Atom

Create Atoms

  1. Choose from the frequently used atom buttons on the Atoms toolbar or simply type the atomic symbol or select an atom from the Periodic Table Dialog.

  2. The chosen atom appears on the tip of the mouse cursor and you can place it on the canvas with a left-click as many times as you like.
    images/download/attachments/1802946/Create_Atoms.png

Special atom types:

  • Deuterium and Tritium symbols (D and T, respectively) are available through keyboard buttons.

  • Query atoms can be placed onto the canvas by keyboard shortcut or through their combo button on the Atoms toolbar.

  • Pseudo atoms are also available among these combo buttons.

  • Star atom (*) can be placed onto the canvas by clicking its button on the Atoms toolbar.

All types of atoms mentioned above are also available from the Atom Properties Dialog.

Draw an Atom List/NOT List

  1. Click the Atom list button on the lower-left corner in the Periodic table dialog.

  2. The selected button is indicated by blue, and an OK button appears on the bottom of the dialog.

  3. Select the atoms you would like to have on your list. The selected atoms are indicated in gray.

  4. Click OK.

  5. The dialog closes and the selected elements of the atom list appear on the tip of the mouse cursor.
    images/download/attachments/1802946/Draw_Atom_List_Not_List.png

Draw Pseudo Atoms

  1. Click the Pseudo atom button in the Query Atoms combo box on the Atom toolbar.

  2. Fill the text field in the Pseudo atom dialog window.
    images/download/attachments/1802946/Pseudo_Atom_Dialog.png

  3. Click OK.

  4. The pseudo atom will appear on the tip of the mouse cursor.

Display of Atoms

Non-metallic atoms are automatically completed with implicit hydrogens according to the free valences of the atom. The visibility of the implicit hydrogens depends on the defined value in the View settings dialog.
Metallic elements are added to the canvas in a zero oxidation state. CPK coloring and monochrome display of the atoms are also possible.

images/download/attachments/1802946/Display_Atoms.png

The figure below shows the fixed place of certain atom properties.

images/download/attachments/1802946/Place_of_Atom_Properties.png

Changing the Atom Properties

Type

Atoms on the canvas can be replaced by inserting a new atom to the same place as the old one. If you select several atoms at the same time, you can also change them simultaneously using the most frequently used atom buttons, the keyboard, or the Periodic System.

The atom type can be changed from the Atom properties menu too.

Charge

Add charge with the charge buttons or from the Atom properties dialog.

Setting charge is also possible by hovering over the atom then typing - or + on the Numeric keypad.

Atom Properties Dialog

In the Atom properties dialog, you can set the values of atomic charges, isotopes, monovalent radicals, enhanced stereo specifications, atom maps, aliases in the Basic tab, and query properties in the Advanced.

For more information, see Atom Properties Dialog.

images/download/attachments/1802946/Atom_Properties_Dialog.png

Delete Atoms

You can delete atoms from the canvas by using the Delete tool: clicking on the atom or dragging until a red rectangle appears around the structure.
It is also possible to select the atom(s) with one of the selection tools first, and click the Delete tool or press the Delete button on the keyboard.

images/download/attachments/1802946/Delete_Atoms.png