Synthesis, characterization, X-ray structure, computational studies, and bioassay of novel compounds combining thiophene and benzimidazole or 1,2,4-triazole moieties
© The Author(s) 2017
Received: 23 November 2016
Accepted: 31 May 2017
Published: 9 June 2017
Due to their interesting and versatile biological activity, thiophene-containing compounds have attracted the attention of both chemists and medicinal chemists. Some of these compounds have anticancer, antibacterial, antiviral, and antioxidant activity. In addition, the thiophene nucleus has been used in the synthesis of a variety of heterocyclic compounds.
In the present work, two novel thiophene-containing compounds, 4-phenyl-2-phenylamino-5-(1H-1,3-a,8-triaza-cyclopenta[α]inden-2-yl)-thiophene-3-carboxylic acid ethyl ester (3) and 5-(1H-Imidazo[1,2-b] [1,2,4] triazol-5-yl)-4-phenyl-2-phenylamino-thiophene-3-carboxylic acid ethyl ester (4), have been synthesized by reaction of 5-(2-bromo-acetyl)-4-phenyl-2-phenylaminothiophene-3-carboxylic acid ethyl ester (2) with 2-aminobenzimidazole and 3-amino-1H-1,2,4-triazole in the presence of triethylamine, respectively. Compound 2, on the other hand, was prepared by bromination of 5-acetyl-4-phenyl-2-phenylaminothiophene-3-carboxylic acid ester (1). Structures of the newly prepared compounds were confirmed by different spectroscopic methods such as 1H-NMR, 13C-NMR, and mass spectrometry, as well as by elemental analysis. Furthermore, bromination of compound 1 led to the formation of two constitutional isomers (2a and 2b) that were obtained in an 80:20 ratio. Molecular structures of 2b were confirmed with the aid of X-ray crystallography. Compound 2 was crystallized in the triclinic, P-1, a = 8.8152 (8) Å, b = 10.0958 (9) Å, c = 12.6892 (10) Å, α = 68.549 (5)°, β = 81.667 (5)°, γ = 68.229 (5)°, V = 976.04 (15) Å3, Z = 2, and was found in two isomeric forms regarding the position of the bromine atom. The antibacterial and antifungal activities of the prepared compounds were evaluated.
Three new thiophene derivatives were synthesized in good yield. Antimicrobial screening revealed that compound 3 was a promising candidate as a potential antibacterial and antifungal agent; it exhibits remarkable activity against the studied bacterial strains, especially the gram negative bacteria E. coli in addition to some fungi. More work is needed to evaluate its safety and efficacy.
KeywordsThiophene-containing compounds X-ray diffraction DFT Antibacterial and antifungal activity Molecular structure
Results and discussion
Shown in Scheme 1 are reactions involved in the synthesis of compounds 2, 3, and 4. 5-Acetyl-4-methyl-2-phenylamino-thiophene-3-carboxylic acid ethyl ester (2), a synthone required in this work, was prepared and characterized according to a procedure outlined by Mabkhot et al.  that involved stirring a mixture of ethyl acetoacetate and anhydrous potassium carbonate followed by addition of phenyl isocyanate and then chloroacetone. Compound 2, on the other hand, was prepared in 90% yield (75% 2a and 15% 2b) from the reaction of compound 1 with bromine in glacial acetic acid as a solvent. Condensation of 2-aminobenzimidazole and compound 2 in ethanol containing triethylamine under reflux afforded compound 3 , whereas treatment of compound 2 with 3-amino-1,2,4-triazol in ethanol under reflux for 7 h yielded compound 4. Structures of compounds 2, 3, and 4 where confirmed with the aid of IR, 1H NMR and 13C NMR spectra and with mass spectrometry, where the NMR spectra were in total agreement with the assigned structures. Similarly, mass spectra displayed the molecular ions corresponding to the respective molecular formulas of prepared compounds.
When compound 2 was prepared, we noticed that part of it dissolves in ethanol. Therefore, when it was recrystallized from this solvent followed by slow evaporation of ethanol, compound 2b was obtained as crystals. This compound was characterized by NMR and x-ray crystallography. In the 1H NMR spectrum, the signal at δ 3.47 ppm has disappeared and a new signal due to a methyl group appeared instead at δ 2.45 ppm. Moreover, the aromatic region in the new compound was different from that of 2a. Compound 2a was obtained via a typical bromination of α-hydrogen of the methyl group next to the carbonyl group. However, bromination was also possible on the activated benzene ring; due to steric effect, substitution took place at the para rather than the ortho position, leading to the formation of compound 2b (formation of compound 2b was achieved via an electrophilic aromatic substitution reaction).
