3D Molecular Animation: A Chemist's Guide to Visual Storytelling ?

On July 29th, I logged in and saw an urgent email. ??

It was from the Managing Director of a Research Center I consult.

The request was simple:

Who could animate individual molecules joining a polymer network?

I joyfully replied, "I could do it!"

(Wisely) I was asked to provide 3?? examples of molecular animations I'd created.

Confidently, I agreed to create and send these by the end of the month.

?? I. Failed. Spectacularly.        

But, after sharing a list of colleagues with experience in molecular animation, I set off to learn the skill.

It took 2 months to create this 1, 17-second animation:

But! I think I can shorten the process for others by sharing a step-by-step recreation guide and a bit about what I learned from the experience:

Fellow Visualizers of the Abstract,

Over the past two months, I embarked on an exciting journey to create a 3D molecular animation of the dehydration synthesis reaction forming maltose from two glucose residues. Today, I'm thrilled to share my experience and insights with you.

Blender: A Powerful Tool for Chemists

The animation was created using Blender, a free 3D modeling software.

Here's a step-by-step guide (to recreate what I did) that can be adapted to create any relatively simple chemical reaction:

First, the Software ???

Links are available here!

1. Blender (Free): Blender is a free, open-source 3D modeling and animation software. It creates high-quality 3D graphics, animations, and rendering.Blender has a steep learning curve but offers various advanced features and tools. It is not specifically designed for molecular visualization but can be used for that purpose with the help of add-ons (more below).
2. PyMOL (Free for Educational Licensing): PyMOL is a popular molecular visualization software used for modeling and visualizing 3D structures of biomolecules, such as proteins, DNA, RNA, and small molecules. It can interpret over 30 file formats and offers nearly 20 ways to represent molecular data.PyMOL has a straightforward graphical user interface and is well-suited for scientific analysis and creating high-quality molecular images.However, PyMOL has limited options for exporting structures and does not preserve color information when exporting (we'll fix that in the step-by-step guide).
3. Atomic Blender (Free): Atomic Blender is a Blender add-on that bridges the gap between molecular visualization software (VMD and PyMOL) and Blender. It allows users to import Protein Data Bank (PDB), VMD Visualization State files, and PyMOL Session files directly into Blender.With Atomic Blender, users can create advanced molecular visualizations and animations in Blender, leveraging the powerful features and rendering capabilities of the 3D software.

Next, the Animation ??

Click here to access (no email or payment required).

The Learning Process: More Than Just Animation

What struck me most during this project was how the act of creating the animation deepened my understanding of these concepts.

For instance, visualizing the electron density distribution in glucose molecules helped me better grasp its impact on reactivity. Similarly, animating the nucleophilic attack from different faces of the molecule reinforced my understanding of stereochemistry in a way that static images never could.

Here are just a few topics I needed to review to animate the reaction:

1. Anomers vs. epimers and the anomeric effect
2. Haworth projections and chair conformations
3. Chirality and cyclization in glucose
4. Electron density distribution and steric hindrance
5. Leaving group ability in dehydration synthesis
6. Hybridization states and orbital interactions
7. Alpha/beta face nucleophilic attacks
8. Enzyme selectivity and substrate specificity
9. Solvent effects on reactivity and the anomeric effect

Incorporating 3D Animation in Chemistry

This experience has convinced me of the immense potential of 3D animation projects in chemistry education and research. Here are a few ways we could integrate this approach:

• Assign animation projects to reinforce complex concepts
• Create an animation for your talk or paper
• Use student-created animations for peer teaching
• Develop visual aids for lectures and online courses

Your Turn to Explore

I've documented my process and am excited to share it with you. Please feel free to ask questions in the comments section below and share any animations you make with the Collective! We'd love to cheer you on.

Stay tuned for more resources!

Off visualizing the abstract,

Vanessa Rosa, Ph.D.

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