Convert reaction mechanisms into accurate 3D movies

In the Mechanism Lab, curved-arrow mechanisms play as 3D animations so students can align a flat line drawing with what the atoms actually do. Draw a mechanism with the Lab tools, read one from a photo or manuscript, or rebuild a library example step by step while the engine checks your arrows.

A curved-arrow mechanism is typically drawn as a flat 2D structure. A 3D representation can help a student understand the regiochemistry or stereochemistry of the reaction, but these have not been commonly available. Students can struggle to map what they draw to the videos they can find.

Combining 2D and 3D makes each reaction pathway clear

The Mechanism Lab allows you to build a mechanism from a document, including hand-drawn answer keys. It also has a short library of mechanisms in 3D: SN2 with inversion, E2, a proton transfer, hydroxide adding to acetone, tert-butyl bromide ionizing and then capturing hydroxide, a three-step SN1 with water, and cyanohydrin formation. Press Watch in 3D on any of them, or on the matching worked example further down the page.

3D animation of an E2 elimination: hydroxide removes a hydrogen from 2-bromobutane, the C=C double bond forms and bromide leaves, with three numbered curved arrows.
E2: hydroxide + 2-bromobutane. Arrow 1 takes the β-hydrogen, arrow 2 makes the C=C π bond and arrow 3 moves the C–Br electrons onto bromine. The hydrogen and bromine start anti-periplanar.

How the 3D frames are built

Each species is embedded with RDKit (ETKDGv3) and relaxed with MMFF. For each step, the product geometry is fitted onto the starting geometry with a weighted Kabsch fit, restricted to proper rotations so a stereocentre is never mirrored, and the frames in between are interpolated. Bonds that form or break are drawn as dashes at the midpoint. One camera is used for the whole mechanism. It is rolled to keep heavy atoms from overlapping on screen, and reagents that are waiting their turn are turned flat to the screen. The motion is a teaching picture of the arrows. It is not a computed reaction path, and the animation says so. Published library animations are rendered once and stored; pressing Watch in 3D plays those frames, so nothing is computed while you wait.

Draw a mechanism or read one from a page

You can start from a reaction you drew with the Lab's own tools on the Mechanism Lab canvas, or from a photo, scan, or page of a PDF—even a handwritten answer key or a figure from a manuscript—under Read a mechanism. Rebuild in 3D on a library example opens the Lab with only the starting structures on the canvas. You draw the arrows one step at a time. Play my steps in 3D animates what you have so far using the same frame-building pipeline described under How the 3D frames are built, and Check my mechanism checks the whole thing.

Contact sheet of the two-step tert-butyl bromide animation: the C–Br bond ionizes to a tertiary carbocation and bromide, then hydroxide bonds to the carbocation to give tert-butyl alcohol.
tert-Butyl bromide in two steps: the C–Br bond ionizes, then hydroxide bonds to the tertiary carbocation.

How a rebuild is checked

  • Each set of arrows is validated against the closed-shell teaching profile and the result is validated again. If the server's result differs from the structure your browser showed, the check stops and asks you to start the rebuild again.
  • After every step the server compares a balance signature: element counts, hydrogens, total charge, radicals and electron count, plus the set of atom IDs. Any change fails the step, as does a valence the engine flags as impossible.
  • Your own route is then built in 3D and has to pass the same geometry checks as the stored animation.

A different route to the same product passes. The server also compares the product after each of your steps with the reference's and reports whether you followed the same route. If a step trips one of the Lab's plausibility rules (a primary carbocation, for example, or a poor leaving group), the note is listed beside the result. It does not change the result. A pass comes with a signed token that is good for 15 minutes and is tied to your account, that version of the reference, and a hash of your steps.

Diels–Alder and Claisen in 3D

Pericyclic reactions have their own videos in the Lab, built from a transition-state template. The Diels–Alder view plays the endo and the exo transition state one after the other. Furan and maleic anhydride is a good one to show a class: endo forms faster, but furan adducts form reversibly, so the exo adduct is the one you isolate.