Crystal structure of compound 2
Crystal data and structure refinement for 2
Crystal system, space group
a, b, c (Å)
8.8152 (8), 10.0958 (9), 12.6892 (10)
α, β, γ (°)
68.549 (5), 81.667 (5), 68.229 (5)
Crystal size (mm)
0.20 × 0.15 × 0.07
Bruker Kappa APEXII Duo diffractometer
Numerical Blessing, 1995
No. of measured, independent and observed [I > 2σ(I)] reflections
25,229, 3426, 2904
R[F 2 > 2σ(F 2 )], wR(F 2 ), S
0.046, 0.141, 1.06
No. of reflections
No. of parameters
No. of restraints
H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)
Energetic and thermodynamic parameters
The calculated energies and thermodynamic parameters of the studied isomers of 2
ZPVE (a. u.)
S (cal mol−1 K−1)
The geometric parameters of both disorders, 2a and 2b (calculated and experimental)
Antibacterial and antifungal activity
Antibacterial and antifungal activity of compounds 2, 3, and 4 (diameter of inhibition zone is given in mm)
A) Antifungal activity
23.7 ± 0.1
19.7 ± 0.2
28.7 ± 0.2
25.4 ± 0.1
16.2 ± 0.4
15.0 ± 0.4
17.6 ± 0.6
21.3 ± 0.4
17.2 ± 0.2
24.6 ± 0.6
17.6 ± 0.6
15.4 ± 0.3
12.6 ± 0.4
B) Antibacterial activity
Gram positive bacteria
Gram negative bacteria
23.8 ± 0.2
32.4 ± 0.3
17.3 ± 0.1
19.9 ± 0.3
16.9 ± 0.6
18.2 ± 0.4
11.9 ± 0.6
18.2 ± 0.1
20.3 ± 0.1
20.3 ± 0.1
12.3 ± 0.6
12.7 ± 0.4
8.5 ± 0.4
Results in Table 4 reveal that compound 3 has remarkable activity against the tested fungi A. fumigates, S. racemosum, and G. candidum, whereas compounds 2 and 4 exhibited moderate activities against these fungi. On the other hand, compound 3 displayed significant activity against the gram positive bacterial strains S. pneumoniae and B. subtilis and showed excellent activity against the gram negative strain E. coli. Compounds 2 and 4 showed moderate activities against the aforementioned bacterial strains. In addition, results suggest that the new skeletons possessing benzimidazole and thiophene moieties may provide valuable leads for the synthesis and development of novel antimicrobial agents. Moreover, compound 3 could be a promising antifungal and antibacterial agent, however, more work is needed to evaluate the safety and efficacy of this compound.
Reagents and instrumentation
Reagents used throughout this work were obtained from commercial sources and were used as received without further purification. Progress of reactions was monitored with TLC using Merck Silica Gel 60 F–254 thin layer plates (Billerica, MA, USA). Infrared Spectra were recorded, as KBr pellets, on a Nicolet 6700 FT-IR Nicolet spectrophotometer (Madison, WI, USA). Melting points were determined on a Gallenkamp apparatus in open glass capillaries and are uncorrected. We acquired 1H- and 13C-NMR spectra with a Varian Mercury Jeol-400 NMR spectrometer (Akishima, Japan) with CDCl3 as solvent. Chemical shifts are reported in ppm (δ) relative to tetramethylsilane as an internal reference and coupling constants, J, are given in Hz. Mass spectral data were obtained with the aid of a Jeol of JMS-600H mass spectrometer (Tokyo, Japan). Single-crystal X-ray diffraction measurements were performed using a Bruker SMART APEX II CCD diffractometer (Karlsruhe, Germany). Elemental analyses were performed on a Euro Vector Elemental Analyzer (EA 3000 A, Via Tortona, Milan, Italy).
