Chemical Education

InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics

Abstract

Interactive molecular dynamics in virtual reality (IMD-VR) simulations provide a digital molecular playground for students as an alternative or complement to traditional molecular modelling kits or 2D illustrations. Previous IMD-VR studies have used molecular mechanics to enable simulations of macromolecules such as proteins and nanostructures for the
classroom setting with considerable success. Here, we present the INTERACHEM molecular visualizer, intended for reactive IMD-VR simulation using semiempirical and ab initio methods.
INTERACHEM visualizes not only the molecular geometry, but also 1) isosurfaces such as molecular orbitals and electrostatic potentials, and 2) two-dimensional graphs of time-varying
simulation quantities such as kinetic/potential energy, internal coordinates, and user-applied force. Additionally, INTERACHEM employs speech recognition to facilitate user interaction and introduces a novel “atom happiness” visualization using emojis to indicate the energetic
feasibility of a particular bonding arrangement. We include a set of accompanying exercises that we have used to teach chemical reactivity in small molecular systems.

Content

Thumbnail image of IMD-ChemArxiv.pdf
download asset IMD-ChemArxiv.pdf 7 MB [opens in a new tab]