Furan + maleic anhydride, endo then exo. Both new σ bonds form in one step (dashed, gold). Press play; the video never starts on its own.
Transcript

Diels–Alder · endo and exo, for furan and maleic anhydride. The diene and dienophile are drawn flat, the diene above and the dienophile below with a gap where the new bonds will form; the drawing then moves onto the 3D model, with the s-cis diene stacked over the dienophile about 3 angstroms apart. Along the reaction both new sigma bonds form together (dashed, gold) in one concerted step, the six pi electrons are delocalised at the transition state, and the product ring keeps one pi bond, between carbons 2 and 3. The geometry is a template built from the computed transition state of butadiene plus ethylene (Houk, 1996), with the rest of each molecule relaxed by a force field; no energies are calculated. ENDO transition state: the acceptor group lies under the diene. This is the favored transition state. Alder endo rule: the π-acceptor sits under the diene (secondary orbital overlap), so the endo adduct forms faster. Furan adducts form reversibly, though: the endo adduct forms first, but the more stable exo adduct is the one isolated once the reaction equilibrates. The video then returns the product to a line drawing. EXO transition state: the acceptor group points away from the diene. The video then returns the product to a line drawing.

The chair view now takes a Claisen rearrangement as well as a Cope. Draw an allyl vinyl ether and it is bent into the same chair: the O–C bond breaks, a new C–C bond forms, and the oxygen ends up in a C=O. Allyl vinyl ether gives pent-4-enal.

Allyl vinyl ether → pent-4-enal through a chair. Positions are numbered C1 to C6 with the oxygen at 3.
Transcript

Claisen rearrangement · chair, for allyl vinyl ether. The allyl vinyl ether is drawn as a zigzag, bent into a U so that carbons 1 and 6 face each other, and redrawn as a chair with carbons 1 and 6 about 2.6 angstroms apart; then the same chair is shown in 3D. Along the reaction the sigma bond between oxygen 3 and carbon 4 breaks (dashed) while a new sigma bond forms between carbons 1 and 6 (dashed, gold); the pi bonds shift from C1=C2 and C5=C6 to C2=O3, a new carbonyl, and C4=C5. The geometry is the Cope template chair with the bonds to oxygen set to typical lengths, an illustration, not an energy calculation. It gives pent-4-enal. The video then unfolds the product chair back to the U and the zigzag drawing.

How the line drawings move

The 3D model comes first. The engine builds the transition state in 3D from a template, and the ball-and-stick picture is drawn from those coordinates. The line drawing you see over the model is the same set of atoms, flattened onto the screen, and drawn as lines instead of balls.

The textbook drawing at the start and end of each video is a separate, tidy 2D layout. In the middle of the video, every atom travels from its place in the textbook drawing to its place in the flattened 3D view. The bonds bend along the way, the way a chain folds, instead of each atom sliding in a straight line.

This is why a double bond can look odd for a moment. A cis C=C seen nearly edge-on in 3D looks almost straight on a flat screen. As the view turns, it opens up and looks cis again. Nothing broke. It is the same bond seen from a different angle.

What must never happen is a cis bond coming out the other side as trans. An earlier version of these videos did that for some molecules. The bond reached the right final shape, but on the way the two groups swapped sides, as if a double bond could rotate. The engine now checks every frame, atom by atom, against the 3D model. A group may pass close to the line of the bond, but it may not cross it. If no motion passes that check, the two drawings fade into each other in place instead, and a video with a wrong frame is not made at all.

Reading a handwritten mechanism

The Lab can also start from a drawing. Under Read a mechanism, upload a photo, a scan or one page of a PDF, such as a handwritten answer key or a student's exam answer. Claude Opus 5.5 reads the page at full resolution and can zoom in on parts of it. It transcribes the mechanism as drawn: the starting structures as atom-mapped SMILES, and each arrow as a move from a lone pair or a bond to an atom. For every step it also records whether the arrows were drawn, partly drawn, or had to be inferred.

The Lab engine replays the transcription step by step and reports four things separately: how the source showed each step, whether the engine can carry it out, what the plausibility rules say, and whether the steps reach the product drawn on the page. If the engine refuses a step, the replay stops there and nothing after it is filled in. Each step is drawn with the Lab's own renderer, so you can compare it with the original. Open in Lab puts the steps on the canvas, where you can edit them and press Animate in 3D.

Reading is available to verified teachers. A reading costs 2 AI Actions, charged only once the starting structures have been read. Anyone can open the sample reading of a handwritten key on the same page for free. Verified teachers can also create one tutorial from an old exam or answer key.

Saving a rebuild

After a pass, Save reference animation adds the stored animation to Your saved 3D animations, along with whether you followed the same route. The save points to the frames already stored, so nothing is rendered again, and only you can see your list. If an animation is withdrawn, your list marks it as unavailable.

Try it

Open the Mechanism Lab and press Watch in 3D on any mechanism in the 3D library. If you teach, press Rebuild in 3D, or upload a page under Read a mechanism. The chair transition state is on the same page.

The 3D ball-and-stick frames are built using xyzrender.