Synthesis of 5-(2-bromo-acetyl)-4-phenyl-2-phenylamino-thiophene-3-carboxylic acid ethyl ester (2)
Compound 2a was synthesized according to the following general procedure: A solution of 5-acetyl-4-phenyl-2-phenylaminothiophene-3-carboxylic acid ester (1) (3.0 g, 10 mmol) in glacial acetic acid (100 mL) was heated to 90–100 °C with vigorous stirring. To this hot solution, bromine (1.1 ml) in glacial acetic acid (50 mL) was added dropwise over a period of 30 min. After complete addition of bromine, the reaction mixture was stirred vigorously at room temperature for further 2 h until evolution of hydrogen bromide gas ceased, then was poured onto ice. The solid product was collected by filtration, washed with water, dried, and recrystallized from ethanol to give 2 as white yellowish crystals. Yield 75%; m.p.: 120–122 °C; IR (KBr): 3452 (NH), 1655 (C=O), 1633 (C=O) cm−1. 1H NMR (400 MHz, CDCl3): δ 0.72 (t, J = 6.0 Hz, 3H, CH3–CH2), 3.47 (s, 2H, CH2–Br), 3.91 (q, J = 6.1 Hz, 2H, CH2–CH3), 7.21–7.51 (m, 10H, aromatic), 10.81 (s, 1H, NH–ph). 13C NMR (100 Hz, CDCl3): δ 28.7 (CH3), 33.0 (CH2Br), 60.1 (CH2O), 110.5, 117.8, 120.5, 121.8, 125.2, 128.3, 129.8, 132.7, 136.7, 138.3. 139.2, 147.8, 166.3 (C=O), 184.4 (C=O). Anal. calcd. For C21H18BrNO3S: C, 56.76; H, 4.08; N, 3.15; S, 7.22; Found: C, 56.66; H, 3.98; N, 3.18; S, 7.34.
Compound 2b. Yield 15%; 1H NMR (400 MHz, DMSO-d6): δ 0.88 (t, J = 6.0 Hz 3H, CH3–CH2), 2.45 (s, 3H, CH3), 3.98 (q, J = 6.2 Hz, 2H, CH2–CH3), 7.45-7.83 (m, 9H, aromatic), 10.48 (s, 1H, NH–amine), ppm. 13C NMR (100 Hz, DMSO-d6): δ 11.9 (CH3), 12.0 (CH3), 60.0 (CH2), 111.2, 113.2, 118.3, 119.2, 122.8, 123.0, 127.8, 132.3, 134.0, 137.8, 150.0, 165.2 (C=O), 180.0 (C=O).
Synthesis of 4-phenyl-2-phenylamino-5-(1H-1,3-a,8-triaza-cyclopenta[α]inden-2-yl)-thiophene-3-carboxylic acid ethyl ester (3)
The following procedure was employed to prepare the title compound: A mixture of compound 2 (0.44 g, 1 mmol) and 2-aminobenzimidazole (0.133 g, 1 mmol) was refluxed in ethanol (15 mL) for 8 h in the presence of 0.5 mL of triethylamine (TEA). After cooling, the solid product was collected by filtration to afford the title compound 3 as a yellow powder. Yield 82%; m.p.: 146–148 °C; IR (KBr): 3452 (NH), 1633 (C=O), 1586 (C=N) cm−1. 1H NMR (400 MHz, CDCl3): δ 0.95 (t, J = 6.0 Hz 3H, CH3–CH2), 3.25 (q, J = 6.1 Hz, 2H, CH2–CH3), 6.57–7.51 (m, 14 H, aromatic), 7.54 (s, 1H, CH-imidazo), 10.73 (s, 1H, NH–ph) 10.81 (s, 1H, NH) ppm. 13C NMR (100 Hz, CDCl3): δ 12.1 (CH3), 54.5 (CH2), 111.0, 119.4, 119.7, 120.0, 126.2, 127.3, 128.0, 131.0, 135.0, 153.0, 164.9 (C=O). MS m/z 478 [M+, 1.2%] calcd. for C28H22N4O2S; 442 (18.9%); 328 (22.6%), 112 (100%); Anal. calcd. For C28H22N4O2S: C, 70.27; H, 4.63; N, 11.71; S, 6.70; Found: C, 70.50; H, 4.53; N, 11.66; S, 6.84.
