯S (0.6%), S⋯N/N⋯S (0.4%), O⋯N/N⋯O (0.4%) and Br⋯O/O⋯Br (0.3%).

Figure 4.

Figure 4

Open in a new tab

The full 2D fingerprint plots for (1), showing (a) all inter­actions, and delineated into (b) H⋯H, (c) N⋯H/H⋯N, (d) O⋯H/H⋯O, (e) C⋯H/H⋯C and (f) Br⋯H/H⋯Br inter­actions. The d i and d e values are the closest inter­nal and external distances (in Å) from given points on the Hirshfeld surface contacts.

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.42, update of September 2021; Groom et al., 2016 ▸) for the 5-bromo-1,3-di­hydro-2H-indol-2-one unit of (1) gave 87 hits. The three compounds most resembling (1) are (I) (COGQAS; Nagalakshmi et al., 2014a ▸), (II) (WOPKAP; Nagalakshmi et al., 2014b ▸) and (III) (XODQOY; Nagalakshmi et al., 2014c ▸), showing very similar conformation of the mol­ecular core.

In the crystal of (I), N—H⋯O hydrogen bonds lead to the formation of chains along the c-axis direction. Within the chains there are further N—H⋯O and C—H⋯O hydrogen bonds enclosing Inline graphic (14) ring motifs. The chains are linked via N—H⋯O and C—H⋯O hydrogen bonds involving the dimethyl sulfoxide solvent mol­ecule which acts as both an acceptor and a donor.

In (II), the asymmetric unit contains two independent mol­ecules (A and B) having similar conformations. In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, forming chains along the a axis which enclose Inline graphic (16) ring motifs. The rings are linked by weak N—H⋯O and C—H⋯O hydrogen bonds, and C—H⋯π inter­actions, forming sheets lying parallel to the (001) plane.

In (III), two intra­molecular N—H⋯O hydrogen bonds are formed, each closing an S(6) loop. In the crystal, strong N—H⋯O hydrogen bonds lead to the formation of zigzag chains along the c axis. These are consolidated in the 3D crystal packing by weak N—H⋯O hydrogen bonding, as well as by C—H⋯O, C—H⋯Br and C—H⋯π inter­actions.

5. Synthesis and crystallization

To a solution of 2-(5-bromo-2-oxoindolin-3-yl­idene)malono­nitrile (1.4 g, 5.1 mmol), which was previously prepared by a known procedure (Negar et al., 2012 ▸), and malono­nitrile (0.34 g, 5.2 mmol) in methanol (25 ml), ethyl­enedi­amine (0.31 g, 5.2 mmol) was added and the mixture was stirred at room temperature for 72 h (Fig. 5 ▸). Methanol (15 ml) was removed from the reaction mixture, which was left overnight. The precipitated crystals were separated by filtration and recrystallized from an ethanol–water (1:1 v/v) solution (yield 69%; m.p. 479–480 K). Single crystals of (1) were grown from DMSO solution.

Figure 5.

Figure 5

Open in a new tab

The synthesis of 5-amino-5′-bromo-2′-oxo-2,3-di­hydro-1H-spiro­[imidazo[1,2-a]pyridine-7,3′-indoline]-6,8-dicarbo­nitrile by a reported procedure (Magerramov et al., 2018 ▸).

1H NMR (300 MHz, DMSO-d 6, ppm): δ 3.50 (t, 4H, 2CH2N), 6.61 (s, 2H, NH2), 6.78 (d, 1H, Ar-H, 3 J H-H = 7.8 Hz), 7.35 (s, 1H, Ar-H), 7.37 (d, 1H, Ar-H, 3 J H-H = 7.8 Hz), 7.73 (s, H, NH), 10.44 (s, H, NH). 13C NMR (75 MHz, DMSO-d 6, ppm): δ 42.46 (CH2N), 45.15 (CH2N), 51.24 (Cquat), 51.71 (=Cquat), 54.69 (=Cquat), 112.02 (CHarom), 114.43 (Br—Carom), 119.63 (CN), 120.15 (CN), 128.02 (CHarom), 131.90 (CHarom), 137.83 (Carom), 140.80 (Carom), 152.19 (=Cquat), 154.76 (=Cquat), 179.67 (O=C).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. The H atoms were included in calculated positions and treated as riding atoms; N—H = 0.90 Å with U iso(H) = 1.2U eq(N), and C—H = 0.95–0.99 Å with U iso(H) = 1.2 or 1.5U eq(C). Both DMSO solvent mol­ecules are disordered over two positions, with final occupancies of 0.90:0.10 for the first and 0.95:0.05 for the second mol­ecule. In the first disordered DMSO molecule, the C17B and C18B atoms of the minor component were refined isotropically. The disordered atoms O2A/O2B, O3A/O3B, C19A/C19B and C20A/C20B were refined with anisotropic displacement parameters, constrained to be the same for both components. The S—C and S—O bond lengths in both disordered DMSO mol­ecules were restrained to similarity.

