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This work seeks to develop and explore conceptual understanding regarding chemical bonding. Our ELI-Chem environment enables interaction with atoms while experiencing attraction and repulsion forces. The theoretical framework is based on embodied cognition theory by relating conceptual learning to intuition development through repeated and varied bodily experiences. The study uses qualitative methods with 14 high-school students in a pretest-intervention-posttest design, capturing students' gestures and articulations. Our findings indicate a shift from a naïve perception of chemical bonds as stationary solid spheres that keep together like magnets to a more scientific understanding that involves the balance of attraction and repulsion forces, describing the atoms as constantly moving around a dynamic equilibrium.