Molecule Lab
Four elements. Three dimensions. Build a molecule and explore its electron clouds.
Drag an atom close to another to connect them. Or click an element to attach it to the selected atom.
Drag atoms to build · Drag empty space to orbit · Scroll to zoom · Click bonds to cycle allowed orders · Shift-click bonds to break
Description
Build small molecules from hydrogen, carbon, nitrogen, and oxygen. Atoms connect when brought close enough and settle toward familiar 3D bonding geometries. Explore tetrahedral carbon, bent water, pyramidal ammonia, planar double-bonded structures, linear triple bonds, lone pairs, and orbital probability clouds.
Instructions
- Drag an element into the workspace. Drop it near another atom to form one single bond if both have room in their valence. Click an element instead to attach it at an open site on the selected atom. If there is no open selected site, a separate atom is added.
- Move the atoms. Drag a sphere in the camera’s screen plane; the molecule responds in three dimensions. A bond stretched beyond about twice its usual length breaks on release. Drag an atom near a new partner to reconnect. Drag empty space to orbit the camera; right-drag or Shift-drag pans it. Scroll to zoom and use Fit view to recover the whole structure.
- Change the bonds. Click a stick to cycle through its allowed single, double, and triple bond orders. A single bond uses one valence site, a double two, and a triple three. Hydrogen allows 1, oxygen 2, nitrogen 3, and carbon 4 in this neutral model. Remove neighboring hydrogens before adding a higher-order bond to a saturated carbon. Shift-click a bond to delete it.
- Build faster. Fill H adds hydrogens to open sites on heavy atoms. Remove deletes the selected atom; the small atom selector supports keyboard selection. Undo restores a previous edit, including Clear. Examples load editable structures, including methane, ethanol, ethene, ethyne, and glycine. Up to 24 atoms fit in one workspace.
- Explore electrons. “Bonding & lone pairs” shows shared σ-bond regions, π-cloud lobes for multiple bonds, and amber lone-pair clouds. “Atomic 1s / 2s / 2p” shows occupied valence atomic orbitals as an illustrative superposition, even within a molecule. “Ball & stick” hides the clouds. Pause samples freezes relaxation and sampling so you can inspect the structure.
- Keyboard and saving. Arrow keys rotate, +/− zoom, Home fits the view, Delete removes the selected atom, and Ctrl/Cmd+Z undoes an edit while the canvas is focused. Palette buttons also work with Enter or Space. Your structure saves in this browser when local storage is available.
What an electron cloud means
An orbital is a wavefunction; its squared magnitude describes a probability density for finding an electron. Electrons do not orbit the nucleus on the little circular tracks often drawn in early atomic diagrams. Here the twinkling dots are repeatedly sampled positions illustrating a distribution, not many separate electrons or tracked particles.
Hydrogen’s isolated 1s cloud is spherical. The illustrated 2s cloud includes a radial node, and 2p clouds have two lobes separated by a nodal plane. Blue and violet distinguish wavefunction sign, not positive versus negative electric charge. All electrons have the same negative charge.
Why molecules bend
Electron-domain repulsion helps explain molecular shapes. The model uses approximate bond lengths and angular preferences: sp³ carbon favors tetrahedral directions near 109.5°, water bends near 104.5°, ammonia is pyramidal near 107°, sp² centers favor planar 120° domains, and sp centers favor 180°. Lone pairs occupy space even though they do not appear as another atom.
Single, double, and triple
A single bond is represented by a σ cloud along the internuclear axis. A double bond adds one π system above and below a plane; a triple bond adds two perpendicular π systems. In the model, neighboring groups on a double bond are encouraged into a shared plane so the depicted p directions can align. The bond-cloud drawings are schematic, localized teaching representations.
Building rather than predicting reactions
This sandbox lets you construct bonding graphs; placing atoms close together is an editing gesture. It does not calculate whether a reaction will occur, whether a substance is stable, or what products a real mixture will form. Open-valence structures are unfinished model fragments. The neutral H/C/N/O valence rules omit ions, radicals, excited states, aromatic resonance, and many important exceptions.
Model and rendering details
Geometry relaxes with bond springs, angular targets, short-range repulsion, and a simple double-bond planarity constraint. This is not a calibrated molecular force field, molecular dynamics trajectory, or quantum-chemical energy minimization. Compact or strained structures can have distorted angles. Atomic orbital samples use scaled hydrogen-like radial and angular functions; heavy-atom core orbitals are omitted, and multi-electron orbitals are not solved self-consistently. Carbon shows two occupied 2p directions; nitrogen and oxygen show three, without treating dot count as electron occupancy. Molecular bonding and lone-pair clouds are Gaussian-based schematics, not computed molecular orbitals. Soft cloud envelopes are schematic guides, not calculated isosurfaces; the point samples carry the illustrated probability distributions. Atomic mode shrinks the atom markers to expose more of the cloud. Cloud sizes, nucleus sizes, and opacity are chosen for visibility and are not mutually to scale.
The workspace uses perspective projection and depth-sorted drawing of 3D spheres, bonds, and probability samples. It runs without WebGL or external libraries. Point counts, atom counts, and undo history are bounded. Activity pauses while the page is hidden. No simulation data leaves your browser.
Background: OpenStax: hybrid atomic orbitals and molecular structure and polarity.