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.

    Available Bonds Icon Shortcut
    Single images/download/thumbnails/20425389/bonds.png 1
    Double images/download/thumbnails/20425389/bond_double24.png 2
    Triple images/download/thumbnails/20425389/bond_triple24.png 3
    Aromatic images/download/thumbnails/20425389/bond_aromatic24.png 4
    Single Up (active only in 2D) images/download/thumbnails/20425389/bond_singleup24.png 5
    Single Down (active only in 2D) images/download/thumbnails/20425389/bond_singledown24.png 6
    Single Up or Down images/download/thumbnails/20425389/bond_singleupordown24.png 7
    Double Cis or Trans images/download/thumbnails/20425389/bond_doublecisortrans24.png N/A
    Double C/T or Unspec images/download/thumbnails/20425389/bond-doublect24.png N/A
    Single or Double images/download/thumbnails/20425389/bond_singleordouble24.png 12
    Single or Aromatic images/download/thumbnails/20425389/bond_singleoraromatic24.png 14
    Double or Aromatic images/download/thumbnails/20425389/bond_doubleoraromatic24.png 24
    Any images/download/thumbnails/20425389/bond-any24.png 0
    Coordinate images/download/thumbnails/20425389/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).


    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


    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.


    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.


    Position Variation Bond

    For details, see Markush structures.