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Drawing atoms and bonds
Adding an atom
Select an element from the toolbar. In the drawing area click where you want to add the atom. If the option "show missing hydrogen atoms" is set, some atoms (e.g. C, N, O, etc.) will be drawn with hydrogen atoms.
Add aditional methyl groups to a C atom by clicking on the atom when element C and single bond are selected in the toolbar.
An atom can be edited by clicking, double clicking or right-clicking (see Editing atoms)
Adding a bond
Select a bond typ from the toolbar. In the drawing area click and drag either on an empty spot or on an existing atom. The red line indicates the direction and lenght of a bond and will lock at certain positions. The locking can be dissable from the menubar (Drawing) or Preferences. You can also connect to existing atoms with a bond.
If the number of bonds is larger as the valence of the connected atoms, a warning will be shown. If you choose to add the bond anyway, the atoms may get charged. The charge can be manually adjusted (Editing atoms).
Bonds with higher hapticity (π-bonding)
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If you draw a bond over another bond, a bond with hapticity η2 is generated. |
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If you draw a bond over a circle, an arc, or a curved line drawing the popup window for bonds with higher hapticity appears.
After selecting atoms by clicking or dragging a selection frame and hitting the continue button a bond with the selected hapticity is drawn. |
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All elemtents of a bond with higher hapticity are highlighted with a red frame. Despite grouping, the atoms, circles or arcs belonging to the bond with higher hapticity can be moved indepentently. |
Bonds that do not count
Dashed and dative bonds by default are not taken into consideration when calculating free valances and charges. Therefore they can be used for example as hydrogen and complex bond.
Other bonds can have the same characteristic. It can be set in the bond-popover "Editing bonds".
Adding an atomgroup
Atomgroupds like NO2 can be added by double clicking an existing atom and entering the atomgroup as text.
Adding explicit hydrogen atoms
Hydrogen atoms can be added to or removed from atoms with free valence by using the according item under "tools" in the main menubar.