Synthesis of 5-(1H-Imidazo[1,2-b][1,2,4]triazol-5-yl)-4-phenyl-2-phenylamino-thiophene-3-carboxylic acid ethyl ester (4)
Compound 4 was prepared according to the procedure employed for the synthesis of compound 3 with some modifications: a mixture of compound 2 (0.44 g, 1 mmol) and 3-amino-1H-1,2,4-triazole (0.84 g, 1 mmol) was heated under reflux for 8 h in ethanol (10 mL) in the presence of 0.5 mL of trimethylamine (TEA). The solid product was collected by filtration to afford the desired product as a brown powder. Yield 49%; mp 150–152 °C; IR (KBr): 3409 (NH), 1658 (C=O), 1627 (C=N), 1586 cm−1 (C=C). 1H NMR (400 MHz, CDCl3): δ 0.69 (t, J = 6.0 Hz 3H, CH3–CH2), 3.52 (q, J = 6.0 Hz, 2H, CH2–CH3), 5.14 (s, 1H, NH–amine), 7.24–7.53 (m, 14 H, aromatic), 7.56 (s, 1H, CH–imidazol), 10.74 (s, 1H, CH–triazol) 10.85 (s, 1H, NH–triazol) ppm. 13C NMR (100 Hz, CDCl3): δ 12.1 (CH3), 54.8 (CH2), 119.1, 119.9, 120.0, 121.3, 125.0, 126.9, 127.2, 127.3, 127.5, 128.1, 128.7, 128.9, 131.6, 131.9, 148.5, 148.7, 164.8 (C=O). MS m/z 429 [M+, 81.3%] calcd. for C23H19N5O2S; 275 (53.8%); 211 (47.4%); 91 (100%); Anal. calcd. For C23H19N5O2S: C, 64.32; H, 4.46; N, 16.31; S, 7.47; Found: C, 64.55; H, 4.39; N, 16.50; S, 7.66.
Crystals of compound of 2 were obtained by slow evaporation from an ethanol solution at room temperature. Crystallographic data were collected on a Bruker Kappa APEXII Duo diffractometer, equipped with graphite monochromatic Mo Kα radiation, λ = 0.71073 Å at 100 (2) K. Cell refinement and data reduction were accomplished with the aid of a Bruker SAINT, whereas structure was solved by means of SHELXT [16, 17]. The final refinement was carried out by full-matrix least-squares techniques with anisotropic thermal data for nonhydrogen atoms on F2. CCDC 1450887 contains the supplementary crystallographic data for compound 2 and can be obtained free of charge from the Cambridge Crystallographic Data Centre via http://www.ccdc.cam.ac.uk/data_request/cif.
X-ray structure coordinates of the two isomers of 2 were employed as input files for comparing their relative stability. Structure optimizations were accomplished using the B3LYP method and 6‒311G(d,p) basis set with the aid of Gaussian 03 software . The optimized geometries gave no imaginary vibrational modes. GaussView4.1  and Chemcraft  programs have been employed to extract the calculation results and to visualize the optimized structures.
In vitro antibacterial screening tests of the newly synthesized compounds were performed against four bacterial strains: two Gram-positive (Streptococcus pneumonia and Bacillis subtilis) and two Gram-negative (P. aeruginosa and E. coli) in addition to four different fungi; A. fumigates, S. racemosum, G. candidum, and C. albicans. The disc diffusion method  was used in this assay and each experiment was performed in triplicate; experimental details of these techniques can be found elsewhere [22, 23]. Readings of the zone of inhibition, which are shown in Table 4, represent the mean value of three readings. Amphotericin B, ampicillin, and gentamicin were employed as standard drugs in this assay.
Three new thiophene derivatives were synthesized in good yield. These newly synthesized compounds were characterized by means of different spectroscopic methods and by elemental analysis. Furthermore, X-ray crystallography was performed on the two isomeric forms of compound 2 in addition to DFT and energy calculations to show the dominance of one of the isomers over the other. Additionally, the new compounds were screened for their antimicrobial activity against a number of bacterial and fungal strains. Results showed that compound 3 was a promising candidate as a potential antibacterial and antifungal agent; it exhibited remarkable activity against the studied bacterial strains, especially the gram negative bacteria E. coli in addition to some fungi. More work is needed to evaluate its safety and efficacy.
YNM and SSA proposed the subject, designed the study, and carried out the synthesis of the new compounds. SMS and MAA carried out the theoretical studies. HAG and MAA did the X-ray part and its discussion. MSM participated in writing and editing results and discussion and undertook writing the manuscript. All authors read and approved the final manuscript.
Authors extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for its funding of this Prolific Research Group (PRG-1437-29).
The authors declare that they have no competing interests.
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