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Chemistry uses multiple representations of molecules and molecular processes to help students acquire accurate mental images and build appropriate schema. However, most chemistry courses tend to use only one representation. We explored online students’ perceptions regarding a simulation that employed multiple representations. Data were collected from lower- and upper-division students (N = 159) enrolled in two online chemistry courses through an anonymous survey. Results indicate positive responses from the students. They reportedly gained a better understanding of molecular bonding through an engaging learning experience. Their recommended suggestions that also implied interest to solve more advanced problems. This study sheds light on ways to increase students’ interest in learning STEM-related topics.