Chem3D Users Manual - CambridgeSoft

You can graphically display partial charges in the
following ways:
• By coloring atoms.
• By varying the size of atom spheres.
• By varying the size of the dot surfaces.
3. Click the Show by Default checkbox in the Solid
Spheres section.
4. Select the Partial Charges radio button.
To display partial charges:
1. From the File menu, choose Model Settings.
2. Click the Model Display tab.
3. Select the Color by Partial Charge radio button.
All of the atoms are colored according to a
scale from blue to white to red. Atoms with a
large negative partial charge are deep blue.
Atoms with a large positive partial charge are
deep red. As the magnitude of the charges
approaches 0, the color of the atom becomes
paler.
In this representation, the oxygen atom and its two
adjacent atoms are large because they have relatively
large partial charges of opposite signs. The rest of
the atoms are relatively small.
You can display dot surfaces whose size is specified
by partial charge.
1. Click the VDW Radius radio button in the Solid
Spheres section.
1. Select the Show By Default check box in the Dot
Surfaces section.
2. Click the Partial Charges radio button.
For phenol, the greatest negative charge is on the
oxygen atom. The greatest positive charge is on the
adjacent carbon atom (with the adjacent hydrogen
atom a close second). The rest of the molecule has
relatively pale atoms; their partial charges are much
closer to zero.
In addition to color, you can vary the size of atom
spheres or dot surfaces by partial charge.
1. Select the Color By Element radio button in
Model Display tab of the Model Settings dialog
box.
2. Click the Atom Display tab.
In this representation, the oxygen atom and its two
adjacent atoms have large dot surface clouds
around them because they have relatively large
partial charges of opposite signs. The rest of the
ChemOffice 2005/Chem3D Chem3D Tutorials • 53
Tutorial 10: Computing Partial Charges