How to Draw Bonds

• Create a new bond:

• Create an aligned double bond

• Replace a bond

• Bold tool

  • Aromatic bonds

• Hashed bond

Create a new bond:

Select a bond type using the Bond toolbar button or by shortcut .

• To link two existing atoms, select a bond type, click on one 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.

Marvin allows you to draw a bond between any two atoms in the molecule. Valence errors are highlighted (if that option is enabled).

• If you add a bond to empty canvas space, a carbon atom is added to each end of the bond.

• To change the orientation of a wedge bond click with the corresponding wedge bond tool on the bond.

• To change the order of bonds which cross each other : Select the bond to move to the front and go to Contextual menu < Arrange < Bring to Front. The selected bond now is drawn in front of all other bonds (or objects). Similarly, the Send to Back option paints the bond behind other bonds(or objects) .

{info} Please note that all bond types are active in 2D, but wedge bonds are inactive in 3D ( e.g., after 3D cleaning ).

Create an aligned double bond

Double bonds can have one of three alignments relative to the chain: above, centered and below

To change the alignment click the double bond tool and click on the existing bond as many times as necessary.

Further bond types applied in Marvin:

• multi-center bond (For details see the Coordination compounds section.)

  

• position variation bond (For details see the Markush structure section.)

  Xle ( J ): is L-Leucine or L-Isoleucine

Replace a bond

• You can replace any bond in the molecule by placing a new bond type on top of it.

• Bond types can also be changed using the Bond pop-up menu .

• Single bonds can be changed to double or triple by left-clicking on them

.

• Additionally, you can change a bond, selecting it and use the following keys shortcut.

  Available Bonds
  Single
  Double
  Triple
  Aromatic
  Single Up
  Single Down
  Single Up or Down
  Double Cis or Trans
  Double C/T or Unspec
  Single or Double
  Single or Aromatic
  Double or Aromatic
  Any
  Coordinate

  1	Single bond
  2	Double bond
  3	Triple bond
  4	Aromatic bond
  5	Single up bond (active only in 2D)
  6	Single down bond (active only in 2D)
  7	Single up or down bond
  12	Single or double bond
  14	Single or aromatic bond
  24	Double or aromatic bond
  0	Any bond

Bold tool

The Bold tool, , is intended to be used for graphical presentations of molecules.

It is located in the Bond menu, on the Tools toolbar and in the Bond pop-up menu by default.

Activate the tool, click on a bond and it will be changed to bold.

In case of single, double, or aromatic bond clicking again you can reestabilish the original bond.

Aromatic bonds

Aromatic bonds has four representations:

• bold single

• bold aromatic up,

• reversed bold aromatic up,

• and single .

  Example

Hashed bond

You can make the selected bond hashed: Choose the icon from the Tools toolbar or the Bond > Hashed menu option. It retains the original single bond type.