InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics

Seritan, Stefan; Wang, Yuanheng; Ford, Jason E.; Valentini, Alessio; Gold, Tom; Martínez, Todd J.

doi:10.1021/acs.jchemed.1c00654

Title: InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics

Journal Article · 08 October 2021 · Journal of Chemical Education

DOI: https://doi.org/10.1021/acs.jchemed.1c00654 · OSTI ID:1873512

^[1]; Wang, Yuanheng ^[1]; Ford, Jason E. ^[1];

^[1]; Gold, Tom ^[2];

^[1]

Stanford Univ., CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)
Stanford Univ., CA (United States)

Interactive molecular dynamics in virtual reality (IMD-VR) simulations provide a digital molecular playground for students as an alternative or complement to traditional molecular modeling 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. Furthermore, we include a set of accompanying exercises that we have used to teach chemical reactivity in small molecular systems.

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Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1873512

Journal Information:: Journal of Chemical Education, Journal Name: Journal of Chemical Education Journal Issue: 11 Vol. 98; ISSN 0021-9584

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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Title: InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics

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