Special bond types
Short answer: Open the bond menu in the left rail (click the bond button twice) to find every bond type. It has three groups: Bonds, Query / stereo and Advanced. Use Dative for metal to ligand bonds and H-bond for hydrogen bonds. Use Thick for the front edge of a ring and query bonds for search patterns.
- Click the bond button in the left rail. Click it again to open the bond menu.
- Pick a bond type. The button now shows that type.
- Drag from atom to atom to draw it, or click an existing bond to change it.
The plain single, double, triple and wedge bonds are on the Draw bonds page. This page covers the rest.
All bond types#
| Menu group | Type | What it means | When to use it |
|---|---|---|---|
| Bonds | Aromatic | A bond in an aromatic ring. Rings show a solid inner circle. | Benzene type rings drawn as one unit. |
| Bonds | Wedge/hash | A stereo center whose direction is unknown. | A mixture, or a center you have not assigned. |
| Bonds | Wavy | Unknown or mixed stereo. | Racemic centers, or an unknown E/Z bond. |
| Query / stereo | Cis/trans | A crossed double bond. E or Z is not set. | A mixture of E and Z isomers. |
| Query / stereo | Dative | A coordinate bond. A dashed line with an arrow head. | Metal to ligand bonds, such as NH₃ on a metal. |
| Query / stereo | Inductive | An arrow on a sigma bond toward the more electronegative atom. | Teaching the inductive effect. |
| Query / stereo | Centroid | A bond from a metal to the centre of a ring (ηⁿ). | Ferrocene, arene complexes. |
| Query / stereo | Any | Any bond order. | Search patterns. |
| Advanced | Single/double | Single or double. | Search patterns. |
| Advanced | Single/arom. | Single or aromatic. | Search patterns. |
| Advanced | Double/arom. | Double or aromatic. | Search patterns. |
| Advanced | H-bond | A dotted line for a hydrogen bond or other weak contact. | Base pairs, enzyme pockets, intramolecular H-bonds. |
| Advanced | Thick | A heavy line. Display only. | The front edge of a chair or a Haworth ring. |
Dative and centroid bonds#
- Dative: drag from the donor atom to the acceptor. The arrow points at the acceptor, usually the metal. Dative bonds do not trigger the too many bonds warning.
- Centroid: start on the metal and release inside the ring face, not on a corner atom. The bond attaches to the ring centre. If you release on empty space, nothing is drawn.
- The Dative tool also links to a ring centre when you release inside a ring.
For sandwich and arene complexes, use the Cp and Tilted arene rings in the ring bar. Clean up leaves these organometallic drawings as drawn.
Hydrogen bonds and other dotted lines#
The H-bond type is dotted and does not use valence. Draw it from the H atom to the acceptor, for example from an amide H to a carbonyl O. It shows a contact, not a real bond.
Thick bonds#
Thick only makes the line heavier. It keeps the bond order, so a thick double bond stays double. Click a thick bond again with the Thick tool to make it normal.
Query bonds#
Any, Single/double, Single/arom. and Double/arom. are query bonds. They describe a pattern, not one molecule. MOL files keep them as query bond types 8, 5, 6 and 7, so search programs can read them.
Click again to change or reset#
Clicking an existing bond with a tool applies that type. Clicking again with the same tool does this:
| Tool | Second click |
|---|---|
| Wedge, hash, wedge/hash | Flips the narrow end to the other atom. |
| Thick | Turns the thick line off. |
| Inductive | Reverses the arrow, then clears it. |
| Other special types | Turns it back into a plain single bond. |
| Double | Moves the second line: centred, right, left. |
You can also select bonds first and then pick a type. Every selected bond changes. This only works on bonds you picked, not on a whole selected molecule.
Double bond position#
A double bond can sit centred or with its second line on either side. Click it with the Double tool, or point at it and press 2, to step through the three positions. See hover keys for more.
Common problems#
| Problem | Fix |
|---|---|
| The arrow on a dative bond points the wrong way | Undo and draw it again from the donor atom. |
| The centroid bond does not appear | Release inside the ring face, not on a ring atom. |
| A red flash after drawing a bond | An atom has too many bonds. Dative, H-bond and query bonds do not cause this. |
| Clicking a bond reset it to single | You clicked a special bond with the same tool. Pick the type again. |
For the theory, read about aromaticity and Hückel's rule and stereoisomers. The inductive arrow is covered in inductive effect arrows.
Questions and answers
How do I draw a dative bond in MolDraw?
Open the bond menu, pick Dative and drag from the donor atom to the metal. The arrow points at the atom where you release.
How do I draw a hydrogen bond?
Open the bond menu, go to Advanced and pick H-bond. Drag from the hydrogen to the acceptor atom to draw a dotted line.
How do I draw a wavy bond?
Open the bond menu and pick Wavy. Drag from the stereo center to the outer atom.
How do I draw ferrocene or a metal to ring bond?
Pick Centroid in the bond menu. Start on the metal and release inside the ring face.
What are query bonds for?
Any, Single/double, Single/arom. and Double/arom. describe search patterns. They are saved in MOL files as query bond types.
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