The present technology report is aimed at demonstrating how the implementation of VR chemistry simulations of atomic structure enhances learning among students. MEL Chemistry VR lessons were incorporated into the classroom for 43 first-year undergraduate ITMO University students. The visualization techniques provided the learners with two important opportunities: (1) connecting the macroscopic and tangible component of chemistry with the submicroscopic component (the real world and the world of molecules) and (2) connecting the submicroscopic component of chemistry with the representational one (atomic structure and orbital diagrams). The results show that implementation of the VR experience into the atomic structure laboratory enhances the learning experience of the students.