Table 2. Experimental details.

Crystal data
Chemical formula C16H11BrN6O·2C2H6OS
M r 539.47
Crystal system, space group Monoclinic, P21/c
Temperature (K) 100
a, b, c (Å) 10.3940 (1), 26.2421 (2), 8.9860 (1)
β (°) 108.056 (1)
V (Å3) 2330.32 (4)
Z 4
Radiation type Cu Kα
μ (mm−1) 4.38
Crystal size (mm) 0.05 × 0.03 × 0.02
 
Data collection
Diffractometer Rigaku XtaLAB Synergy Dualflex HyPix
Absorption correction Multi-scan (CrysAlis PRO; Rigaku OD, 2021 ▸)
T min, T max 0.793, 0.899
No. of measured, independent and observed [I > 2σ(I)] reflections 31508, 5062, 5047
R int 0.029
(sin θ/λ)max (Å−1) 0.638
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.039, 0.094, 1.17
No. of reflections 5062
No. of parameters 331
No. of restraints 6
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.63, −0.41
Open in a new tab

Computer programs: CrysAlis PRO (Rigaku OD, 2021 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL (Sheldrick, 2015b ▸), ORTEP-3 for Windows (Farrugia, 2012 ▸) and PLATON (Spek, 2020 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989022004741/zv2013sup1.cif

e-78-00554-sup1.cif (939.1KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989022004741/zv2013Isup2.hkl

e-78-00554-Isup2.hkl (402.9KB, hkl)

CCDC reference: 2170241

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors would like to thank Baku State University and the Ministry of Education and Science of the Russian Federation for their support of this research. Authors’ contributions are as follows. Conceptualization, FNN and IGM; methodology, FNN and IGM; investigation, FNN, MA and APN; writing (original draft), MA and IGM; writing (review and editing of the manuscript), MA and FNN; visualization, MA, FNN and IGM; funding acquisition, VNK, RMR and FNN; resources, AAA, VNK and FNN; supervision, IGM and MA.

supplementary crystallographic information

Crystal data

C16H11BrN6O·2C2H6OS F(000) = 1104
Mr = 539.47 Dx = 1.538 Mg m−3
Monoclinic, P21/c Cu Kα radiation, λ = 1.54184 Å
a = 10.3940 (1) Å Cell parameters from 27880 reflections
b = 26.2421 (2) Å θ = 3.4–79.2°
c = 8.9860 (1) Å µ = 4.38 mm−1
β = 108.056 (1)° T = 100 K
V = 2330.32 (4) Å3 Prism, colourless
Z = 4 0.05 × 0.03 × 0.02 mm
Open in a new tab

Data collection

Rigaku XtaLAB Synergy Dualflex HyPix diffractometer 5062 independent reflections
Radiation source: micro-focus sealed X-ray tube 5047 reflections with I > 2σ(I)
Detector resolution: 0 pixels mm-1 Rint = 0.029
φ and ω scans θmax = 79.4°, θmin = 3.4°
Absorption correction: multi-scan (CrysAlis PRO; Rigaku OD, 2021) h = −13→13
Tmin = 0.793, Tmax = 0.899 k = −31→33
31508 measured reflections l = −11→11
Open in a new tab

Refinement

Refinement on F2 Hydrogen site location: mixed
Least-squares matrix: full H-atom parameters constrained
R[F2 > 2σ(F2)] = 0.039 w = 1/[σ2(Fo2) + (0.0287P)2 + 4.5523P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.094 (Δ/σ)max = 0.003
S = 1.17 Δρmax = 0.63 e Å−3
5062 reflections Δρmin = −0.41 e Å−3
331 parameters Extinction correction: SHELXL (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
6 restraints Extinction coefficient: 0.00068 (7)
Open in a new tab

