Adding Atoms

Molecular editor allows to build molecules in 3D by atoms (see also Drawing in 3D). Imagine, for example, that we want to draw the acetone molecule:

Select "Add Atom" from the "Edit" menu:

Program opens two dialogs: "Select Atom Type" dialog (which contains Periodic Table of Elements, Atom types panel and Connection panel ) and "Select Atom" dialog:

Atom types panel is used to select the Atom type of atom which will be used internally for filling empty valences and geometry optimization.

Since we want to start drawing from the Carbon sceleton we select Carbon in the Periodic Table:

Atom type panel shows several possible covalent states of Carbon atom (sp3 is its default state).

Shift-left mouse clicking in the main window we create out first Carbon atom:

Zoom out Carbon atom:

We need to select Carbon atom in order to add the other one:

Position the cursor on the spot in the Main Window where you want to place a new atom:

While holding down the Shift key on the keyboard press the Left mouse button and program will generate a new atom:

Following the same procedure we'll generate the third Carbon atom:

To add the Oxygen atom we need to select it first in the Periodic Table:

then select its atom type (sp2)

and, finally, to place it in the Main Window:

When generating the Hydrogen atoms we'll use the predefined C-H bond length of 1.1 Angstrom typical for aliphatic compounds. To do so one needs to check the "Predefined Bond Length" checkbox and to select "1.1" in the combobox:

When the "Predefined Bond Length" checkbox is checked the mouse cursor sets only the direction of the bond vector while the real bond length is equal to the value selected in the combobox (1.1 A in our case):

There is more simple method for generating Hydrogens using "Add Hydrogens" facility however in this example we learn how to draw a molecule in 3D.

Generate the rest of Hydrogen atoms:

Although our final structure is far from ideal

it can be easily optimized using either internal geometry optimizer (will be implemented soon) or external program.

Send all questions, suggestions and comments to Vlad (

Dr. Vladislav Vasilyev

Supercomputer Facility,

The Australian National University,

Canberra, ACT, 0200, Australia