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Determine the raw spin density alone, not mapped
onto the charge density surface.
1. On the Surfaces toolbar, point to Surface, and
select Total Spin Density.
2. From the Surfaces menu, point to Surfaces, and
choose Wire Mesh.
3. Set Isospin to 0.001.
There is a large concentration of unpaired spin over
each of the terminal carbons and a small
concentration over the central hydrogen. This extra
little bit of spin density is not very significant—you
could not even see it when looking at the mapped
display earlier, but the calculations show that it is, in
fact, there.
Tutorial 10:
Computing Partial
Charges
To compute the charge of a molecule, the number
of electrons contributed by each of its atoms can be
subtracted from the number of protons in the
nucleus of each of its atoms. Each atom of a
molecule contributes an integral charge to the
molecule as a whole. This integral contribution is
known as the formal charge of each atom.
Certain types of atoms in Chem3D deal with this
explicitly by having non-integral formal charges.
For example, the two oxygen atoms in nitrobenzene
each have charges of -0.500 because there
is one electron that is shared across the two N-O
bonds.
However, as shown above, electrons in molecules
actually occupy areas of the molecule that are not
associated with individual atoms and can also be
attracted to different atomic nucleii as they move
across different atomic orbitals. In fact, bonds are a
representation of the movement of these electrons
between different atomic nucleii.
Because electrons do not occupy the orbitals of a
single atom in a molecule, the actual charge of each
atom is not integral, but is based on the average
number of electrons in the model that are
occupying the valence shells of that atom at any
given instant. By subtracting this average from the
number of protons in the molecule, the partial
charge of each atom is determined.
Visualizing the partial charge of the atoms in a
molecule is another way to understand the model's
reactivity. Typically the greater the partial charge on
an atom, the more likely it is to form bonds with
other atoms whose partial charge is the opposite
sign.
Using the theories in Extended Hückel, MOPAC,
or Gaussian, you can compute the partial charges
for each atom. In the following example, the partial
charges for phenol are computed by Extended
Hückel.
1. From the File menu, choose New.
Click the Text Building tool , click in the
model window, type PhOH in the text box, and
press the Enter key.
A molecule of phenol is created.
To compute Extended Hückel charges:
• From the Calculations menu, point to Extended
Hückel and choose Calculate Charges.
Messages are added to the Output box, listing
the partial charge of each atom.
48 •Chem3D Tutorials CambridgeSoft
Tutorial 10: Computing Partial Charges