Tutorial: caffeine, from ring to slide

Draw caffeine from an empty canvas — a fused ring system, four nitrogens, two carbonyls and three methyls — then check the SMILES, save it, and put it on a slide.

Caffeine is a good first molecule because it exercises nearly every tool in Molecule Studio and nothing it cannot do: a six-membered ring fused to a five-membered one, heteroatoms swapped into ring positions, two carbonyls, three N-methyls, and not a single stereocentre — which matters, because wedges and hashes never make it into the SMILES.

Allow ten minutes the first time. Every step below is a real click in the shipped editor.

Open a blank canvas#

In the dashboard sidebar, open Studio → Molecule Studio, press New molecule, and choose Blank — "Start from an empty canvas". The studio opens with the name Untitled molecule, the formula chip reading empty, and the Bond tool already selected.

Step one — the six-membered ring#

Click Cyclohexane in the left rail under Rings & templates. The status bar changes to "Click empty to drop the ring · click a bond to fuse it".

Click once in the middle of the canvas. Six carbons appear as a regular hexagon, and the formula chip reads C6H12. Press F if you want it centred.

Cyclohexane rather than benzene: this ring becomes a pyrimidinedione, not an aromatic ring, and we want plain single bonds to start from.

Step two — fuse the five-membered ring#

Click Cyclopentane in the same rail, then click one of the hexagon's bonds — the one on the right-hand side is easiest to work with afterwards.

The five-ring appears sharing that bond, grown on the side away from the rest of the molecule. The status bar now reads 9 atoms · 10 bonds and the formula chip C9H16. The two atoms of the shared bond are the fusion pair, and every instruction below is relative to them.

Step three — the four nitrogens#

Press N, or click N in the Atoms rail. The status line reads "Atom N — click empty to place, click an atom to change it, drag to bond". Clicking an existing atom changes what it is.

• In the five-ring, click the two atoms that neighbour the fusion pair. Leave the apex atom — the one furthest from the shared bond — as carbon.
• In the six-ring, start at either fusion atom and walk around the ring away from the shared bond. Click the first atom you reach, skip the second, click the third.

You should now have four nitrogens, no two of them adjacent, and the formula chip should read C5H12N4.

Step four — the two carbonyls#

Press O. This time drag rather than click: dragging from an atom draws a bond out to a new atom of the selected element.

• Drag outward, away from the ring, from the six-ring carbon that sits between the two nitrogens. An oxygen appears on a single bond.
• Drag outward from the other six-ring carbon that is not part of the fusion pair — the one with a nitrogen on one side and a fusion atom on the other.

Press B for the Bond tool and click each of the two new carbon–oxygen bonds once. Each goes from single to double. Clicking again would take it to triple, and once more back to single.

Step five — the two ring double bonds#

Stay on the Bond tool.

• Click the shared fusion bond once. It becomes the double bond between the two ring systems.
• Click the bond from the five-ring's apex carbon to one of its two nitrogens. Pick the nitrogen whose fusion neighbour also touches a ring nitrogen — not the one whose fusion neighbour touches a carbonyl carbon. That second nitrogen is about to take a methyl, and a nitrogen cannot carry both.

Step six — the three methyls#

Still on the Bond tool, click — do not drag — each of these three nitrogens once:

• both six-ring nitrogens,
• the five-ring nitrogen you left out of the double bond.

Each click grows a carbon on a single bond, aimed into the widest gap between the bonds that atom already has, so the methyls space themselves. A methyl draws as a bare line: carbon takes no letter unless it is charged or unbonded.

Step seven — check the readout#

Look at the inspector on the right.

• Formula should read C8H10N4O2.
• The status bar should read 14 atoms · 15 bonds.
• SMILES holds a valid caffeine string. It will not look like the CN1C=NC2=C1C(=O)N(C(=O)N2C)C on the Caffeine template button — the writer is valid, not canonical, and writes atoms in the order you drew them.

If the formula shows more hydrogens than it should, a bond you meant to double is still single: hydrogens are implied from the bonds actually present. Click the offending bond with the Bond tool.

Press F to fit the view, then V for Select & move to nudge any methyl that landed on top of a neighbour. A drag is previewed live and committed once, so tidying costs one undo step each.

Step eight — name it and let it save#

Click the name field in the top bar, type Caffeine, and press Enter. The save chip goes Saving… and then Saved. Esc in that field puts the old name back, and a blank name is ignored.

That is the whole document: it is in your library, it is in this browser, and — signed in — in your account. Library or Done takes you back to the grid, where the card shows the name, the atom count and today's date.

Step nine — put it on a slide#

Click the SMILES box in the inspector; the whole string selects. Copy it.

Open a deck and choose Insert → Molecule. The object arrives as caffeine already, so paste your string over the SMILES field in the inspector and click away — the field commits when it loses focus. The structure redraws.

To keep editing it on the slide, double-click the structure, or press Draw in Molecule Studio. The typed string is imported into an editable structure once, and from then on the drawing is the truth. The slide's copy and the library's are independent: Save to library copies one way, and nothing links them afterwards.

Step ten — style it#

In the slide inspector:

• name — Caffeine, with Show name set to On for a caption under the structure.
• Atoms — Colour gives nitrogen and oxygen their conventional hues; Ink draws everything in the paper's ink for a monochrome figure.
• Hydrogens — Implicit or Explicit. This governs a molecule that is still only a typed string; a drawn structure always labels the hydrogens its heteroatoms imply.

Drag the object's handles to resize. The generated drawing scales in the editor and presenter view. Image and PDF exports capture it at the selected resolution; they do not preserve vector artwork. PowerPoint uses an image capture where available. See Import & export.

What to try next#

• Draw pyridine the fast way: press 6 for benzene, click the canvas, then press N and click one ring carbon. The aromatic flag survives the element change, so the SMILES comes out lower-case.
• Give an atom a formal charge with the Add + charge tool, or the Charge stepper under Selected atom, and watch it appear in the SMILES as a bracket atom.
• Share the molecule and leave a comment on a single atom — select it first, and the thread anchors there and follows it.
• Read SMILES and structure data before you rely on the string anywhere else.