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.
Open in a new tab

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq Occ. (<1)
Br1 0.43785 (3) 0.56355 (2) 0.19141 (3) 0.02651 (10)
O1 0.84018 (19) 0.31921 (7) 0.4894 (2) 0.0262 (4)
N1 0.7688 (2) 0.33596 (8) −0.0737 (2) 0.0236 (4)
H1 0.846974 0.349380 −0.079035 0.028*
C1 0.7948 (2) 0.36248 (9) 0.4575 (3) 0.0195 (5)
N2 0.8234 (2) 0.40340 (8) 0.5544 (2) 0.0223 (4)
H2 0.883850 0.403189 0.650976 0.027*
C2 0.6818 (3) 0.30219 (12) −0.1925 (3) 0.0311 (6)
H2A 0.730367 0.270499 −0.201996 0.037*
H2B 0.651308 0.319271 −0.295753 0.037*
C3 0.5622 (3) 0.29063 (10) −0.1340 (3) 0.0269 (6)
H3A 0.476650 0.303812 −0.207158 0.032*
H3B 0.553120 0.253560 −0.119462 0.032*
N4 0.5981 (2) 0.31762 (8) 0.0156 (2) 0.0181 (4)
C5 0.5237 (2) 0.31827 (8) 0.1184 (3) 0.0162 (4)
N5 0.4101 (2) 0.28990 (8) 0.0779 (2) 0.0206 (4)
H5A 0.387282 0.271975 −0.011822 0.025*
H5B 0.357158 0.288865 0.140338 0.025*
C6 0.5691 (2) 0.34678 (9) 0.2534 (3) 0.0175 (4)
C7 0.6955 (2) 0.37927 (9) 0.2964 (3) 0.0164 (4)
C8 0.7672 (2) 0.37480 (9) 0.1734 (3) 0.0170 (4)
C8A 0.7175 (2) 0.34454 (9) 0.0441 (3) 0.0169 (4)
C9 0.4989 (3) 0.34610 (9) 0.3650 (3) 0.0227 (5)
N9 0.4511 (3) 0.34703 (10) 0.4650 (3) 0.0313 (5)
C10 0.8877 (3) 0.40296 (9) 0.1953 (3) 0.0219 (5)
N10 0.9860 (3) 0.42647 (10) 0.2186 (3) 0.0321 (5)
C11 0.7468 (2) 0.44627 (9) 0.4847 (3) 0.0198 (5)
C12 0.6681 (2) 0.43415 (9) 0.3327 (3) 0.0173 (4)
C13 0.5776 (2) 0.46901 (9) 0.2424 (3) 0.0187 (5)
H13 0.523468 0.461160 0.138649 0.022*
C14 0.5690 (2) 0.51605 (9) 0.3097 (3) 0.0208 (5)
C15 0.6498 (3) 0.52928 (10) 0.4587 (3) 0.0244 (5)
H15 0.642919 0.562266 0.499107 0.029*
C16 0.7414 (3) 0.49383 (10) 0.5490 (3) 0.0243 (5)
H16 0.798109 0.502105 0.651194 0.029*
S1A 0.13352 (7) 0.39460 (3) 0.95312 (8) 0.02416 (16) 0.9
O2A −0.0128 (3) 0.38792 (11) 0.8623 (5) 0.0249 (7) 0.9
