Chains and group abbreviations
Short answer: Pick the Chain tool in the left rail and drag to draw a zigzag carbon chain. Numbers on each atom show the length. To grow a chain from an atom, point at it and press a number from 1 to 9. Type groups such as OMe, CO2Et or Boc on an atom. To expand one, right click it and pick Show as Full Structure.
- Click the Chain tool in the left rail. It sits next to the bond button.
- Press on an atom to grow the chain from it, or press on empty canvas for a free chain.
- Drag. Each new atom shows a number, so you can count the carbons.
- Release when the count is right.
How the Chain tool works#
- The chain is a zigzag with 120° angles, the usual skeletal style.
- Each bond has the document bond length. The direction follows Bond angle snap in Settings, Bonds (30° by default).
- When you start on an atom, the first bond points into the open space next to it.
- Drag back to make the chain shorter before you release.
- With the Chain tool active, hold Ctrl and drag on empty canvas to select instead of drawing.
On a phone, the Chain tool is in the Bond strip of the bottom bar.
Add a chain with a number key#
You do not need the Chain tool for short chains. Point the mouse at an atom and press a number key.
- 1 to 9 add a carbon chain of that many atoms.
- The chain leaves the atom on the side away from its other bonds.
- This works with any tool. See Draw faster with hover keys for the other keys.
Group abbreviations#
An abbreviation is a short label that stands for a whole group, such as CO2Me for a methyl ester. The basics of typing a label are on the Atom labels and R-groups page. This page lists the groups that MolDraw understands.
To type one fast, select one atom and start typing. Or point at an atom with a bond or ring tool active and type. A list of suggestions opens. Press Tab or Enter to accept one.
Groups that expand#
These labels expand into full atoms. Letter case does not matter.
| Type | Labels |
|---|---|
| Alkyl | Me, Et, nPr, iPr, nBu, iBu, sBu, tBu, vinyl, allyl, propargyl |
| Aryl and benzyl | Ph, Bn, OPh, SPh |
| Oxygen groups | OH, OMe, OEt, OPr, OtBu, CHO, Ac, COOH, CO2H, COONa |
| Esters and amides | COOMe, CO2Me, COOEt, CO2Et, CONH2 |
| Nitrogen and others | NH2, NO2, NO, CN, CF3, CCl3, SH, SO3H, SO2Me |
| Protecting groups | Boc, Cbz, Fmoc, Ts, Tos, Ms, TFA, PMB, Trt, MOM, THP, MEM, SEM, BOM |
| Silyl groups | TMS, TES, TBS, TBDMS, TIPS, TBDPS |
Condensed formulas also expand. For example CH2CH2OH or C(CH3)3 become the right atoms and bonds.
Expand a label#
Right click the labelled atom and pick Show as Full Structure. The anchor atom and its bonds stay in place, so wedges next to the group keep their meaning. Press Ctrl+Z to go back.
A label MolDraw does not know stays as text. It still prints on your figure.
Show short labels on drawn groups#
Settings, General, Condensed group labels shows end groups as compact text such as CH₃ or NH₂. It is off by default.
Common problems#
| Problem | Fix |
|---|---|
| The chain goes the wrong way | Undo, then start the drag on the other side of the atom. Or use a number key on the atom. |
| A number key changed a bond instead | The pointer was over a bond. Move it onto the atom. |
| Typing a letter switched tools | Some letters are tool keys, such as V and L. Select the atom first, or double click it, then type. |
| Show as Full Structure is missing | The atom has no label, or the label is plain text that MolDraw does not know. |
For ready-made groups you can click instead of type, open the Library. To name the groups in a molecule, try the functional group identifier.
Questions and answers
How do I draw a long carbon chain in MolDraw?
Pick the Chain tool in the left rail and drag. The numbers on each atom count the carbons, so release when the count is right.
How do I add a butyl group to an atom quickly?
Point the mouse at the atom and press 4. A four carbon chain grows from it.
Which abbreviations can MolDraw expand?
Common alkyl, aryl, ester, nitrogen, protecting and silyl groups such as Et, Ph, CO2Me, NO2, Boc and TBS. Condensed formulas like CH2CH2OH expand too.
How do I expand an abbreviation into atoms?
Right click the labelled atom and pick Show as Full Structure.
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