Chem3D Users Manual - CambridgeSoft

Administrator
To save the iterations as a movie, click Record Each
Iteration.
The following illustration shows the distances
between atom pairs at the completion of the
docking computation. The distances in the Actual
cell are close to the distances in the Optimal cell.
iteration
values
Note that while the docking computation proceeds,
one molecule remains stationary and the second
molecule moves.
To stop the docking computation before it reaches
it’s preset RMS values, click Stop Calculation
on the Calculation toolbar. Both docking and
recording are stopped.
The Status bar displays the values describing each
iteration of the docking computation.
The following illustration shows the docked
polymer molecules.
Your results may not exactly match those described
here. The relative position of the two fragments or
molecules at the start of the docking computation
can affect your results. For more accurate results,
lower the minimum RMS gradient.
Tutorial 8: Viewing
Molecular Surfaces
Frontier molecular orbital theory says that the
highest occupied molecular orbitals (HOMO) and
lowest unoccupied molecular orbitals (LUMO) are
the most important MOs affecting a molecule’s
reactivity. This tutorial examines the reactivity of
double bonds by looking at the simplest molecule
containing a double bond, ethene.
Create an ethene model:
1. From the File menu, choose New.
2. Draw a double bond in the ChemDraw panel.
A molecule of ethene appears.
Before you can view the molecular orbital surface,
you must calculate it.
48 •Chem3D Tutorials CambridgeSoft
Tutorial 8: Viewing Molecular Surfaces