C17A 0.2226 (3) 0.38206 (13) 0.8160 (4) 0.0335 (7) 0.9
H17A 0.214127 0.345875 0.787662 0.050* 0.9
H17B 0.318415 0.390664 0.863195 0.050* 0.9
H17C 0.184208 0.402768 0.721890 0.050* 0.9
C18A 0.1618 (4) 0.46142 (14) 0.9724 (5) 0.0453 (9) 0.9
H18A 0.126943 0.477575 0.869331 0.068* 0.9
H18B 0.259115 0.468053 1.015790 0.068* 0.9
H18C 0.115059 0.475458 1.042574 0.068* 0.9
S1B 0.0823 (6) 0.4388 (2) 0.9322 (8) 0.0235 (12) 0.1
O2B −0.024 (3) 0.3988 (13) 0.874 (6) 0.0249 (7) 0.1
C17B 0.224 (2) 0.4099 (11) 1.073 (3) 0.035 (6)* 0.1
H17D 0.252431 0.379726 1.026836 0.053* 0.1
H17E 0.198648 0.399764 1.165015 0.053* 0.1
H17F 0.299037 0.434301 1.104281 0.053* 0.1
C18B 0.150 (4) 0.4529 (15) 0.778 (3) 0.048 (8)* 0.1
H18D 0.168102 0.421089 0.730947 0.072* 0.1
H18E 0.234154 0.472179 0.819275 0.072* 0.1
H18F 0.084401 0.473284 0.697880 0.072* 0.1
S2A 0.11696 (8) 0.28805 (3) 0.26820 (8) 0.0263 (2) 0.948 (2)
O3A 0.24507 (19) 0.25919 (7) 0.2727 (2) 0.0245 (4) 0.95
C19A 0.1529 (3) 0.32357 (12) 0.4465 (4) 0.0286 (7) 0.95
H19A 0.214320 0.351728 0.444556 0.043* 0.95
H19B 0.195632 0.301184 0.535359 0.043* 0.95
H19C 0.068477 0.337256 0.457128 0.043* 0.95
C20A 0.0076 (3) 0.24245 (15) 0.3136 (6) 0.0422 (11) 0.95
H20A −0.027573 0.219286 0.224693 0.063* 0.95
H20B −0.067876 0.260108 0.334906 0.063* 0.95
H20C 0.058216 0.222893 0.406131 0.063* 0.95
S2B 0.0451 (16) 0.2982 (5) 0.2263 (16) 0.0263 (2) 0.052 (2)
O3B 0.165 (3) 0.2865 (13) 0.169 (4) 0.0245 (4) 0.05
C19B 0.149 (6) 0.306 (3) 0.425 (3) 0.0286 (7) 0.05
H19D 0.244796 0.302777 0.430774 0.043* 0.05
H19E 0.127063 0.279408 0.490034 0.043* 0.05
H19F 0.133444 0.339513 0.463042 0.043* 0.05
C20B 0.045 (10) 0.240 (2) 0.326 (11) 0.0422 (11) 0.05
H20D −0.020108 0.241711 0.385397 0.063* 0.05
H20E 0.135442 0.233028 0.398604 0.063* 0.05
H20F 0.018655 0.211771 0.250113 0.063* 0.05
Open in a new tab

