The teaching of Chemistry represents one of the most expressive examples of the impact that mobile technologies can promote regarding the teaching-learning process. Virtual Reality and Augmented Reality are significant representations of these technological advances promoted by mobile devices. And, in this way, they contribute to dynamic learning, arousing students curiosity to understand and visualize theories from a new perspective.Augmented reality, one of the most sophisticated virtual reality technologies and effective as a learning medium, qualifies to integrate education with the visualization of chemical and biological structures, allowing for impressive and immersive experiences. Thus, the integration of smartphones with Augmented Reality applications is an innovative method of teaching spatial reasoning skills to chemistry students.The purpose of this application was to use free software such as Avogadro, Blender 2.79, Unity and Vuforia, to model molecular structures that can illustrate the concepts of Molecular Geometry and Spatial Isomerism. The use of these tools makes it possible to build molecules with the application of 3D interactivity for the Android system of mobile devices that provide greater involvement of students in the teaching-learning process. In this way, increasing the cognitive work capacity of students and teachers both in the face-to-face environment and in distance learning.