Host–guest binding selectivity of ethylated pillar[5]arene (EtP5A) towards octane, 1,7-octadiene, and 1,7-octadiyne: a computational investigation

Abstract

Host−guest binding selectivity of the perethylated pillar [5]arene (EtP5A) macrocycles with aliphatic modi ed hydrocarbons, i.e., octane, 1,7-octadiene, and 1,7-octadiyne as guests, has been investigated computationally employing molecular docking simulations. Density Functional Theory (DFT) investigations were also performed on these host-guest complexes using the dispersion-corrected approach BLYP-D3(BJ)/TZP/COSMO calculations as implemented in the ADF program and two dispersion-corrected density functionals, ωB97XD and B97D, along with the 6-311G* basis set, coupled with the PCM solvation model as implemented in the Gaussian software. We performed analysis of the frontier molecular orbitals (FMO) and Natural Bond Orbitals (NBO), Energy Decomposition Analysis (EDA), and Non-Covalent Interaction (NCI-RDG) analysis. The study sheds light on the structures and binding energetics of EtP5A with the above-mentioned guests as well as on the physicochemical nature of the noncovalent interactions involved in these host-guest inclusion complexes. Based on the docking simulations, the EtP5A host revealed slightly better binding ability in the complex with the alkyne guest than with the octane and alkene, corroborated by the EDA analysis. The results showed that the complexation of EtP5A with the hydrocarbons is mainly governed by the interplay of electrostatic interactions and dispersive noncovalent interactions. These results agree well with NCI-RDG and NBO analysis showing that host − guest binding interactions result predominantly from electrostatic CH•••π and van der Waals forces, the H-bonding being weak or not observed. The results obtained using different computational methods were found to be in good agreement and complementary.The three-dimensional EtP5A host-guest complexes including the hydrocarbon molecules, octane, 1,7octadiene, and 1,7-octadiyne, were generated from the pdb format using Autodock-Vina software [46], which allows to predict the binding free energy of complexes. The EtP5A host was used as a rigid receptor, and Autodock Tools [47] was used to determine the possible rotations of bonds by molecular docking. During the simulation, the ligands (guest molecules) were docked to the EtP5A with box dimensions set to the grid (22 × 24 × 24) Å 3 in volume, and the cartesian coordinates center was set to 0.017, -0.021, and − 0.097 Å. The docking con guration with the highest free-energy score (ΔG) was used as the starting geometry conformations for the DFT calculations.The structures of all species, including the host, the guests, and their three complexes, generated by Autodock Tools docking simulations, were reoptimized in both gas and implicit solvent phases using the DFT approaches as implemented in two quantum chemistry programs: Amsterdam Density Functional ADF2021.107 program release [48, 49] and the Gaussian 09 program package [50].

A comparative analysis of the influence of hydrofluoroethers as diluents on solvation structure and electrochemical performance in non-flammable electrolytes

“…It has been shown in several studies that NCI can be employed to analyse interactions in both simple and complex systems, including giving insights on NMR results. 25,27,66,67…”

“…† It has been shown in several studies that NCI can be employed to analyse interactions in both simple and complex systems, including giving insights on NMR results. 25,27,66,67 In the conventional electrolyte system, Li + bonds to four oxygen atoms: one TEP double-bonded oxygen (1.88 Å), two oxygens close to CH 2 group (2.0 Å), and one FSI oxygen (also 2.0 Å). In the case of the HCE, the same bond length is observed, but Li + bonds to two FSI oxygens, which cause the uorine atoms to change direction compared to the conventional regime.…”

“…A brief overview of the method, as well as a detailed discussion of the results, can be found in the ESI. † It has been shown in several studies that NCI can be employed to analyse interactions in both simple and complex systems, including giving insights on NMR results 25,27,66,67. In the conventional electrolyte system, Li + bonds to four oxygen atoms: one TEP double-bonded oxygen (1.88 Å), two oxygens close to CH 2 group (2.0 Å), and one FSI oxygen (also 2.0 Å).…”