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
Br1 0.02864 (16) 0.01708 (14) 0.03326 (17) 0.00539 (10) 0.00878 (11) 0.00476 (10)
O1 0.0292 (10) 0.0233 (9) 0.0252 (9) 0.0092 (7) 0.0069 (8) 0.0058 (7)
N1 0.0255 (11) 0.0263 (11) 0.0216 (10) −0.0070 (9) 0.0111 (9) −0.0061 (8)
C1 0.0192 (11) 0.0212 (11) 0.0186 (11) 0.0012 (9) 0.0067 (9) 0.0025 (9)
N2 0.0216 (10) 0.0247 (11) 0.0165 (9) 0.0033 (8) −0.0002 (8) 0.0011 (8)
C2 0.0280 (14) 0.0391 (16) 0.0275 (13) −0.0081 (12) 0.0106 (11) −0.0137 (12)
C3 0.0325 (14) 0.0252 (13) 0.0228 (12) −0.0088 (11) 0.0085 (11) −0.0084 (10)
N4 0.0179 (9) 0.0202 (10) 0.0161 (9) −0.0034 (8) 0.0054 (8) −0.0035 (8)
C5 0.0178 (10) 0.0130 (10) 0.0179 (10) 0.0018 (8) 0.0056 (9) 0.0032 (8)
N5 0.0214 (10) 0.0218 (10) 0.0192 (10) −0.0040 (8) 0.0074 (8) −0.0034 (8)
C6 0.0196 (11) 0.0148 (10) 0.0188 (11) −0.0009 (9) 0.0068 (9) −0.0007 (8)
C7 0.0185 (11) 0.0136 (10) 0.0164 (10) 0.0000 (8) 0.0044 (9) −0.0004 (8)
C8 0.0196 (11) 0.0144 (10) 0.0169 (11) −0.0012 (8) 0.0054 (9) 0.0008 (8)
C8A 0.0176 (11) 0.0136 (10) 0.0192 (11) 0.0012 (8) 0.0052 (9) 0.0021 (8)
C9 0.0247 (12) 0.0192 (11) 0.0240 (12) −0.0048 (9) 0.0073 (10) −0.0059 (9)
N9 0.0330 (12) 0.0352 (13) 0.0300 (12) −0.0105 (10) 0.0162 (10) −0.0130 (10)
C10 0.0263 (13) 0.0197 (11) 0.0204 (11) −0.0026 (10) 0.0084 (10) −0.0031 (9)
N10 0.0312 (12) 0.0331 (13) 0.0339 (13) −0.0126 (10) 0.0130 (10) −0.0100 (10)
C11 0.0201 (11) 0.0202 (11) 0.0168 (11) −0.0012 (9) 0.0025 (9) 0.0007 (9)
C12 0.0187 (11) 0.0159 (11) 0.0171 (11) −0.0023 (8) 0.0052 (9) −0.0025 (8)
C13 0.0205 (11) 0.0169 (11) 0.0170 (11) −0.0019 (9) 0.0037 (9) −0.0004 (9)
C14 0.0204 (11) 0.0170 (11) 0.0251 (12) 0.0004 (9) 0.0069 (10) 0.0029 (9)
C15 0.0307 (13) 0.0180 (11) 0.0258 (13) −0.0031 (10) 0.0106 (11) −0.0058 (10)
C16 0.0273 (13) 0.0243 (12) 0.0195 (11) −0.0049 (10) 0.0046 (10) −0.0065 (10)
S1A 0.0207 (3) 0.0278 (4) 0.0216 (3) −0.0033 (3) 0.0030 (3) 0.0009 (3)
O2A 0.0197 (10) 0.0340 (18) 0.0191 (12) −0.0052 (12) 0.0032 (8) 0.0003 (13)
C17A 0.0303 (16) 0.0348 (17) 0.0396 (18) −0.0050 (13) 0.0172 (14) 0.0012 (14)
C18A 0.046 (2) 0.0296 (18) 0.064 (3) −0.0077 (17) 0.0228 (19) −0.0129 (17)
S1B 0.023 (3) 0.011 (3) 0.041 (3) 0.004 (2) 0.017 (3) 0.005 (2)
O2B 0.0197 (10) 0.0340 (18) 0.0191 (12) −0.0052 (12) 0.0032 (8) 0.0003 (13)
S2A 0.0283 (4) 0.0275 (3) 0.0226 (3) 0.0065 (3) 0.0074 (3) 0.0015 (3)
O3A 0.0256 (10) 0.0235 (9) 0.0263 (10) 0.0008 (8) 0.0108 (8) −0.0013 (7)
C19A 0.0278 (14) 0.0235 (15) 0.0378 (16) −0.0057 (13) 0.0148 (12) −0.0156 (12)
C20A 0.028 (2) 0.0434 (18) 0.062 (2) −0.0157 (15) 0.023 (2) −0.0283 (17)
S2B 0.0283 (4) 0.0275 (3) 0.0226 (3) 0.0065 (3) 0.0074 (3) 0.0015 (3)
O3B 0.0256 (10) 0.0235 (9) 0.0263 (10) 0.0008 (8) 0.0108 (8) −0.0013 (7)
C19B 0.0278 (14) 0.0235 (15) 0.0378 (16) −0.0057 (13) 0.0148 (12) −0.0156 (12)
C20B 0.028 (2) 0.0434 (18) 0.062 (2) −0.0157 (15) 0.023 (2) −0.0283 (17)
Open in a new tab

