About this project

Why we are doing this

     We established this website to share videos of representative trajectories for a variety of organic reactions, with a focus on those taught in undergraduate organic chemistry courses.

     Our goal is to provide instructors with videos they can show students of molecules vibrating in meaningful ways while reacting. In our experience, students generally come away from organic courses thinking that molecular structures transform smoothly from reactant(s) to transition state structure (TSS) to product(s) — a misconception against which we intend to fight.

     First, we use density functional theory (DFT) methods to locate a TSS for a given reaction. We calculate an intrinsic reaction coordinates (IRC) for the reaction and display this as a movie. The changes in geometries shown in an IRC correspond to moving along a potential energy surface (PES).

     We also subject our TSS to direct dynamics trajectory simulations. In these simulations, internal vibrations of a reacting molecule are included. Unlike IRC movies, trajectory movies clearly show that bonds that do not break, for example, vibrate as molecules move from reactant(s) to product(s).

     For each reaction, we post videos of representative trajectories (we calculate many to make sure those shown capture the most common features). We also include videos of examples of rare trajectories to emphasize that these occur.

     We envision this databank expanding continuously over time.

Introduction to Dynamics Calculation

What is dynamics?

     For an introduction to dynamics simulations, we invite you to read Dean’s “Wiggling and Jiggling” article for American Scientist.

Methods we are using

     The program we are using is called Progdyn.

     Details about how we setup the calculation can be found here.



     This work is supported by NSF funding (CHE-1856416).

     This website is build using jekyll, html5 and bootstrap 4. Jekyll theme sakura @Kimfucious. Responsive images build with Gulp. Blog with Bootstrap 4 and Sass. Publishing with Netlify.

     The calculation by Tiffy were performed using XSEDE. The calculations by Misa were performed using Research Center for Computational Science, Okazaki, Japan. Figures are generated with Schrodinger, BioRender, PyMOL, ChemDraw, molview.


Cite our work

     This project is about to be published here: DOI