The role of water and iodine in supramolecular assembly of a 2D coordination of benzimidazole derivate: X-ray crystallography and DFT calculations

Abstract

To understand the relationships between molecular structure and properties, as well as to validate predictive models, density functional theory (DFT) and experimental characterization of molecules are essential. In this study, we describe the synthesis and crystal structure of the 1,3-dimethyl-3H-benzimidazol-1-ium iodide monohydrate (DBZIW), which crystallizes in a monoclinic system with the space group P2₁/c, a = 8.9323(4) Å, b = 7.1654(3) Å, c = 17.6425(8) Å, β = 101.432(2)°, V = 1106.78(8) ų, Z = 4, T = 293(2) K, μ(MoKα) = 2.860 mm^-1, Dcalc = 1.753 g/cm³, 9452 reflections measured (4.652° ≤ 2Θ ≤ 55.512°), 2547 unique (R_int = 0.0244, R_sigma = 0.0222) which were used in all calculations. The asymmetric unit comprises a [C₉H₁₁N₂]⁺ molecule, an iodine ion (I^-), and a water molecule. The B3LYP/6-311++G(d,p)  diffuse function was used to optimize the structures of 1,3-dimethyl-3H-benzimidazol-1-ium (DBZ) and 1,3-dimethyl-3H-benzimidazol-1-ium monohydrate (DBZW), while the structures of 1,3-dimethyl-3H-benzimidazol-1-ium iodine (DBZI) and 1,3-dimethyl-3H-benzimidazol-1-ium iodide monohydrate (DBZIW) were optimized using the B3LYP/Def2-TZVP method due to the presence of the iodine ion. These optimizations were performed using Gaussian09 software, and both models accurately predicted the bond lengths, bond angles, and torsion angles of the molecules. Furthermore, DFT calculations were employed to determine the HOMO-LUMO energy levels, energy gap, softness, hardness, and other quantum chemical parameters. A strong intermolecular hydrogen bond interaction, along with the aromatic ring system and the fusion of benzene and imidazole, constitutes a small but highly significant structure that has been confirmed. The O1 atom of the water molecule and the iodine ion (I^-) participate in a significant hydrogen bond interaction (O-H···I) within the molecular packing of DBZIW. Furthermore, the network of C-H···O hydrogen bond contacts plays a crucial role in the stability of the structure. Hirshfeld surface analysis was carried out to identify the various hydrogen bonds. The energy frameworks for the compounds were constructed through based on intermolecular interaction energies to know ascertain dominant interaction energy involved contributing to the strength of the packing. Molecular studies indicated that DBZIW had exhibits high binding affinity for thyroid-stimulating hormone receptor (TSHR) protein targets (4QT5).