Geometric parameters (Å, º)

Br1—C14 1.909 (2) C16—H16 0.9500
O1—C1 1.229 (3) S1A—O2A 1.497 (3)
N1—C8A 1.344 (3) S1A—C18A 1.778 (4)
N1—C2 1.464 (3) S1A—C17A 1.787 (3)
N1—H1 0.9000 C17A—H17A 0.9800
C1—N2 1.356 (3) C17A—H17B 0.9800
C1—C7 1.559 (3) C17A—H17C 0.9800
N2—C11 1.408 (3) C18A—H18A 0.9800
N2—H2 0.8999 C18A—H18B 0.9800
C2—C3 1.523 (4) C18A—H18C 0.9800
C2—H2A 0.9900 S1B—O2B 1.497 (4)
C2—H2B 0.9900 S1B—C18B 1.777 (5)
C3—N4 1.462 (3) S1B—C17B 1.787 (5)
C3—H3A 0.9900 C17B—H17D 0.9800
C3—H3B 0.9900 C17B—H17E 0.9800
N4—C5 1.377 (3) C17B—H17F 0.9800
N4—C8A 1.381 (3) C18B—H18D 0.9800
C5—N5 1.347 (3) C18B—H18E 0.9800
C5—C6 1.378 (3) C18B—H18F 0.9800
N5—H5A 0.8996 S2A—O3A 1.521 (2)
N5—H5B 0.8999 S2A—C20A 1.782 (3)
C6—C9 1.412 (3) S2A—C19A 1.790 (3)
C6—C7 1.513 (3) C19A—H19A 0.9800
C7—C8 1.517 (3) C19A—H19B 0.9800
C7—C12 1.523 (3) C19A—H19C 0.9800
C8—C8A 1.369 (3) C20A—H20A 0.9800
C8—C10 1.414 (3) C20A—H20B 0.9800
C9—N9 1.154 (4) C20A—H20C 0.9800
C10—N10 1.156 (4) S2B—O3B 1.522 (4)
C11—C16 1.384 (4) S2B—C20B 1.782 (5)
C11—C12 1.394 (3) S2B—C19B 1.790 (4)
C12—C13 1.381 (3) C19B—H19D 0.9800
C13—C14 1.390 (3) C19B—H19E 0.9800
C13—H13 0.9500 C19B—H19F 0.9800
C14—C15 1.386 (4) C20B—H20D 0.9800
C15—C16 1.397 (4) C20B—H20E 0.9800
C15—H15 0.9500 C20B—H20F 0.9800
C8A—N1—C2 111.7 (2) C11—C16—H16 121.1
C8A—N1—H1 124.1 C15—C16—H16 121.1
C2—N1—H1 124.2 O2A—S1A—C18A 106.15 (19)
O1—C1—N2 126.2 (2) O2A—S1A—C17A 105.0 (2)
O1—C1—C7 125.0 (2) C18A—S1A—C17A 98.23 (18)
N2—C1—C7 108.8 (2) S1A—C17A—H17A 109.5
C1—N2—C11 111.5 (2) S1A—C17A—H17B 109.5
C1—N2—H2 124.2 H17A—C17A—H17B 109.5
C11—N2—H2 124.3 S1A—C17A—H17C 109.5
N1—C2—C3 104.8 (2) H17A—C17A—H17C 109.5
N1—C2—H2A 110.8 H17B—C17A—H17C 109.5
C3—C2—H2A 110.8 S1A—C18A—H18A 109.5
N1—C2—H2B 110.8 S1A—C18A—H18B 109.5
C3—C2—H2B 110.8 H18A—C18A—H18B 109.5
H2A—C2—H2B 108.9 S1A—C18A—H18C 109.5
N4—C3—C2 102.6 (2) H18A—C18A—H18C 109.5
N4—C3—H3A 111.3 H18B—C18A—H18C 109.5
C2—C3—H3A 111.3 O2B—S1B—C18B 107 (2)
N4—C3—H3B 111.3 O2B—S1B—C17B 108 (2)
C2—C3—H3B 111.3 C18B—S1B—C17B 101.7 (16)
H3A—C3—H3B 109.2 S1B—C17B—H17D 109.5
C5—N4—C8A 121.9 (2) S1B—C17B—H17E 109.5
C5—N4—C3 125.9 (2) H17D—C17B—H17E 109.5
C8A—N4—C3 112.2 (2) S1B—C17B—H17F 109.5
N5—C5—N4 116.1 (2) H17D—C17B—H17F 109.5
N5—C5—C6 124.8 (2) H17E—C17B—H17F 109.5
N4—C5—C6 119.1 (2) S1B—C18B—H18D 109.5
C5—N5—H5A 119.8 S1B—C18B—H18E 109.5
C5—N5—H5B 120.2 H18D—C18B—H18E 109.5
H5A—N5—H5B 120.0 S1B—C18B—H18F 109.5
C5—C6—C9 120.5 (2) H18D—C18B—H18F 109.5
C5—C6—C7 124.4 (2) H18E—C18B—H18F 109.5
C9—C6—C7 115.1 (2) O3A—S2A—C20A 105.94 (15)
C6—C7—C8 110.72 (19) O3A—S2A—C19A 107.28 (13)
C6—C7—C12 112.51 (19) C20A—S2A—C19A 96.65 (19)
