Single Crystal, DFT and Docking Studies of a Benzimidazolium Salt
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Single Crystal, DFT and Docking Studies of a Benzimidazolium Salt S. Akkoça,*, S. Çağlar Yavuzb, B. Türkmenoğluc, İ. Özer İlhand, and M. Akkurte a Department
of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Suleyman Demirel University, Isparta, 32260 Turkey Sefaatli Vocational School, Department of Veterinary, Yozgat Bozok University, Yozgat, 66800 Turkey c Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Erzincan Binali Yıldırım University, Erzincan, 24100 Turkey d Department of Chemistry, Faculty of Sciences, Erciyes University, Kayseri, 38000 Turkey e Department of Physics, Faculty of Sciences, Erciyes University, Kayseri, 38000 Turkey *e-mail: [email protected], [email protected] b
Received April 25, 2020; revised May 13, 2020; accepted May 14, 2020
Abstract—A single-crystal of (C18H18N3)+Br–, namely, 3-[(2-cyanophenyl)methyl]-1-propyl-1Hbenzo[d]imidazol-3-ium bromide, was studied using X-ray diffraction techniques. This compound crystallizes in the triclinic space group P 1 , with Z = 2, a = 8.9153(9) Å, b = 10.2681(8) Å, c = 10.6528(10) Å, and V = 858.69 (14) Å3. Ions are linked by C–H⋅⋅⋅Br hydrogen bonds in the crystal. The geometrical parameters (bond length, and angles), the highest occupied molecular orbital energy, and the lowest unoccupied molecular orbital energy of this S2 molecule were calculated using the Spartan 10 program. The structural data were calculated by the density functional method using the ground state with the 6-311++G** basic set. Furthermore, a molecular docking analysis was performed to determine the binding mode in the active site of tyrosinase with S2 ligand. DOI: 10.1134/S1063774520070032
INTRODUCTION Organic compounds having a benzimidazole nucleus are very important heterocycles and widely synthesized due to their kinds of biological activities, such as anticancer [1–4], antimicrobial [5–7], anti-inflammatory [8], antioxidant [9], and α-glucosidase inhibitors [10]. More recently, Akkoç et al. [11] reported that the two 1,3-disubstituted benzimidazolium salts have promising antiproliferative activity and are more effective than positive control drug cisplatin, which is clinically used against the human breast cancer cell line (MDA-MB-231) with IC50 values of 1.26 ± 0.85, 2.01 ± 0.96 μM. On the other hand, molecules having a benzimidazole core have other applications in medical and chemical industries. For example, benzimidazole-based molecules are effective as catalysts in reactions such as Suzuki–Miyaura [12–14] and Mizoroki–Heck [15] cross-coupling and arylation [13, 16, 17]. Currently used theoretical calculation methods lead to the fact that various properties of molecules can be calculated without the use of experimental studies. In some studies, even more sensitive and reliable results can be obtained experimentally. In a single experiment, there is no way to get more information, such as molecular structure, formation temperature, dipole moment, ionization potential, electron loads, electron density, and bon
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