Kharkiv University Bulletin. Chemical Series

Local Structure and Li-ion Transport Mechanism in LiFSI/DME/BTFE Electrolyte Revealed by Molecular Dynamics Simulation

Kateryna Dikarieva — 2025-12-30

Fluorinated ether-based electrolytes represent a promising avenue for improving lithium-ion battery performance and safety, yet the molecular mechanisms governing ion transport in these systems remain insufficiently understood. To elucidate the solvation behavior and ion dynamics in mixed solvents, molecular dynamics simulations of 1M (bisfluorosulfonyl)imide (LiFSI) / 1,2-dimethoxyethane (DME) / bis (2,2,2-trifluoroethyl)ether (BTFE) (1:1) system were performed. The results reveal a distinct solvation preference: Li⁺ form predominantly anion-rich aggregates (FSI₃DME₁BTFE₀, 28.9%) instead of traditional solvent-separated structures, with fluorinated BTFE completely excluded from the first coordination shell despite its equimolar presence. Diffusion analysis showed significant mobility differences – BTFE diffuses 17-18 times faster than ionic species−while van Hove correlation function demonstrate that Li⁺transport proceeds via hopping between confined regions rather than continuous diffusion. Cluster analysis reveals small weakly charged aggregates dominating the electrolyte structure, explaining the system’s efficient charge transport. These molecular insights provide design principles for optimizing fluorinated ether electrolytes with enhanced ionic conductivity.

Comparative Evaluation of Computational Methods for Modeling SARS-CoV-2 Spike Protein RBD - Antibody Complexes

Vira Morozova — 2025-12-30

Computational modeling of protein-protein interactions (PPIs) is a high priority because it is essential for understanding nearly all cellular functions and for addressing the limitations of time-consuming experimental methods. This approach is crucial for drug discovery, as it enables rapid identification of disease targets, the design of therapeutics that modulate PPIs, and the simulation of interactions under realistic, crowded cellular conditions. The SARS-CoV-2 Spike protein's Receptor-Binding Domain (RBD) is the crucial region that directly engages the human ACE2 receptor to initiate infection. Therefore, studying the RBD and its interactions with neutralizing antibodies is paramount for understanding immune protection, assessing the threat posed by viral variants, and guiding the design of effective vaccines and antibody-based therapeutics. Here, we evaluated the performance of several computational tools for modeling complexes between the SARS-CoV-2 Spike protein receptor-binding domain (RBD) and various neutralizing antibodies. Recent breakthroughs in computational chemistry have moved beyond traditional protein-protein docking towards various generative methods and co-folding tools that predict a protein's 3D structure and binding poses from its sequence. Therefore, this motivates us to compare the performance of traditional docking methods, such as pyDockWEB and ClusPro, with that of novel, promising AI-driven tools, such as AlphaFold 3, Boltz-2, Protenix, and Chai-1. All these methods were systematically evaluated for their ability to reproduce the 3D structures of known Spike RBD-antibody complexes. We found that traditional docking tools, such as ClusPro and pyDockWeb, perform well at capturing correct protein-protein interactions for relatively small antibodies with well-defined interaction interfaces, but fall short at reproducing more complex protein-protein assemblies. AlphaFold 3 performs best at reproducing the 3D structures of the five studied RBD-antibody complexes among the four AI-driven prediction tools considered. Our study sheds light on understanding protein-protein interactions and provides a practical guide for accurate modeling of viral Spike protein RBD-antibody interactions.

Molecular Dynamic Modeling of Pertechnate Ion in Aqueous Solution

Maksym Volobuiev — 2025-12-30

A molecular dynamics simulation of an aqueous solution of pertechnate ion was performed. To determine the thermodynamic, structural, and dynamic properties of an infinitely dilute solution of pertechnate ion, the following systems were simulated at 25ºC using the MDNAES software package: 400 H2O molecules; 1+399 H2O. The SPC/E water model was used. A classical description of intermolecular interactions via paired (site-site) potentials was chosen, consisting of a sum of short-range Lennard-Jones potentials (12–6) and a Coulomb component.

Atomic charges within the ion were obtained from a quantum chemical calculation using the Gaussian package at the level of second-order Møller-Plesset excitation theory, using the def2QZVP basis set. To verify the obtained model potential parameters, quantum chemical calculations in Gaussian were performed for both pertechnate and perchlorate ions using the method described above, reproducing literature data on atomic charges for which the calculation procedure was considered correct. Atomic charges for the pertechnate ion were then obtained using this method and used in subsequent MD simulations.

The ion's enthalpy of solvation, radial distribution functions, current coordination numbers, and autocorrelation functions were calculated. It was found that the absolute value of the pertechnate ion's enthalpy of solvation is lower than that of the perchlorate ion, as the larger pertechnate ion hydrates less readily.

Based on the calculations, a model for the arrangement of water molecules in the immediate environment of the pertechnate ion was proposed. It was found that the pertechnate ion is located in a deformed octahedral environment of six water molecules. It has been shown that water molecules behave identically in the context of translational dynamics in the first and second solvation shells and in the bulk solution. The dynamics of water molecules are fundamentally the same in the bulk solution and in the solvation shells of the ion, and also differ little in the nature of the ion's dynamics. Thus, the integration of the anion into the water structure occurs with minimal changes in the latter.