C8—C7—C12 113.31 (19) S2A—C19A—H19A 109.5
C6—C7—C1 110.56 (19) S2A—C19A—H19B 109.5
C8—C7—C1 108.74 (19) H19A—C19A—H19B 109.5
C12—C7—C1 100.51 (18) S2A—C19A—H19C 109.5
C8A—C8—C10 120.4 (2) H19A—C19A—H19C 109.5
C8A—C8—C7 121.5 (2) H19B—C19A—H19C 109.5
C10—C8—C7 118.2 (2) S2A—C20A—H20A 109.5
N1—C8A—C8 128.9 (2) S2A—C20A—H20B 109.5
N1—C8A—N4 108.7 (2) H20A—C20A—H20B 109.5
C8—C8A—N4 122.3 (2) S2A—C20A—H20C 109.5
N9—C9—C6 174.4 (3) H20A—C20A—H20C 109.5
N10—C10—C8 177.5 (3) H20B—C20A—H20C 109.5
C16—C11—C12 121.8 (2) O3B—S2B—C20B 97 (4)
C16—C11—N2 128.7 (2) O3B—S2B—C19B 93 (3)
C12—C11—N2 109.4 (2) C20B—S2B—C19B 72 (4)
C13—C12—C11 120.7 (2) S2B—C19B—H19D 109.5
C13—C12—C7 129.7 (2) S2B—C19B—H19E 109.5
C11—C12—C7 109.5 (2) H19D—C19B—H19E 109.5
C12—C13—C14 117.1 (2) S2B—C19B—H19F 109.5
C12—C13—H13 121.4 H19D—C19B—H19F 109.5
C14—C13—H13 121.4 H19E—C19B—H19F 109.5
C15—C14—C13 122.8 (2) S2B—C20B—H20D 109.5
C15—C14—Br1 119.25 (19) S2B—C20B—H20E 109.5
C13—C14—Br1 117.94 (18) H20D—C20B—H20E 109.5
C14—C15—C16 119.6 (2) S2B—C20B—H20F 109.5
C14—C15—H15 120.2 H20D—C20B—H20F 109.5
C16—C15—H15 120.2 H20E—C20B—H20F 109.5
C11—C16—C15 117.8 (2)
O1—C1—N2—C11 −175.7 (2) C2—N1—C8A—C8 −178.1 (3)
C7—C1—N2—C11 5.0 (3) C2—N1—C8A—N4 0.9 (3)
C8A—N1—C2—C3 1.0 (3) C10—C8—C8A—N1 0.9 (4)
N1—C2—C3—N4 −2.3 (3) C7—C8—C8A—N1 −179.2 (2)
C2—C3—N4—C5 −178.4 (2) C10—C8—C8A—N4 −178.0 (2)
C2—C3—N4—C8A 3.0 (3) C7—C8—C8A—N4 1.9 (3)
C8A—N4—C5—N5 −179.2 (2) C5—N4—C8A—N1 178.8 (2)
C3—N4—C5—N5 2.4 (3) C3—N4—C8A—N1 −2.6 (3)
C8A—N4—C5—C6 0.3 (3) C5—N4—C8A—C8 −2.1 (3)
C3—N4—C5—C6 −178.2 (2) C3—N4—C8A—C8 176.5 (2)
N5—C5—C6—C9 2.8 (4) C1—N2—C11—C16 175.8 (3)
N4—C5—C6—C9 −176.6 (2) C1—N2—C11—C12 −2.6 (3)
N5—C5—C6—C7 −178.9 (2) C16—C11—C12—C13 −2.4 (4)
N4—C5—C6—C7 1.7 (3) N2—C11—C12—C13 176.2 (2)
C5—C6—C7—C8 −1.8 (3) C16—C11—C12—C7 −179.5 (2)
C9—C6—C7—C8 176.6 (2) N2—C11—C12—C7 −1.0 (3)
C5—C6—C7—C12 126.2 (2) C6—C7—C12—C13 −55.6 (3)
C9—C6—C7—C12 −55.4 (3) C8—C7—C12—C13 70.9 (3)
C5—C6—C7—C1 −122.3 (2) C1—C7—C12—C13 −173.2 (2)
C9—C6—C7—C1 56.1 (3) C6—C7—C12—C11 121.2 (2)
O1—C1—C7—C6 56.6 (3) C8—C7—C12—C11 −112.3 (2)
N2—C1—C7—C6 −124.1 (2) C1—C7—C12—C11 3.6 (2)
O1—C1—C7—C8 −65.2 (3) C11—C12—C13—C14 0.0 (4)
N2—C1—C7—C8 114.1 (2) C7—C12—C13—C14 176.5 (2)
O1—C1—C7—C12 175.6 (2) C12—C13—C14—C15 2.3 (4)
N2—C1—C7—C12 −5.1 (2) C12—C13—C14—Br1 −176.74 (18)
C6—C7—C8—C8A 0.0 (3) C13—C14—C15—C16 −2.1 (4)
C12—C7—C8—C8A −127.5 (2) Br1—C14—C15—C16 176.9 (2)
C1—C7—C8—C8A 121.6 (2) C12—C11—C16—C15 2.5 (4)
C6—C7—C8—C10 179.8 (2) N2—C11—C16—C15 −175.7 (2)
C12—C7—C8—C10 52.4 (3) C14—C15—C16—C11 −0.3 (4)
C1—C7—C8—C10 −58.5 (3)
Open in a new tab

