Learn to use ChemModel

Tutorials

Short step-by-step guides to get the most out of every ChemModel tool: molecular Studio, isomerism, reactions, biomolecule viewer and sharing.

Need help? Every tool has a ? button that brings you here.

Molecular Studio

Search for any molecule or draw it, and view it in 3D with its properties.

Step by step

  1. 1Type a molecule name in the search box (English or Spanish: “aspirin”, “cafeína”) and press Search or Enter. Formulas (“C8H10N4O2”) and SMILES (“CC(=O)O”) also work.
  2. 2The structure appears in the 2D editor (left) and the 3D viewer (right). Drag to rotate and use the mouse wheel (or pinch on mobile) to zoom.
  3. 3Change the style with the buttons on the viewer edge: sticks, ball & stick, spheres (CPK) or lines. “Auto-rotate” spins it and “Dark background” toggles the background. Hover over a button to see its name.
  4. 4Press “Properties” to see formula, molar mass, SMILES, InChIKey and XLogP.
  5. 5To draw your own molecule, use the 2D editor tools and press ➜ to generate its 3D.
  6. 6Save or share: 🔗 copies a link to the molecule, “Download” saves PNG or SDF, “Share as PNG” creates an image with name and formula, and 🕐 opens your search history.

💡 Tips

  • If you misspell a name (“ibuprofemo”, “asprin”), the AI tries to correct it and tells you how it was interpreted.
  • Salts are shown without their counter-ions (tartrazine without Na⁺) and, if PubChem has no 3D structure, ChemModel computes one: you will see “approximate geometry”.
Open the toolTry an example

Isomerism Studio

Compare two or more molecules side by side and find out what kind of isomers they are.

Step by step

  1. 1Type one molecule in panel A and another in panel B (name or SMILES) and press Search in each.
  2. 2The detected type appears at the top: constitutional, geometric (cis/trans), enantiomers, diastereomers, same compound or “not isomers”.
  3. 3Read the explanation: what they are, how to identify them and a tip to remember it.
  4. 4Turn on “Sync rotation” to rotate all 3D models together and compare them from the same angle.
  5. 5Press “🔍 Find isomers” in a panel to see other compounds with the same formula and load them into any panel.
  6. 6Use “+ Panel” to compare up to 4 molecules, or the Examples button to load classic pairs (butane/isobutane, D/L-alanine, cocoa…).

💡 Tips

  • You can type names in English or Spanish, even misspelled: the AI interprets them as in the Studio.
  • For stereoisomers, use names with configuration (“L-alanine”, “trans-2-butene”) or SMILES with @ and / \: a generic name may not specify stereochemistry.
Open the toolTry an example

Chemical reactions

Draw or pick a reaction and check whether it is balanced, what type it is and what its molecules look like in 3D.

Step by step

  1. 1Pick a template (combustion, neutralization, esterification, cocoa fermentation…) or draw reactants and products in the editor and join them with the reaction arrow in the toolbar.
  2. 2Know the reaction name? Type it in “Search by name” (e.g. “bromination of propanol” or “butane combustion”). ChemModel recognizes it or interprets it with AI, checks that it can be balanced and shows its title; check that it is the one you wanted.
  3. 3Need more drawing tools? Switch the editor to “Advanced (Ketcher)”: it has functional-group templates, atom mapping and RXN/MOL export. The first time it downloads about 6 MB; the reaction you have drawn moves to the new editor.
  4. 4Press Analyze. You will see the equation with formulas and whether it is balanced (✔) or not (⚠).
  5. 5If it is not balanced, check the suggested coefficients and press Apply. The “Atoms per element” table shows how many atoms of each element are on each side.
  6. 6Read the reaction type and its explanation, and explore each reactant and product in its 3D viewer.
  7. 7Export the reaction as a PNG image, copy a link or copy the code to embed it in your website or blog.

💡 Tips

  • No drawing needed: type a “reaction SMILES” such as CC(=O)O.CCO>>CCOC(C)=O.O (reactants >> products, molecules separated by dots).
  • To set a coefficient while drawing, repeat the molecule (two O₂ = coefficient 2).
  • With the advanced editor you can map the atoms: number which reactant atom ends up in each product. ChemModel then shows which bonds break, which form and the reaction pattern (addition, elimination, substitution, cycloaddition…). Press “Map atoms automatically” or map by hand with the tool next to the arrow.
  • Automatic mapping is an estimate and sometimes gets it wrong (repeated numbers or unmapped atoms). ChemModel checks it and warns you; fixing it by hand is a good exercise to understand the reaction.
  • The classification is rule-based: right for textbook cases, but not for every reaction.
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Biomolecule viewer

Explore proteins, DNA and other large structures from the Protein Data Bank.

Step by step

  1. 1Type a 4-character PDB code (e.g. 4HHB, hemoglobin) and press Load, or try one of the examples.
  2. 2You can also upload your own .pdb, .cif, .sdf, .mol or .mol2 file.
  3. 3Change the representation: Cartoon (secondary structure), Ball & Stick, Surface, Ribbon or Licorice, and a light or dark background.
  4. 4Drag to rotate, scroll to zoom and right-click to pan.

💡 Tips

  • Find PDB codes at rcsb.org by searching for the protein name.
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Share and embed

Bring ChemModel molecules and reactions into your classes, blog or presentations.

Step by step

  1. 1Direct link: chemmodel.com/en/lab/?mol=caffeine opens the Studio with the molecule loaded.
  2. 2Embed a 3D viewer: use an iframe with chemmodel.com/embed?mol=… If you use a SMILES, add &label=Name to show the name.
  3. 3Embed a reaction: in the reaction editor, press “</> Embed” and paste the code into your page. You can also embed it by name: chemmodel.com/embed/reaccion?q=bromination of propanol. The “Embed reactions” guide (in the footer) explains every option, including WordPress.
  4. 4For images: use 🖼️ in the Studio or “Export PNG” in Reactions.

💡 Tips

  • The Share page lists every parameter, code examples and the public JSON API.
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