Virtual classrooms based on the metaverse or virtual reality are useful and effective for imparting basic chemistry concepts. Interactive and immersive environments can effectively teach fundamental chemistry concepts, such as chemical bonding and formulas, thereby making these otherwise abstract and intangible ideas more accessible and understandable. With the outbreak of COVID-19, e-learning platforms have also been developed for chemistry education. However, these platforms are unable to make learning chemistry interactive and enjoyable. Therefore, there is a need to motivate students to learn basic chemistry concepts in an immersive and interactive environment. In this paper, we propose an immersive virtual reality-based Virtual Chemistry Classroom for Chemical Bonding (VC3B) to facilitate the learning of chemical bonding and formulas through a game-based learning approach. It includes two different games for learning chemical bonding and formulas. In the first game, molecule construction, students reconstruct the structure of molecules by rearranging the atoms in order to learn about chemical bonding. In the second game, chemical formula, students compose the chemical formula of a given compound to help them memorize chemical formulas. The study, conducted on 90 middle school students, employed a randomized controlled study design, dividing participants into three groups. Each group learned about chemical bonding and formulas through three different mediums. After conducting the experiment, the students were given a questionnaire to evaluate the usability of VC3B. The results of the study were positive, with participants finding the VC3B to be more interactive than traditional book and online lecture methods. Participants were also motivated to learn and enhance their knowledge of chemistry.