Molecular Simulation Animations for Teaching Chemistry

I love that molecular simulations allow us to see the microscopic world as dynamic instead of static. If my students learn nothing else from my 4th year class, it's the dynamic nature of the chemical world. Whenever I can, I try to use visualizations of molecular dynamics simulations in my undergraduate lectures. Students immediately snap to attention when the animation starts. There are many concepts that are vague when described with figures and words but are totally intuitive when they are visualized. These are some of the videos I use in my undergraduate lectures. Most of them are for my 4000-level statistical thermodynamics course, but I also use some in general chemistry and high school outreach lectures. After having done the work to make the animations, I thought that they should be available for use by other instructors, so I put them on my YouTube Channel and on from Wikimedia Commons. They are released under a Creative Commons Attribution-Share Alike 4.0 International license.

This is a molecular dynamics simulation of liquid water (TIP4P). Hydrogen bonds are indicated by dashed red lines. I use this animation in my first year general chemistry class to illustrate the dynamic nature of liquids and hydrogen bonding.

This is a trajectory of a Monte Carlo simulation of liquid argon. I teach Monte Carlo methods before I teach molecular dynamics. I think that this animation communicates the sampling of configurational space through translational moves well.

This is an molecular dynamics simulation of liquid argon. I use this animation to illustrate molecular dynamics simulations of liquids.

This is an NVE simulation of liquid argon in a periodic cell. All but one of the argon atoms are rendered as transparent red spheres. One tagged atom is rendered in blue to show the stochastic diffusion of the particles through the liquid.

This is a NVT molecular dynamics simulation of liquid hydrogen sulfide. I use as a simple demonstration of molecular dynamics and periodic boundary conditions. I had made it for my research but I like the example because it's something different than a water box.

This is a molecular dynamics simulation of the anti-cancer drug erlotinib (magenta) bound to EGFR tyrosine kinase (PDB ID: 4HJO). I use this when I do outreach demonstrations to high school students.

This is a molecular dynamics simulation of TIP3P water in a periodic unit cell. The pressure and temperature are regulated by a Nose-Hoover barostat/thermostat combination. I use this simulation to illustrate the concept of unit-cell scaling in NpT simulations.

I use this animation to illustrate hydrophobic solvation of small solutes. A fixed argon atom (orange) is surrounded by water molecules. The water molecules form a hydrogen bonding network around the argon (red dashed lines).

I present QM/MM methods at the end of my 4th year course. My M.Sc. student Saleh had generated this trajectory from a project we did on Mg(II) solvation. The Mg(II) and the inner coordination sphere of 6 waters are rendered in blue.