This work integrates Talanquer's model of the chemical knowledge space, focusing on developing an educational animation and a virtual/augmented reality object. We designed the animation concerning bimolecular nucleophilic substitution, offering a multifaceted learning approach incorporating theoretical calculations and three-dimensional molecular modeling. This method facilitates a deeper understanding of complex chemical reactions and engages students in a more immersive and interactive learning experience. The use of advanced software like Blender 3D for 3D editing and animating, as well as Gaussian for generating accurate structures and electronic configurations, along with a well-thought-out pedagogical framework, allows for a higher level of abstraction in depicting how molecules interact. Our approach enhances the quality of the lessons and helps students gain a better understanding of chemistry's conceptual and practical aspects.