Students perceive molecular bonding as an abstract concept; therefore, learning this concept seems uninteresting and difficult. A strategically designed learning object (LO), such as in the form of a simulation, can be used to help students acquire accurate mental images and build appropriate schema in addition to providing a concrete learning experience and encouraging knowledge construction. This paper presents an evaluation of the design and development of the "Making Molecules" simulation through students' perceptions of the previous version and recommendations for improving a future version. Data were collected from two online chemistry courses (N = 159) through an anonymous online survey. Results suggest that students responded positively to the use of the simulation. They reported gaining a better understanding of molecular bonding through an interactive learning experience. One of their recommendations was to include more learning tasks related to complex molecules, expressing an interest in learning more about chemistry. This paper provides insights for educators and instructional designers regarding selection and/or design of an LO for optimizing student learning of complex topics.