Create conformational analysis videos that help students bridge 2D and 3D representations

Four 3D-native conformation videos rendered from the molecule on your canvas: a Newman rotation with its energy curve, the double Newman of a chair, the 1,3-diaxial figure, and the full chair flip through the boat, each with a transcript and MP4, GIF and poster downloads.

Conformational analysis is typically taught with still pictures and we ask students to picture the motion. A Newman projection is a snapshot of a bond mid-rotation; a chair drawing captures one part of a ring flip. ChemIllusion can now render that motion for the molecule you already have on the canvas: four conformation videos, built from a real 3D model with a real force field, that fade into the textbook drawings students know.

  • Newman rotation — look down one C–C bond while the back carbon sweeps a relaxed torsion scan; the energy curve carries a cursor.
  • Double Newman — a cyclohexane chair spins until two parallel ring bonds point at you and the two-circle Newman fades in, axial groups vertical, equatorial groups slanted.
  • 1,3-Diaxial figure — the same view with an axial substituent and its two 1,3-partners picked out.
  • Chair flip — chair → half-chair → twist-boat → boat → twist-boat → half-chair → chair, with the energy profile drawn as it happens.
Methylcyclohexane, axial → equatorial. The ring carbons follow the known half-chair, twist-boat and boat geometries; the substituents relax at every step. MMFF94 energies above the lowest point (the equatorial chair): axial chair 1.5, half-chair 12.3, twist-boat 6.3, boat 7.1 kcal/mol, so the barrier from the starting chair is 10.8.
Transcript

Methylcyclohexane: chair flip, axial → equatorial. A cyclohexane chair, seen from its textbook viewpoint, flips to the other chair through the known sequence: half-chair, twist-boat, boat, twist-boat, half-chair. The CH3 on C2 goes from axial to equatorial; it stays on the down face. On the MMFF94 profile, with the ring held on the Cremer–Pople pathway and energies in kcal/mol above the lowest point, the starting chair is at 1.5, the half-chair 12.3, the twist-boat 6.3, the boat 7.1 and the flipped chair 0.0. The barrier from the starting chair is 10.8 kcal/mol. The line drawing fades into the three-dimensional model. The ring flips, the energy cursor climbing to the half-chair, resting in the twist-boat, crossing the boat and descending to the other chair. The model cross-fades into the chair line drawing.

Four videos, one tool

Every video starts and ends on a line drawing — a Newman projection or a textbook chair — and crosses into the 3D model only while something is moving. That is deliberate. The drawing is what students will have to produce on an exam, so the video exists to show what the drawing stands for, not to replace it.

(S)-2-Bromobutane down C2–C3. The camera opens the hidden bond sideways, the Newman cross-fades into the 3D model and a wedge/dash drawing, then back. The stereocentre is read back from the drawing and checked against the model on every frame.
Transcript

(S)-2-Bromobutane, down C2–C3 (Br in front). The viewer looks down the C3–C2 bond; the front carbon's three groups are fixed and the back carbon turns. The back carbon rotates from -180° (anti) to 60° (gauche). The camera tilts sideways to 60°, the hidden bond opens up and the Newman circle fades into the three-dimensional model. The model cross-fades into a wedge-and-dash line structure drawn from the same view: wedges come toward the viewer, hashes go away. The line structure fades back into the model. The camera tilts back until the bond points at the viewer again and the Newman projection returns. The back carbon rotates from 60° (gauche) to -180° (anti). The camera tilts sideways to 40°, the hidden bond opens up and the Newman circle fades into the three-dimensional model. The camera tilts back until the bond points at the viewer again and the Newman projection returns. Relative MMFF94 energies: minimum at -170° and maximum 8.0 kcal/mol above it at 120°.

Methylcyclohexane with the methyl equatorial. The chair turns 90° into the double Newman: C1 bridges the front carbons, C4 the back ones, and every substituent keeps its axial (vertical) or equatorial (slanted) direction.
Transcript

Methylcyclohexane, methyl equatorial on C6 (front, left). A chair cyclohexane viewed down two parallel ring bonds at once, C6 toward C5 and C2 toward C3, so two Newman circles appear side by side; C1 joins the two front carbons at the top and C4 joins the two back carbons at the bottom. C6 carries CH3 equatorial. Axial groups point straight up or down; equatorial groups slant outward. The line drawing fades into the three-dimensional model. The chair spins about its own axis until the two bonds point straight at the viewer and the double Newman projection fades in. The chair spins back to its textbook view. The model cross-fades into the chair line drawing.

The 1,3-diaxial movie. The axial methyl and the axial hydrogens two carbons away on the same face are haloed and connected in all three views; the legend gives the MMFF94 axial − equatorial gap.
Transcript

Methylcyclohexane, axial methyl on C6: 1,3-diaxial. A chair cyclohexane viewed down two parallel ring bonds at once, C6 toward C5 and C2 toward C3, so two Newman circles appear side by side; C1 joins the two front carbons at the top and C4 joins the two back carbons at the bottom. C6 carries CH3 axial. Axial groups point straight up or down; equatorial groups slant outward. The line drawing fades into the three-dimensional model. The chair spins about its own axis until the two bonds point straight at the viewer and the double Newman projection fades in. The chair spins back to its textbook view. The model cross-fades into the chair line drawing.

