Draw Bonds

To select any bond type use the Bond button or press the associated shortcut. The table below shows the available bond types and their shortcuts.

Since version 20.11, when a bond tool is active and the cursor is over an atom, gray-colored feedback appears in the selected bond type. Pressing the Shift key changes the direction of the bond.

Clicking on the atom places the bond in this position. The length of the bond is the default value and a carbon atom is placed on its other end.

Available Bonds

Icon

Shortcut

Single

images/download/thumbnails/1805980/bonds.png

1

Double

images/download/thumbnails/1805980/bond_double24.png

2

Triple

images/download/thumbnails/1805980/bond_triple24.png

3

Aromatic

images/download/thumbnails/1805980/bond_aromatic24.png

4

Single Up (active only in 2D)

images/download/thumbnails/1805980/bond_singleup24.png

5

Single Down (active only in 2D)

images/download/thumbnails/1805980/bond_singledown24.png

6

Single Up or Down

images/download/thumbnails/1805980/bond_singleupordown24.png

7

Double Cis or Trans

images/download/thumbnails/1805980/bond_doublecisortrans24.png

N/A

Double C/T or Unspec

images/download/thumbnails/1805980/bond-doublect24.png

N/A

Single or Double

images/download/thumbnails/1805980/bond_singleordouble24.png

12

Single or Aromatic

images/download/thumbnails/1805980/bond_singleoraromatic24.png

14

Double or Aromatic

images/download/thumbnails/1805980/bond_doubleoraromatic24.png

24

Any

images/download/thumbnails/1805980/bond-any24.png

0

Coordinate

images/download/thumbnails/1805980/bond_coordinative24.png

N/A

To link two existing atoms, select a bond type then click one of the atoms then drag the cursor to the other.

To draw a bond from a single atom, simply click the atom. A carbon atom is added at the other end of the bond.

MarvinSketch allows you to draw a bond between any atoms. Valence errors are highlighted (if the associated option is enabled).

It is possible to add a bond to an empty canvas. In this case, a carbon atom is added to each end of the bond.

To change the orientation of a wedge bond, click the bond with the corresponding wedge bond tool. Alternatively, you can select the bond to be changed and press the shortcut of the desired bond.

To change the order of bonds that cross each other, select the bond to be moved to the front and right-click to open the context menu, and navigate to Arrange > Bring to Front. The selected bond is now drawn in front of all other bonds (or objects). Similarly, the Send to Back option draws the selected bond behind other bonds (or objects).

images/download/attachments/1805980/adamantane.png

Replace a Bond

To replace any bond, simply overwrite it by placing the new bond on top of it.

Alternatively, a bond can be changed by using the context menu or the shortcuts.

Single bonds can be changed into double or triple bonds by clicking them when the single bond tool is the active tool.

Create an Aligned Double Bond

Double bonds can have one of three alignments relative to the chain.

These alignments are as follows:

  • Above

  • Centered

  • Below

images/download/attachments/1805980/Double_bond_aligment.png

To change the alignment, select the double bond tool and click the existing bond to alternate between the different alignments.

Bold Tool

The Bold tool can be used for the graphical presentation of molecules.

The tool can be found on the Tools toolbar, in the Bond menu, and the Bond context menu.

In the case of single, double, and aromatic bonds you can alternate bold and the original representation by clicking the bond with the Bold tool.

images/download/attachments/1805980/boldaromatic.png

Hashed Bond

You can make the selected bond hashed by choosing the Hashed Bond tool from the Tools toolbar or the Bond > Hashed menu option.

Other Bond Types in MarvinSketch

Multi-center Bond

For details, see How to draw coordination compounds.
images/download/attachments/1805980/multiferro.PNG

Position Variation Bond

For details, see Markush structures.
images/download/attachments/1805980/Xle.PNG