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
N1—H1···O2Ai 0.90 1.98 2.855 (4) 165
N1—H1···O2Bi 0.90 2.00 2.87 (4) 160
N2—H2···O2Aii 0.90 1.91 2.793 (5) 166
N2—H2···O2Bii 0.90 1.94 2.82 (5) 166
N5—H5A···O3Aiii 0.90 2.20 3.034 (3) 155
N5—H5B···O3A 0.90 2.06 2.918 (3) 160
C2—H2B···N9iv 0.99 2.59 3.469 (4) 148
C19A—H19A···N9 0.98 2.41 3.114 (5) 128
C19A—H19C···O1v 0.98 2.52 3.392 (4) 148
C20A—H20B···O1v 0.98 2.46 3.359 (4) 152
Open in a new tab

Symmetry codes: (i) x+1, y, z−1; (ii) x+1, y, z; (iii) x, −y+1/2, z−1/2; (iv) x, y, z−1; (v) x−1, y, z.

Funding Statement

Funding for this research was provided by: Ministry of Education and Science of the Russian Federation (award No. 075-03-2020-223 (FSSF-2020-0017)).

References

  1. Abdelhamid, A. A., Mohamed, S. K., Khalilov, A. N., Gurbanov, A. V. & Ng, S. W. (2011). Acta Cryst. E67, o744. [DOI] [PMC free article] [PubMed]
  2. Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.
  3. Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.
  4. Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. [DOI] [PMC free article] [PubMed]
  5. Han, F., Shioda, N., Moriguchi, S., Yamamoto, Y., Raie, A. Y. A., Yamaguchi, Y., Hino, M. & Fukunaga, K. (2008). J. Pharmacol. Exp. Ther. 326, 127–134. [DOI] [PubMed]
  6. Jun, J., Juan, L., Xinhua, L., Hongxin, L., Haiyan, W. & Hong-Ping, X. (2019). Synlett, 30, 1241–1245.
  7. Khalilov, A. N., Tüzün, B., Taslimi, P., Tas, A., Tuncbilek, Z. & Cakmak, N. K. (2021). J. Mol. Liq. 344, 117761.
  8. Lu, L., Deyan, W., Xiangmin, L., Sinan, W., Hao, L., Jian, L. & Wei, W. (2012). Chem. Commun. 48, 1692–1694.
  9. Magerramov, A. M., Nagiev, F. N., Mamedova, G. Z. Kh. A., Asadov, Kh. A. & Mamedov, I. G. (2018). Russ. J. Org. Chem. 54, 1713–1715.
  10. Mamedov, I., Naghiyev, F., Maharramov, A., Uwangue, O., Farewell, A., Sunnerhagen, P. & Erdelyi, M. (2020). Mendeleev Commun. 30, 498–499.
  11. Nagalakshmi, R. A., Suresh, J., Sivakumar, S., Kumar, R. R. & Lakshman, P. L. N. (2014a). Acta Cryst. E70, o604–o605. [DOI] [PMC free article] [PubMed]
  12. Nagalakshmi, R. A., Suresh, J., Sivakumar, S., Kumar, R. R. & Lakshman, P. L. N. (2014b). Acta Cryst. E70, o971–o972. [DOI] [PMC free article] [PubMed]
  13. Nagalakshmi, R. A., Suresh, J., Sivakumar, S., Kumar, R. R. & Lakshman, P. L. N. (2014c). Acta Cryst. E70, o816–o817. [DOI] [PMC free article] [PubMed]
  14. Naghiyev, F. N., Cisterna, J., Khalilov, A. N., Maharramov, A. M., Askerov, R. K., Asadov, K. A., Mamedov, I. G., Salmanli, K. S., Cárdenas, A. & Brito, I. (2020). Molecules, 25, 2235–2248. [DOI] [PMC free article] [PubMed]
  15. Naghiyev, F. N., Grishina, M. M., Khrustalev, V. N., Khalilov, A. N., Akkurt, M., Akobirshoeva, A. A. & Mamedov, İ. G. (2021a). Acta Cryst. E77, 195–199. [DOI] [PMC free article] [PubMed]
  16. Naghiyev, F. N., Tereshina, T. A., Khrustalev, V. N., Akkurt, M., Khalilov, A. N., Akobirshoeva, A. A. & Mamedov, İ. G. (2021b). Acta Cryst. E77, 512–515. [DOI] [PMC free article] [PubMed]
  17. Negar, L., Ghodsi Mohammadi, Z., Alireza, B. & Parisa, G. (2012). Eur. J. Chem. 3, 310–313.
  18. Rigaku OD (2021). CrysAlis PRO. Rigaku Oxford Diffraction Ltd, Yarnton, England.
  19. Samaneh, A., Homa, A. & Javad, A. (2021). J. Chin. Chem. Soc. 68, 1090–1103.
  20. Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.
  21. Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.
  22. Spek, A. L. (2020). Acta Cryst. E76, 1–11. [DOI] [PMC free article] [PubMed]
  23. Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. The University of Western Australia.
  24. Yadigarov, R. R., Khalilov, A. N., Mamedov, I. G., Nagiev, F. N., Magerramov, A. M. & Allakhverdiev, M. A. (2009). Russ. J. Org. Chem. 45, 1856–1858.
  25. Yin, J., Khalilov, A. N., Muthupandi, P., Ladd, R. & Birman, V. B. (2020). J. Am. Chem. Soc. 142, 60–63. [DOI] [PubMed]

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, global. DOI: 10.1107/S2056989022004741/zv2013sup1.cif

e-78-00554-sup1.cif (939.1KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989022004741/zv2013Isup2.hkl

e-78-00554-Isup2.hkl (402.9KB, hkl)

CCDC reference: 2170241

Additional supporting information: crystallographic information; 3D view; checkCIF report

Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

RESOURCES