From the molecule on your canvas

Draw or paste a substituted cyclohexane and the Generator notices: the right dock says Conformation video available with the two most useful offers, and Chem Assistant shows the same offers as chips. A butane-like chain gets the Newman offer instead. Dismiss it once and it stays quiet for that molecule.

The Generator's right dock with methylcyclohexane active: a blue card titled Conformation video available with two buttons, Chair flip of this ring and 1,3-Diaxial figure of this ring, and a dismiss cross.
The dock offer for methylcyclohexane. Each button opens the video modal with the kind, the ring and the substituent already chosen.

The Newman projection tool can also be accessed by click or chat. Once you have confirmed a canvas bond, Animate in 3D hands that exact bond to the video modal.

The Newman projection tool's canvas bond picker showing butane's C2–C3 bond with Use this bond and a new Animate in 3D button.
Animate in 3D on the Newman tool's bond picker.
The Conformation video modal for methylcyclohexane: the molecule from the canvas, four kind cards with Newman rotation greyed out because the ring has no butane-like bond, Chair flip selected, the substituent and axial/equatorial choice, and quality radio buttons.
The modal explains why a kind is unavailable for this molecule instead of hiding it; here the ring has no acyclic bond to look down.

The Chair tool

Rings get their own tool at https://chemillusion.com/generator?tool=chair, with four tabs: Double Newman, 1,3-Diaxial, Chair flip and Chair drawing. The last one is a still image, not a video: the start chair as a textbook line drawing with axial bonds exactly vertical and equatorial bonds parallel to the ring bond once removed, inserted on the canvas as an editable figure. It needs no account.

The Chair tool dialog with tabs Double Newman, 1,3-Diaxial, Chair flip and Chair drawing, the molecule CC1CCCCC1 from the canvas, Ring found with C1: CH3, the Double Newman kind card, the substituent and placement choices and the quality options.
The Chair tool over the canvas molecule.
The Chair drawing tab of the Chair tool: a preview of the methylcyclohexane chair line drawing with the methyl axial, a legend line, ring-number and ring-hydrogen options and an Add to canvas button.
The Chair drawing tab renders the still in about two seconds and adds it to the canvas.

What the engine actually computes

Nothing here is a cartoon. The molecule is embedded in 3D with RDKit, and every frame comes from an MMFF94 geometry. For the Newman rotation that is a relaxed torsion scan: the dihedral is held and everything else minimised, which is why the curve shows the gauche minimum and the eclipsed maxima at the right heights for the molecule rather than for an idealised ethane.

The chair flip is the interesting one. The six ring carbons are placed on the Cremer–Pople pathway — the puckering coordinates that define the half-chair, twist-boat and boat exactly — and held there while the substituents and the pucker amplitude relax. The route through the twelve possible twist meridians is chosen by the lowest barrier. The result is a profile with the right shape and the right ordering (chair < twist-boat < boat < half-chair), labelled as MMFF94. Bare cyclohexane comes out at twist-boat +6.1, boat +6.9 and half-chair +10.8 kcal/mol against the textbook +5.5, +6.5 and +10.

A contact sheet of seven frames from the methylcyclohexane chair flip: chair, half-chair, twist-boat, boat, twist-boat, half-chair and the flipped chair, each with the energy cursor at its station.
The seven stations of the flip, from the engine's own contact sheet. Every axial substituent ends equatorial and the engine refuses to publish a video where that check fails.

The chair line drawing deliberately departs from the 3D projection for its substituent bonds. A faithful projection of an axial methyl is foreshortened and slanted; the textbook draws it vertical and the same length as every other substituent. So the ring stays the true projection while the substituent bonds are idealised, and the drawing fades out before its bonds slide to where the model has them. The video shows both, and shows the hand-off.

Downloads, decks and the brand strip

A finished video gives you MP4, GIF, a poster frame, the transcript and its alt text, and Add to canvas, which places the poster with the video attached so a slide deck or a chapter can pick it up later. In Deck Creator the same asset drops in as its GIF with the poster as fallback, and the reader plays it inline with the transcript underneath.

  • Free accounts get three videos a month at 720p with a small ChemIllusion strip, plus the chair drawing and the detector without limit.
  • MyMol Plus and up render clean, with more videos a month; Premium adds 1080p. A branded video can be re-rendered clean once you upgrade.
  • Teachers with a class on ChemIllusion are not metered.

Alt text, transcripts and no autoplay

Every render writes two pieces of text along with the video. The alt text is a one-sentence description for screen readers and for the alt field of a post or LMS page. The transcript describes each segment in turn, with the energies the panel plots. Both are written by the engine from the same geometry as the frames, not by a language model, so they cannot quote a number the video does not show.

  • On your result: the alt text is shown under the video with Copy alt text and a .txt download, and the transcript opens with Show transcript and downloads on its own.
  • On the share page and on this blog: the poster waits until you press Play, the alt text labels the poster and the player, and the transcript sits under each video.
  • In Deck Creator and on the canvas: the asset carries the alt text as its alt text and the transcript as its long description, so they reach exported slides and chapters. A deck shows the video as its GIF, which loops like any GIF on a slide; use the poster if a slide should stay still.

Try it

Draw methylcyclohexane in the Generator and take the offer, open the Chair tool directly, or start from the Newman projection tool and press Animate in 3D. The still chair drawing and the detector work without an account; free email registration unlocks the videos.