Bringing Molecules to Life in the Classroom: Real-Time Molecular Dynamics Visualization of the Microstructure of Alcohol–Water Mixtures

To address the challenge of teaching the abstract concepts underlying solution microstructures in physical chemistry, we developed a progressive instructional module integrating molecular dynamics (MD) simulations, which was successfully implemented in undergraduate physical chemistry and statistical thermodynamics courses. This scaffolded learning approach employs three representative systems (methanol–water, ethanol–water–sodium carbonate, and butanol–water systems) across three sequential phases: (1) model construction using GROMACS software, (2) simulation and dynamic visualization of nanocluster formation, and (3) quantitative analysis of microscopic structural features including radial distribution functions, hydrogen-bonding networks, and three-dimensional spatial density distributions. Assessment data indicate that incorporating molecular simulation into courses enhances students’ understanding of theory and concepts, which are often difficult to convey through traditional lectures or media. The module also successfully stimulated student interest in computational chemistry research. Implemented nationally through China’s Virtual Simulation Platform (2,700 participants), this work provides a transferable model for incorporating research-based molecular simulation methods into physical chemistry education.