Chem3D Users Manual - CambridgeSoft

Administrator
Chemical
symbol
++ barium di-cation + 2 electrons
_
Equivalent to...
borohydride halogen, or nitrate
anion minus electron
= sulfate, oxalate di-anion minus 2
electrons
Sparkles are represented in Chem3D by adding a
charged dummy atom to the model.
TIP: Dummy atoms are created with the uncoordinated
bond tool. You must add the charge after creating the dummy.
The output file shows the the chemical symbol as
XX.
Optimizing Geometry
Chem3D uses the Eigenvector Following (EF)
routine as the default geometry optimization
routine for minimization calculations. EF is
generally superior to the other minimizers, and is
the default used by MOPAC 2002. (Earlier versions
of MOPAC used BFGS as the default.) The other
alternatives are described below.
TS
The TS optimizer is used to optimize a transition
state. It is inserted automatically when you select
Optimize to Transition State from the MOPAC
Interface submenu.
BFGS
For large models (over about 500-1,000 atoms) the
suggested optimizer is the Broyden-Fletcher-
Goldfarb-Shanno procedure. By specifying BFGS,
this procedure will be used instead of EF.
LBFGS
For very large systems, the LBFGS optimizer is
often the only method that can be used. It is based
on the BFGS optimizer, but calculates the inverse
Hessian as needed rather than storing it. Because it
uses little memory, it is preferred for optimizing
very large systems. It is, however, not as efficient as
the other optimizers.
MOPAC Files
CS MOPAC can use standard MOPAC text files for
input, and creates standard MOPAC output files.
These are especially useful when running repeat
computations.
Using the *.out file
In addition to the Messages window, MOPAC
creates two text files that contain information about
the computations.
Each computation performed using MOPAC
creates a *.out file containing all information
concerning the computation. A summary *.arax file
is also created, (where x increments from a to z after
each run). The *.out file is overwritten for each run,
but a new summary *.arax, file is created after each
computation (*.araa, *.arab, and so on.)
176•MOPAC Computations
CambridgeSoft
Optimizing Geometry